LMU BioDB 2024 - User contributions [en]

Hivanson Week 15

2024-05-03T18:03:31Z

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ yeastract tool

===Electronic laboratory notebook for weeks 14-15===
I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out [[Data_Analysts_Week_14|here]]. I ran the sanity check to find the ideal B&H p-value (goal: significance of ~25%).
I made the expression table to send to the coder/designers. There are two sheets in the expression table, each containing ONLY the ID in column 1, and Log2 Fold Change data for EITHER control OR CHP at each timepoint for each trial.
An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated by adding in the proper data to the ANOVA sheet, and re-running the Bonferroni and B&H corrections. The sanity check values were readjusted for the CHP data.

I also used the "ORF List <-> Gene List" tool at YEASTRACT to get the standard names for the significant genes in profile 41. This tool was also used to determine whether the transcription factors were part of our GRNmap cluster (Katie did this, but I converted the gene names).

I helped Charlotte and Katie run the Stem analysis. Steps outlined [[Data_Analysts_Week_14|here]].

I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.

For the final presentation, I made the flow chart using Goodnotes5, I made the outline, I wrote the Sha et al. background, I put together and interpreted the GRNmaps from what Dr. Dahlquist sent us, and I drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.

For the final paper, I wrote the introduction, added figure captions to some of the Data Analysts section, helped with the conclusion, and imported and updated the references.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts, these past few weeks during class and in person to complete the rest of the data analyst's sections as well as all of the final deliverables. The [[Yeast_Beasts|whole team]] communicated via text, call, FaceTime, and in person to work on the final presentation and paper.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:28, 3 May 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Data Analysts Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_14
*LMU BioDB 2024. (2024). Data Analysts Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_15
*LMU BioDB 2024. (2024). Week 9. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 10. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
*LMU BioDB 2024. (2024). Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14
*LMU BioDB 2024. (2024). Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

{{Yeast Beasts}}
{{Hivanson}}

Hivanson Week 15

2024-05-03T17:50:41Z

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ some more info on expression table and more detail on the presentation contributions

===Electronic laboratory notebook for weeks 14-15===
I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out [[Data_Analysts_Week_14|here]]. I ran the sanity check to find the ideal B&H p-value (goal: significance of ~25%).
I made the expression table to send to the coder/designers. There are two sheets in the expression table, each containing ONLY the ID in column 1, and Log2 Fold Change data for EITHER control OR CHP at each timepoint for each trial.
An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated by adding in the proper data to the ANOVA sheet, and re-running the Bonferroni and B&H corrections. The sanity check values were readjusted for the CHP data.

I helped Charlotte and Katie run the Stem analysis. Steps outlined [[Data_Analysts_Week_14|here]].

I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.

For the final presentation, I made the flow chart using Goodnotes5, I made the outline, I wrote the Sha et al. background, I put together and interpreted the GRNmaps from what Dr. Dahlquist sent us, and I drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.

For the final paper, I wrote the introduction, added figure captions to some of the Data Analysts section, helped with the conclusion, and imported and updated the references.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts, these past few weeks during class and in person to complete the rest of the data analyst's sections as well as all of the final deliverables. The [[Yeast_Beasts|whole team]] communicated via text, call, FaceTime, and in person to work on the final presentation and paper.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:28, 3 May 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Data Analysts Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_14
*LMU BioDB 2024. (2024). Data Analysts Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_15
*LMU BioDB 2024. (2024). Week 9. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 10. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
*LMU BioDB 2024. (2024). Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14
*LMU BioDB 2024. (2024). Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

{{Yeast Beasts}}
{{Hivanson}}

Yeast Beasts

2024-05-03T17:44:08Z

Hivanson: /* Week 15 */ 14 & 15

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

[[Yeast Beasts Deliverables]]

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Weeks 14 and 15===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*During weeks 14 and 15, Charlotte, Katie, and I completed milestones 3-5. I oversaw what they did and helped complete all tasks on the shared Excel file, and communicated with the coder/designers about what was needed from them to finish the database. From there, the whole team worked to complete all of the deliverables.
*I thought it was still working well to split up, with Natalija going with the coder/designers and me going with data analysis. It felt easier to split up the work for the final project deliverables this way as well. It also worked well to use the online shared Excel file.
*It did not work to not assign people exact things that they were doing for the final project deliverables. It is also difficult to enforce deadlines and quality standards for work.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:43, 3 May 2024 (PDT)

====Dean's Reflection====
# This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
# Each team member should reflect on the team's progress:
## The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
## The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
## To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

====Katie's Reflection Weeks 14/15====
Due to the wiki being down during Week 14, we had to combine our reflections for Week 14/15 into one. During Week 14, Charlotte, Hailey, and I worked on completing milestone 3 on the Data Analysts page, which contained instructions on how to complete the ANOVA analysis on our new Log2 transformed data. After determining our suitable cut-off p-value, we filtered our data to fit that value. We then worked on completing Milestone 4, which involved clustering with stem and then putting that data into YEASTRACT. More detailed instructions can be seen on our Data Analysts Week 14 journal entry. We had a better experience of working together this week. With the ANOVA data, we were able to use Microsoft Excel online and work at the same time to compute our ANOVA values. We still had some trouble with divvying up the steps for obtaining our stem and YEASTRACT data, as only one person could use their computer to run the data through these programs. During Week 15, we worked with Dean to complete Milestone 5, who helped design queries to obtain our GRNmap input data. Again, a more detailed description of what was done can be seen on our Data Analysts Week 15 and the Coder's individual journal pages. After the input data was sent to Dr. Dahlquist, she was able to run GRNmap and upload the output data. Once this was done, we analyzed our results and worked as a group to complete our presentation, the group report, and uploaded all of the deliverables that were outlined by Dr. Dahlquist. We had some trouble coordinating a time that would work for everybody to meet, but we were able to work both in person and virtually to complete everything for the project. If I were to do this project again, I would try to have organized our time just a little bit better, as we were completing this during finals week and had limited opportunities.

===Andrew's Section===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

The class website did not work.

 3. What will I do next to fix what didn't work?

I don't have a fix but it meant that I took notes and did not have them save, so I lost some of my detailed notes on the methods for the past week. I am trying to determine what I would have saved them as.

Yeast Beasts

2024-05-03T17:43:54Z

Hivanson: /* Week 14 */ delete wk 14 header

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

[[Yeast Beasts Deliverables]]

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Week 15===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*During weeks 14 and 15, Charlotte, Katie, and I completed milestones 3-5. I oversaw what they did and helped complete all tasks on the shared Excel file, and communicated with the coder/designers about what was needed from them to finish the database. From there, the whole team worked to complete all of the deliverables.
*I thought it was still working well to split up, with Natalija going with the coder/designers and me going with data analysis. It felt easier to split up the work for the final project deliverables this way as well. It also worked well to use the online shared Excel file.
*It did not work to not assign people exact things that they were doing for the final project deliverables. It is also difficult to enforce deadlines and quality standards for work.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:43, 3 May 2024 (PDT)

====Dean's Reflection====
# This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
# Each team member should reflect on the team's progress:
## The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
## The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
## To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

====Katie's Reflection Weeks 14/15====
Due to the wiki being down during Week 14, we had to combine our reflections for Week 14/15 into one. During Week 14, Charlotte, Hailey, and I worked on completing milestone 3 on the Data Analysts page, which contained instructions on how to complete the ANOVA analysis on our new Log2 transformed data. After determining our suitable cut-off p-value, we filtered our data to fit that value. We then worked on completing Milestone 4, which involved clustering with stem and then putting that data into YEASTRACT. More detailed instructions can be seen on our Data Analysts Week 14 journal entry. We had a better experience of working together this week. With the ANOVA data, we were able to use Microsoft Excel online and work at the same time to compute our ANOVA values. We still had some trouble with divvying up the steps for obtaining our stem and YEASTRACT data, as only one person could use their computer to run the data through these programs. During Week 15, we worked with Dean to complete Milestone 5, who helped design queries to obtain our GRNmap input data. Again, a more detailed description of what was done can be seen on our Data Analysts Week 15 and the Coder's individual journal pages. After the input data was sent to Dr. Dahlquist, she was able to run GRNmap and upload the output data. Once this was done, we analyzed our results and worked as a group to complete our presentation, the group report, and uploaded all of the deliverables that were outlined by Dr. Dahlquist. We had some trouble coordinating a time that would work for everybody to meet, but we were able to work both in person and virtually to complete everything for the project. If I were to do this project again, I would try to have organized our time just a little bit better, as we were completing this during finals week and had limited opportunities.

===Andrew's Section===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

The class website did not work.

 3. What will I do next to fix what didn't work?

I don't have a fix but it meant that I took notes and did not have them save, so I lost some of my detailed notes on the methods for the past week. I am trying to determine what I would have saved them as.

Yeast Beasts

2024-05-03T17:43:23Z

Hivanson: /* Hailey's Reflection [Quality Assurance] */ signed it

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

[[Yeast Beasts Deliverables]]

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Week 14===
===Week 15===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*During weeks 14 and 15, Charlotte, Katie, and I completed milestones 3-5. I oversaw what they did and helped complete all tasks on the shared Excel file, and communicated with the coder/designers about what was needed from them to finish the database. From there, the whole team worked to complete all of the deliverables.
*I thought it was still working well to split up, with Natalija going with the coder/designers and me going with data analysis. It felt easier to split up the work for the final project deliverables this way as well. It also worked well to use the online shared Excel file.
*It did not work to not assign people exact things that they were doing for the final project deliverables. It is also difficult to enforce deadlines and quality standards for work.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:43, 3 May 2024 (PDT)

====Dean's Reflection====
# This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
# Each team member should reflect on the team's progress:
## The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
## The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
## To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

====Katie's Reflection Weeks 14/15====
Due to the wiki being down during Week 14, we had to combine our reflections for Week 14/15 into one. During Week 14, Charlotte, Hailey, and I worked on completing milestone 3 on the Data Analysts page, which contained instructions on how to complete the ANOVA analysis on our new Log2 transformed data. After determining our suitable cut-off p-value, we filtered our data to fit that value. We then worked on completing Milestone 4, which involved clustering with stem and then putting that data into YEASTRACT. More detailed instructions can be seen on our Data Analysts Week 14 journal entry. We had a better experience of working together this week. With the ANOVA data, we were able to use Microsoft Excel online and work at the same time to compute our ANOVA values. We still had some trouble with divvying up the steps for obtaining our stem and YEASTRACT data, as only one person could use their computer to run the data through these programs. During Week 15, we worked with Dean to complete Milestone 5, who helped design queries to obtain our GRNmap input data. Again, a more detailed description of what was done can be seen on our Data Analysts Week 15 and the Coder's individual journal pages. After the input data was sent to Dr. Dahlquist, she was able to run GRNmap and upload the output data. Once this was done, we analyzed our results and worked as a group to complete our presentation, the group report, and uploaded all of the deliverables that were outlined by Dr. Dahlquist. We had some trouble coordinating a time that would work for everybody to meet, but we were able to work both in person and virtually to complete everything for the project. If I were to do this project again, I would try to have organized our time just a little bit better, as we were completing this during finals week and had limited opportunities.

===Andrew's Section===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

The class website did not work.

 3. What will I do next to fix what didn't work?

I don't have a fix but it meant that I took notes and did not have them save, so I lost some of my detailed notes on the methods for the past week. I am trying to determine what I would have saved them as.

Yeast Beasts

2024-05-03T17:43:08Z

Hivanson: /* Week 15 */ team reflection

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

[[Yeast Beasts Deliverables]]

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Week 14===
===Week 15===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*During weeks 14 and 15, Charlotte, Katie, and I completed milestones 3-5. I oversaw what they did and helped complete all tasks on the shared Excel file, and communicated with the coder/designers about what was needed from them to finish the database. From there, the whole team worked to complete all of the deliverables.
*I thought it was still working well to split up, with Natalija going with the coder/designers and me going with data analysis. It felt easier to split up the work for the final project deliverables this way as well. It also worked well to use the online shared Excel file.
*It did not work to not assign people exact things that they were doing for the final project deliverables. It is also difficult to enforce deadlines and quality standards for work.

====Dean's Reflection====
# This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
# Each team member should reflect on the team's progress:
## The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
## The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
## To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

====Katie's Reflection Weeks 14/15====
Due to the wiki being down during Week 14, we had to combine our reflections for Week 14/15 into one. During Week 14, Charlotte, Hailey, and I worked on completing milestone 3 on the Data Analysts page, which contained instructions on how to complete the ANOVA analysis on our new Log2 transformed data. After determining our suitable cut-off p-value, we filtered our data to fit that value. We then worked on completing Milestone 4, which involved clustering with stem and then putting that data into YEASTRACT. More detailed instructions can be seen on our Data Analysts Week 14 journal entry. We had a better experience of working together this week. With the ANOVA data, we were able to use Microsoft Excel online and work at the same time to compute our ANOVA values. We still had some trouble with divvying up the steps for obtaining our stem and YEASTRACT data, as only one person could use their computer to run the data through these programs. During Week 15, we worked with Dean to complete Milestone 5, who helped design queries to obtain our GRNmap input data. Again, a more detailed description of what was done can be seen on our Data Analysts Week 15 and the Coder's individual journal pages. After the input data was sent to Dr. Dahlquist, she was able to run GRNmap and upload the output data. Once this was done, we analyzed our results and worked as a group to complete our presentation, the group report, and uploaded all of the deliverables that were outlined by Dr. Dahlquist. We had some trouble coordinating a time that would work for everybody to meet, but we were able to work both in person and virtually to complete everything for the project. If I were to do this project again, I would try to have organized our time just a little bit better, as we were completing this during finals week and had limited opportunities.

===Andrew's Section===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

The class website did not work.

 3. What will I do next to fix what didn't work?

I don't have a fix but it meant that I took notes and did not have them save, so I lost some of my detailed notes on the methods for the past week. I am trying to determine what I would have saved them as.

Hivanson Week 15

2024-05-03T17:36:40Z

Hivanson: /* References */ added data analysts week 14

===Electronic laboratory notebook for weeks 14-15===
I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out [[Data_Analysts_Week_14|here]]. I ran the sanity check to find the ideal B&H p-value (significance of ~25%).
I made the expression table to send to the coder/designers.
An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated and the sanity check values were readjusted for the CHP data.

I helped Charlotte and Katie run the Stem analysis. Steps outlined [[Data_Analysts_Week_14|here]].

I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.

For the final presentation, I made the flow chart, the outline, the Sha et al. background, put together and interpreted the GRNmaps, and drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.

For the final paper, I wrote the introduction, added figure captions to some of the Data Analysts section, helped with the conclusion, and imported and updated the references.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts, these past few weeks during class and in person to complete the rest of the data analyst's sections as well as all of the final deliverables. The [[Yeast_Beasts|whole team]] communicated via text, call, FaceTime, and in person to work on the final presentation and paper.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:28, 3 May 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Data Analysts Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_14
*LMU BioDB 2024. (2024). Data Analysts Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_15
*LMU BioDB 2024. (2024). Week 9. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 10. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
*LMU BioDB 2024. (2024). Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14
*LMU BioDB 2024. (2024). Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

{{Yeast Beasts}}
{{Hivanson}}

Hivanson Week 15

2024-05-03T17:36:10Z

Hivanson: /* Acknowledgments */ refs actually

===Electronic laboratory notebook for weeks 14-15===
I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out [[Data_Analysts_Week_14|here]]. I ran the sanity check to find the ideal B&H p-value (significance of ~25%).
I made the expression table to send to the coder/designers.
An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated and the sanity check values were readjusted for the CHP data.

I helped Charlotte and Katie run the Stem analysis. Steps outlined [[Data_Analysts_Week_14|here]].

I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.

For the final presentation, I made the flow chart, the outline, the Sha et al. background, put together and interpreted the GRNmaps, and drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.

For the final paper, I wrote the introduction, added figure captions to some of the Data Analysts section, helped with the conclusion, and imported and updated the references.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts, these past few weeks during class and in person to complete the rest of the data analyst's sections as well as all of the final deliverables. The [[Yeast_Beasts|whole team]] communicated via text, call, FaceTime, and in person to work on the final presentation and paper.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:28, 3 May 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Data Analysts Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_15
*LMU BioDB 2024. (2024). Week 9. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 10. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
*LMU BioDB 2024. (2024). Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14
*LMU BioDB 2024. (2024). Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

{{Yeast Beasts}}
{{Hivanson}}

Hivanson Week 15

2024-05-03T17:28:23Z

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ acknowledgments

Hivanson Week 15

2024-05-03T17:19:43Z

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ steps outlined

Hivanson Week 15

2024-05-03T17:18:30Z

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ refs

Hivanson Week 15

2024-05-03T17:17:09Z

Hivanson: templates

Hivanson Week 15

2024-05-03T17:16:39Z

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ for presentation

Hivanson Week 15

2024-05-03T17:10:03Z

Hivanson: header and filling for journal

Yeast Beasts Deliverables

2024-05-03T12:01:00Z

Hivanson: link to self

# [[Yeast_Beasts_Deliverables|Organized Team deliverables wiki page with table of contents]]
# Group Report (''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
# Group PowerPoint presentation (given on Thursday, May 2, ''.pptx'' or ''.pdf'' file) [[Media:Yeast_Beasts_Presentation.pdf|Presentation]]
# Sample-data relationship table in Excel (''.xlsx'') [[Media:Sample_Data_Table.xlsx | Sample-data Relationship Table]]
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'') [[Media:ANOVA_STEM.xlsx | ANOVA and STEM Spreadsheet]]
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNmap/GRNsight output networks [[Media:ANOVAslides.pdf | PPT of ANOVA, STEM, and Networks]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file) [https://lmu.app.box.com/file/1512445828707 GO List Zipped Files] and [https://lmu.app.box.com/file/1512445314285 Gene List Zipped Files]
# YEASTRACT "rank by TF" results (''.xlsx'') [https://lmu.app.box.com/file/1513580824058 YEASTRACT Results]
# GRNmap input workbook (''.xlsx'') [[media:GRNmap_930PM.xlsx|GRNmap Input Workbook]]
# GRNmap output workbook (''.xlsx'') and output plots (''.jpg'') zipped together [https://lmu.box.com/s/rathfd4jhdqdjzuci4kdagmptq1jbxeb link to Box with GRNmap Output]
# MS Access database, including all tables (''.accdb'') [https://lmu.box.com/s/2mcetil8n7vxzwe100avt5yhmc7psuh5 Database]
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.docx'', ''.pdf'') [https://lmu.box.com/s/0j6y9p1mrb3dji8wuvn8zhfwrb6lpo97 Database Diagram]
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access; or SQL code, ''.txt'') [https://lmu.box.com/s/y6x97kqcjlxfezhnbpvck4h4oe4pm366 Query Designs]
# Electronic notebook corresponding to these the microarray results files ([[Week 13]], [[Week 14]], and [[Week 15]]) to support ''reproducible research'' 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.

{{Yeast_Beasts}}
[[Template:Yeast_Beasts]]

Hivanson Week 15

2024-05-02T17:03:03Z

Hivanson: It would not upload for the life of me on my end.

[[Media:~$Yeast_Beasts_Presentation_(1).pptx.zip]]

Coder/Designer

2024-05-02T05:03:35Z

Hivanson: /* Milestone 6: Document the schema and design queries to create the GRNmap input workbook */ creat --> create

{{Final Project Links}}

The Coder/Designers are responsible for creating the Microsoft Access database that will be used by the Data Analysts to prepare an input workbook for GRNmap for the microarray dataset they are analyzing. The Coder/Designers are also the resident experts on the technology being used—assorted software, file management, version control, and troubleshooting. He or she coordinates with Dr. Dahlquist and fellow Coders/Designers in developing the Access database and storing it on Box.

== Guild Members ==

* Dean
* Andrew

== Milestones ==

The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together. However, Milestone 3 is a hard prerequisite for proceeding to Milestone 4, so ideally the Coder/Coder guild should finish these milestones (they require some coordination; see below) as soon as possible.

* Coder/Designers can have a shared ''individual'' journal entry. Both students will be given the same grade and are expected to contribute equally to the electronic lab notebook.
* Detailed notes should be taken throughout consistent with reproducible research and contributing to the final deliverables.

=== Milestone 1: Journal Club Presentation ===

* The Coder/Designers will work with one of the QA's to create and deliver a Journal Club presentation about to their assigned paper.

=== Milestone 2: Working Environment Setup ===

Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.
* Microsoft Access
* Box account (provided by LMU)
** Databases created by the teams will be kept in a [https://lmu.box.com/s/lorqp5d5hkzqb7q161ldb66mhqfham3f "BIOL367_Spring2024" Box folder].
** Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.
** This folder will serve as as the version control mechanism for the Coder/Designer guild.

=== Milestone 3: Design a database to store data needed to create a GRNmap input workbook ===

* Designer/Coders will work with the QA's to create a MS Access Database that will contain data needed to create a GRNmap input workbook. It will need to have the following tables:
** A <code>gene</code> table that contains all of the gene IDs for the entire yeast genome, obtained from [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine].
** An <code>expression</code> table to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts. You will consult with the Data Analysts and QA's to figure out the sample-data relationships and how that should be encoded as fields in the database.
** A <code>degradation_rates</code> table that contains degradation rates from Neymotin et al. (2014). This table is provided at [[Media:Degradation_rates.txt| this link]].
** A <code>production_rates</code> table that contains initial guesses for the production rates for each gene. This table is provided at [[Media:Production_rates.txt | this link]].
** A <code>network</code> table that contains the gene regulatory network data from the Harbison et al. (2004) paper. [[Media:Pvalbygene_forpaper_abbr.xls | Here is the link to the data.]]
** A <code>metadata</code> table that encodes information about the database itself, i.e., other tables in the database.
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.

=== Milestone 4: Build the database ===

* Once the design work has been completed, you need to actually import the data into the database.

=== Milestone 5: Validation, Quality Assurance, and Documentation of the Database ===

* The QA will perform quality assurance to make sure that the database is correct and accurate.
** In particular, the QA's need to make sure that all of the rows of data were imported into the database for each table.
** The QA's will make sure that both the ID (SGD systematic name) and Standard Names are included in the expression table and are correct.
* QA's will communicate to the Coder/Designers any changes needed to the database.
* With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]

=== Milestone 6: Document the schema and design queries to create the GRNmap input workbook ===

* Assist the Data Analysts with the queries needed to create a GRNmap input workbook
* This is a sample of a GRNmap input workbook: [[Media:15-genes_28-edges_sample-GRNmap_Sigmoid_estimation.xlsx | 15-genes_28-edges_sample-GRNmap_Sigmoid_estimation.xlsx]]
** '''''Note that you will need to match the column ids and worksheet names exactly, including case. The worksheets need to be in the exact order of the sample workbook as well.'''''
* This is a description of what needs to go into each worksheet:
** <code>production_rates</code>: two columns
*** <code>id</code>: standard names of the genes encoding the regulatory transcription factors in the network, in alphabetical order
*** <code>production_rate</code>: mRNA production rates for each of the genes
** <code>degradation_rates</code>
*** <code>id</code>: standard names of the genes encoding the regulatory transcription factors in the network, in alphabetical order
*** <code>degradation_rate</code>: mRNA production rates for each of the genes
** <code>wt_log2_expression</code>
*** <code>id</code>: standard names of the genes encoding the regulatory transcription factors in the network, in alphabetical order
*** Log2 fold changes for each gene for all the timepoints and replicates to be included in the analysis. The timepoints should be arranged in chronological order with the replicates grouped. The column headers are the time in minutes (just the number). See the sample for how it should be arranged.
** <code>network</code>
*** Cell A1 needs to have <code>cols regulators/rows targets</code>
*** This is an adjacency matrix encoding the network connections. All genes to be included in the network should appear in column 1 and row 1 in alphabetical order.
*** A "0" indicates no connection between them.
*** A "1" indicates that the transcription factor in the column regulates the corresponding transcription factor in the row.
** <code>network_weights</code>
*** This sheet should be identical to the <code>network</code> sheet. It represents the initial guesses for the weight values for the modeling.
** <code>optimization_parameters</code>: this worksheet contains information needed for Matlab to run the model. This sheet should be copied from the sample and only two lines need to be modified:
*** <code>expression_timepoints</code>: this row should list the expression timepoints corresponding to the timepoints in the <code>wt_log2_expression</code> worksheet.
*** <code>simulation_timepoints</code>: this row is a list of timepoints that the model will simulate from the estimated parameters. It should begin and end with the same timepoint, but the intervals between the timepoints should be shorter than the experimental expression data.
** <code>threshold_b</code>: two columns
*** <code>id</code>: standard names of the genes encoding the regulatory transcription factors in the network, in alphabetical order
*** <code>threshold_b</code>: all 0. This represents the initial guesses for the threshold b parameter in the network.

==== Using Microsoft Access Query Design ====

This is a loose set of instructions on how to use your Microsoft Access database to make the GRNmap input workbook.

# Import a table into the database that is the list of regulatory transcription factors that need to be included in the network (get from the Data Analysis team).
# Go to the Query Design view and select the tables that you need for the query. (For example, the TF table you just imported and the production_rates table).
# Link the ID fields that are equivalent.
# Right-click on the line between the fields and set the join properties:
#* Include all the records from the TF table, and only those records from the other table that match.
# Select the fields from the tables that you want to be output in the query and drag them to the grids at the bottom of the window.
# Choose "Make Table" query so that your results will be stored in a table.
# Run the query.
# Export the table created as tab-delimited text file. Bring it into Excel.
# Repeat as needed to create all of the worksheets you need.

{{Final Project Links}}

[[Category:Team Project]]

Main Page

2024-04-18T21:01:41Z

Hivanson: /* Upcoming Seminars */ oops missed the detail on the srivastava talk. deleted that too.

__NOTOC__
<div style="text-align: center; font-size: 175%">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''BIOL 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Spring 2024</div>

<div style="float: right;">__TOC__</div>

== Announcements ==

* Don't forget to sign your class journal entries with your wiki signature! '''<nowiki>~~~~</nowiki>'''

=== Upcoming Seminars ===

* '''Biology Department Seminar''', Friday, April 19, 3:00 PM, '''''PER 140''''', Dr. Deepak Srivastava (Gladstone Institutes), ''From Genes To Cures: Emergence of the Biocentury''
** [https://forms.office.com/r/pM3w5xVDGK RSVP for lunch] with the speaker on Friday, 12:30-1:30 PM.

=== Online Extra Credit Seminar Option ===

* You may earn 1 extra credit seminar by watching a video seminar and doing a 1-page write-up of what you learned from the seminar.
** Select a seminar from the [https://www.ibiology.org/research-talks/genetics-and-gene-regulation/ iBiology series on Genetics and Gene Regulation].
** It needs to be a seminar (with one scientist talking + slides) not an educational video.
** The total length of the seminar needs to be >= 50 minutes. You might need to watch two parts to achieve that length.
** Write a one-page reflection on what you learned from the seminar.
** Reflections are due in hard copy on the last day of class, Thursday, April 25.

== Instructor ==
* [[User:Kdahlquist|Kam D. Dahlquist]]

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:Hivanson| Hailey Ivanson]]
| style="padding-right: 1em" | [[User:Asandle1| Andrew Sandler]]
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" | [[User:Ckapla12| Charlotte Kaplan]]
| style="padding-right: 1em" | [[User:Nstojan1| Natalija Stojanovic]]
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" | [[User:Kmill104| Katherine Miller]]
| style="padding-right: 1em" | [[User:Msymond1| Dean Symonds]]
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" |
| style="padding-right: 1em" |
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|}

{{Final Project Links}}

== Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Thursdays at 12:01am. In cases where subsequent revisions or corrections will be accepted, the instructor will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.

{| class="wikitable"
|-
! Week 
! Date 
! Before Class Reading 
! During Class Topic
! After Class Assignment
|- style="vertical-align:bottom;"
| rowspan="2" | 1
| 9-Jan
| 
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies
* Wiki account setup
| rowspan="2" | [[Week 1]] (due 12:01am 1/18) [[Class Journal Week 1]] 
|- style="vertical-align:bottom;"
| 11-Jan
| [https://peerj.com/preprints/3215v1/ Dahlquist et al. (2017) ''An Invitation to Modeling'']
|
* What is a model?
* Model of a cell/model of a computer 
|- style="vertical-align:bottom;"
| rowspan="2" | 2
| 16-Jan
|
* Denning [http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''], [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] (also available on [http://brightspace.lmu.edu/ Brightspace]).
* Janovy ''On Becoming a Biologist'' Chapter 1, available on [http://brightspace.lmu.edu/ Brightspace].
* Note that there are some ''before'' questions you should answer before completing these readings. See [[Week 1]].
|
* Discuss the Week 1 assignment
** Wiki syntax overview
** Lab session to setup User wiki page 
| rowspan="2" | [[Week 2]] (due 12:01am 1/25) [[Class Journal Week 2]] 
|- style="vertical-align:bottom;"
| 18-Jan
|
* [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Brown, T.A. (2002) Ch. 1 ''Genomes 2'']
* [http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]
| DNA structure
|- style="vertical-align:bottom;"
| rowspan="2" | 3
| 23-Jan
|
* On [http://brightspace.lmu.edu Brightspace]:
** [https://www.sciencedirect.com/science/article/pii/S0968000403003025 Nirenberg (2004) ''Deciphering the Genetic Code'']
** [https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(04)00083-0 Kaji & Kaji (2004) ''Setting the Record Straight'']
** Moody (2004) ''Digital Code of Life'', Ch. 1
** Hayes (2004) ''Ode to the Code''
| Aipotu work session
| rowspan="2" | [[Week 3]] (due 12:01am 2/1) [[Class Journal Week 3]] 
|- style="vertical-align:bottom;"
| 25-Jan
| 
|
* Genes as models
* Central model of molecular biology
** [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
** This [https://dnalc.cshl.edu/resources/animations/ web site] has links to animations of the replication, transcription, and translation processes.
** [http://brightspace.lmu.edu Slides on Brightspace]
* [[Media:BIOL367_Spring2024_GeneticCode-CentralModel.pdf | Paper and pencil exercise]]

|- style="vertical-align:bottom;"
| rowspan="2" | 4
| 30-Jan
|
* [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford, Paul. “What is Code?” ''Business Week'', June 11, 2015.]
* [[Media:L01_DataManagement.pptx | DataONE: Data Management Slides]]
|
Introduction to biological databases ([[Media:2024-01-30_biological-databases-part1.pdf | part 1 slides]]) 
* What is bioinformatics?
* Open Science Ecosystem
* DataONE: Data management and the life cycle of data
* Terminology, types, four "Gold Standard" databases
| rowspan="2" | [[Week 4]] (due 12:01am 2/8) [[Class Journal Week 4]] 
|- style="vertical-align:bottom;"
| 1-Feb
|
* [[Media:L02_DataSharing.pptx | DataONE: Data Sharing Slides]]
* [https://doi.org/10.1093/nar/gkad1173 Rigden & Fernández (2024) ''NAR'' Database Issue editorial]
|
Introduction to biological databases ([[Media:2024-02-01_biological-databases-part2.pdf | part 2 slides]]) 
* A closer look at evaluating biological databases
* DataONE: Data sharing
|- style="vertical-align:bottom;"
| rowspan="2" | 5
| 6-Feb
| 
|
* Presentation Guidelines ([https://brightspace.lmu.edu .pptx is on Brightspace])
* Week 4 work session 
| rowspan="2" | [[Week 5]] (due 12:01am 2/15) [[Class Journal Week 5]] 
|- style="vertical-align:bottom;"
| 8-Feb
| 
|
Database presentations
* [[Media:Nemo_presentation.pdf | NeMO by Hailey & Dean]]
* [https://docs.google.com/presentation/d/1C74eHcvpTo0rnbQFcUnDsmG_AIPpIqLvM0t-DV95Obk/edit#slide=id.g1f0192797b8_0_30 Monarch Initiative by Katie & Andrew]
* [[Media:The_AgeAnnoMo_Database.pdf | AgeAnnoMO by Charlotte & Natalija]]

|- style="vertical-align:bottom;"
|- style="background-color:#dae8fc;"
| colspan="5" | '''Part 2: Going Deeper (Gene Expression Data and Relational Databases)'''
|-
| rowspan="2" | 6
| 13-Feb
|
* Moody (2004) ''Digital Code of Life'', Ch. 6 (on [https://brightspace.lmu.edu Brightspace])
* Original (2001) Human Genome Project articles in [https://www.nature.com/nature/volumes/409/issues/6822 ''Nature''] & [https://www.science.org/toc/science/291/5507 ''Science'']
* Special issues (2021) "The Human Genome at 20" in [https://www.nature.com/collections/febigehfbg ''Nature''] & [https://www.science.org/toc/science/371/6529 ''Science'']
| Human Genome Project
| rowspan="2" | [[Week 6]] (due 12:01am 2/22) [[Class Journal Week 6]] 
|- style="vertical-align:bottom;"
| 15-Feb
|
|
Where's my Stuff?
* Slides are on Brightspace
* An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
|- style="vertical-align:bottom;"
| rowspan="2" | 7
| 20-Feb
| 
| [[Week 6]] work session
* Please bring ear buds/headphones if possible.

| rowspan="2" | No Week 7 Assignment
|- style="vertical-align:bottom;"
| 22-Feb
|
* [http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]
* [https://www.youtube.com/watch?v=0ATUjAxNf6U Microarray animation]
* [https://doi.org/10.1038/4462 Brown. & Botstein (1999)]
* Campbell, A.M. and Heyer, L.J. (2003), Ch 4 ([http://brightspace.lmu.edu on Brightspace])
* [https://doi.org/10.1126/science.278.5338.680 DeRisi, et al. (1997)]
| 'omics analysis
|- style="vertical-align:bottom; background-color:#e5fee8;"
| rowspan="2" | Spring Break
| 27-Feb
| rowspan="2" colspan="3" | No class
|- style="vertical-align:bottom; background-color:#e5fee8;"
| 29-Feb
|- style="vertical-align:bottom;"
| rowspan="2" | 8
| 5-Mar
|
* [https://www.seas.upenn.edu/~zives/03f/cis550/codd.pdf Ted Codd’s seminal paper “A Relational Model of Data for Large Shared Data Banks”]
* [https://dondi.lmu.build/share/db/super-basic-database-diagramming.pdf Super basic relational database concepts]
| Guest lecture: Dr. Dionisio
* Relational Databases part 1
| rowspan="2" | [[Week 8]] (due 12:01am 3/14) [[Class Journal Week 8]] 
|- style="vertical-align:bottom;"
| 7-Mar
| [https://dondi.lmu.build/share/db/super-basic-sql.pdf Super basic SQL crib sheet]
| Guest lecture: Dr. Dionisio
* Relational Databases part 2
|- style="vertical-align:bottom;"
| rowspan="2" | 9
| 12-Mar
| 
| [[Week 8]] work session 
| rowspan="2" | [[Week 9]] (due 12:01am 3/21) [[Class Journal Week 9]] 
|- style="vertical-align:bottom;"
| 14-Mar
| 
| Transcriptomic analysis (part 1)
* ANOVA
|- style="vertical-align:bottom;"
| rowspan="2" | 10
| 19-Mar
| [https://xkcd.com/882/ "Significant"]
| Transcriptomic analysis (part 2)
* Multiple testing problem, p value corrections
| rowspan="2" | [[Week 10]] (due 12:01am 4/4, interim deadlines on 3/26 and 4/2) [[Class Journal Week 10]] 
|- style="vertical-align:bottom;"
| 21-Mar
|
* [https://academic.oup.com/bioinformatics/article/21/suppl_1/i159/203147 Ernst, J., & Bar-Joseph, Z. (2006). STEM]
* [https://doi.org/10.1038/75556 Ashburner et al. (2000). Gene Ontology]
| Transcriptomic analysis (part 3)
* Clustering and GO term enrichment analysis
|- style="vertical-align:bottom;"
| 11
| 26-Mar
|
* [https://doi.org/10.1093/nar/gkac1041 Teixeira, et al. (2023) YEASTRACT+]
* [https://link.springer.com/article/10.1007/s11538-015-0092-6 Dahlquist et al. (2015) GRNmap]
* [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) GRNsight]
|
* Transcriptomic analysis (part 4)
** GRN modeling and visualization
| rowspan="2" | Continue with [[Week 10]] assignment
|- style="vertical-align:bottom; background-color:#e5fee8;"
| Easter
| 28-Mar
| colspan="2" | No class
|- style="background-color:#dae8fc;"
| colspan="5" | '''Part 3: Integrating for Research (GRNsight Gene Expression Database Project)'''
|-
|- style="vertical-align:bottom;"
| rowspan="2" | 12
| 2-Apr
| 
| Discussion of [[Week 10]] results
| rowspan="2" | [[Week 12]] (due 12:01am 4/11) 
|- style="vertical-align:bottom;"
| 4-Apr
| 
| Begin Database Project
* Overview of project
* Work session for journal club
|- style="vertical-align:bottom;"
| rowspan="2" | 13
| 9-Apr
| 
| Work session for journal club
| rowspan="2" | [[Week 13]] (due 12:01am 4/18) 
|- style="vertical-align:bottom;"
| 11-Apr
| 
|
* Journal Club Presentations
* Work session to organize milestones
|- style="vertical-align:bottom;"
| rowspan="2" | 14
| 16-Jan
| 
|
* Status report
* Work session
| rowspan="2" | [[Week 14]] (due 12:01am 4/25) 
|- style="vertical-align:bottom;"
| 18-Apr
| 
|
* Status report
* Work session
|- style="vertical-align:bottom;"
| rowspan="2" | 15
| 23-Apr
| 
|
* Status report
* Work session
| rowspan="2" | [[Week 15]] (due 12:00 noon 5/3) 
|- style="vertical-align:bottom;"
| 25-Apr
| 
|
* Status report
* Work session
|- style="vertical-align:bottom; background-color:#ffccc9;"
| rowspan="2" | Finals
| 2-May
|
| '''Final Presentations 11:00am''' 
| rowspan="2" |
|- style="vertical-align:bottom; background-color:#ffccc9;"
| 3-May
|
| '''Project Deliverables Due 12:00 noon''' 
|}

== Course Information ==

=== Instructor ===

==== [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]] ====
: http://kdahlquist.github.io/DahlquistLab/index.htm
: '''Phone:''' (310) 338-7697
: '''E-mail:''' kdahlquist at lmu dot edu
: '''Office:''' Life Sciences Building 289
: '''Office Hours (Spring 2024):''' Mondays 2:00-3:30 PM, Tuesdays 3:15-4:45, and by appointment; check [https://brightspace.lmu.edu Brightspace] for a Calendly link to make an appointment for a Zoom or in-person meeting.

=== Prerequisites/Recommended Background ===

BIOL 201 and MATH 123 or MATH 132 or MATH 204 or MATH 205.

=== Class Meetings and Attendance ===
TR 1:45-3:00pm, Seaver 120 

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 12 point (2.5%) deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. The instructor should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is January 12. The withdrawal or credit/no-credit status deadline is April 5.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructor is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

# As an LMU Lion, by the [http://studentaffairs.lmu.edu/wellness/lmucares/aboutlmucares/livethelionscode/ Lion’s code], you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students.
# You are responsible for your own learning and for being a good class citizen.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
# You are expected to bring the required materials to each class session.
# Cell phones and other ancillary devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises, '''''provided that you have confirmed with the instructor that you have the correct versions of software installed for the exercise'''''. If, however, the laptops/tablets are being used for other purposes and become distracting to you or others, you will be asked to put them away.
# All students are governed by the [https://lmu.box.com/s/urox7s2vkxtoofg0rmmnv5h7ik5rahof Student Conduct Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code.

=== Course Website ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/spring2024/. You will need to have a user account on this wiki to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in the course page on [http://brightspace.lmu.edu Brightspace]. The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times I will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email address. Messages sent to the instructor at night or on the weekend will be answered the next school day.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on this wiki or [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder or folder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to back-up data
* Account for this wiki
* [http://www.github.com GitHub account]

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-to-day science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from your discipline and different disciplines

==== University Core Curriculum ====

This course fulfills the following requirements in the University Core Curriculum:
* Integrations: Interdisciplinary Connections

=== Course Work and Grading ===

Your work in this course will be assessed in the following areas:

{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments, individual (usually 12 points each)
| style="text-align: right" | 168 
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (usually 3 points each)
| style="text-align: right" | 42 
| points
|-
| Oral presentations (3 @ 35, 45, 60 points)
| style="text-align: right" | 140
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 100
| points
|-
| '''Total'''
| style="text-align: right" | '''450''' 
| '''points'''
|}

Final course grading scale:
94.0-100.0% A
90.0- 93.9% A-
86.0- 89.9% B+
82.0- 85.9% B
78.0- 81.9% B-
74.0- 77.9% C+
70.0- 73.9% C
67.0- 69.9% C-
60.0- 66.9% D
≤ 59.9% F

Current grades will be made available at [http://brightspace.lmu.edu Brightspace].

==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow.” For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki that we will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferable to other applications.

You will create an individual user page and make weekly entries that the instructor will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every 12:01am on Thursday Pacific time; consult the schedule for specific due dates for each assignment.
* Each weekly assignment has an individual component and a shared component. You will earn 12 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructor will read and comment on how to improve your journal entries on your user talk pages.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* For most weeks in the semester, you will be assigned a "homework partner". You will be expected to consult with your partner in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.'''''

==== Final Group Project ====



In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, May 3 at 12:00pm. The Final Written Report must be completed to receive a passing grade in the course.'''''

==== Life happens, what do I do then? Use your tokens! ====

To succeed in this course it is important to come to each class session and keep up with the work. However, I understand that circumstances may arise from time-to-time that could interfere with this. To responsibly manage these circumstances, the following token system is in place.

* Each student begins the semester with 4 tokens that can be used as follows:
** 1 token = turning in a individual journal entry up to one week later without penalty '''''or''''' dropping a missed shared journal entry from the final grade without penalty.
** 3 tokens = dropping a missed individual journal club entry from the final grade without penalty.
** 4 tokens = excusing an absence without penalty beyond the two automatically excused.
* To use tokens, the instructor must be emailed about your intention to use the token(s) at the day/time of usage (due date or absence). Requests to use tokens after one week from the due date or absence has passed will not be honored. Unused tokens have no point value.
* Up to two additional tokens may be earned by attending extra credit seminars (see below).

==== Extra Credit ====

Students may accumulate up to 12.5 points toward their final grade in extra credit by attending Biology Department seminars and completing the seminar sheets. Each seminar attended is worth 2.5 points with up to 5 seminars (12.5 points) total.

Alternately, you may elect to earn a token for attending the seminar instead of the extra credit points. Only two tokens may be earned this way, and the instructor must be notified of your intention to earn a token instead of extra credit at the time of the seminar by writing it on the seminar sheet on the day of the seminar.

Certain non-Biology Department seminars may be approved in advance for extra credit at the instructor's discretion. To receive credit for these seminars, you must turn in a one-page '''''hard copy''''' of your summary of the seminar '''''in class, within one week''''' of the date of the seminar or they will not count as extra credit.

===== Biology Department Seminar Attendance Policy =====

* To receive course credit for attending a Biology Department Seminar, students must do the following:
** Arrive early at the seminar venue (usually FEA auditorium) and obtain a paper seminar sheet from a faculty member.
*** Seminar sheets will only be available until 3:05 PM, at which time no further sheets will be distributed.
*** You must pick up the seminar sheet yourself. You may not obtain seminar sheets for others.
** Completely fill out the seminar sheet during the seminar, including:
*** Your name as it appears on PROWL
*** All course numbers, section numbers, professor and TA names for the courses for which you would like to receive credit
*** Day and time of seminar, speaker name, and title
*** Answer the other questions on the seminar sheet.
** Stay quietly in your seat for the entire seminar, including the question and answer period.
** At the end of the seminar, take a picture of the seminar sheet and upload it to the survey link accessed via a posted QR code.
** Turn in the paper seminar sheet to a faculty member before exiting the room.
*** You must turn in your own seminar sheet; you may not turn it in for someone else.
* Note that students arriving after 3:05 PM will not receive a seminar sheet and must enter through the back entrance on the second floor of the FEA auditorium so as not to disturb the seminar in progress.

=== Work Load Expectations ===

In line with [https://academics.lmu.edu/media/lmuacademics/provost/documents/LMU%20Credit%20Hour%20Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

=== University Policy on Academic Honesty ===

Loyola Marymount University is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences. '''''The minimum penalty for an instance of academic dishonesty in this course, even on a 1-point assignment or extra credit assignment, is a one-letter grade penalty in the course and a zero on the assignment.''''' It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including the Internet) without properly acknowledging the source. Note that students may not submit assignment or paper prompts to CourseHero, Chegg, online artificial intelligence tools, or any other such website; answers or papers derived from such sites are considered to be a direct violation of the Academic Honesty policy. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

You are required to sign the [[Media:BIOL367_Spring2024_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]] for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Spring2024_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [https://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic-Honesty-Policy-2021.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Guidelines for Using and Citing Sources]
* [[Media:BIOL367_Spring2024_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== Americans with Disabilities Act—Special Accommodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit http://www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructor early in the semester to discuss any accommodations for this course for which you have been approved.

=== Health and Wellness ===

There are many resources for student wellness on campus. A central website for students is: http://lionwellness.lmu.edu.

==== COVID-19 ====

All University mandated COVID-19 safety guidelines are to be followed. The [https://www.lmu.edu/together/ LMU Together] and [https://www.lmu.edu/together/resources/matrix/ Need to Know A-Z Index] websites contain updated information. If you have COVID-19 symptoms and/or test positive, please contact the COVID Support Team ([mailto:COVIDSupportTeam@lmu.edu COVIDSupportTeam@lmu.edu] or 310-568-6868) for instructions.

=== Emergency Preparedness ===

To report an emergency or suspicious activity, contact the LMU Department of Public Safety by phone (x222 or 310-338-2894) or at the nearest emergency call box. In the event of an evacuation, follow the evacuation signage throughout the building to the designated safe refuge area where you will receive further instruction from Public Safety or a Building Captain. For more safety information and preparedness tips, visit http://www.lmu.edu/emergency.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/spring2024/.

Main Page

2024-04-18T21:00:32Z

Hivanson: /* Upcoming Seminars */ thursday talk happened

__NOTOC__
<div style="text-align: center; font-size: 175%">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''BIOL 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Spring 2024</div>

<div style="float: right;">__TOC__</div>

== Announcements ==

* Don't forget to sign your class journal entries with your wiki signature! '''<nowiki>~~~~</nowiki>'''

=== Upcoming Seminars ===

** To receive credit for attending this seminar, you need to submit a 1-page write-up of what you learned (hard copy) due in class on Thursday, April 25.
* '''Biology Department Seminar''', Friday, April 19, 3:00 PM, '''''PER 140''''', Dr. Deepak Srivastava (Gladstone Institutes), ''From Genes To Cures: Emergence of the Biocentury''
** [https://forms.office.com/r/pM3w5xVDGK RSVP for lunch] with the speaker on Friday, 12:30-1:30 PM.

=== Online Extra Credit Seminar Option ===

* You may earn 1 extra credit seminar by watching a video seminar and doing a 1-page write-up of what you learned from the seminar.
** Select a seminar from the [https://www.ibiology.org/research-talks/genetics-and-gene-regulation/ iBiology series on Genetics and Gene Regulation].
** It needs to be a seminar (with one scientist talking + slides) not an educational video.
** The total length of the seminar needs to be >= 50 minutes. You might need to watch two parts to achieve that length.
** Write a one-page reflection on what you learned from the seminar.
** Reflections are due in hard copy on the last day of class, Thursday, April 25.

== Instructor ==
* [[User:Kdahlquist|Kam D. Dahlquist]]

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:Hivanson| Hailey Ivanson]]
| style="padding-right: 1em" | [[User:Asandle1| Andrew Sandler]]
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" | [[User:Ckapla12| Charlotte Kaplan]]
| style="padding-right: 1em" | [[User:Nstojan1| Natalija Stojanovic]]
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" | [[User:Kmill104| Katherine Miller]]
| style="padding-right: 1em" | [[User:Msymond1| Dean Symonds]]
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" |
| style="padding-right: 1em" |
| style="padding-right: 1em" |
| style="padding-right: 1em" |
|}

{{Final Project Links}}

== Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Thursdays at 12:01am. In cases where subsequent revisions or corrections will be accepted, the instructor will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.

{| class="wikitable"
|-
! Week 
! Date 
! Before Class Reading 
! During Class Topic
! After Class Assignment
|- style="vertical-align:bottom;"
| rowspan="2" | 1
| 9-Jan
| 
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies
* Wiki account setup
| rowspan="2" | [[Week 1]] (due 12:01am 1/18) [[Class Journal Week 1]] 
|- style="vertical-align:bottom;"
| 11-Jan
| [https://peerj.com/preprints/3215v1/ Dahlquist et al. (2017) ''An Invitation to Modeling'']
|
* What is a model?
* Model of a cell/model of a computer 
|- style="vertical-align:bottom;"
| rowspan="2" | 2
| 16-Jan
|
* Denning [http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''], [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] (also available on [http://brightspace.lmu.edu/ Brightspace]).
* Janovy ''On Becoming a Biologist'' Chapter 1, available on [http://brightspace.lmu.edu/ Brightspace].
* Note that there are some ''before'' questions you should answer before completing these readings. See [[Week 1]].
|
* Discuss the Week 1 assignment
** Wiki syntax overview
** Lab session to setup User wiki page 
| rowspan="2" | [[Week 2]] (due 12:01am 1/25) [[Class Journal Week 2]] 
|- style="vertical-align:bottom;"
| 18-Jan
|
* [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Brown, T.A. (2002) Ch. 1 ''Genomes 2'']
* [http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]
| DNA structure
|- style="vertical-align:bottom;"
| rowspan="2" | 3
| 23-Jan
|
* On [http://brightspace.lmu.edu Brightspace]:
** [https://www.sciencedirect.com/science/article/pii/S0968000403003025 Nirenberg (2004) ''Deciphering the Genetic Code'']
** [https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(04)00083-0 Kaji & Kaji (2004) ''Setting the Record Straight'']
** Moody (2004) ''Digital Code of Life'', Ch. 1
** Hayes (2004) ''Ode to the Code''
| Aipotu work session
| rowspan="2" | [[Week 3]] (due 12:01am 2/1) [[Class Journal Week 3]] 
|- style="vertical-align:bottom;"
| 25-Jan
| 
|
* Genes as models
* Central model of molecular biology
** [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
** This [https://dnalc.cshl.edu/resources/animations/ web site] has links to animations of the replication, transcription, and translation processes.
** [http://brightspace.lmu.edu Slides on Brightspace]
* [[Media:BIOL367_Spring2024_GeneticCode-CentralModel.pdf | Paper and pencil exercise]]

|- style="vertical-align:bottom;"
| rowspan="2" | 4
| 30-Jan
|
* [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford, Paul. “What is Code?” ''Business Week'', June 11, 2015.]
* [[Media:L01_DataManagement.pptx | DataONE: Data Management Slides]]
|
Introduction to biological databases ([[Media:2024-01-30_biological-databases-part1.pdf | part 1 slides]]) 
* What is bioinformatics?
* Open Science Ecosystem
* DataONE: Data management and the life cycle of data
* Terminology, types, four "Gold Standard" databases
| rowspan="2" | [[Week 4]] (due 12:01am 2/8) [[Class Journal Week 4]] 
|- style="vertical-align:bottom;"
| 1-Feb
|
* [[Media:L02_DataSharing.pptx | DataONE: Data Sharing Slides]]
* [https://doi.org/10.1093/nar/gkad1173 Rigden & Fernández (2024) ''NAR'' Database Issue editorial]
|
Introduction to biological databases ([[Media:2024-02-01_biological-databases-part2.pdf | part 2 slides]]) 
* A closer look at evaluating biological databases
* DataONE: Data sharing
|- style="vertical-align:bottom;"
| rowspan="2" | 5
| 6-Feb
| 
|
* Presentation Guidelines ([https://brightspace.lmu.edu .pptx is on Brightspace])
* Week 4 work session 
| rowspan="2" | [[Week 5]] (due 12:01am 2/15) [[Class Journal Week 5]] 
|- style="vertical-align:bottom;"
| 8-Feb
| 
|
Database presentations
* [[Media:Nemo_presentation.pdf | NeMO by Hailey & Dean]]
* [https://docs.google.com/presentation/d/1C74eHcvpTo0rnbQFcUnDsmG_AIPpIqLvM0t-DV95Obk/edit#slide=id.g1f0192797b8_0_30 Monarch Initiative by Katie & Andrew]
* [[Media:The_AgeAnnoMo_Database.pdf | AgeAnnoMO by Charlotte & Natalija]]

|- style="vertical-align:bottom;"
|- style="background-color:#dae8fc;"
| colspan="5" | '''Part 2: Going Deeper (Gene Expression Data and Relational Databases)'''
|-
| rowspan="2" | 6
| 13-Feb
|
* Moody (2004) ''Digital Code of Life'', Ch. 6 (on [https://brightspace.lmu.edu Brightspace])
* Original (2001) Human Genome Project articles in [https://www.nature.com/nature/volumes/409/issues/6822 ''Nature''] & [https://www.science.org/toc/science/291/5507 ''Science'']
* Special issues (2021) "The Human Genome at 20" in [https://www.nature.com/collections/febigehfbg ''Nature''] & [https://www.science.org/toc/science/371/6529 ''Science'']
| Human Genome Project
| rowspan="2" | [[Week 6]] (due 12:01am 2/22) [[Class Journal Week 6]] 
|- style="vertical-align:bottom;"
| 15-Feb
|
|
Where's my Stuff?
* Slides are on Brightspace
* An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
|- style="vertical-align:bottom;"
| rowspan="2" | 7
| 20-Feb
| 
| [[Week 6]] work session
* Please bring ear buds/headphones if possible.

| rowspan="2" | No Week 7 Assignment
|- style="vertical-align:bottom;"
| 22-Feb
|
* [http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]
* [https://www.youtube.com/watch?v=0ATUjAxNf6U Microarray animation]
* [https://doi.org/10.1038/4462 Brown. & Botstein (1999)]
* Campbell, A.M. and Heyer, L.J. (2003), Ch 4 ([http://brightspace.lmu.edu on Brightspace])
* [https://doi.org/10.1126/science.278.5338.680 DeRisi, et al. (1997)]
| 'omics analysis
|- style="vertical-align:bottom; background-color:#e5fee8;"
| rowspan="2" | Spring Break
| 27-Feb
| rowspan="2" colspan="3" | No class
|- style="vertical-align:bottom; background-color:#e5fee8;"
| 29-Feb
|- style="vertical-align:bottom;"
| rowspan="2" | 8
| 5-Mar
|
* [https://www.seas.upenn.edu/~zives/03f/cis550/codd.pdf Ted Codd’s seminal paper “A Relational Model of Data for Large Shared Data Banks”]
* [https://dondi.lmu.build/share/db/super-basic-database-diagramming.pdf Super basic relational database concepts]
| Guest lecture: Dr. Dionisio
* Relational Databases part 1
| rowspan="2" | [[Week 8]] (due 12:01am 3/14) [[Class Journal Week 8]] 
|- style="vertical-align:bottom;"
| 7-Mar
| [https://dondi.lmu.build/share/db/super-basic-sql.pdf Super basic SQL crib sheet]
| Guest lecture: Dr. Dionisio
* Relational Databases part 2
|- style="vertical-align:bottom;"
| rowspan="2" | 9
| 12-Mar
| 
| [[Week 8]] work session 
| rowspan="2" | [[Week 9]] (due 12:01am 3/21) [[Class Journal Week 9]] 
|- style="vertical-align:bottom;"
| 14-Mar
| 
| Transcriptomic analysis (part 1)
* ANOVA
|- style="vertical-align:bottom;"
| rowspan="2" | 10
| 19-Mar
| [https://xkcd.com/882/ "Significant"]
| Transcriptomic analysis (part 2)
* Multiple testing problem, p value corrections
| rowspan="2" | [[Week 10]] (due 12:01am 4/4, interim deadlines on 3/26 and 4/2) [[Class Journal Week 10]] 
|- style="vertical-align:bottom;"
| 21-Mar
|
* [https://academic.oup.com/bioinformatics/article/21/suppl_1/i159/203147 Ernst, J., & Bar-Joseph, Z. (2006). STEM]
* [https://doi.org/10.1038/75556 Ashburner et al. (2000). Gene Ontology]
| Transcriptomic analysis (part 3)
* Clustering and GO term enrichment analysis
|- style="vertical-align:bottom;"
| 11
| 26-Mar
|
* [https://doi.org/10.1093/nar/gkac1041 Teixeira, et al. (2023) YEASTRACT+]
* [https://link.springer.com/article/10.1007/s11538-015-0092-6 Dahlquist et al. (2015) GRNmap]
* [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) GRNsight]
|
* Transcriptomic analysis (part 4)
** GRN modeling and visualization
| rowspan="2" | Continue with [[Week 10]] assignment
|- style="vertical-align:bottom; background-color:#e5fee8;"
| Easter
| 28-Mar
| colspan="2" | No class
|- style="background-color:#dae8fc;"
| colspan="5" | '''Part 3: Integrating for Research (GRNsight Gene Expression Database Project)'''
|-
|- style="vertical-align:bottom;"
| rowspan="2" | 12
| 2-Apr
| 
| Discussion of [[Week 10]] results
| rowspan="2" | [[Week 12]] (due 12:01am 4/11) 
|- style="vertical-align:bottom;"
| 4-Apr
| 
| Begin Database Project
* Overview of project
* Work session for journal club
|- style="vertical-align:bottom;"
| rowspan="2" | 13
| 9-Apr
| 
| Work session for journal club
| rowspan="2" | [[Week 13]] (due 12:01am 4/18) 
|- style="vertical-align:bottom;"
| 11-Apr
| 
|
* Journal Club Presentations
* Work session to organize milestones
|- style="vertical-align:bottom;"
| rowspan="2" | 14
| 16-Jan
| 
|
* Status report
* Work session
| rowspan="2" | [[Week 14]] (due 12:01am 4/25) 
|- style="vertical-align:bottom;"
| 18-Apr
| 
|
* Status report
* Work session
|- style="vertical-align:bottom;"
| rowspan="2" | 15
| 23-Apr
| 
|
* Status report
* Work session
| rowspan="2" | [[Week 15]] (due 12:00 noon 5/3) 
|- style="vertical-align:bottom;"
| 25-Apr
| 
|
* Status report
* Work session
|- style="vertical-align:bottom; background-color:#ffccc9;"
| rowspan="2" | Finals
| 2-May
|
| '''Final Presentations 11:00am''' 
| rowspan="2" |
|- style="vertical-align:bottom; background-color:#ffccc9;"
| 3-May
|
| '''Project Deliverables Due 12:00 noon''' 
|}

== Course Information ==

=== Instructor ===

==== [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]] ====
: http://kdahlquist.github.io/DahlquistLab/index.htm
: '''Phone:''' (310) 338-7697
: '''E-mail:''' kdahlquist at lmu dot edu
: '''Office:''' Life Sciences Building 289
: '''Office Hours (Spring 2024):''' Mondays 2:00-3:30 PM, Tuesdays 3:15-4:45, and by appointment; check [https://brightspace.lmu.edu Brightspace] for a Calendly link to make an appointment for a Zoom or in-person meeting.

=== Prerequisites/Recommended Background ===

BIOL 201 and MATH 123 or MATH 132 or MATH 204 or MATH 205.

=== Class Meetings and Attendance ===
TR 1:45-3:00pm, Seaver 120 

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 12 point (2.5%) deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. The instructor should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is January 12. The withdrawal or credit/no-credit status deadline is April 5.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructor is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

# As an LMU Lion, by the [http://studentaffairs.lmu.edu/wellness/lmucares/aboutlmucares/livethelionscode/ Lion’s code], you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students.
# You are responsible for your own learning and for being a good class citizen.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
# You are expected to bring the required materials to each class session.
# Cell phones and other ancillary devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises, '''''provided that you have confirmed with the instructor that you have the correct versions of software installed for the exercise'''''. If, however, the laptops/tablets are being used for other purposes and become distracting to you or others, you will be asked to put them away.
# All students are governed by the [https://lmu.box.com/s/urox7s2vkxtoofg0rmmnv5h7ik5rahof Student Conduct Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code.

=== Course Website ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/spring2024/. You will need to have a user account on this wiki to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in the course page on [http://brightspace.lmu.edu Brightspace]. The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times I will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email address. Messages sent to the instructor at night or on the weekend will be answered the next school day.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on this wiki or [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder or folder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to back-up data
* Account for this wiki
* [http://www.github.com GitHub account]

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-to-day science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from your discipline and different disciplines

==== University Core Curriculum ====

This course fulfills the following requirements in the University Core Curriculum:
* Integrations: Interdisciplinary Connections

=== Course Work and Grading ===

Your work in this course will be assessed in the following areas:

{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments, individual (usually 12 points each)
| style="text-align: right" | 168 
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (usually 3 points each)
| style="text-align: right" | 42 
| points
|-
| Oral presentations (3 @ 35, 45, 60 points)
| style="text-align: right" | 140
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 100
| points
|-
| '''Total'''
| style="text-align: right" | '''450''' 
| '''points'''
|}

Final course grading scale:
94.0-100.0% A
90.0- 93.9% A-
86.0- 89.9% B+
82.0- 85.9% B
78.0- 81.9% B-
74.0- 77.9% C+
70.0- 73.9% C
67.0- 69.9% C-
60.0- 66.9% D
≤ 59.9% F

Current grades will be made available at [http://brightspace.lmu.edu Brightspace].

==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow.” For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki that we will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferable to other applications.

You will create an individual user page and make weekly entries that the instructor will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every 12:01am on Thursday Pacific time; consult the schedule for specific due dates for each assignment.
* Each weekly assignment has an individual component and a shared component. You will earn 12 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructor will read and comment on how to improve your journal entries on your user talk pages.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* For most weeks in the semester, you will be assigned a "homework partner". You will be expected to consult with your partner in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.'''''

==== Final Group Project ====



In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, May 3 at 12:00pm. The Final Written Report must be completed to receive a passing grade in the course.'''''

==== Life happens, what do I do then? Use your tokens! ====

To succeed in this course it is important to come to each class session and keep up with the work. However, I understand that circumstances may arise from time-to-time that could interfere with this. To responsibly manage these circumstances, the following token system is in place.

* Each student begins the semester with 4 tokens that can be used as follows:
** 1 token = turning in a individual journal entry up to one week later without penalty '''''or''''' dropping a missed shared journal entry from the final grade without penalty.
** 3 tokens = dropping a missed individual journal club entry from the final grade without penalty.
** 4 tokens = excusing an absence without penalty beyond the two automatically excused.
* To use tokens, the instructor must be emailed about your intention to use the token(s) at the day/time of usage (due date or absence). Requests to use tokens after one week from the due date or absence has passed will not be honored. Unused tokens have no point value.
* Up to two additional tokens may be earned by attending extra credit seminars (see below).

==== Extra Credit ====

Students may accumulate up to 12.5 points toward their final grade in extra credit by attending Biology Department seminars and completing the seminar sheets. Each seminar attended is worth 2.5 points with up to 5 seminars (12.5 points) total.

Alternately, you may elect to earn a token for attending the seminar instead of the extra credit points. Only two tokens may be earned this way, and the instructor must be notified of your intention to earn a token instead of extra credit at the time of the seminar by writing it on the seminar sheet on the day of the seminar.

Certain non-Biology Department seminars may be approved in advance for extra credit at the instructor's discretion. To receive credit for these seminars, you must turn in a one-page '''''hard copy''''' of your summary of the seminar '''''in class, within one week''''' of the date of the seminar or they will not count as extra credit.

===== Biology Department Seminar Attendance Policy =====

* To receive course credit for attending a Biology Department Seminar, students must do the following:
** Arrive early at the seminar venue (usually FEA auditorium) and obtain a paper seminar sheet from a faculty member.
*** Seminar sheets will only be available until 3:05 PM, at which time no further sheets will be distributed.
*** You must pick up the seminar sheet yourself. You may not obtain seminar sheets for others.
** Completely fill out the seminar sheet during the seminar, including:
*** Your name as it appears on PROWL
*** All course numbers, section numbers, professor and TA names for the courses for which you would like to receive credit
*** Day and time of seminar, speaker name, and title
*** Answer the other questions on the seminar sheet.
** Stay quietly in your seat for the entire seminar, including the question and answer period.
** At the end of the seminar, take a picture of the seminar sheet and upload it to the survey link accessed via a posted QR code.
** Turn in the paper seminar sheet to a faculty member before exiting the room.
*** You must turn in your own seminar sheet; you may not turn it in for someone else.
* Note that students arriving after 3:05 PM will not receive a seminar sheet and must enter through the back entrance on the second floor of the FEA auditorium so as not to disturb the seminar in progress.

=== Work Load Expectations ===

In line with [https://academics.lmu.edu/media/lmuacademics/provost/documents/LMU%20Credit%20Hour%20Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

=== University Policy on Academic Honesty ===

Loyola Marymount University is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences. '''''The minimum penalty for an instance of academic dishonesty in this course, even on a 1-point assignment or extra credit assignment, is a one-letter grade penalty in the course and a zero on the assignment.''''' It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including the Internet) without properly acknowledging the source. Note that students may not submit assignment or paper prompts to CourseHero, Chegg, online artificial intelligence tools, or any other such website; answers or papers derived from such sites are considered to be a direct violation of the Academic Honesty policy. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

You are required to sign the [[Media:BIOL367_Spring2024_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]] for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Spring2024_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [https://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic-Honesty-Policy-2021.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Guidelines for Using and Citing Sources]
* [[Media:BIOL367_Spring2024_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== Americans with Disabilities Act—Special Accommodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit http://www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructor early in the semester to discuss any accommodations for this course for which you have been approved.

=== Health and Wellness ===

There are many resources for student wellness on campus. A central website for students is: http://lionwellness.lmu.edu.

==== COVID-19 ====

All University mandated COVID-19 safety guidelines are to be followed. The [https://www.lmu.edu/together/ LMU Together] and [https://www.lmu.edu/together/resources/matrix/ Need to Know A-Z Index] websites contain updated information. If you have COVID-19 symptoms and/or test positive, please contact the COVID Support Team ([mailto:COVIDSupportTeam@lmu.edu COVIDSupportTeam@lmu.edu] or 310-568-6868) for instructions.

=== Emergency Preparedness ===

To report an emergency or suspicious activity, contact the LMU Department of Public Safety by phone (x222 or 310-338-2894) or at the nearest emergency call box. In the event of an evacuation, follow the evacuation signage throughout the building to the designated safe refuge area where you will receive further instruction from Public Safety or a Building Captain. For more safety information and preparedness tips, visit http://www.lmu.edu/emergency.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/spring2024/.

Yeast Beasts

2024-04-18T06:36:20Z

Hivanson: /* [User:Hivanson|Hailey's]] Reflection [Quality Assurance] */ actually i missed a bracket

Yeast Beasts

2024-04-18T06:36:03Z

Hivanson: /* Hailey's Reflection [Quality Assurance] */ linked my page

Yeast Beasts

2024-04-18T06:35:38Z

Hivanson: /* Week 13 */ reflection

Hivanson Week 13

2024-04-18T06:23:56Z

Hivanson: /* We completed Milestone 2 */ are-->were

===We completed Milestone 2===
# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# I reported on the following quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments were grouped together
#* Replicates were grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:21, 17 April 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Quality Assurance. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Quality_Assurance
*LMU BioDB 2024. (2024). Week 9. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

{{Hivanson}}
{{Yeast_Beasts}}

Hivanson Week 13

2024-04-18T06:23:38Z

Hivanson: /* We completed Milestone 2 */ I fixed the tense of a sentence

===We completed Milestone 2===
# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# I reported on the following quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments are grouped together
#* Replicates are grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:21, 17 April 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Quality Assurance. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Quality_Assurance
*LMU BioDB 2024. (2024). Week 9. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

{{Hivanson}}
{{Yeast_Beasts}}

Hivanson Week 13

2024-04-18T06:22:51Z

Hivanson: really actually fixing classmate page links

===We completed Milestone 2===
# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments are grouped together
#* Replicates are grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

===Acknowledgments===
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:21, 17 April 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Quality Assurance. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Quality_Assurance
*LMU BioDB 2024. (2024). Week 9. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

{{Hivanson}}
{{Yeast_Beasts}}

Hivanson Week 13

2024-04-18T06:22:14Z

Hivanson: /* Acknowledgments */ fixed classmate links

===We completed Milestone 2===
# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments are grouped together
#* Replicates are grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

===Acknowledgments===
I worked closely with [[Kmill104|Katie]] and [[Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:21, 17 April 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Quality Assurance. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Quality_Assurance
*LMU BioDB 2024. (2024). Week 9. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

{{Hivanson}}
{{Yeast_Beasts}}

Hivanson Week 13

2024-04-18T06:21:59Z

Hivanson: /* Acknowledgments */ signed acknowledgments

===We completed Milestone 2===
# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments are grouped together
#* Replicates are grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

===Acknowledgments===
I worked closely with [[Kmill104 Katie]] and [[Ckapla12 Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:21, 17 April 2024 (PDT)

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Quality Assurance. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Quality_Assurance
*LMU BioDB 2024. (2024). Week 9. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

{{Hivanson}}
{{Yeast_Beasts}}

Hivanson Week 13

2024-04-18T06:20:04Z

Hivanson: References

===We completed Milestone 2===
# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments are grouped together
#* Replicates are grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

===Acknowledgments===
I worked closely with Katie and Charlotte, the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.

===References===
*LMU BioDB 2024. (2024). Data Analysis. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
*LMU BioDB 2024. (2024). Quality Assurance. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Quality_Assurance
*LMU BioDB 2024. (2024). Week 9. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
*LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

{{Hivanson}}
{{Yeast_Beasts}}

Hivanson Week 13

2024-04-18T06:07:00Z

Hivanson: template

Hivanson Week 13

2024-04-18T05:58:17Z

Hivanson: header

Hivanson Week 13

2024-04-18T05:57:59Z

Hivanson: all milestone 2 described

# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* '''Are all the samples described in the paper in the dataset?'''
#**As described above, the samples listed in the paper were all present in the dataset.
#* '''Are all the samples in the dataset described in the paper?'''
#**Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
# We came up with consistent column headers that summarize this information
#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
# I ensured the data were organized in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) was in the first column
#* Data columns were to the right, in increasing chronological order, using the column header pattern we created
#* Treatments are grouped together
#* Replicates are grouped together
# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

Hivanson Week 13

2024-04-18T04:02:07Z

Hivanson: editing to fit what actually happened

# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
#*The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
# Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* Are all the samples described in the paper in the dataset?
#* Are all the samples in the dataset described in the paper?
# Come up with consistent column headers that summarize this information
#* For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.
#* Do not use any special characters except for "-" or "_" (e.g., no commas, etc.)
# Organize the data in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) is in the first column
#* Data columns are to the right, in increasing chronological order, using the column header pattern you created
#* Treatments are grouped together
#* Replicates are grouped together
# This information needs to be relayed to the Coder/Designers so that they can design an appropriate <code>expression</code> table.

Hivanson Week 13

2024-04-18T03:57:16Z

Hivanson: paste milestone 2

# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip Link to processed dataset from SGD.]
#* For your reference, this is the link to the dataset at the GEO Database:[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GSE26169]. However, we will use the dataset processed by SGD.
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
# Report on these quality measures:
#* Are all the samples described in the paper in the dataset?
#* Are all the samples in the dataset described in the paper?
# Come up with consistent column headers that summarize this information
#* For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.
#* Do not use any special characters except for "-" or "_" (e.g., no commas, etc.)
# Organize the data in a worksheet in an Excel workbook so that:
#* ID (SGD systematic name) is in the first column
#* Data columns are to the right, in increasing chronological order, using the column header pattern you created
#* Treatments are grouped together
#* Replicates are grouped together
# This information needs to be relayed to the Coder/Designers so that they can design an appropriate <code>expression</code> table.

File:GSE7645.reorganized.xlsx

2024-04-18T03:33:27Z

Hivanson: Hivanson uploaded a new version of File:GSE7645.reorganized.xlsx

== Summary ==
reorganized sdg

Hivanson Week 12

2024-04-18T02:26:52Z

Hivanson: deleted everything because I didn't include references. You can see what I did in the last version

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:56:14Z

Hivanson: /* Bibliographic Entry */ more bib

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* '''What country is the journal published in?'''
*#**The United States
*# '''How long has the journal been in operation?'''
*#* 18 years (Since 2006)
*# '''Are the articles in this journal peer-reviewed?'''
*#* Yes
*# '''Provide a link to the scientific advisory board/editorial board of the journal.'''
*#*[https://journals.plos.org/plosone/static/editorial-board? editorial board]
*# '''What is the journal impact factor?'''
*#*3.7
*# '''On what date was the article submitted?'''
*#*May 10, 2013
*# '''On what date was the article accepted?'''
*#*August 7, 2013
*# '''Did the article undergo any revisions before acceptance?'''
*#*No
*# '''When was the article published?'''
*#*September 20, 2013
*# '''What is the approximate elapsed time between submission and publication?'''
*#*4 months
*# '''What are the institutions with which the authors are affiliated?'''
*#*"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Bioinformatics Research Division, University of North Carolina at Charlotte, Kannapolis, North Carolina, United States of America." [https://pubmed.ncbi.nlm.nih.gov/24073228/ via PubMed]
*# '''Have the authors published other articles on this subject?'''
*#*Sha has other articles that [https://doi.org/10.1002/yea.1442 relate to yeast metabolism] and [https://doi.org/10.1016/j.freeradbiomed.2011.03.002 the effects of oxidative stress].
*# '''Is there a conflict of interest for any of the authors?'''
*#*None declared
*# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
*#* '''How many articles does this article cite?'''
*#**79
*#* '''How many articles cite this article?'''
*#**26

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:53:42Z

Hivanson: /* Bibliographic Entry */ editorial board

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* What country is the journal published in?
*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
*# Are the articles in this journal peer-reviewed?
*# '''Provide a link to the scientific advisory board/editorial board of the journal.'''
*#*[https://journals.plos.org/plosone/static/editorial-board? editorial board]
*# '''What is the journal impact factor?'''
*#*3.7
*# '''On what date was the article submitted?'''
*#*May 10, 2013
*# '''On what date was the article accepted?'''
*#*August 7, 2013
*# '''Did the article undergo any revisions before acceptance?'''
*#*No
*# '''When was the article published?'''
*#*September 20, 2013
*# '''What is the approximate elapsed time between submission and publication?'''
*#*4 months
*# '''What are the institutions with which the authors are affiliated?'''
*#*"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Bioinformatics Research Division, University of North Carolina at Charlotte, Kannapolis, North Carolina, United States of America." [https://pubmed.ncbi.nlm.nih.gov/24073228/ via PubMed]
*# '''Have the authors published other articles on this subject?'''
*#*Sha has other articles that [https://doi.org/10.1002/yea.1442 relate to yeast metabolism] and [https://doi.org/10.1016/j.freeradbiomed.2011.03.002 the effects of oxidative stress].
*# '''Is there a conflict of interest for any of the authors?'''
*#*None declared
*# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
*#* '''How many articles does this article cite?'''
*#**79
*#* '''How many articles cite this article?'''
*#**26

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:52:05Z

Hivanson: /* Bibliographic Entry */ bottom half of bibliography

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* What country is the journal published in?
*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
*# Are the articles in this journal peer-reviewed?
*# Provide a link to the scientific advisory board/editorial board of the journal.
*# '''What is the journal impact factor?'''
*#*3.7
*# '''On what date was the article submitted?'''
*#*May 10, 2013
*# '''On what date was the article accepted?'''
*#*August 7, 2013
*# '''Did the article undergo any revisions before acceptance?'''
*#*No
*# '''When was the article published?'''
*#*September 20, 2013
*# '''What is the approximate elapsed time between submission and publication?'''
*#*4 months
*# '''What are the institutions with which the authors are affiliated?'''
*#*"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Bioinformatics Research Division, University of North Carolina at Charlotte, Kannapolis, North Carolina, United States of America." [https://pubmed.ncbi.nlm.nih.gov/24073228/ via PubMed]
*# '''Have the authors published other articles on this subject?'''
*#*Sha has other articles that [https://doi.org/10.1002/yea.1442 relate to yeast metabolism] and [https://doi.org/10.1016/j.freeradbiomed.2011.03.002 the effects of oxidative stress].
*# '''Is there a conflict of interest for any of the authors?'''
*#*None declared
*# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
*#* '''How many articles does this article cite?'''
*#**79
*#* '''How many articles cite this article?'''
*#**26

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:42:10Z

Hivanson: /* Presentation Prep */ more bib progress

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* What country is the journal published in?
*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
*# Are the articles in this journal peer-reviewed?
*# Provide a link to the scientific advisory board/editorial board of the journal.
*# What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
*# On what date was the article submitted?
*# On what date was the article accepted?
*# Did the article undergo any revisions before acceptance?
*# When was the article published?
*# What is the approximate elapsed time between submission and publication?
*# What are the institutions with which the authors are affiliated?
*#*"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Bioinformatics Research Division, University of North Carolina at Charlotte, Kannapolis, North Carolina, United States of America." [https://pubmed.ncbi.nlm.nih.gov/24073228/ via PubMed]
*# '''Have the authors published other articles on this subject?'''
*#*Sha has other articles that [https://doi.org/10.1002/yea.1442 relate to yeast metabolism] and [https://doi.org/10.1016/j.freeradbiomed.2011.03.002 the effects of oxidative stress].
*# '''Is there a conflict of interest for any of the authors?'''
*#*None declared
*# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
*#* '''How many articles does this article cite?'''
*#**79
*#* '''How many articles cite this article?'''
*#**26

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:34:32Z

Hivanson: /* Bibliographic Entry */ COI

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* What country is the journal published in?
*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
*# Are the articles in this journal peer-reviewed?
*# Provide a link to the scientific advisory board/editorial board of the journal.
*# What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
*# On what date was the article submitted?
*# On what date was the article accepted?
*# Did the article undergo any revisions before acceptance?
*# When was the article published?
*# What is the approximate elapsed time between submission and publication?
*# What are the institutions with which the authors are affiliated?
*# Have the authors published other articles on this subject? (How will you find this out?) Hint:
*#* [http://scholar.google.com/ Google Scholar]
*#* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link)]
*#* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
*#**
*# '''Is there a conflict of interest for any of the authors?'''
*#*None declared
*# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
*#* '''How many articles does this article cite?'''
*#**79
*#* '''How many articles cite this article?'''
*#**26

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:33:19Z

Hivanson: /* Bibliographic Entry */ three ones from the bottom bib

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* What country is the journal published in?
*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
*# Are the articles in this journal peer-reviewed?
*# Provide a link to the scientific advisory board/editorial board of the journal.
*# What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
*# On what date was the article submitted?
*# On what date was the article accepted?
*# Did the article undergo any revisions before acceptance?
*# When was the article published?
*# What is the approximate elapsed time between submission and publication?
*# What are the institutions with which the authors are affiliated?
*# Have the authors published other articles on this subject? (How will you find this out?) Hint:
*#* [http://scholar.google.com/ Google Scholar]
*#* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link)]
*#* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
*# Is there a conflict of interest for any of the authors?
*# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
*#* '''How many articles does this article cite?'''
*#**79
*#* '''How many articles cite this article?'''
*#**26

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:28:04Z

Hivanson: /* Presentation Prep */ paste bibliographic entry

==Presentation Prep==

===Purpose===
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
# '''What mathematical/statistical method did they use to analyze the data?'''
#*Robust Multichip Average and ANOVA
# '''Are the data publicly available for download? From which web site?'''
#*GEO Database and SGD.
#'''Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.'''
#*''Figure 1''
#**X represents Concentration in µM; Y represents Time in minutes
#**Quantification by HPLC
#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
#*''Figure 2''
#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
#**Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.

# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

===Bibliographic Entry===
* For your assigned journal article, answer/provide the following on your individual journal entry.
*# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
*# The link to the abstract from [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link].
*# The link to the full text of the article in [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral] (if not available, write N/A).
*# The link to the full text of the article (HTML format) from the publisher web site.
*# The link to the full PDF version of the article from the publisher web site.
*# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
*#* Additionally, is the article available under a Creative Commons license?
*# How is the article available to you?
*#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
*#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
*#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
*#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
*# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
*# What organization is the publisher of the journal?
*#* What type of organization is it?
*#** Is the publisher for-profit or non-profit?
*#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
*#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
*#* What country is the journal published in?
*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
*# Are the articles in this journal peer-reviewed?
*# Provide a link to the scientific advisory board/editorial board of the journal.
*# What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
*# On what date was the article submitted?
*# On what date was the article accepted?
*# Did the article undergo any revisions before acceptance?
*# When was the article published?
*# What is the approximate elapsed time between submission and publication?
*# What are the institutions with which the authors are affiliated?
*# Have the authors published other articles on this subject? (How will you find this out?) Hint:
*#* [http://scholar.google.com/ Google Scholar]
*#* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link)]
*#* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
*# Is there a conflict of interest for any of the authors?
*# Are the data associated with this article available? If so, provide a link to the dataset.
*# Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):
*#* How many articles does this article cite?
*#* How many articles cite this article?

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T01:26:33Z

Hivanson: /* Questions about your article */ fig 2

Hivanson Week 12

2024-04-18T01:12:16Z

Hivanson: /* Questions about your article */ fig 1

Hivanson Week 12

2024-04-18T01:08:28Z

Hivanson: /* Presentation Prep */ RNA treatment, math, and where available.

Hivanson Week 12

2024-04-18T00:54:28Z

Hivanson: /* Defining 10 unknown biological terms */ all words to define

==Presentation Prep==
===Defining 10 unknown biological terms===
#Thioredoxin system:
#Glutathione system:
#Leucine zipper proteins:
#Lignin:
#Capillariy electrophoresis:
#Photodiode Array Detector:
#Trehalose:
#MAPK signaling:
#Regulon:
#Isoenzymes:
#Rho zero petites:

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#*
# What mathematical/statistical method did they use to analyze the data?
# Are the data publicly available for download? From which web site?
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent (if applicable)?
#* How were the measurements made?
#* What trends are shown by the plots and what conclusions can you draw from the data?
# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T00:38:05Z

Hivanson: /* Questions about your article */ bolded a question

==Presentation Prep==
===Defining 10 unknown biological terms===

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# '''What media did they grow them in? What temperature? What type of incubator? For how long?'''
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#*
# What mathematical/statistical method did they use to analyze the data?
# Are the data publicly available for download? From which web site?
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent (if applicable)?
#* How were the measurements made?
#* What trends are shown by the plots and what conclusions can you draw from the data?
# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T00:36:16Z

Hivanson: template and acknowledgments

==Presentation Prep==
===Defining 10 unknown biological terms===

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# What media did they grow them in? What temperature? What type of incubator? For how long?
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
# What mathematical/statistical method did they use to analyze the data?
# Are the data publicly available for download? From which web site?
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent (if applicable)?
#* How were the measurements made?
#* What trends are shown by the plots and what conclusions can you draw from the data?
# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==Acknowledgments==

==References==

{{Hivanson}}

Hivanson Week 12

2024-04-18T00:32:19Z

Hivanson: /* Questions about your article */ conditions grown

==Presentation Prep==
===Defining 10 unknown biological terms===

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# What media did they grow them in? What temperature? What type of incubator? For how long?
#*2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
#*30ºC
#*New Brunswick BioFlo fermentors
#*Grown until OD600 of 1.5
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
# What mathematical/statistical method did they use to analyze the data?
# Are the data publicly available for download? From which web site?
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent (if applicable)?
#* How were the measurements made?
#* What trends are shown by the plots and what conclusions can you draw from the data?
# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==References==

Hivanson Week 12

2024-04-18T00:28:21Z

Hivanson: /* Questions about your article */ replicates

==Presentation Prep==
===Defining 10 unknown biological terms===

===Questions about your article===
# '''What is the main result presented in this paper?'''
#*CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
#**Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
# '''What is the importance or significance of this work?'''
#*This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
#*The researchers found that ''Yap3'', ''5'', and ''7'' are involved in the yeast OSR, and that their functions were not previously known.
# '''What were the limitations in previous studies that led them to perform this work?'''
#*Some similar studies did not have biological replicates, nor control groups.
#*This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
# '''How did they treat the yeast cells (what experiment were they doing?)'''
#*CHP, or cumene hydroperoxide, exposure
# '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?'''
#*Diploid strain ''BY4743'' was used.
# What media did they grow them in? What temperature? What type of incubator? For how long?
# '''What controls did they use? '''
#*The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
# '''How many replicates did they perform per treatment or timepoint?'''
#*3
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
# What mathematical/statistical method did they use to analyze the data?
# Are the data publicly available for download? From which web site?
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent (if applicable)?
#* How were the measurements made?
#* What trends are shown by the plots and what conclusions can you draw from the data?
# How does this work compare with previous studies?
# What are the important implications of this work?
# What future directions should the authors take?
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

==Presentation==
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]

==References==