ASAP - Revision history

127.0.0.1: /Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

2010-05-23T00:11:02Z

/Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

← Older revision		Revision as of 00:11, 23 May 2010
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	{\| id="B497edd17ef856" class=" tableEdit Database_table"		{\| {{Prettytable}} width='30%' align="right" id="B497edd17ef856" class=" tableEdit Database_table"

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	!align=left \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
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	[https://asap.ahabs.wisc.edu/asap/logon.php A Systematic Annotation Package (ASAP)]		[https://asap.ahabs.wisc.edu/asap/logon.php A Systematic Annotation Package (ASAP)]

	\|-		\|-
	!align=left \|What:		!align=left {{table heading style}} \|What:
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	Comprehensive genome information for several enteric bacteria with community annotation.		Comprehensive genome information for several enteric bacteria with community annotation.
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	!align=left \|Who:		!align=left {{table heading style}} \|Who:
	\|\|		\|\|
	Nicole Perna, Univ. of Wisconsin		Nicole Perna, Univ. of Wisconsin

	\|-		\|-
	!align=left \|Updates:		!align=left {{table heading style}} \|Updates:
	\|\|		\|\|

	\|-		\|-
	!align=left \|Upcoming events:		!align=left {{table heading style}} \|Upcoming events:
	\|\|		\|\|

	\|-		\|-
	!align=left \|Web Services:		!align=left {{table heading style}} \|Web Services:
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127.0.0.1: Update TableEdit tables.

2010-01-09T00:07:26Z

Update TableEdit tables.

← Older revision		Revision as of 00:07, 9 January 2010
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	!align=left ~~{{table heading style}}~~ \|Link/URL:		!align=left \|Link/URL:
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	[https://asap.ahabs.wisc.edu/asap/logon.php A Systematic Annotation Package (ASAP)]		[https://asap.ahabs.wisc.edu/asap/logon.php A Systematic Annotation Package (ASAP)]

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	!align=left ~~{{table heading style}}~~ \|What:		!align=left \|What:
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	Comprehensive genome information for several enteric bacteria with community annotation.		Comprehensive genome information for several enteric bacteria with community annotation.
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	!align=left ~~{{table heading style}}~~ \|Who:		!align=left \|Who:
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	Nicole Perna, Univ. of Wisconsin		Nicole Perna, Univ. of Wisconsin

	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Updates:		!align=left \|Updates:
	\|\|		\|\|

	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Upcoming events:		!align=left \|Upcoming events:
	\|\|		\|\|

	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Web Services:		!align=left \|Web Services:
	\|\|		\|\|


	\|-class=~~'sortbottom'~~		\|- class="tableEdit_footer"
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127.0.0.1: Fixing references section.

2009-06-26T16:03:06Z

Fixing references section.

← Older revision		Revision as of 16:03, 26 June 2009
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	==References==		==References==
			{{BacktoTop}}
	{{RefHelp}}		{{RefHelp}}
	<references/>		<references />
	J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. ''Nucleic Acids Res.'' 31(1):147-151. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12519969 PubMed] [http://nar.oupjournals.org/cgi/content/full/31/1/147 full text] [http://nar.oupjournals.org/cgi/content/abstract/31/1/147 abstract]		J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. ''Nucleic Acids Res.'' 31(1):147-151. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12519969 PubMed] [http://nar.oupjournals.org/cgi/content/full/31/1/147 full text] [http://nar.oupjournals.org/cgi/content/abstract/31/1/147 abstract]

	==External Links==		==External Links==
	*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page]		*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page]

Amandasupak: add home page jpg

2009-06-10T20:21:11Z

add home page jpg

← Older revision		Revision as of 20:21, 10 June 2009
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	==About {{PAGENAME}}==		==About {{PAGENAME}}==
			[[Image:ASAP_home.jpg\|right\|Home Page\|thumb\|350px]]
	[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}}] is a comprehensive source of genome information for several enteric bacteria, including ''E. coli'' K-12 MG1655 and W3110. ASAP annotations are based on community annotation curated by ASAP staff.		[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}}] is a comprehensive source of genome information for several enteric bacteria, including ''E. coli'' K-12 MG1655 and W3110. ASAP annotations are based on community annotation curated by ASAP staff.

Amandasupak: Table edited by Amandasupak via TableEdit

2009-06-03T20:04:52Z

Table edited by Amandasupak via TableEdit

← Older revision		Revision as of 20:04, 3 June 2009
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	{\|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align=right		{\|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

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	!align=left {{table heading style}} \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
	\|\|		\|\|
	[https://asap.ahabs.wisc.edu/asap/logon.php ASAP]		[https://asap.ahabs.wisc.edu/asap/logon.php A Systematic Annotation Package (ASAP)]

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JimHu at 04:17, 2 June 2009

2009-06-02T04:17:34Z

← Older revision		Revision as of 04:17, 2 June 2009
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	[[Category:Databases]]		[[Category:Databases]]
	[[Category:E. coli Databases]]		[[Category:E. coli Databases]]
			[[Category:IECA_Portal]]
	<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856-->		<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856-->
	<!--		<!--

JimHu: Table edited by JimHu via TableEdit

2009-01-27T10:10:00Z

Table edited by JimHu via TableEdit

← Older revision		Revision as of 10:10, 27 January 2009
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	!align=left {{table heading style}} \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
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			[https://asap.ahabs.wisc.edu/asap/logon.php ASAP]

	\|-		\|-
	!align=left {{table heading style}} \|What:		!align=left {{table heading style}} \|What:
			\|\|
			Comprehensive genome information for several enteric bacteria with community annotation.


	\|-		\|-
	!align=left {{table heading style}} \|Who:		!align=left {{table heading style}} \|Who:
			\|\|
			Nicole Perna, Univ. of Wisconsin

	\|-		\|-
	!align=left {{table heading style}} \|Updates:		!align=left {{table heading style}} \|Updates:
			\|\|

	\|-		\|-
	!align=left {{table heading style}} \|Upcoming events:		!align=left {{table heading style}} \|Upcoming events:
			\|\|

	\|-		\|-
	!align=left {{table heading style}} \|Web Services:		!align=left {{table heading style}} \|Web Services:
			\|\|


	\|-class='sortbottom'		\|-class='sortbottom'
	\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856&page=1635&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table]		\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856&page=1635&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] \|\|
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JimHu at 10:08, 27 January 2009

2009-01-27T10:08:24Z

← Older revision		Revision as of 10:08, 27 January 2009
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	[[Category:Databases]]		[[Category:Databases]]
	[[Category:E. coli Databases]]		[[Category:E. coli Databases]]
	{\|{{Prettytable}} width='30%' align = 'right'		<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856-->
	~~\|- align='center' bgcolor = '#ddddff'~~		<!--
	~~\| colspan = '2' \| '''{{PAGENAME}}'''~~		******************************************************************************************
			*
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			*
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			{\|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align=right

	\|-		\|-
	~~\| width~~=~~'30%'~~ \| ~~Who~~:		!align=left {{table heading style}} \|Link/URL:
	~~\| Nicole Perna, Univ. of Wisconsin~~
	\|-		\|-
	~~\| width~~=~~'30%'~~ \| What:		!align=left {{table heading style}} \|What:
	~~\| Comprehensive genome information for several enteric bacteria with community annotation.~~
	\|-		\|-
	~~\| Where:~~		!align=left {{table heading style}} \|Who:
	~~\| [https://asap.ahabs.wisc.edu/asap/logon.php~~ {{~~PAGENAME~~}}]
	\|-		\|-
	\| Updates		!align=left {{table heading style}} \|Updates:
	\|
	\|-		\|-
	\| Upcoming events		!align=left {{table heading style}} \|Upcoming events:
	~~\| ''link to event calendar, if applicable''~~
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	\| Web Services		!align=left {{table heading style}} \|Web Services:
	\|
			\|-class='sortbottom'
			\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856&page=1635&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table]
	\|}		\|}
	=About {{PAGENAME}}=		<!--box uid=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856--></protect>
			==About {{PAGENAME}}==
	[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}}] is a comprehensive source of genome information for several enteric bacteria, including ''E. coli'' K-12 MG1655 and W3110. ASAP annotations are based on community annotation curated by ASAP staff.		[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}}] is a comprehensive source of genome information for several enteric bacteria, including ''E. coli'' K-12 MG1655 and W3110. ASAP annotations are based on community annotation curated by ASAP staff.

	=Content=		==Content==
	Content at ASAP covers genomes of many enteric bacteria, and is very extensive for individual genomes. ASAP includes:		Content at ASAP covers genomes of many enteric bacteria, and is very extensive for individual genomes. ASAP includes:
	:*Annotations generated by ASAP curators and user community. These are therefore nonredundant with other sites.		:*Annotations generated by ASAP curators and user community. These are therefore nonredundant with other sites.
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	ASAP has a page that [https://asap.ahabs.wisc.edu/asap/db_summary.php?LocationID=&SequenceVersionID=&GenomeID=&ExpSetID=#WIS_MG1655 lists feature types and annotation types]		ASAP has a page that [https://asap.ahabs.wisc.edu/asap/db_summary.php?LocationID=&SequenceVersionID=&GenomeID=&ExpSetID=#WIS_MG1655 lists feature types and annotation types]

	=Using {{PAGENAME}}=		==Using {{PAGENAME}}==
	==Browsing==		==Browsing==
	ASAP has its own genome browser, which runs as a Java Applet. On some browsers, this does not open to the selected gene, and does not allow clicking to a nearby gene page. ASAP also includes a Synteny Browser.		ASAP has its own genome browser, which runs as a Java Applet. On some browsers, this does not open to the selected gene, and does not allow clicking to a nearby gene page. ASAP also includes a Synteny Browser.

	==Searching==		===Searching===
	[[Image:ASAP_query.jpg\|thumb\|ASAP query page ]]Entering ASAP brings up a query page that allows a fairly customizable search. Most users will probably use two kinds of searches, Location and Basic Options		[[Image:ASAP_query.jpg\|thumb\|ASAP query page ]]Entering ASAP brings up a query page that allows a fairly customizable search. Most users will probably use two kinds of searches, Location and Basic Options
	===by Location===		====by Location====
	Enter the boundaries of the desired location and submit.		Enter the boundaries of the desired location and submit.
	===by Feature (gene) name===		====by Feature (gene) name====
	A simple search on gene names is done by entering the name into feature name. Submitting the query brings up a list of features matching the query. The table includes the genome coordinates for any genes found. ASAP recognizes synonyms. For example, searching for groP returns pages for dnaK, dnaJ, and dnaB. T		A simple search on gene names is done by entering the name into feature name. Submitting the query brings up a list of features matching the query. The table includes the genome coordinates for any genes found. ASAP recognizes synonyms. For example, searching for groP returns pages for dnaK, dnaJ, and dnaB. T

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	*see only tRNAs between 200kbp and 500kbp, select tRNAs while using 200000 and 500000 in the Chromosome Location section.		*see only tRNAs between 200kbp and 500kbp, select tRNAs while using 200000 and 500000 in the Chromosome Location section.

	===Displaying the Results===		====Displaying the Results====
	Clicking on a feature link brings up a display for that feature. The feature pages are in two frames. The left frame has links to a variety of information. The right page has lists of Annotations, Overlapping Features, Orthologs and Paralogs, Similarity Searches, Molecular Interactions, and Experimental Data.		Clicking on a feature link brings up a display for that feature. The feature pages are in two frames. The left frame has links to a variety of information. The right page has lists of Annotations, Overlapping Features, Orthologs and Paralogs, Similarity Searches, Molecular Interactions, and Experimental Data.
	feature ID mapped to gene name (https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=114900		feature ID mapped to gene name (https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=114900

	==Usage examples==		===Usage examples===
	''Add links to additional pages describing success stories here.''		''Add links to additional pages describing success stories here.''

	=Other sites with related content=		=Other sites with related content=
	=Technology=		==Technology==
	ASAP is written in PHP. The original Univ. of WIsconsin version uses an underlying MySQL database; the ERIC version migrates this to Oracle.		ASAP is written in PHP. The original Univ. of WIsconsin version uses an underlying MySQL database; the ERIC version migrates this to Oracle.

	ASAP offers downloadable data in different forms.		ASAP offers downloadable data in different forms.
	==Web Services/API==		===Web Services/API===
	None available		None available

	=Discussion=		==Discussion==
	ASAP has lots of important content. For example, it is easy in ASAP to find the locations of different kinds of features, even if you can't always search for them by name. For example, by selecting prophage, you can find the locations of 10 cryptic prophage in MG1655. However, you can't find specific prophage by searching for e14 or rac. By contrast, searching for rac in [[EcoCyc]] does return hits. But it's easier to see how many prophage are there using ASAP; EcoCyc returns hits for every prophage gene when you search for "prophage".		ASAP has lots of important content. For example, it is easy in ASAP to find the locations of different kinds of features, even if you can't always search for them by name. For example, by selecting prophage, you can find the locations of 10 cryptic prophage in MG1655. However, you can't find specific prophage by searching for e14 or rac. By contrast, searching for rac in [[EcoCyc]] does return hits. But it's easier to see how many prophage are there using ASAP; EcoCyc returns hits for every prophage gene when you search for "prophage".

	ASAP can be frustrating in some cases from problems with its user interface. For example, in the simple query page, the search box for ASAP FeatureID(s) is prominently placed but is going to be used rarely by naive users (it is not clear to me who uses that search field at all [[User:JimHu\|JimHu]] 06:27, 4 July 2006 (CDT)). If they do type a gene name there, they will get no hits. Feature name is also nonintuitive as a surrogate for gene name. ASAP also can surprise the user with links that lead to long load times. For example, clicking on Published Annotation in the Annotation lists often loads the entire genome record from NCBI. Loading the genome and synteny browsers can also be so slow that the user may think that the program is not responding.		ASAP can be frustrating in some cases from problems with its user interface. For example, in the simple query page, the search box for ASAP FeatureID(s) is prominently placed but is going to be used rarely by naive users (it is not clear to me who uses that search field at all [[User:JimHu\|JimHu]] 06:27, 4 July 2006 (CDT)). If they do type a gene name there, they will get no hits. Feature name is also nonintuitive as a surrogate for gene name. ASAP also can surprise the user with links that lead to long load times. For example, clicking on Published Annotation in the Annotation lists often loads the entire genome record from NCBI. Loading the genome and synteny browsers can also be so slow that the user may think that the program is not responding.

	=References=		==References==
			{{RefHelp}}
			<references/>
	J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. ''Nucleic Acids Res.'' 31(1):147-151. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12519969 PubMed] [http://nar.oupjournals.org/cgi/content/full/31/1/147 full text] [http://nar.oupjournals.org/cgi/content/abstract/31/1/147 abstract]		J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. ''Nucleic Acids Res.'' 31(1):147-151. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12519969 PubMed] [http://nar.oupjournals.org/cgi/content/full/31/1/147 full text] [http://nar.oupjournals.org/cgi/content/abstract/31/1/147 abstract]

	=External Links=		==External Links==
	*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page]		*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page]
	*[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}} at the University of Wisconsin]		*[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}} at the University of Wisconsin]
	*[http://www.ericbrc.org/ {{PAGENAME}} as part of ERIC]		*[http://www.ericbrc.org/ {{PAGENAME}} as part of ERIC]
	==Discussion of {{PAGENAME}} on other websites==		==Discussion of {{PAGENAME}} on other websites==

Dbaumler: /* External Links */

2007-08-06T21:20:37Z

External Links

← Older revision		Revision as of 21:20, 6 August 2007
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	*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page]		*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page]
	*[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}} at the University of Wisconsin]		*[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}} at the University of Wisconsin]
	*[http://www.ericbrc.org/~~asap/home.php~~ {{PAGENAME}} as part of ERIC]		*[http://www.ericbrc.org/ {{PAGENAME}} as part of ERIC]
	==Discussion of {{PAGENAME}} on other websites==		==Discussion of {{PAGENAME}} on other websites==

Japodaca: /* Content */

2007-08-06T20:40:52Z

Content

← Older revision		Revision as of 20:40, 6 August 2007
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	Content at ASAP covers genomes of many enteric bacteria, and is very extensive for individual genomes. ASAP includes:		Content at ASAP covers genomes of many enteric bacteria, and is very extensive for individual genomes. ASAP includes:
	:*Annotations generated by ASAP curators and user community. These are therefore nonredundant with other sites.		:*Annotations generated by ASAP curators and user community. These are therefore nonredundant with other sites.
	:*Experimental data, including published microarray and proteomic data).		:*Experimental data, including published microarray and proteomic data.
	:*Strain descriptions from the Blattner lab		:*Strain descriptions from the Blattner lab
	ASAP has a page that [https://asap.ahabs.wisc.edu/asap/db_summary.php?LocationID=&SequenceVersionID=&GenomeID=&ExpSetID=#WIS_MG1655 lists feature types and annotation types]		ASAP has a page that [https://asap.ahabs.wisc.edu/asap/db_summary.php?LocationID=&SequenceVersionID=&GenomeID=&ExpSetID=#WIS_MG1655 lists feature types and annotation types]