https://xmlpipedb.lmucs.io/biodb/fall2017/api.php?action=feedcontributions&feedformat=atom&user=Hhinsch 2026-06-15T17:58:05Z User contributions MediaWiki 1.29.0 https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5863 2017-12-15T23:44:23Z

<p>Hhinsch: fixed invocation of presentation file and group report file</p> <hr /> <div><br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:PageDesignGroupReport.pdf|Page Design Group Report]]<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx|Page Design Final Presentation]]<br /> # Code (GitHub pull request)<br /> #*[https://github.com/bhamilton18/GRNsight/tree/master/web-client/public/gene GitHub Pull Request for our code]<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*[[File:PageDesignREADME.txt]]<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See Page Designer Deliverables template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5860 2017-12-15T23:43:02Z

<p>Hhinsch: added group report</p> <hr /> <div><br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[File:PageDesignGroupReport.pdf|Page Design Group Report]<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #*[https://github.com/bhamilton18/GRNsight/tree/master/web-client/public/gene GitHub Pull Request for our code]<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*[[File:PageDesignREADME.txt]]<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See Page Designer Deliverables template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:PageDesignGroupReport.pdf&diff=5859 2017-12-15T23:42:00Z

<p>Hhinsch: uploaded page desiigner group report</p> <hr /> <div>uploaded page desiigner group report</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5852 2017-12-15T23:30:18Z

<p>Hhinsch: added github pull request</p> <hr /> <div><br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #*[https://github.com/bhamilton18/GRNsight/tree/master/web-client/public/gene GitHub Pull Request for our code]<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*[[File:PageDesignREADME.txt]]<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See Page Designer Deliverables template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Schedule&diff=5804 2017-12-15T15:14:40Z

<p>Hhinsch: struckout presentation</p> <hr /> <div>=[[Page Desiigner Schedule]]=<br /> ==Page Desiigner Deliverables==<br /> The Page Design team is responsible for the visual appearance and internal behavior of the gene page. The core deliverable of the team is the HTML/CSS/JavaScript code for this page, in a form that can be dynamically populated based on the gene chosen by the GRNsight user. The final page design shall also design messages and alerts for errors and warnings, such as when the user attempts to display a gene page for a node that does not correspond to a S. cerevisiae gene.<br /> &lt;br&gt;<br /> The Data Analyst will complete the analysis of microarray data for the dCIN5 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.<br /> <br /> ==Schedule of Deliverables==<br /> #&lt;s&gt;Coder and Designer present journal club presentation on &#039;&#039;&#039;November 14&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Project Manager and Data Analysis add annotated bibliographies to the team page by &#039;&#039;&#039;November 14&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Project Manager and Data Analysis present journal club presentation on &#039;&#039;&#039;November 21&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Coder and Designer complete milestones 0-3 and begin milestone 4 by &#039;&#039;&#039;November 21&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Entire group will give a final group PowerPoint presentation in class during the final exam period on &#039;&#039;&#039;Tuesday, December 12, 2:00pm&#039;&#039;&#039;&lt;/s&gt;<br /> #&#039;&#039;&#039;Final due date for all other deliverables is no later than Friday, December 15, 4:30pm (according to official final exam schedule for fall, 2017)&#039;&#039;&#039;</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5803 2017-12-15T15:14:02Z

<p>Hhinsch: moved powerpoint presentation section, fixed link to readme</p> <hr /> <div><br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*[[File:PageDesignREADME.txt]]<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See Page Designer Deliverables template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5802 2017-12-15T15:12:28Z

<p>Hhinsch: added the readme</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*File:PageDesignREADME.txt<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See Page Designer Deliverables template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Pagedesiigner&diff=5801 2017-12-15T15:11:56Z

<p>Hhinsch: added our read me to uploaded files</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> {{ GRNsight Gene Page Project Links }}<br /> <br /> ===Page Desiigner Deliverables Page===<br /> [[Page Desiigner Deliverables Page]]<br /> ===Page Desiigner Schedule===<br /> [[Page Desiigner Schedule]]<br /> <br /> ===Uploaded Files===<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> &lt;br&gt;<br /> [[File:PageDesignREADME.txt]]<br /> ===Individual Contributer Pages===<br /> [[User:ArashLari|Arash Lari]]<br /> &lt;br&gt;<br /> [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> [[User:Nicolekalcic|Nicole Kalcic]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:PageDesignREADME.txt&diff=5800 2017-12-15T15:10:49Z

<p>Hhinsch: uploaded our readme</p> <hr /> <div>uploaded our readme</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Pagedesiigner&diff=5799 2017-12-15T15:09:21Z

<p>Hhinsch: added link to our deliverables page</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> {{ GRNsight Gene Page Project Links }}<br /> <br /> ===Page Desiigner Deliverables Page===<br /> [[Page Desiigner Deliverables Page]]<br /> ===Page Desiigner Schedule===<br /> [[Page Desiigner Schedule]]<br /> <br /> ===Uploaded Files===<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> ===Individual Contributer Pages===<br /> [[User:ArashLari|Arash Lari]]<br /> &lt;br&gt;<br /> [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> [[User:Nicolekalcic|Nicole Kalcic]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_15&diff=5798 2017-12-15T15:03:34Z

<p>Hhinsch: fixed a typo in electronic notebook</p> <hr /> <div>[[Category:Journal Entry]]<br /> [[Category:Group Projects]]<br /> [[Category:Page Desiigner]]<br /> ==Electronic Notebook==<br /> *This week I served as a floater again in order to help the other team members if they needed it. <br /> *I planned out the layout for our final paper and presentation.<br /> *I completed the presentation aside from the coder and data analyst section.<br /> *I also completed the intro and conclusion section of the paper as well as delegated tasks for the final paper.<br /> *I needed to reread the journal club article Mary and I reviewed in order to connect our paper to theirs. <br /> *I found that we had a really interesting similarity. Dr. Dahlquist&#039;s data showed the same two patterns as theirs did. There were genes that were upregulated in response to cold shock and downregulated in response to heat shock, then there were genes that were downregulated in response to cold shock and upregulated in response to heat shock. <br /> *The rest of my time was spent managing the team members to ensure completion of deliverables as well as writing my statement of work, assessment, and reflection. <br /> *I emailed my statement of work etc. to the professors while our teams deliverables can be found on our [[Page Desiigner Deliverables Page]].<br /> *Our final page can be found here https://github.com/bhamilton18/GRNsight/tree/page-design .<br /> ===Page Design Team&#039;s Deliverables Page===<br /> *Our team&#039;s deliverables can be found [[Page Desiigner Deliverables Page|Here]] ([[Page Desiigner Deliverables Page]])<br /> <br /> <br /> <br /> ==Acknowledgments==<br /> #I worked with [[User:ArashLari|Arash Lari]], [[User:Mbalducc|Mary Balducci]] and [[User:Nicolekalcic|Nicole Kalcic]] in person and over text to complete the deliverables of this assignment.<br /> #I worked with the other QA&#039;s in order to become familiar with the information to be provided on the page.<br /> #Dr. Dahlquist helped me to better understand the overall content of the paper.<br /> #Most of the students in BIOL/CMSI 367-01 shared information with me so that I may better understand the concepts.<br /> #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. <br /> ==References==<br /> #LMU BioDB 2017. (2017). Week 15. Retrieved December 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15<br /> #Github. (2017). bhamilton18/GRNsight, Retrieved December 10, 2017, from https://github.com/bhamilton18/GRNsight/tree/page-design<br /> #The journal club article I reviewed is: Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> {{hhinsch}}<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5797 2017-12-15T15:01:43Z

<p>Hhinsch: clarified my individual deliverables section</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See Page Designer Deliverables template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Pagedesiigner&diff=5796 2017-12-15T14:55:07Z

<p>Hhinsch: added final presentation to uploaded files section of our template</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> {{ GRNsight Gene Page Project Links }}<br /> <br /> <br /> ===Page Desiigner Schedule===<br /> [[Page Desiigner Schedule]]<br /> <br /> ===Uploaded Files===<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> ===Individual Contributer Pages===<br /> [[User:ArashLari|Arash Lari]]<br /> &lt;br&gt;<br /> [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> [[User:Nicolekalcic|Nicole Kalcic]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5795 2017-12-15T14:53:35Z

<p>Hhinsch: added mary&#039;s week 15 page</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> #*[[Mbalducc Week 15|Week 15]]<br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> *[[Mbalducc Week 15| Week 15]]<br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_15&diff=5794 2017-12-15T14:51:15Z

<p>Hhinsch: added my electronic notebook section as well as acknowledgments and references</p> <hr /> <div>[[Category:Journal Entry]]<br /> [[Category:Group Projects]]<br /> [[Category:Page Desiigner]]<br /> ==Electronic Notebook==<br /> *This week I served as a floater again in order to help the other team members if they needed it. <br /> *I planned out the layout for our final paper and presentation.<br /> *I completed the presentation aside from the coder and data analyst section.<br /> *I also completed the intro and conclusion section of the paper as well as delegated tasks for the final paper.<br /> *I needed to reread the journal club article Mary and I reviewed in order to connect our paper to theirs. <br /> *I found that we had a really interesting similarity. Dr. Dahlquist&#039;s data showed the same two patterns as theirs did. There were genes that were upregulated in response to cold shock and downregulated in response to heat shock, then there were genes that were downregulated in response to cold shock and upregulated in response to heat shock. <br /> *The rest of my time was spent managing the team members to ensure completion of deliverables as well as writing my statement of work, assessment, and reflection. <br /> *I emailed my statement of work etc. to the professors while our teams deliverables can be found on our [[Page Desiigner Deliverables Page]].<br /> *Our final page can be found here [.https://github.com/bhamilton18/GRNsight/tree/page-design ].<br /> ===Page Design Team&#039;s Deliverables Page===<br /> *Our team&#039;s deliverables can be found [[Page Desiigner Deliverables Page|Here]] ([[Page Desiigner Deliverables Page]])<br /> <br /> <br /> <br /> ==Acknowledgments==<br /> #I worked with [[User:ArashLari|Arash Lari]], [[User:Mbalducc|Mary Balducci]] and [[User:Nicolekalcic|Nicole Kalcic]] in person and over text to complete the deliverables of this assignment.<br /> #I worked with the other QA&#039;s in order to become familiar with the information to be provided on the page.<br /> #Dr. Dahlquist helped me to better understand the overall content of the paper.<br /> #Most of the students in BIOL/CMSI 367-01 shared information with me so that I may better understand the concepts.<br /> #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. <br /> ==References==<br /> #LMU BioDB 2017. (2017). Week 15. Retrieved December 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15<br /> #Github. (2017). bhamilton18/GRNsight, Retrieved December 10, 2017, from https://github.com/bhamilton18/GRNsight/tree/page-design<br /> #The journal club article I reviewed is: Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> {{hhinsch}}<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_15&diff=5793 2017-12-15T14:33:01Z

<p>Hhinsch: created my week 15 individual page</p> <hr /> <div>[[Category:Journal Entry]]<br /> [[Category:Group Projects]]<br /> [[Category:Page Desiigner]]<br /> ==Electronic Notebook==<br /> ===Page Design Team&#039;s Deliverables Page===<br /> *Our team&#039;s deliverables can be found [[Page Desiigner Deliverables Page|Here]] ([[Page Desiigner Deliverables Page]])<br /> <br /> <br /> <br /> <br /> {{hhinsch}}<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Hhinsch&diff=5792 2017-12-15T14:28:51Z

<p>Hhinsch: added week 15 to my template and link to devilerables page</p> <hr /> <div>[[Category:Journal Entry]]<br /> ===Assignments===<br /> [[Week 1]]<br /> &lt;br&gt;<br /> [[Week 2]]<br /> &lt;br&gt;<br /> [[Week 3]]<br /> &lt;br&gt;<br /> [[Week 4]]<br /> &lt;br&gt;<br /> [[Week 5]]<br /> &lt;br&gt;<br /> [[Week 6]]<br /> &lt;br&gt;<br /> [[Week 7]]<br /> &lt;br&gt;<br /> [[Week 8]]<br /> &lt;br&gt;<br /> [[Week 9]]<br /> &lt;br&gt;<br /> [[Week 10]]<br /> &lt;br&gt;<br /> [[Week 11]]<br /> &lt;br&gt;<br /> [[Week 12]]<br /> &lt;br&gt;<br /> [[Week 14]]<br /> &lt;br&gt;<br /> [[Week 15]]<br /> ===Hayden&#039;s Individual Journal Entries===<br /> [[Week 1 Journal Entry|hhinsch Week 1]]<br /> &lt;br&gt;<br /> [[hhinsch Week 2]]<br /> &lt;br&gt;<br /> [[hhinsch Week 3]]<br /> &lt;br&gt;<br /> [[hhinsch Week 4]]<br /> &lt;br&gt;<br /> [[hhinsch Week 5]]<br /> &lt;br&gt;<br /> [[hhinsch Week 6]]<br /> &lt;br&gt;<br /> [[hhinsch Week 7]]<br /> &lt;br&gt;<br /> [[hhinsch Week 8]]<br /> &lt;br&gt;<br /> [[hhinsch Week 9]]<br /> &lt;br&gt;<br /> [[hhinsch Week 10]]<br /> &lt;br&gt;<br /> [[hhinsch Week 11]]<br /> &lt;br&gt;<br /> [[hhinsch Week 12]]<br /> &lt;br&gt;<br /> [[hhinsch Week 14]]<br /> &lt;br&gt;<br /> [[hhinsch Week 15]]<br /> &lt;br&gt;<br /> [[Page Desiigner Deliverables Page]]<br /> <br /> ===Class Journal Entries===<br /> [[Class Journal Week 1]]<br /> &lt;br&gt;<br /> [[Class Journal Week 2]]<br /> &lt;br&gt;<br /> [[Class Journal Week 3]]<br /> &lt;br&gt;<br /> [[Class Journal Week 4]]<br /> &lt;br&gt;<br /> [[Class Journal Week 5]]<br /> &lt;br&gt;<br /> [[Class Journal Week 6]]<br /> &lt;br&gt;<br /> [[Class Journal Week 7]]<br /> &lt;br&gt;<br /> [[Class Journal Week 8]]<br /> &lt;br&gt;<br /> [[Class Journal Week 9]]<br /> &lt;br&gt;<br /> [[Class Journal Week 10]]<br /> &lt;br&gt;<br /> [[Page Desiigner]]<br /> ===Electronic Notebook===<br /> [[Hhinsch Electronic Notebook]]<br /> <br /> ===Hayden&#039;s User Page===<br /> [[user:hhinsch|Hayden Hinsch]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5791 2017-12-15T14:27:01Z

<p>Hhinsch: added my week 15 page link</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Page Desiigner Deliverables Page==<br /> <br /> [[Page Desiigner Deliverables Page]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:Pagedesignprototype.zip]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> <br /> ====Hayden====<br /> # What worked?<br /> #* We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.<br /> # What didn&#039;t work?<br /> #* We still need to complete the prototype and add the other groups&#039; deliverables to our page.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We completed the basic structure of the page, and everyone was able to finish their work in time despite my absence on Thursday. <br /> # What didn&#039;t work?<br /> #* We haven&#039;t finalized anything yet, or implemented any information into the page. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will talk with everyone in class, including the Dahlquist and Dionisio in order to make final decisions moving into Week 15. <br /> <br /> <br /> ===[[Week 15]] Team Progress Reflections===<br /> ====Arash====<br /> This week I worked on adding the finishing touches to our info.html file in order to make the information easier to digest and nicer to look at. I also worked on my parts of the group presentation and report, which basically entailed me writing out, in detail, everything I did for the GRNsight project. I also wrote an individual statement of work that I emailed to the professors.<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 22:44, 14 December 2017 (PST)<br /> [[ArashLari_Week_15|ArashLari Week 15]]<br /> ====Hayden====<br /> This week I helped complete the final presentation for our team as well as the final paper. I made sure all of the deliverables were accurately produced as well as formulates the final presentation and final paper layout. In regards to what worked and what didn&#039;t work, everything was completed on time and we all communicated fairly effectively so I don&#039;t have anything to note on. Our deliverables can be found on my [[Page Desiigner Deliverables Page]] page. A More detailed summary of work can be found on my [[hhinsch Week 15]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:21, 15 December 2017 (PST)<br /> <br /> ====Mary====<br /> ====Nicole====<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5790 2017-12-15T14:22:05Z

<p>Hhinsch: removed my bulltepoint</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Page Desiigner Deliverables Page==<br /> <br /> [[Page Desiigner Deliverables Page]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:Pagedesignprototype.zip]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> <br /> ====Hayden====<br /> # What worked?<br /> #* We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.<br /> # What didn&#039;t work?<br /> #* We still need to complete the prototype and add the other groups&#039; deliverables to our page.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We completed the basic structure of the page, and everyone was able to finish their work in time despite my absence on Thursday. <br /> # What didn&#039;t work?<br /> #* We haven&#039;t finalized anything yet, or implemented any information into the page. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will talk with everyone in class, including the Dahlquist and Dionisio in order to make final decisions moving into Week 15. <br /> <br /> <br /> ===[[Week 15]] Team Progress Reflections===<br /> ====Arash====<br /> This week I worked on adding the finishing touches to our info.html file in order to make the information easier to digest and nicer to look at. I also worked on my parts of the group presentation and report, which basically entailed me writing out, in detail, everything I did for the GRNsight project. I also wrote an individual statement of work that I emailed to the professors.<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 22:44, 14 December 2017 (PST)<br /> [[ArashLari_Week_15|ArashLari Week 15]]<br /> ====Hayden====<br /> This week I helped complete the final presentation for our team as well as the final paper. I made sure all of the deliverables were accurately produced as well as formulates the final presentation and final paper layout. In regards to what worked and what didn&#039;t work, everything was completed on time and we all communicated fairly effectively so I don&#039;t have anything to note on. Our deliverables can be found on my [[Page Desiigner Deliverables Page|hhinsch Week 15]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:21, 15 December 2017 (PST)<br /> <br /> ====Mary====<br /> ====Nicole====<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5789 2017-12-15T14:21:26Z

<p>Hhinsch: added my progress reflection</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Page Desiigner Deliverables Page==<br /> <br /> [[Page Desiigner Deliverables Page]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:Pagedesignprototype.zip]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> <br /> ====Hayden====<br /> # What worked?<br /> #* We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.<br /> # What didn&#039;t work?<br /> #* We still need to complete the prototype and add the other groups&#039; deliverables to our page.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We completed the basic structure of the page, and everyone was able to finish their work in time despite my absence on Thursday. <br /> # What didn&#039;t work?<br /> #* We haven&#039;t finalized anything yet, or implemented any information into the page. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will talk with everyone in class, including the Dahlquist and Dionisio in order to make final decisions moving into Week 15. <br /> <br /> <br /> ===[[Week 15]] Team Progress Reflections===<br /> ====Arash====<br /> This week I worked on adding the finishing touches to our info.html file in order to make the information easier to digest and nicer to look at. I also worked on my parts of the group presentation and report, which basically entailed me writing out, in detail, everything I did for the GRNsight project. I also wrote an individual statement of work that I emailed to the professors.<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 22:44, 14 December 2017 (PST)<br /> [[ArashLari_Week_15|ArashLari Week 15]]<br /> ====Hayden====<br /> *This week I helped complete the final presentation for our team as well as the final paper. I made sure all of the deliverables were accurately produced as well as formulates the final presentation and final paper layout. In regards to what worked and what didn&#039;t work, everything was completed on time and we all communicated fairly effectively so I don&#039;t have anything to note on. Our deliverables can be found on my [[Page Desiigner Deliverables Page|hhinsch Week 15]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:21, 15 December 2017 (PST)<br /> <br /> ====Mary====<br /> ====Nicole====<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5788 2017-12-15T14:17:51Z

<p>Hhinsch: added my electronic signature</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> <br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See template I created above.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 06:17, 15 December 2017 (PST)<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5787 2017-12-15T13:35:30Z

<p>Hhinsch: added notes to my individual deliverable</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> <br /> ===Project Manager/Quality Assurance Deliverables===<br /> *See template I created above.<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5786 2017-12-15T13:34:16Z

<p>Hhinsch: added one if the deliveablres</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*[[Page Desiigner Deliverables Page]]<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*Most group members emailed their statements of work, assessments, and reflections to the professors.<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> <br /> ===Project Manager/Quality Assurance Deliverables===<br /> #Group report<br /> #Individual statement of work, assessment and reflection was emailed to professors<br /> #Github pull<br /> #[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Hhinsch&diff=5785 2017-12-15T11:58:06Z

<p>Hhinsch: added week 15/ deliverables page to my template</p> <hr /> <div>[[Category:Journal Entry]]<br /> ===Assignments===<br /> [[Week 1]]<br /> &lt;br&gt;<br /> [[Week 2]]<br /> &lt;br&gt;<br /> [[Week 3]]<br /> &lt;br&gt;<br /> [[Week 4]]<br /> &lt;br&gt;<br /> [[Week 5]]<br /> &lt;br&gt;<br /> [[Week 6]]<br /> &lt;br&gt;<br /> [[Week 7]]<br /> &lt;br&gt;<br /> [[Week 8]]<br /> &lt;br&gt;<br /> [[Week 9]]<br /> &lt;br&gt;<br /> [[Week 10]]<br /> &lt;br&gt;<br /> [[Week 11]]<br /> &lt;br&gt;<br /> [[Week 12]]<br /> &lt;br&gt;<br /> [[Week 14]]<br /> ===Hayden&#039;s Individual Journal Entries===<br /> [[Week 1 Journal Entry|hhinsch Week 1]]<br /> &lt;br&gt;<br /> [[hhinsch Week 2]]<br /> &lt;br&gt;<br /> [[hhinsch Week 3]]<br /> &lt;br&gt;<br /> [[hhinsch Week 4]]<br /> &lt;br&gt;<br /> [[hhinsch Week 5]]<br /> &lt;br&gt;<br /> [[hhinsch Week 6]]<br /> &lt;br&gt;<br /> [[hhinsch Week 7]]<br /> &lt;br&gt;<br /> [[hhinsch Week 8]]<br /> &lt;br&gt;<br /> [[hhinsch Week 9]]<br /> &lt;br&gt;<br /> [[hhinsch Week 10]]<br /> &lt;br&gt;<br /> [[hhinsch Week 11]]<br /> &lt;br&gt;<br /> [[hhinsch Week 12]]<br /> &lt;br&gt;<br /> [[hhinsch Week 14]]<br /> &lt;br&gt;<br /> [[Page Desiigner Deliverables Page|hhinsch Week 15]]<br /> <br /> ===Class Journal Entries===<br /> [[Class Journal Week 1]]<br /> &lt;br&gt;<br /> [[Class Journal Week 2]]<br /> &lt;br&gt;<br /> [[Class Journal Week 3]]<br /> &lt;br&gt;<br /> [[Class Journal Week 4]]<br /> &lt;br&gt;<br /> [[Class Journal Week 5]]<br /> &lt;br&gt;<br /> [[Class Journal Week 6]]<br /> &lt;br&gt;<br /> [[Class Journal Week 7]]<br /> &lt;br&gt;<br /> [[Class Journal Week 8]]<br /> &lt;br&gt;<br /> [[Class Journal Week 9]]<br /> &lt;br&gt;<br /> [[Class Journal Week 10]]<br /> &lt;br&gt;<br /> [[Page Desiigner]]<br /> ===Electronic Notebook===<br /> [[Hhinsch Electronic Notebook]]<br /> <br /> ===Hayden&#039;s User Page===<br /> [[user:hhinsch|Hayden Hinsch]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5784 2017-12-15T11:42:30Z

<p>Hhinsch: reformatted deliverables page</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Page Designer Deliverables ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> #*<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> #*<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> #*[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> #*<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> #*[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> #*[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> #*[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> #*[[mbalducc Week 8|Week 8]]<br /> #*[[mbalducc Week 10|Week 10]]<br /> #*[[mbalducc Week 11|Week 11]]<br /> #*[[mbalducc Week 12|Week 12]]<br /> #*[[mbalducc Week 14|Week 14]]<br /> <br /> ===Project Manager/Quality Assurance Deliverables===<br /> #Group report<br /> #Individual statement of work, assessment and reflection was emailed to professors<br /> #Github pull<br /> #[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5783 2017-12-15T11:38:25Z

<p>Hhinsch: added some of my deliverables</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Deliverables Checklist ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> <br /> ===Project Manager/Quality Assurance Deliverables===<br /> #Group report<br /> #Individual statement of work, assessment and reflection was emailed to professors<br /> #Github pull<br /> #[[File:BiodbPageDesignFinalPresentation_.pptx]]<br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5683 2017-12-12T21:50:57Z

<p>Hhinsch: added link to new final presentation file on downloads section</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Page Desiigner Deliverables Page==<br /> <br /> [[Page Desiigner Deliverables Page]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:Pagedesignprototype.zip]]<br /> &lt;br&gt;<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> <br /> ====Hayden====<br /> # What worked?<br /> #* We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.<br /> # What didn&#039;t work?<br /> #* We still need to complete the prototype and add the other groups&#039; deliverables to our page.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We completed the basic structure of the page, and everyone was able to finish their work in time despite my absence on Thursday. <br /> # What didn&#039;t work?<br /> #* We haven&#039;t finalized anything yet, or implemented any information into the page. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will talk with everyone in class, including the Dahlquist and Dionisio in order to make final decisions moving into Week 15. <br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5682 2017-12-12T21:49:35Z

<p>Hhinsch: added link to new final presentation file</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation_.pptx]] <br /> <br /> == Deliverables Checklist ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> <br /> <br /> <br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:BiodbPageDesignFinalPresentation_.pptx&diff=5681 2017-12-12T21:47:48Z

<p>Hhinsch: final presentation update</p> <hr /> <div>final presentation update</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5668 2017-12-12T07:38:29Z

<p>Hhinsch: added final presentation powerpoint</p> <hr /> <div><br /> ===Group PowerPoint Presentation===<br /> [[File:BiodbPageDesignFinalPresentation.pptx]] <br /> <br /> == Deliverables Checklist ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> <br /> <br /> <br /> ===Data Analyst Deliverables===<br /> #[[Media:Mbalducc_week8_dCIN5.zip|Excel file for the ANOVA of dCIN5]]<br /> #[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]<br /> #[[media:Mbalduccgene&amp;GOlists.zip|Gene lists and GO lists]]<br /> #[[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 from YEASTRACT &quot;Rank by TF&quot; results]]<br /> #[[media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx|GRNmap input Workbook]]<br /> #[[media:Mbalducc_GRNmapoutputfiles.zip|GRNmap output files]]<br /> <br /> &#039;&#039;&#039;My electronic notebooks that outline the process I followed:&#039;&#039;&#039;<br /> *[[mbalducc Week 8|Week 8]]<br /> *[[mbalducc Week 10|Week 10]]<br /> *[[mbalducc Week 11|Week 11]]<br /> *[[mbalducc Week 12|Week 12]]<br /> *[[mbalducc Week 14|Week 14]]<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 12:39, 11 December 2017 (PST)<br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:BiodbPageDesignFinalPresentation.pptx&diff=5667 2017-12-12T07:36:39Z

<p>Hhinsch: final presentation for page design</p> <hr /> <div>final presentation for page design</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Deliverables_Page&diff=5476 2017-12-05T23:54:39Z

<p>Hhinsch: created our deliverable&#039;s page</p> <hr /> <div>== Deliverables Checklist ==<br /> <br /> # Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)<br /> # Group Report (&#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Individual statements of work, assessments, reflections (wiki page, &#039;&#039;.doc&#039;&#039;, &#039;&#039;.docx&#039;&#039;, &#039;&#039;.pdf&#039;&#039;, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)<br /> # Group PowerPoint presentation (given on Tuesday, December 12, &#039;&#039;.ppt&#039;&#039;, &#039;&#039;.pptx&#039;&#039; or &#039;&#039;.pdf&#039;&#039; file)<br /> # Code (GitHub pull request)<br /> #* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the &#039;&#039;original&#039;&#039; GRNsight GitHub repository as a single, unified pull request from the class project’s fork<br /> # Supply a README that summarizes the functionality of your team&#039;s new feature (&#039;&#039;.txt&#039;&#039; or &#039;&#039;.md&#039;&#039;, &#039;&#039;one README per team&#039;&#039;)<br /> # Excel spreadsheet with ANOVA results/stem formatting (&#039;&#039;.xlsx&#039;&#039;)<br /> # PowerPoint of screenshots of stem results (&#039;&#039;.pptx&#039;&#039;)<br /> # Gene List and GO List files from each significant profile (&#039;&#039;.txt&#039;&#039; compressed together in a &#039;&#039;.zip&#039;&#039; file)<br /> # YEASTRACT &quot;rank by TF&quot; results (&#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap input workbook (with network adjacency matrix, &#039;&#039;.xlsx&#039;&#039;)<br /> # GRNmap output workbook (&#039;&#039;.xlsx&#039;&#039;)<br /> # Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support &#039;&#039;reproducible research&#039;&#039; so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.<br /> <br /> <br /> {{pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5473 2017-12-05T23:53:44Z

<p>Hhinsch: added prototype page to the uploaded files section and created link to groups deliverables page</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Page Desiigner Deliverables Page==<br /> <br /> [[Page Desiigner Deliverables Page]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> <br /> ====Hayden====<br /> # What worked?<br /> #* We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.<br /> # What didn&#039;t work?<br /> #* We still need to complete the prototype and add the other groups&#039; deliverables to our page.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We completed the basic structure of the page, and everyone was able to finish their work in time despite my absence on Thursday. <br /> # What didn&#039;t work?<br /> #* We haven&#039;t finalized anything yet, or implemented any information into the page. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will talk with everyone in class, including the Dahlquist and Dionisio in order to make final decisions moving into Week 15. <br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5386 2017-12-05T04:19:43Z

<p>Hhinsch: added my progress reflection</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> <br /> ====Hayden====<br /> # What worked?<br /> #* We did a pretty good job getting everything done we needed to get done this week in a timely fashion while dealing with adversity.<br /> # What didn&#039;t work?<br /> #* We still need to complete the prototype and add the other groups&#039; deliverables to our page.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We just simply need to take a final assessment of the deliverables as well as gather feedback from the entire class regarding the final layout of the page.<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* <br /> # What didn&#039;t work?<br /> #* <br /> # What will I do next to fix what didn&#039;t work?<br /> #* <br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5385 2017-12-05T04:16:12Z

<p>Hhinsch: added my week 14 exec summary</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> This week I served as a &quot;floater&quot;. I worked with Nicole and Arash in order to come up with how the page design prototype would look. We decided to use the ACT1 design along with Nicole&#039;s sketch in order to find a balance between aesthetic and function. The design we used is downloadable from this page and my [[hhinsch Week 14]] page. My [[hhinsch Week 14]] page has some more information regarding why we chose our current prototype design. I also spoke with Mary to make sure she knew I was there to help with her deliverables if needed. I also spent time with the other QA&#039;s this week in order to familiarize myself with the deliverables of the other groups. This was necessary for me to make sure we added everything to the page that is required. I uploaded images to my [hhinsch Week 14]] page as well as this page in order to further clarify our thought process behind the page prototype. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 20:16, 4 December 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_14&diff=5384 2017-12-05T04:09:44Z

<p>Hhinsch: fixed github reference</p> <hr /> <div><br /> [[Category:Journal Entry]]<br /> ==Week 14 Electronic Notebook==<br /> *This week I worked with the other QA&#039;s to become familiar with what each team will be contributing to the page.<br /> *I worked with Arash and Nicole in order to come to an agreement regarding the design of the page. <br /> *In order to do this Arash and I looked over some of the favorite gene pages in class and decided we liked the layout of ACT1. I provided an image of the ACT1 page below.<br /> [[File:ACT1screenshot.png|500px]]<br /> *We decided to use a layout similar to the ACT1 page because it organizes the information well without crowding the page too much.<br /> *Nicole came up with the sketch below.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is very similar to the ACT1 page and although it as a rough sketch, we felt it would serve as the best option to keep the page aesthetically pleasing as well as give all of the information required.<br /> *Arash spent time coding the specific things we needed into this template. <br /> *The information we needed to put onto the page are as follows:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *Although the page prototype does not have all of the information listed above yet, it is easily inputted into the code. <br /> *I also spent time this week getting to know the information that other teams will be providing to the page.<br /> *I spent the most time with the JASPAR team because it was some gene information I have not encountered thus far. I found the frequency matrix most interesting.<br /> *This week I also spent time with Mary to understand her YEASTRACT assignment and made sure she got any help she needed completing the deliverable.<br /> *Arash and I then communicated to make sure we had everything we needed. <br /> *Arash directed me to the github for our project and I downloaded all of the files. <br /> *After downloading the files I renamed the &lt;code&gt;gene&lt;/code&gt; file to &lt;code&gt;pagedesignprototype&lt;/code&gt; and uploaded it to the wiki and created a link on our team page.<br /> *The file containing the html file of the page prototype is below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Acknowledgments==<br /> #I worked with [[User:ArashLari|Arash Lari]], [[User:Mbalducc|Mary Balducci]] and [[User:Nicolekalcic|Nicole Kalcic]] in person and over text to complete the deliverables of this assignment.<br /> #I worked with the other QA&#039;s in order to become familiar with the information to be provided on the page.<br /> #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 19:58, 4 December 2017 (PST)<br /> ==References==<br /> #LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14<br /> #Github. (2017). bhamilton18/GRNsight, Retrieved December 4, 2017, from https://github.com/bhamilton18/GRNsight/tree/page-design<br /> {{pagedesiigner}}<br /> {{hhinsch}}<br /> <br /> [[Category:Journal Entry]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_14&diff=5382 2017-12-05T04:08:13Z

<p>Hhinsch: added category and github reference</p> <hr /> <div><br /> [[Category:Journal Entry]]<br /> ==Week 14 Electronic Notebook==<br /> *This week I worked with the other QA&#039;s to become familiar with what each team will be contributing to the page.<br /> *I worked with Arash and Nicole in order to come to an agreement regarding the design of the page. <br /> *In order to do this Arash and I looked over some of the favorite gene pages in class and decided we liked the layout of ACT1. I provided an image of the ACT1 page below.<br /> [[File:ACT1screenshot.png|500px]]<br /> *We decided to use a layout similar to the ACT1 page because it organizes the information well without crowding the page too much.<br /> *Nicole came up with the sketch below.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is very similar to the ACT1 page and although it as a rough sketch, we felt it would serve as the best option to keep the page aesthetically pleasing as well as give all of the information required.<br /> *Arash spent time coding the specific things we needed into this template. <br /> *The information we needed to put onto the page are as follows:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *Although the page prototype does not have all of the information listed above yet, it is easily inputted into the code. <br /> *I also spent time this week getting to know the information that other teams will be providing to the page.<br /> *I spent the most time with the JASPAR team because it was some gene information I have not encountered thus far. I found the frequency matrix most interesting.<br /> *This week I also spent time with Mary to understand her YEASTRACT assignment and made sure she got any help she needed completing the deliverable.<br /> *Arash and I then communicated to make sure we had everything we needed. <br /> *Arash directed me to the github for our project and I downloaded all of the files. <br /> *After downloading the files I renamed the &lt;code&gt;gene&lt;/code&gt; file to &lt;code&gt;pagedesignprototype&lt;/code&gt; and uploaded it to the wiki and created a link on our team page.<br /> *The file containing the html file of the page prototype is below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Acknowledgments==<br /> #I worked with [[User:ArashLari|Arash Lari]], [[User:Mbalducc|Mary Balducci]] and [[User:Nicolekalcic|Nicole Kalcic]] in person and over text to complete the deliverables of this assignment.<br /> #I worked with the other QA&#039;s in order to become familiar with the information to be provided on the page.<br /> #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 19:58, 4 December 2017 (PST)<br /> ==References==<br /> #LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14<br /> #Github. (2017). bhamilton18/GRNsight, Retrieved December 4, 2017, github.com/bhamilton18/GRNsight/tree/page-design.<br /> {{pagedesiigner}}<br /> {{hhinsch}}<br /> <br /> [[Category:Journal Entry]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5381 2017-12-05T03:59:42Z

<p>Hhinsch: fixed a typo</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype.zip&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_14&diff=5380 2017-12-05T03:58:42Z

<p>Hhinsch: linked prototype page design, added references and acknowledgments</p> <hr /> <div>==Week 14 Electronic Notebook==<br /> *This week I worked with the other QA&#039;s to become familiar with what each team will be contributing to the page.<br /> *I worked with Arash and Nicole in order to come to an agreement regarding the design of the page. <br /> *In order to do this Arash and I looked over some of the favorite gene pages in class and decided we liked the layout of ACT1. I provided an image of the ACT1 page below.<br /> [[File:ACT1screenshot.png|500px]]<br /> *We decided to use a layout similar to the ACT1 page because it organizes the information well without crowding the page too much.<br /> *Nicole came up with the sketch below.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is very similar to the ACT1 page and although it as a rough sketch, we felt it would serve as the best option to keep the page aesthetically pleasing as well as give all of the information required.<br /> *Arash spent time coding the specific things we needed into this template. <br /> *The information we needed to put onto the page are as follows:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *Although the page prototype does not have all of the information listed above yet, it is easily inputted into the code. <br /> *I also spent time this week getting to know the information that other teams will be providing to the page.<br /> *I spent the most time with the JASPAR team because it was some gene information I have not encountered thus far. I found the frequency matrix most interesting.<br /> *This week I also spent time with Mary to understand her YEASTRACT assignment and made sure she got any help she needed completing the deliverable.<br /> *Arash and I then communicated to make sure we had everything we needed. <br /> *Arash directed me to the github for our project and I downloaded all of the files. <br /> *After downloading the files I renamed the &lt;code&gt;gene&lt;/code&gt; file to &lt;code&gt;pagedesignprototype&lt;/code&gt; and uploaded it to the wiki and created a link on our team page.<br /> *The file containing the html file of the page prototype is below.<br /> [[File:Pagedesignprototype.zip]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Acknowledgments==<br /> #I worked with [[User:ArashLari|Arash Lari]], [[User:Mbalducc|Mary Balducci]] and [[User:Nicolekalcic|Nicole Kalcic]] in person and over text to complete the deliverables of this assignment.<br /> #I worked with the other QA&#039;s in order to become familiar with the information to be provided on the page.<br /> #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 19:58, 4 December 2017 (PST)<br /> ==References==<br /> #LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14<br /> {{pagedesiigner}}<br /> {{hhinsch}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5379 2017-12-05T03:54:18Z

<p>Hhinsch: added the page prototype zip file</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *A zip file containing the html file of prototype page can be downloaded by clicking the &lt;code&gt;pagedesignprototype&lt;/code&gt; link below.<br /> [[File:Pagedesignprototype.zip]]<br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Executive Summaries===<br /> ====Arash====<br /> This week I worked on implementing our designs for the web page. Nicole and Hayden helped come up with some design ideas. We ended up deciding that ACT1 was a very well designed page and that it would be best to follow the format of that page. There&#039;s only a few things left to do but our portion of the project is nearly complete, the generic version of every gene&#039;s page needs just a few finishing touches. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 18:19, 4 December 2017 (PST)<br /> <br /> ====Mary====<br /> This week I finished the Week 10 assignment, using YEASTRACT and GRNsight. I specifically chose one profile from the STEM results to use in YEASTRACT to find transcription factors that regulate a cluster of genes. First I uploaded the genes from profile #22 into YEASTRACT to find 20 significant transcription factors that regulate them. Then, I used Excel to get rid of the transcription factors that were not related to other transcription factors. Once I had those, I imported them into GRNsight to create a map of the transcription factors and their relations to each other. I took a screenshot of this map and uploaded it to my [[mbalducc Week 14| Week 14]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:14, 4 December 2017 (PST)<br /> <br /> ====Nicole====<br /> <br /> <br /> ====Hayden====<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> ===[[Week 14]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #* Our design idea turned out pretty nicely, and was not that difficult to implement.<br /> # What didn&#039;t work?<br /> #* Coming up with what the final aesthetics will look like.<br /> # What will I do next to fix what didn&#039;t work?<br /> #* We will discuss the matter in class with the professors and our fellow students to see what works best for everyone.<br /> <br /> ====Mary====<br /> #What worked?<br /> #*Using YEASTRACT, Excel, and GRNsight to create a map of significant transcription factors in the profile I chose.<br /> #What didn&#039;t work?<br /> #*I have not fixed Weeks 8 and 10 as much as I would have wanted to.<br /> #What will I do next to fix what didn&#039;t work?<br /> #*Take more time, make sure I do things right the first time so I don&#039;t have to back and fix them later.<br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:Pagedesignprototype.zip&diff=5378 2017-12-05T03:50:35Z

<p>Hhinsch: uploaded a zip file for a page design prototype</p> <hr /> <div>uploaded a zip file for a page design prototype</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_14&diff=5377 2017-12-05T03:49:25Z

<p>Hhinsch: fixed page desiigner template and added entries to my electronic notebook</p> <hr /> <div>==Week 14 Electronic Notebook==<br /> *This week I worked with the other QA&#039;s to become familiar with what each team will be contributing to the page.<br /> *I worked with Arash and Nicole in order to come to an agreement regarding the design of the page. <br /> *In order to do this Arash and I looked over some of the favorite gene pages in class and decided we liked the layout of ACT1. I provided an image of the ACT1 page below.<br /> [[File:ACT1screenshot.png|500px]]<br /> *We decided to use a layout similar to the ACT1 page because it organizes the information well without crowding the page too much.<br /> *Nicole came up with the sketch below.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is very similar to the ACT1 page and although it as a rough sketch, we felt it would serve as the best option to keep the page aesthetically pleasing as well as give all of the information required.<br /> *Arash spent time coding the specific things we needed into this template. <br /> *The information we needed to put onto the page are as follows:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> *Although the page prototype does not have all of the information listed above yet, it is easily inputted into the code. <br /> *I also spent time this week getting to know the information that other teams will be providing to the page.<br /> *I spent the most time with the JASPAR team because it was some gene information I have not encountered thus far. I found the frequency matrix most interesting.<br /> *This week I also spent time with Mary to understand her YEASTRACT assignment and made sure she got any help she needed completing the deliverable.<br /> *Arash and I then communicated to make sure we had everything we needed. <br /> *Arash directed me to the github for our project and I downloaded all of the files. <br /> *After downloading the files I renamed the &lt;code&gt;gene&lt;/code&gt; file to &lt;code&gt;pagedesignprototype&lt;/code&gt; and uploaded it to the wiki and created a link on our team page.<br /> *The file containing the html file of the page prototype is below.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Acknowledgments==<br /> <br /> ==References==<br /> <br /> {{pagedesiigner}}<br /> {{hhinsch}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Hhinsch_Week_14&diff=5370 2017-12-05T03:24:00Z

<p>Hhinsch: created week 14 page</p> <hr /> <div>==Week 14 Electronic Notebook==<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Acknowledgments==<br /> <br /> ==References==<br /> <br /> {{pagedesiigner]]<br /> {{hhinsch}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Hhinsch&diff=5369 2017-12-05T03:22:46Z

<p>Hhinsch: added week 14 to my template</p> <hr /> <div>[[Category:Journal Entry]]<br /> ===Assignments===<br /> [[Week 1]]<br /> &lt;br&gt;<br /> [[Week 2]]<br /> &lt;br&gt;<br /> [[Week 3]]<br /> &lt;br&gt;<br /> [[Week 4]]<br /> &lt;br&gt;<br /> [[Week 5]]<br /> &lt;br&gt;<br /> [[Week 6]]<br /> &lt;br&gt;<br /> [[Week 7]]<br /> &lt;br&gt;<br /> [[Week 8]]<br /> &lt;br&gt;<br /> [[Week 9]]<br /> &lt;br&gt;<br /> [[Week 10]]<br /> &lt;br&gt;<br /> [[Week 11]]<br /> &lt;br&gt;<br /> [[Week 12]]<br /> &lt;br&gt;<br /> [[Week 14]]<br /> ===Hayden&#039;s Individual Journal Entries===<br /> [[Week 1 Journal Entry|hhinsch Week 1]]<br /> &lt;br&gt;<br /> [[hhinsch Week 2]]<br /> &lt;br&gt;<br /> [[hhinsch Week 3]]<br /> &lt;br&gt;<br /> [[hhinsch Week 4]]<br /> &lt;br&gt;<br /> [[hhinsch Week 5]]<br /> &lt;br&gt;<br /> [[hhinsch Week 6]]<br /> &lt;br&gt;<br /> [[hhinsch Week 7]]<br /> &lt;br&gt;<br /> [[hhinsch Week 8]]<br /> &lt;br&gt;<br /> [[hhinsch Week 9]]<br /> &lt;br&gt;<br /> [[hhinsch Week 10]]<br /> &lt;br&gt;<br /> [[hhinsch Week 11]]<br /> &lt;br&gt;<br /> [[hhinsch Week 12]]<br /> &lt;br&gt;<br /> [[hhinsch Week 14]]<br /> ===Class Journal Entries===<br /> [[Class Journal Week 1]]<br /> &lt;br&gt;<br /> [[Class Journal Week 2]]<br /> &lt;br&gt;<br /> [[Class Journal Week 3]]<br /> &lt;br&gt;<br /> [[Class Journal Week 4]]<br /> &lt;br&gt;<br /> [[Class Journal Week 5]]<br /> &lt;br&gt;<br /> [[Class Journal Week 6]]<br /> &lt;br&gt;<br /> [[Class Journal Week 7]]<br /> &lt;br&gt;<br /> [[Class Journal Week 8]]<br /> &lt;br&gt;<br /> [[Class Journal Week 9]]<br /> &lt;br&gt;<br /> [[Class Journal Week 10]]<br /> &lt;br&gt;<br /> [[Page Desiigner]]<br /> ===Electronic Notebook===<br /> [[Hhinsch Electronic Notebook]]<br /> <br /> ===Hayden&#039;s User Page===<br /> [[user:hhinsch|Hayden Hinsch]]</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5309 2017-12-02T00:01:02Z

<p>Hhinsch: changed the pixel count of act1 screenshot</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png|500px]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> <br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner&diff=5308 2017-12-02T00:00:00Z

<p>Hhinsch: added some of the page layout details</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> <br /> <br /> ==Page Design Team Members==<br /> Coder: [[User:ArashLari|Arash Lari]]&lt;!--Replicated from home page--&gt;<br /> &lt;br&gt;<br /> Project Manager/ Quality Assurance: [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> Data Analyst: [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> Designer: [[User:Nicolekalcic|Nicole Kalcic]]<br /> <br /> ==Team Schedule==<br /> [[Page Desiigner Schedule]]<br /> <br /> ==Page Desiigner Uploaded Files==<br /> <br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> &lt;br&gt;<br /> [[File:Data Driven Design.zip]]<br /> <br /> ==Page Layout==<br /> *&lt;code&gt;Below are a series of rough ideas we will use to create the layout of the page&lt;/code&gt;<br /> [[File:ACT1screenshot.png]]<br /> *We will be using a layout similar to the ACT1 gene page.<br /> [[File:Sketchofpagedesign.png]]<br /> *This is a rough sketch of what the page will look like.<br /> *The section labeled &#039;&#039;&#039;description&#039;&#039;&#039; on the sketch will include the following:<br /> **Gene ID from each database<br /> **Description/Function (ensembl)<br /> *Within the dropdown menus we will be incorporating the following:<br /> **DNA Sequence (ensembl)<br /> **Protein Sequence (UniProt)<br /> **Locus tag (NCBI)<br /> **Also Known As (NCBI)<br /> **Consensus Sequence (JASPAR)<br /> **Regulation (SGD)<br /> **Interaction (SGD)<br /> **Similar Proteins (UniProt)<br /> **Gene Ontology (SGD)<br /> **JASPAR<br /> ***Matrix ID <br /> ***Class Heat shock factors<br /> ***Family HSF factors<br /> ***Sequence Logo <br /> ***Frequency Matrix<br /> <br /> ==Annotated Bibliography==<br /> ===Mary&#039;s contribution:===<br /> Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> *PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18723660<br /> *PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *HTML format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/<br /> *PDF format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf<br /> *Copyright: 2008 American Society for Microbiology. It is open access.<br /> *Publisher: American Society for Microbiology. This is a scientific society.<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> <br /> Homma, Iwahashi, Komatsu. (2003) Yeast Gene Expression During Growth at Low Temperature. &#039;&#039;Cryobiology&#039;&#039;, 46, doi: 10.1016/S0011-2240(03)00028-2<br /> *PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212<br /> *PubMed Central: <br /> *HTML format: http://www.sciencedirect.com/science/article/pii/S0011224003000282?via%3Dihub<br /> *PDF format: https://ac.els-cdn.com/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=aa7fa05e-c5d2-11e7-88ae-00000aacb361&amp;acdnat=1510289609_6ec25501ce7af9dcc6b521ef8a024164<br /> *Copyright 2003 Elsevier Science (USA). It is open access.<br /> *Publisher: Elsevier. This is a for-profit publisher<br /> *Availability: Online and in print<br /> *Did LMU pay a fee for this article: No<br /> *I could not find the data associated with this article.<br /> <br /> ===Hayden&#039;s Contribution===<br /> <br /> Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., &amp; Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504<br /> * PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/<br /> * Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6<br /> * Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf<br /> * Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.<br /> * Publisher: Bulletin of Mathematical Biology(scientific society)<br /> * Availability: Online<br /> * Did LMU pay a fee for this article: No<br /> * Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip<br /> <br /> <br /> Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x<br /> * PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656<br /> * PubMed Central: N/A<br /> * Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1<br /> * Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf<br /> * Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.<br /> * Publisher: Published by Oxford University Press(respected open access organization)<br /> * Availability: Online and in print<br /> * Did LMU pay a fee for this article: No<br /> * Data: I couldn&#039;t find any supplementary data other than the data provided in the article.<br /> <br /> <br /> <br /> <br /> ==Journal Club Presentations==<br /> ===Powerpoint Slides and Respective Articles===<br /> [[File:Data Driven Design.zip]]<br /> * Liikkanen, L. (2017). The Data-Driven Design Era in Professional Web Design. Accessed November 13, 2017, from http://delivery.acm.org/10.1145/3130000/3121355/p52-liikkanen.pdf?ip=157.242.223.254&amp;id=3121355&amp;acc=ACTIVE%20SERVICE&amp;key=80B0E63637265656%2E958C566062FD1C18%2E4D4702B0C3E38B35%2E4D4702B0C3E38B35&amp;CFID=829067610&amp;CFTOKEN=20249523&amp;__acm__=1510614806_1e8b314e23f771f9b139d99596801365<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> *Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. &quot;Applied and Environmental Microbiology&quot;, 74, 6358-6368, doi:10.1128/AEM.00602-08<br /> <br /> ==Executive Summaries==<br /> <br /> <br /> ===[[Week 11]] Executive Summaries===<br /> ====Arash====<br /> This week, I worked on researching the given article and the development terms within it as well as prepare a presentation on the article. I also began thinking of some page layout ideas with Nicole to prepare to implement in the coming weeks. All of this information could be found on my Week 11 page: [[ArashLari_Week_11|ArashLari Week 11]].<br /> [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 02:09, 14 November 2017 (PST)<br /> ====Mary====<br /> This week, I worked on creating an annotated bibliography. The articles I found were primary sources about experiments done involving cold shock on yeast, and the use of microarrays to show results. I used multiple databases to find these articles, and while doing so I learned what key words got me the results closest to what I wanted. While writing the annotated bibliography, I also learned more about the articles, such as when they were written, who published them, what kind of publisher they are, and other information. All of this is recorded in my [[mbalducc Week 11| Week 11]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 23:03, 13 November 2017 (PST)<br /> <br /> ====Nicole====<br /> This past week, I read the article &#039;&#039;The Data-Driven Design Era in Professional Web Design&#039;&#039; by L.A. Liikkanen. This allowed me to complete my individual journal: an informative outline of the article and list of ten definitions. Arash and I worked together to complete a 15 minute presentation that we are going to give on Tuesday. The presentation gives an overview of our individual journals and what we each learned. You can access more information on what I did this week here: [[Nicolekalcic Week 11]].<br /> [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 01:27, 14 November 2017 (PST)<br /> ====Hayden====<br /> This week I created part of the annotated bibliography we will be using for our final project. I conducted searched for &quot;yeast cold shock microarray&quot; articles and found which two articles I was going to use for the bibliography. The majority of the time this week was spent on finding the information needed for the annotated bibliography which can be found below on this page. More detailed information can be found on my [[hhinsch Week 11]] page. This week I became proficient in finding reliable article to use for our final project. This week we also created the group&#039;s template and wiki page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:43, 13 November 2017 (PST)<br /> <br /> ===[[Week 12]] Executive Summaries===<br /> ====Arash====<br /> This week was rather light compared to the previous week. We mostly set up the files on our personal computers, which was convenient because as a computer science major I already had most of the necessary files. Nicole and I talked about some preliminary designs and set up a rough schedule that we&#039;ll make concrete after the break. This can be found on my week 12 page [[ArashLari Week 12] | Arash Lari Week 12]. [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 20:43, 20 November 2017 (PST)<br /> <br /> ====Mary====<br /> This week I read an article about an experiment done on wine and lab strains of yeast in different temperatures. The experimenters used DNA microarrays to determine which genes were affected by the change in temperatures and which were different based on the different strains of yeast. While reading the article, I can across words I had never seen before, so I also found and recorded the definitions of these words. I then made an outline of the article, to use as a basis for my presentation with our project manager, [[user:hhinsch| Hayden]]. All of this is on my [[mbalducc Week 12| Week 12]] page.<br /> <br /> [[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 19:51, 19 November 2017 (PST)<br /> <br /> ====Nicole====<br /> Because Arash and I presented last week, we didn&#039;t have a heavy work load this week. Arash explained a lot of technical things to me, and we completed the first coding milestones and talked about design possibilities. I officially have a GitHub (nicolekal). I also downloaded the software I needed but didn&#039;t have onto my laptop. A full update can be found on: [[Nicolekalcic Week 12] | Nicole Kalcic Week 12]. [[User:Nicolekalcic|Nicolekalcic]] ([[User talk:Nicolekalcic|talk]]) 23:45, 20 November 2017 (PST)<br /> <br /> ====Hayden====<br /> This week I worked with Mary specifically in order to complete our journal club presentation. As a group we worked together to make corrections to the [[Page Desiigner]] group page in order to complete the deliverables for this week. Mary and I created a schedule for our group along with helpful links. As a class we decided we will be using WhatsApp to communicate. I spent most of this week outlining the article (it was a pretty difficult read) and defining terms on my [[hhinsch Week 12]] page. [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 17:42, 20 November 2017 (PST)<br /> <br /> ==Team Progress Reflections==<br /> <br /> ===[[Week 11]] Team Progress Reflections===<br /> <br /> ====Nicole====<br /> # What worked?<br /> #* We all work well in our positions. Arash and I worked together recently, so it was easy to coordinate what we are going to do as coder and designer. Everyone was open to opinions on the page and team name. Also, everyone communicated what they were having trouble finishing. <br /> # What didn&#039;t work?<br /> #* Like Mary said, we weren&#039;t able to meet in person. We planned out our meetup during class, but Friday ended up being a busy day for everyone. <br /> # What will I do next to fix what didn&#039;t work?<br /> #* Next week I will make sure to check in more with my partners. Even if we don&#039;t meet up, it is important to make sure everyone is caught up on the assignment and their individual parts. <br /> ====Mary====<br /> # What worked?<br /> #*I think as a team, we did a good job communicating and figuring out what needed to be done, and who would do each part.<br /> # What didn&#039;t work?<br /> #*We did not meet up outside of class. We had planned to, but we all ended up having conflicts so we couldn&#039;t meet.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I think this can be fixed just by making sure we all communicate in other ways, which is what we did. Through text messages we were able to talk about the assignment and help each other.<br /> ====Hayden====<br /> # What worked?<br /> #*We are all doing well communicating and completing our deliverables as individuals and as a group.<br /> # What didn&#039;t work?<br /> #*Everything worked well in regards to the group, but I did have some trouble finding all the information needed to create an annotated bibliography for the articles I used. Google Scholar gave me way too many results, and PubMed did not have a lot of articles that were either free or LMU had paid for.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will continue to ask questions in class. I also feel more confident about finding useful articles after the completion of this assignment, so it shouldn&#039;t be a problem.<br /> [[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:44, 13 November 2017 (PST)<br /> <br /> ====Arash====<br /> <br /> # What worked?<br /> #*We were good at maintaining our own individual tasks and keeping each other updated via text message.<br /> <br /> # What didn&#039;t work?<br /> #*We were unable to schedule time to meet and work effectively. <br /> <br /> # What will I do next to fix what didn&#039;t work?<br /> #*Hopefully we will have lighter course loads and more free time for the next assignment, but besides that we will begin working sooner and try to work in person more than digitally.<br /> <br /> <br /> ===[[Week 12]] Team Progress Reflections===<br /> <br /> ====Arash====<br /> # What worked?<br /> #*I think we all got a better grasp of the assignment and time management for the assignment. We have a clear idea where we&#039;re headed.<br /> # What didn&#039;t work?<br /> #* I wish we had more time to dedicate to this class, as often our schedules don&#039;t line up. <br /> # What will I do next to fix what didn&#039;t work?<br /> #*We&#039;ll try to be more proactive about all our tasks so they don&#039;t pile up. I&#039;m planning on starting some work during the thanksgiving break to lighten the load afterwards.<br /> ====Mary====<br /> # What worked?<br /> #*I think that this week I felt more comfortable with the project as a whole. I also liked presenting after the other guilds because I got to see their presentations to get a better idea of what we should include in ours.<br /> # What didn&#039;t work?<br /> #*I wish that I had more time to read the article and make the presentation. I felt that I didn&#039;t understand the article completely, and had to read it a few times to be happy with the way that I understood it and formed my outline of it. Because of this, I couldn&#039;t spend as much time as I would&#039;ve wanted on making the presentation.<br /> # What will I do next to fix what didn&#039;t work?<br /> #*I will try to spend more time on the entire project, instead of just one part.<br /> <br /> ====Nicole====<br /> #What Worked?<br /> #*Arash and I communicated via text and had a better idea of what we needed to do earlier on in the week, which made it easier to progress and do quality, time efficient work. <br /> #What didn&#039;t work?<br /> #*We weren&#039;t all able to meet in person. I don&#039;t know if this was a huge issue this week, but scheduling conflicts might become more of a problem in December. <br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try to make plans with the group on Tuesday. I am assuming everyone is going out of town for Thanksgiving, but perhaps we can make certain dates within the week to have things done by so the rest of the group can look over the work.<br /> <br /> ====Hayden====<br /> #What Worked?<br /> #*This week we were a little more prepared to work together and complete the deliverables. As time goes by the end goal is becoming more apparent.<br /> #What didn&#039;t work?<br /> #*I spent a lot of time reading the article multiple times and it is still a bit confusing to me. A lot of the vocabulary wasn&#039;t even found in the dictionaries we provided and a lot of the information needed a lot of background knowledge to comprehend.<br /> #What will I do next week to fix what didn&#039;t work?<br /> #*Next week I will try and do the bulk of the assignment earlier in the week rather than on the weekend, so I may have more time to understand the material.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 21:09, 20 November 2017 (PST)<br /> <br /> <br /> {{Pagedesiigner}}</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:Sketchofpagedesign.png&diff=5307 2017-12-01T23:52:28Z

<p>Hhinsch: this is the sketch of our page design</p> <hr /> <div>this is the sketch of our page design</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=File:ACT1screenshot.png&diff=5306 2017-12-01T23:51:17Z

<p>Hhinsch: screenshot of act1 page</p> <hr /> <div>screenshot of act1 page</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Page_Desiigner_Schedule&diff=5287 2017-11-30T23:54:00Z

<p>Hhinsch: crossed off some of the calendar items</p> <hr /> <div>=[[Page Desiigner Schedule]]=<br /> ==Page Desiigner Deliverables==<br /> The Page Design team is responsible for the visual appearance and internal behavior of the gene page. The core deliverable of the team is the HTML/CSS/JavaScript code for this page, in a form that can be dynamically populated based on the gene chosen by the GRNsight user. The final page design shall also design messages and alerts for errors and warnings, such as when the user attempts to display a gene page for a node that does not correspond to a S. cerevisiae gene.<br /> &lt;br&gt;<br /> The Data Analyst will complete the analysis of microarray data for the dCIN5 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.<br /> <br /> ==Schedule of Deliverables==<br /> #&lt;s&gt;Coder and Designer present journal club presentation on &#039;&#039;&#039;November 14&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Project Manager and Data Analysis add annotated bibliographies to the team page by &#039;&#039;&#039;November 14&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Project Manager and Data Analysis present journal club presentation on &#039;&#039;&#039;November 21&#039;&#039;&#039;&lt;/s&gt;<br /> #&lt;s&gt;Coder and Designer complete milestones 0-3 and begin milestone 4 by &#039;&#039;&#039;November 21&#039;&#039;&#039;&lt;/s&gt;<br /> #Entire group will give a final group PowerPoint presentation in class during the final exam period on &#039;&#039;&#039;Tuesday, December 12, 2:00pm&#039;&#039;&#039;<br /> #&#039;&#039;&#039;Final due date for all other deliverables is no later than Friday, December 15, 4:30pm (according to official final exam schedule for fall, 2017)&#039;&#039;&#039;</div>

Hhinsch https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Template:Pagedesiigner&diff=4950 2017-11-21T05:12:14Z

<p>Hhinsch: got rid of a bulletpoint on page desiigner schedule</p> <hr /> <div>[[Category:Page Desiigner]]<br /> [[Category:Group Projects]]<br /> <br /> {| class=&quot;wikitable&quot; style=&quot;width: 100%; text-align: center&quot;<br /> ! colspan=&quot;8&quot;|GRNsight Gene Page Project Links<br /> |-<br /> ! rowspan=&quot;2&quot;|[[GRNsight Gene Page Project|Overview]]<br /> ! rowspan=&quot;2&quot;| [[GRNsight Gene Page Project Deliverables|Deliverables]]<br /> | rowspan=&quot;2&quot;|[https://peerj.com/about/author-instructions/#reference-format Reference Format]<br /> ! Guilds<br /> | [[Project Manager]]<br /> | [[Quality Assurance]]<br /> | [[Data Analysis]]<br /> | [[Coder]]<br /> |-<br /> ! Teams<br /> | [[Page Desiigner]]<br /> | [[Lights, Camera, InterACTION!]]<br /> | [[White Chicks]]<br /> | [[JASPAR the Friendly Ghost]]<br /> |}<br /> <br /> <br /> ===Page Desiigner Schedule===<br /> [[Page Desiigner Schedule]]<br /> <br /> ===Uploaded Files===<br /> [[File:Data Driven Design.zip]]<br /> &lt;br&gt;<br /> [[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]<br /> ===Individual Contributer Pages===<br /> [[User:ArashLari|Arash Lari]]<br /> &lt;br&gt;<br /> [[User:hhinsch|Hayden Hinsch]]<br /> &lt;br&gt;<br /> [[User:Mbalducc|Mary Balducci]]<br /> &lt;br&gt;<br /> [[User:Nicolekalcic|Nicole Kalcic]]</div>

Hhinsch