Taur.vil Week 13 - Revision history

Taur.vil: /* gmbuilder coding in class */ bit more eclipse editing

2013-11-21T18:35:53Z

‎gmbuilder coding in class: bit more eclipse editing

2013-11-21T18:34:55Z

‎Microarray Data: future steps

2013-11-21T18:28:36Z

‎Microarray Data

2013-11-21T18:27:55Z

‎gmbuilder coding in class

2013-11-21T18:04:45Z

‎gmbuilder coding in class

2013-11-21T05:43:10Z

‎Import-Export Cycle

2013-11-21T05:42:55Z

‎TIGR4 IMP-EXP C3

2013-11-21T05:12:36Z

‎TIGR4 IMP-EXP C2

2013-11-19T18:32:30Z

‎gmbuilder coding in class

2013-11-19T18:31:11Z

‎Laboratory Journal

@@ Line 63: / Line 63: @@
 *Discovered we had linked to the wrong database
 *Went back into eclipse and linked files to http://bacteria.ensembl.org/streptococcus_pneumoniae_tigr4/Gene/Summary?g=~
-*Copied over dist_20131121 to flash drive
+*Added VC-like code to adjust gene IDs to match microarray data, XML, and database
 *Will use for I-E C4

@@ Line 75: / Line 75: @@
 **Various other formats exist for controls
 *Gene names for TIGR4 database are as SP_####
 ==Template==
 {{Team ATK}}

@@ Line 74: / Line 74: @@
 **spr#### is used for R6
 **Various other formats exist for controls
 ==Template==
 {{Team ATK}}

@@ Line 65: / Line 65: @@
 *Copied over dist_20131121 to flash drive
 *Will use for I-E C4
 ==Template==
 {{Team ATK}}

@@ Line 60: / Line 60: @@
 *Copied over dist folder (what Dondi called the baby gmbuilder) onto my flash drive
 *Will use for additional export cycle.
 ==Template==
 {{Team ATK}}

@@ Line 47: / Line 47: @@
 *Executed gmbuilder.sql (the new version, see bellow) in SQL
 **Verified success by the 159 tables created
-==Import-Export Cycle==
+===Import-Export Cycle===
 *Opened new version of gmbuilder-32bit.bat
 *Connected to database created earlier

← Older revision		Revision as of 05:42, 21 November 2013
Line 41:		Line 41:

	==TIGR4 IMP-EXP C3==		==TIGR4 IMP-EXP C3==
		+	===Collecting files===
		+	*Verified that goa and XML files had not been updated
		+	*Downloaded Nov. 20, 2013 obo-xml file from [http://beta.geneontology.org/page/download-ontology]
		+	*created new database in pgAdminIII called tATK_TIGR4_2013NOV20
		+	*Executed gmbuilder.sql (the new version, see bellow) in SQL
		+	**Verified success by the 159 tables created
		+	==Import-Export Cycle==
		+	*Opened new version of gmbuilder-32bit.bat
		+	*Connected to database created earlier
		+	*Imported UniProt XML file: 20131118_UniProtXML_tATK_TIGR4_TPV.xml
		+	*Imported the obo-xml file: 20131120_OBOXML_tATK_TPV.obo-xml
		+	*Imported the goa file: 20131118_GOA_tATK_TIGR4_TPV.goa
		+	*Exported to 20131120_E3_tATK_TIGR4.gdb

	==gmbuilder coding in class==		==gmbuilder coding in class==

@@ Line 38: / Line 38: @@
 *Imported goa file: 20131118_GOA_tATK_TIGR4_TPV.goa
 *Exported as 20131118_E2_tATK_TIGR4.gdb
 ==gmbuilder coding in class==

← Older revision		Revision as of 18:32, 19 November 2013
Line 44:		Line 44:
	*Copied over dist folder (what Dondi called the baby gmbuilder) onto my flash drive		*Copied over dist folder (what Dondi called the baby gmbuilder) onto my flash drive
	*Will use for additional export cycle.		*Will use for additional export cycle.
		+
		+	==Template==
		+	{{Team ATK}}

← Older revision		Revision as of 18:31, 19 November 2013
Line 38:		Line 38:
	*Imported goa file: 20131118_GOA_tATK_TIGR4_TPV.goa		*Imported goa file: 20131118_GOA_tATK_TIGR4_TPV.goa
	*Exported as 20131118_E2_tATK_TIGR4.gdb		*Exported as 20131118_E2_tATK_TIGR4.gdb
		+
		+	==gmbuilder coding in class==
		+	*Checked out gmbuilder in eclipse, labeled it tATK_gmbuilder3
		+	*Edited StrptococcusPenumoniaeTIGR4UniProtSpeciesProfile.java in the src folder to include the appropriate species id of 170189 and gene identifier of http://www.streppneumoniae.com/gene_detail_output.asp?id=2741&name=~
		+	*Copied over dist folder (what Dondi called the baby gmbuilder) onto my flash drive
		+	*Will use for additional export cycle.