Marmas Week 15 - Revision history

Marmas: /* Acknowledgments */ added a reference

2019-12-13T07:49:48Z

‎Acknowledgments: added a reference

Marmas: /* Conclusion */ fixed a typo

2019-12-13T07:48:13Z

‎Conclusion: fixed a typo

Marmas: /* Conclusion */ added conclusion

2019-12-13T07:48:02Z

‎Conclusion: added conclusion

Marmas: added methods for week 15

2019-12-13T07:25:38Z

added methods for week 15

Marmas: /* Data and Files */ added files

2019-12-13T06:56:11Z

‎Data and Files: added files

Marmas: /* Data and Files */ added files

2019-12-13T06:55:05Z

‎Data and Files: added files

Marmas: /* Data and Files */ added some files

2019-12-13T06:42:54Z

‎Data and Files: added some files

Marmas: /* Purpose */ added purpose

2019-12-13T06:24:25Z

‎Purpose: added purpose

Marmas: copied over, edited headers, added acknoledgments

2019-12-13T06:19:05Z

copied over, edited headers, added acknoledgments

New page

{{marmas}}
==Purpose==

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.
===Week 15===

==Data and Files==

==Conclusion==

==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her help with the formation of the database and understanding the expression data.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi and Delisa for helping with the creation of the database.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.'''<br>
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 21:37, 20 November 2019 (PST)

← Older revision		Revision as of 07:49, 13 December 2019
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	Except for what is noted above, this individual journal entry was completed by me and not copied from another source.'''<br>		Except for what is noted above, this individual journal entry was completed by me and not copied from another source.'''<br>
	[[User:Marmas\|Marmas]] ([[User talk:Marmas\|talk]]) 21:37, 20 November 2019 (PST)		[[User:Marmas\|Marmas]] ([[User talk:Marmas\|talk]]) 21:37, 20 November 2019 (PST)
		+	==References==
		+	*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. doi: 10.1021/es015705v.

@@ Line 51: / Line 51: @@
 ==Conclusion==
-The project is just beginning to wrap up. The database was completed in MS Access and linked together to find inputs for a GRNmap Input workbook. This part of the pipeline will give the resulting weighted adjacency matrix and gene regulatory network. A relationship report was created to show how the database is linked. This was performed using the relationship tools found in MS Access. These tools allowed for the linkage between data tables, and between the metadata sheets. A ReadMe document was created to explain these relationships formed in the database. Additionally, it explains how the metadata tables are linked to the rest of the data tables. Finally, a the final presenation and report are being started for turn-in next week.
+The project is just beginning to wrap up. The database was completed in MS Access and linked together to find inputs for a GRNmap Input workbook. This part of the pipeline will give the resulting weighted adjacency matrix and gene regulatory network. A relationship report was created to show how the database is linked. This was performed using the relationship tools found in MS Access. These tools allowed for the linkage between data tables, and between the metadata sheets. A ReadMe document was created to explain these relationships formed in the database. Additionally, it explains how the metadata tables are linked to the rest of the data tables. Finally, a the final presentation and report are being started for turn-in next week.
 ==Acknowledgments==

← Older revision		Revision as of 07:48, 13 December 2019
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	==Conclusion==		==Conclusion==
		+	The project is just beginning to wrap up. The database was completed in MS Access and linked together to find inputs for a GRNmap Input workbook. This part of the pipeline will give the resulting weighted adjacency matrix and gene regulatory network. A relationship report was created to show how the database is linked. This was performed using the relationship tools found in MS Access. These tools allowed for the linkage between data tables, and between the metadata sheets. A ReadMe document was created to explain these relationships formed in the database. Additionally, it explains how the metadata tables are linked to the rest of the data tables. Finally, a the final presenation and report are being started for turn-in next week.

	==Acknowledgments==		==Acknowledgments==

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 *[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
 *[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
 ==Conclusion==

@@ Line 30: / Line 30: @@
 *[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
 *[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
 ==Conclusion==

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 *Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.
 ===Week 15===
 ==Data and Files==

← Older revision		Revision as of 06:42, 13 December 2019
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	==Data and Files==		==Data and Files==
		+	*[[Media:Metadata_Sheet_(1).xlsx \| Sample-Data Relationship Table (Metadata Sheet)]]
		+	*[[Media:FunGals_Final_Presentation.pptx \| Final Presentation]]

	==Conclusion==		==Conclusion==

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 {{marmas}}
 ==Purpose==
 ==Account of Activity==