Coder/Designer - Revision history

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

2024-05-02T05:03:35Z

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

2024-04-26T16:51:52Z

‎Using Microsoft Access Query Design: add instructions for query.

2024-04-26T16:46:11Z

‎Milestone 6: Document the schema and design queries to create the GRNmap input workbook: add section for query design

2024-04-23T20:59:40Z

‎Milestone 6: Document the schema and design queries to create the GRNmap input workbook: note about exact matching to sampe

2024-04-23T16:32:46Z

‎Milestone 6: Document the schema and design queries to create the GRNmap input workbook: describe optimization_parameters worksheet

2024-04-23T16:28:51Z

‎Milestone 6: Document the schema and design queries to create the GRNmap input workbook: description of the worksheets in the input workbook

2024-04-23T16:15:42Z

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

2024-04-23T16:15:13Z

‎Milestone 6: Document the schema and design queries to create the GRNmap input workbook: add link to sample workbook

2024-04-23T16:11:06Z

‎Milestone 6: Document the schema and design queries to create the GRNmap input workbook: start to talk about sample GRNmap input workbook

2024-04-17T20:56:38Z

‎Milestone 3: Design a database to store data needed to create a GRNmap input workbook: changed back the name

@@ Line 54: / Line 54: @@
 === Milestone 6: Document the schema and design queries to create the GRNmap input workbook ===
-* Assist the Data Analysts with the queries needed to creat a 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.'''''

@@ Line 83: / Line 83: @@
 ==== Using Microsoft Access Query Design ====
 {{Final Project Links}}
 [[Category:Team Project]]

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 *** <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.
 {{Final Project Links}}
 [[Category:Team Project]]

@@ Line 56: / Line 56: @@
 * Assist the Data Analysts with the queries needed to creat 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]]
 * This is a description of what needs to go into each worksheet:
 ** <code>production_rates</code>: two columns

@@ Line 73: / Line 73: @@
 ** <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>
+** <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>threshold_b</code>: two columns
 *** <code>id</code>: standard names of the genes encoding the regulatory transcription factors in the network, in alphabetical order

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 ** 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]].
+** 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.]]