Ntesfaio Week 10 - Revision history

Ntesfaio: /* Acknowledgments */ added to acknowledgments

2019-11-07T02:41:40Z

‎Acknowledgments: added to acknowledgments

Ntesfaio: /* References */ added to references

2019-11-07T02:41:05Z

‎References: added to references

Ntesfaio: /* References */ added signature

2019-11-07T02:40:00Z

‎References: added signature

Ntesfaio: /* Conclusion */ added to conclusion

2019-11-07T00:07:09Z

‎Conclusion: added to conclusion

Ntesfaio: /* References */ added to references

2019-11-07T00:03:53Z

‎References: added to references

Ntesfaio: /* Dynamical Systems Modeling of your Gene Regulatory Network */ added to methods

2019-11-07T00:01:15Z

‎Dynamical Systems Modeling of your Gene Regulatory Network: added to methods

Ntesfaio: /* threshold_b sheet */ added to methods

2019-11-06T23:57:00Z

‎threshold_b sheet: added to methods

Ntesfaio: /* optimization_parameters sheet */ added to methods

2019-11-06T23:55:59Z

‎optimization_parameters sheet: added to methods

Ntesfaio: /* network_weights sheet */ I added to methods

2019-11-06T23:54:14Z

‎network_weights sheet: I added to methods

Ntesfaio: /* network sheet */ added to methods

2019-11-06T23:52:26Z

‎network sheet: added to methods

← Older revision		Revision as of 02:41, 7 November 2019
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	My homework partners this week are Aby [[User:Ymesfin]] and David [[User:Dramir36]]. We worked together on running the different databases such as GRNmap and YEASTRACT.		My homework partners this week are Aby [[User:Ymesfin]] and David [[User:Dramir36]]. We worked together on running the different databases such as GRNmap and YEASTRACT.
		+
		+	"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

	==References==		==References==

← Older revision		Revision as of 02:41, 7 November 2019
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	Matlab. Retrieved on November 6, 2019 from MATLAB R2014b.		Matlab. Retrieved on November 6, 2019 from MATLAB R2014b.
		+
		+	LMU BioDB 2019. (2019). Week 10. Retrieved November 6, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10
		+

	[[User:Ntesfaio\|Ntesfaio]] ([[User talk:Ntesfaio\|talk]]) 18:40, 6 November 2019 (PST)		[[User:Ntesfaio\|Ntesfaio]] ([[User talk:Ntesfaio\|talk]]) 18:40, 6 November 2019 (PST)

← Older revision		Revision as of 02:40, 7 November 2019
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	Matlab. Retrieved on November 6, 2019 from MATLAB R2014b.		Matlab. Retrieved on November 6, 2019 from MATLAB R2014b.
		+
		+	[[User:Ntesfaio\|Ntesfaio]] ([[User talk:Ntesfaio\|talk]]) 18:40, 6 November 2019 (PST)

	==Data and Files==		==Data and Files==

← Older revision		Revision as of 00:07, 7 November 2019
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	==Conclusion==		==Conclusion==
		+
		+	The purpose of this week's assignment was to continue working on the network excel spreadsheet. This spreadsheet was analyzed as the gene's time periods from 15-60 logs were considered. Using GrNsight I was able to view my results after matlab ran the expression plots. An xlsx, .mat, and .jpeg output was made from the Matlab run and uploaded to this wikipedia.

	==Acknowledgments==		==Acknowledgments==

← Older revision		Revision as of 00:03, 7 November 2019
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	==References==		==References==
		+
		+	GRNmap. Retrieved on November 6, 2019 from http://kdahlquist.github.io/GRNmap/downloads/.
		+
		+	Matlab. Retrieved on November 6, 2019 from MATLAB R2014b.

	==Data and Files==		==Data and Files==

← Older revision		Revision as of 00:01, 7 November 2019
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	===Dynamical Systems Modeling of your Gene Regulatory Network===		===Dynamical Systems Modeling of your Gene Regulatory Network===
		+
		+	* I Downloaded the GRNmap v1.10 code from the GRNmap Downloads page.
		+
		+	This is a direct link to start downloading (81 MB).
		+	Unzip the file. (Right-click, 7-zip > Extract here)
		+	Launched MATLAB R2014b.
		+
		+	* I opened GRNmodel.m, which will be in the directory that you unzipped GRNmap-1.10 > matlab
		+	Clicked the Run button (green "play" arrow).
		+
		+	* I selected the input workbook.
		+
		+
		+	When the run is over, expression plots displayed.
		+
		+	Output .xlsx and .mat files will be saved in the same folder as the input folder, along with .jpg files containing the optimization diagnostic and individual expression plots. I saved these files.
		+
		+	I uploaded the .xlsx file into GRNsight to visualize the results!

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 23:57, 6 November 2019
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	===threshold_b sheet===		===threshold_b sheet===
		+
		+	*There should be two columns.
		+
		+	*The left-most column should contain the header "id" and list the standard names for the genes in the model in the same order as in the other sheets.
		+
		+	*The second column should have the header "threshold_b" and should contain the initial guesses, we are going to use all 0.

	===Dynamical Systems Modeling of your Gene Regulatory Network===		===Dynamical Systems Modeling of your Gene Regulatory Network===

← Older revision		Revision as of 23:55, 6 November 2019
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	===optimization_parameters sheet===		===optimization_parameters sheet===
		+
		+	* The optimization_parameters sheet should have two columns (from left to right) entitled, "optimization_parameter" and "value".
		+
		+	This worksheet was copied from the sample workbook provided. The only row that you need to modify is row 15, "Strain". Include just the strain designations for which you have a corresponding STRAIN_log2_expression sheet. If you don't have the dgln3, dhap4, or dcin5 expression sheets, then you will delete those from this row. If you do so, make sure that you don't leave any gaps between cells.

	===threshold_b sheet===		===threshold_b sheet===

← Older revision		Revision as of 23:54, 6 November 2019
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	===network_weights sheet===		===network_weights sheet===
		+
		+	* These are the initial guesses for the estimation of the weight parameters, w.
		+
		+	Since these weights are initial guesses which will be optimized by GRNmap, the content of this sheet can be identical to the "network" sheet.

	===optimization_parameters sheet===		===optimization_parameters sheet===

← Older revision		Revision as of 23:52, 6 November 2019
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	===network sheet===		===network sheet===
		+
		+	*The network derived from the YEASTRACT database for the Week 9 assignment can be copied and pasted into this sheet directly.
		+
		+	*This sheet contained an adjacency matrix representation of the gene regulatory network.
		+
		+	*The columns correspond to the transcription factors and the rows correspond to the target genes controlled by those transcription factors.
		+
		+	*A “1” means there is an edge connecting them and a “0” means that there is no edge connecting them.
		+
		+	The upper-left cell (A1) should contain the text “cols regulators/rows targets”. This text is there as a reminder of the direction of the regulatory relationships specified by the adjacency matrix.
		+	The rest of row 1 should contain the names of the transcription factors that are controlling the other genes in the network, one transcription factor name per column.
		+	The rest of column A should contain the names of the target genes that are being controlled by the transcription factors heading each of the columns in the matrix, one target gene name per row.
		+	The transcription factor names should correspond to the "id" in the other sheets in the workbook. They should be capitalized the same way and occur in the same order along the top and side of the matrix. The matrix needs to be symmetric, i.e., the same transcription factors should appear along the top and left side of the matrix. The genes should be listed in the same order in all the sheets in the Excel workbook.
		+	Each cell in the matrix should then contain a zero (0) if there is no regulatory relationship between those two transcription factors, or a one (1) if there is a regulatory relationship between them. Again, the columns correspond to the transcription factors and the rows correspond to the target genes controlled by those transcription factors.

	===network_weights sheet===		===network_weights sheet===