Help:Gbrowse - Revision history

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T22:01:59Z

Information displayed in Gbrowse

← Older revision		Revision as of 22:01, 24 May 2012
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	*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.		*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.

	[[~~http://ecoliwiki.net/colipedia/index.php/~~File:GBrowse_update2.jpg\|center\|600px]]		[[File:GBrowse_update2.jpg\|center\|600px]]

	*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button.		*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button.

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T21:59:01Z

Information displayed in Gbrowse

← Older revision		Revision as of 21:59, 24 May 2012
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	*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.		*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.

	[[GBrowse_update2.jpg~~\|thumb~~\|center\|600px]]		[[http://ecoliwiki.net/colipedia/index.php/File:GBrowse_update2.jpg\|center\|600px]]

	*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button.		*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button.

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T21:57:56Z

Information displayed in Gbrowse

← Older revision		Revision as of 21:57, 24 May 2012
Line 31:		Line 31:
	*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.		*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.

	[[~~Image:Gbrowse GenePulldownMenu~~.jpg\|thumb\|center\|600px]]		[[GBrowse_update2.jpg\|thumb\|center\|600px]]

	*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button.		*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button.

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T21:44:01Z

Information displayed in Gbrowse

← Older revision		Revision as of 21:44, 24 May 2012
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	*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').		*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').

	[[~~Image~~:~~Gbrowse_middle~~.~~jpg~~\|thumb\|center\|600px]]		[[File:Gbrowse_for_ecoliwiki.jpeg\|thumb\|center\|600px]]

	*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.		*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene.

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T21:37:19Z

Information displayed in Gbrowse

← Older revision		Revision as of 21:37, 24 May 2012
Line 24:		Line 24:
	The information in Gbrowse is displayed in tracks, as shown in the image below.		The information in Gbrowse is displayed in tracks, as shown in the image below.
	*'''Overview''' is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.		*'''Overview''' is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.
	*'''Region''' displays 400 kb on either side of the position being viewed.		*'''Region''' displays 400 kb on either side of the position being viewed. This can change w/ scale.
	*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').		*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T21:29:14Z

Information displayed in Gbrowse

← Older revision		Revision as of 21:29, 24 May 2012
Line 24:		Line 24:
	The information in Gbrowse is displayed in tracks, as shown in the image below.		The information in Gbrowse is displayed in tracks, as shown in the image below.
	*'''Overview''' is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.		*'''Overview''' is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.
	*'''Region''' displays 50 kb on either side of the ~~gene~~ being viewed.		*'''Region''' displays 400 kb on either side of the position being viewed.
	*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').		*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').

Johnlew: /* Information displayed in Gbrowse */

2012-05-24T20:45:43Z

Information displayed in Gbrowse

← Older revision		Revision as of 20:45, 24 May 2012
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	==Information displayed in Gbrowse==		==Information displayed in Gbrowse==
	The information in Gbrowse is displayed in tracks, as shown in the image below.		The information in Gbrowse is displayed in tracks, as shown in the image below.
	*'''Overview''' is a linear display of the entire genome with ~~a vertical bar~~ marking the location of the region being viewed.		*'''Overview''' is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.
	*'''Region''' displays 50 kb on either side of the gene being viewed.		*'''Region''' displays 50 kb on either side of the gene being viewed.
	*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').		*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB''').
Line 36:		Line 36:

	[[Image:Gbrowse_possible_tracks.jpg\|thumb\|center\|600px]]		[[Image:Gbrowse_possible_tracks.jpg\|thumb\|center\|600px]]

	== See also ==		== See also ==
	=== Genome-specific information ===		=== Genome-specific information ===

JimHu: /* Additional functionalities */

2012-05-10T21:46:15Z

Additional functionalities

← Older revision		Revision as of 21:46, 10 May 2012
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	=== Additional functionalities ===		=== Additional functionalities ===
	* [[Help:Gbrowse/Uploading_user_data_to_EcoliWiki_Gbrowse\|Uploading private data]]		* [[Help:Gbrowse/Uploading_user_data_to_EcoliWiki_Gbrowse\|Uploading private data]]
	* [[Help:Gbrowse/~~Uploading_user_data_to_EcoliWiki_Gbrowse~~\|~~Uploading private data~~]]		* [[Help:Gbrowse/PCR primers\|PCR primers]]

	[[Category:Help\|Gbrowse]]		[[Category:Help\|Gbrowse]]

JimHu: /* Selecting a genome to view */

2012-05-10T21:45:16Z

Selecting a genome to view

← Older revision		Revision as of 21:45, 10 May 2012
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	== Selecting a genome to view ==		== Selecting a genome to view ==
			Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu.
	[[File:Gbrowse_data_source_menu.png\|thumb\|center\|300px]]		[[File:Gbrowse_data_source_menu.png\|thumb\|center\|300px]]
	~~Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu.~~

	Contact us if there is a genome that you would like to see in the browser.		Contact us if there is a genome that you would like to see in the browser.

JimHu at 21:44, 10 May 2012

2012-05-10T21:44:58Z

← Older revision		Revision as of 21:44, 10 May 2012
Line 1:		Line 1:
	== Selecting a genome to view ==		== Selecting a genome to view ==
	[[File:Gbrowse_data_source_menu.png\|thumb\|300px]]		[[File:Gbrowse_data_source_menu.png\|thumb\|center\|300px]]
	Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu.		Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu.