SMD Annotating Batch Files - Revision history

JimHu at 02:23, 31 May 2013

2013-05-31T02:23:23Z

← Older revision		Revision as of 02:23, 31 May 2013
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	==Related Tutorials and Resources==		==Related Tutorials and Resources==
	*[[http://ecoliwiki.net/colipedia/index.php/Category:Expression_data Step 1]] List of microarray papers to be annotated.		*[[http://ecoliwiki.net/colipedia/index.php/Category:Expression_data Step 1]] List of microarray papers to be annotated.
	*[[SMD_Affy_Ecoli_2.0_sets Step 2]] Guide on how to set up a batch file.		*[[http://tetramer.tamu.edu/team/wiki/index.php/SMD_Affy_Ecoli_2.0_sets Step 2]] Guide on how to set up a batch file.
	*[ Step 3 ] Guide on how to Annotate batch files.		*[ Step 3 ] Guide on how to Annotate batch files.
	*[[Loading_Microarrays_into_SMD Step 4]] Tutorial on how to load batch files into SMD.		*[[http://tetramer.tamu.edu/team/wiki/index.php/Loading_Microarrays_into_SMD Step 4]] Tutorial on how to load batch files into SMD.
	*[[SMD-How_to_Make_a_Publication Step 5]] Guide on how to make a publication.		*[[http://tetramer.tamu.edu/team/wiki/index.php/SMD-How_to_Make_a_Publication Step 5]] Guide on how to make a publication.

	==Categories==		==Categories==
	[[Category:Expression_data]]		[[Category:Expression_data]]

JimHu: /* Related Tutorials and Resources */

2013-05-31T02:21:39Z

Amandasupak: /* Experiment Description */

2011-09-02T15:15:10Z

Experiment Description

← Older revision		Revision as of 15:15, 2 September 2011
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	* Here are some examples of what you DO NOT want to put		* Here are some examples of what you DO NOT want to put
	** (Don't type WT after the strain name) K-12 BW25113 WT		** (Don't type WT after the strain name) K-12 BW25113 WT
			**You Don't need to put "bio.rep. 1", just put rep. 1

	===Individual Annotation Fields===		===Individual Annotation Fields===

Siegele: /* Conventions for the field */

2011-08-16T04:16:30Z

Conventions for the field

← Older revision		Revision as of 04:16, 16 August 2011
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	*Growth medium information		*Growth medium information
	**LB		**LB
	**MOPS minimal medium + carbon source (~~You don~~'t ~~need~~ to include the concentration ~~of carbon source~~, ~~unless~~ it is ~~a variable in the experiment~~.)		**MOPS minimal medium + carbon source (0.xx%) (It isn't essential to include the concentration, but DAS usually does because it is information she would want to have.)
	**M9 minimal medium + carbon source (")		**M9 minimal medium + carbon source (0.xx%) (")
	**M63 minimal medium + carbon source (")		**M63 minimal medium + carbon source (0.xx%) (")
	*Optical Density		*Optical Density
	**OD600=0.3		**OD600=0.3

Amandasupak: /* Conventions for the field */

2011-06-10T16:54:04Z

Conventions for the field

← Older revision		Revision as of 16:54, 10 June 2011
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	====Conventions for the <c-2>field====		====Conventions for the <c-2>field====
	*Put the name of relevant <b>mutant alleles or plasmids</b> between the <c-2> and </c-2> tags.		*Put the name of relevant <b>mutant alleles or plasmids</b> between the <c-2> and </c-2> tags.
			** <c-2>ygjK726(del)::FRT-kan-FRT</c-2>
	*Don't use special characters because the database won't accept them. Some of our substitutions are listed below:		*Don't use special characters because the database won't accept them. Some of our substitutions are listed below:
	**Instead of ∆ for deletion, put (del) after the gene name and allele number.		**Instead of ∆ for deletion, put (del) after the gene name and allele number.

Amandasupak: /* Conventions for the field */

2011-06-10T16:53:04Z

Conventions for the field

← Older revision		Revision as of 16:53, 10 June 2011
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	*Optical Density		*Optical Density
	**OD600=0.3		**OD600=0.3
			*List of things you should NOT PUT:
			** Do not list the number of grams for glass wool
			** Do not list the rpm a solution was shaking at
			**
	*Other Examples		*Other Examples
	**LB + glucose (1 g/L), glucose/MgSO4-fed batch culture, OD595=11.5, 50C for 15 min (shifted from 37C)		**LB + glucose (1 g/L), glucose/MgSO4-fed batch culture, OD595=11.5, 50C for 15 min (shifted from 37C)

Amandasupak: /* Experiment Description */

2011-06-10T16:51:08Z

Experiment Description

← Older revision		Revision as of 16:51, 10 June 2011
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	**K-12 BW25113 hha-745(del)::FRT-Kan-FRT, 4 hr Biofilm, LB		**K-12 BW25113 hha-745(del)::FRT-Kan-FRT, 4 hr Biofilm, LB
	**K-12 ATCC 25404 + R1drd19 Plasimd, 24 h biofilm		**K-12 ATCC 25404 + R1drd19 Plasimd, 24 h biofilm
			* Here are some examples of what you DO NOT want to put
			** (Don't type WT after the strain name) K-12 BW25113 WT

	===Individual Annotation Fields===		===Individual Annotation Fields===

Amandasupak: /* Conventions for the field */

2011-06-10T16:49:50Z

Conventions for the field

← Older revision		Revision as of 16:49, 10 June 2011
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	** <c-1>K-12 BW25113 yjgK726(del)::FRT-kan-FRT</c-1>		** <c-1>K-12 BW25113 yjgK726(del)::FRT-kan-FRT</c-1>
	*If the experiment uses an E. coli strain other than MG1655, BW25113, or W3110, check whether it has a page in EcoliWiki. If it doesn't, make one or ask someone else to make one.		*If the experiment uses an E. coli strain other than MG1655, BW25113, or W3110, check whether it has a page in EcoliWiki. If it doesn't, make one or ask someone else to make one.
	* To find the allele number, go [[http://cgsc.biology.yale.edu/MutationQueryForm.php here]] and type the gene of interest (yjgK for example) in the field labeled "Mutation of gene."		* To find the allele number, go [http://cgsc.biology.yale.edu/MutationQueryForm.php here] and type the gene of interest (yjgK for example) in the field labeled "Mutation of gene."

	====Conventions for the <c-2>field====		====Conventions for the <c-2>field====

Amandasupak: /* Conventions for the field */

2011-06-10T16:48:55Z

Conventions for the field

← Older revision		Revision as of 16:48, 10 June 2011
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	**<c-1>K-12 W3110</c-1>		**<c-1>K-12 W3110</c-1>
	**<c-1>O157-H7 EDL933</c-1>		**<c-1>O157-H7 EDL933</c-1>
			** <c-1>K-12 BW25113 yjgK726(del)::FRT-kan-FRT</c-1>
	*If the experiment uses an E. coli strain other than MG1655, BW25113, or W3110, check whether it has a page in EcoliWiki. If it doesn't, make one or ask someone else to make one.		*If the experiment uses an E. coli strain other than MG1655, BW25113, or W3110, check whether it has a page in EcoliWiki. If it doesn't, make one or ask someone else to make one.
			* To find the allele number, go [[http://cgsc.biology.yale.edu/MutationQueryForm.php here]] and type the gene of interest (yjgK for example) in the field labeled "Mutation of gene."

	====Conventions for the <c-2>field====		====Conventions for the <c-2>field====

Siegele: /* Conventions for the field */

2011-06-07T02:58:20Z

Conventions for the field

← Older revision		Revision as of 02:58, 7 June 2011
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	====Conventions for the <c-1> field====		====Conventions for the <c-1> field====
	*Put the name of the organism and strain background between the <c-1> and </c-1> tags.		*Put the name of the organism and strain background between the <c-1> and </c-1> tags.
	*Do not include mutant alleles or plasmids~~, because they~~ will be added to the <c-2> field.		*<s>Do not</s> '''Do include''' relevant mutant alleles or plasmids; these will also be added to the <c-2> field.[[User:Siegele\|Siegele]] 02:58, 7 June 2011 (UTC)
	*Here are some examples:		*Here are some examples:
	**<c-1>K-12 MG155</c-1>		**<c-1>K-12 MG155</c-1>
			**<c-1>K-12 MG155 rpoS::Tn10</c-1>
	**<c-1>K-12 BW25113</c-1>		**<c-1>K-12 BW25113</c-1>
	**<c-1>K-12 W3110</c-1>		**<c-1>K-12 W3110</c-1>

← Older revision		Revision as of 02:21, 31 May 2013
Line 205:		Line 205:
	==Related Tutorials and Resources==		==Related Tutorials and Resources==
	*[[http://ecoliwiki.net/colipedia/index.php/Category:Expression_data Step 1]] List of microarray papers to be annotated.		*[[http://ecoliwiki.net/colipedia/index.php/Category:Expression_data Step 1]] List of microarray papers to be annotated.
	*[[~~http://tetramer.tamu.edu/team/wiki/index.php/~~SMD_Affy_Ecoli_2.0_sets Step 2]] Guide on how to set up a batch file.		*[[SMD_Affy_Ecoli_2.0_sets Step 2]] Guide on how to set up a batch file.
	*[ Step 3 ] Guide on how to Annotate batch files.		*[ Step 3 ] Guide on how to Annotate batch files.
	*[[~~http://tetramer.tamu.edu/team/wiki/index.php/~~Loading_Microarrays_into_SMD Step 4]] Tutorial on how to load batch files into SMD.		*[[Loading_Microarrays_into_SMD Step 4]] Tutorial on how to load batch files into SMD.
	*[[~~http://tetramer.tamu.edu/team/wiki/index.php/~~SMD-How_to_Make_a_Publication Step 5]] Guide on how to make a publication.		*[[SMD-How_to_Make_a_Publication Step 5]] Guide on how to make a publication.

	==Categories==		==Categories==
	[[Category:Expression_data]]		[[Category:Expression_data]]