ISEEM:Project - Revision history

Guillaume Jospin at 19:08, 1 March 2010

Guillaume Jospin — Mon, 01 Mar 2010 19:08:56 GMT

←Older revision		Revision as of 19:08, 1 March 2010
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	9. Pennisi, E., Metagenomics. Massive microbial sequence project proposed. Science, 2007. 315(5820): p. 1781.		9. Pennisi, E., Metagenomics. Massive microbial sequence project proposed. Science, 2007. 315(5820): p. 1781.

-	~~==Software and Downloads==~~
-	* [[AMPHORA]] - automated phylogenomic analysis for genomes and metagenomics.
-	* [[STAP]] - ss-rRNA Taxonomy Assigning Pipeline - rRNA alignment and taxonomy pipeline.
	</div>		</div>

Guillaume Jospin: /* Software and Downloads */

Guillaume Jospin — Thu, 25 Feb 2010 19:52:16 GMT

Software and Downloads

←Older revision		Revision as of 19:52, 25 February 2010
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	==Software and Downloads==		==Software and Downloads==
		+	* [[AMPHORA]] - automated phylogenomic analysis for genomes and metagenomics.
	* [[STAP]] - ss-rRNA Taxonomy Assigning Pipeline - rRNA alignment and taxonomy pipeline.		* [[STAP]] - ss-rRNA Taxonomy Assigning Pipeline - rRNA alignment and taxonomy pipeline.
	</div>		</div>

Guillaume Jospin: /* Software and Downloads */

Guillaume Jospin — Thu, 25 Feb 2010 19:48:20 GMT

Software and Downloads

←Older revision		Revision as of 19:48, 25 February 2010
Line 68:		Line 68:

	==Software and Downloads==		==Software and Downloads==
-	* [[STAP]] - rRNA alignment and taxonomy pipeline.	+	* [[STAP]] - ss-rRNA Taxonomy Assigning Pipeline - rRNA alignment and taxonomy pipeline.
	</div>		</div>

Guillaume Jospin at 19:42, 25 February 2010

Guillaume Jospin — Thu, 25 Feb 2010 19:42:43 GMT

←Older revision		Revision as of 19:42, 25 February 2010
Line 66:		Line 66:

	9. Pennisi, E., Metagenomics. Massive microbial sequence project proposed. Science, 2007. 315(5820): p. 1781.		9. Pennisi, E., Metagenomics. Massive microbial sequence project proposed. Science, 2007. 315(5820): p. 1781.
-	~~</div>~~	+
	==Software and Downloads==		==Software and Downloads==
	* [[STAP]] - rRNA alignment and taxonomy pipeline.		* [[STAP]] - rRNA alignment and taxonomy pipeline.
		+	</div>

Guillaume Jospin at 19:42, 25 February 2010

Guillaume Jospin — Thu, 25 Feb 2010 19:42:11 GMT

←Older revision		Revision as of 19:42, 25 February 2010
Line 67:		Line 67:
	9. Pennisi, E., Metagenomics. Massive microbial sequence project proposed. Science, 2007. 315(5820): p. 1781.		9. Pennisi, E., Metagenomics. Massive microbial sequence project proposed. Science, 2007. 315(5820): p. 1781.
	</div>		</div>
		+	==Software and Downloads==
		+	* [[STAP]] - rRNA alignment and taxonomy pipeline.

Bill Flanagan at 22:51, 24 November 2008

Bill Flanagan — Mon, 24 Nov 2008 22:51:42 GMT

←Older revision		Revision as of 22:51, 24 November 2008
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-	<div style="width: 800px;border-top-width: 4px;border-bottom-width: 4px;border-top-style: solid;border-bottom-style: solid;border-top-color: #333333;border-right-color: #333333;border-bottom-color: #333333;border-left-color: #333333;">[[Image:header6.jpg]]</div><div style="color: #999999; background-color: #FFF; width: 800px;text-align: center;">	+	{{ISEEM}}
-	~~[[iSEEM \| <font face="arial" style="color:#333333"> '''Home''' </font>]]~~	+
-	~~   ~~	+
-	~~[[iSEEM:What We Do \| <font face="arial" style="color:#333333"> '''Project''' </font>]]   ~~	+
-	~~[[iSEEM:Who We Are \| <font face="arial" style="color:#333333"> '''People''' </font>]]    ~~	+
-	~~[[iSEEM:Publications, Talks & Media \| <font face="arial" style="color:#333333"> '''News''' </font>]]    ~~	+
-	~~[[iSEEM:Group Members Only \| <font face="arial" style="color:#333333"> '''Members Only''' </font>]]    ~~	+
-	~~[[iSEEM:Calendar \| <font face="arial" style="color:#333333"> '''Calendar''' </font>]]    ~~	+
-	~~[http://www.citeulike.org/group/6072/library <font face="arial" style="color:#333333"> '''Library''' </font>]    ~~	+
-	~~</div><br>~~	+

	<div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px;">		<div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px;">

Steven Green: /* Proposed research areas */

Steven Green — Tue, 11 Nov 2008 20:57:56 GMT

Proposed research areas

←Older revision		Revision as of 20:57, 11 November 2008
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	Though each of these projects can be considered separate activities, they are highly interdependent and the interdisciplinary nature of the labs involved is critical for the success of the project. For example, we propose to use phylogenetic analysis to search for new types of organisms and genes (project 1.2 led by Eisen). The results of this phylogenetic analysis will also be used to assess the phylogenetic structure of communities (project 1.3 led by Green) and to study evolution of gene families across environments (project 2.2 led by Pollard). Similarly, the statistical methods developed for comparative metagenomics (project 3 led by Pollard) will be used in the population genomic studies (project 2.1 led by Eisen) as well as in the development of biodiversity estimators (project 1.4 led by Green). To achieve this integration we plan to have active feedback between each of the PIs and each of the projects. To do this we propose a management plan that will help guide these interactions. We believe that by taking this integrated approach – both in terms of the research topics and by combining separate fields of study, we will not only make important scientific discoveries about microbial communities but we will also build and develop novel methods and approaches of great utility to the metagenomics community.		Though each of these projects can be considered separate activities, they are highly interdependent and the interdisciplinary nature of the labs involved is critical for the success of the project. For example, we propose to use phylogenetic analysis to search for new types of organisms and genes (project 1.2 led by Eisen). The results of this phylogenetic analysis will also be used to assess the phylogenetic structure of communities (project 1.3 led by Green) and to study evolution of gene families across environments (project 2.2 led by Pollard). Similarly, the statistical methods developed for comparative metagenomics (project 3 led by Pollard) will be used in the population genomic studies (project 2.1 led by Eisen) as well as in the development of biodiversity estimators (project 1.4 led by Green). To achieve this integration we plan to have active feedback between each of the PIs and each of the projects. To do this we propose a management plan that will help guide these interactions. We believe that by taking this integrated approach – both in terms of the research topics and by combining separate fields of study, we will not only make important scientific discoveries about microbial communities but we will also build and develop novel methods and approaches of great utility to the metagenomics community.

		+	<div style="width: 720px;border-bottom-width: 2px;;border-bottom-style: solid;border-bottom-color: #333333;font-family: Arial, Helvetica, sans-serif;font-size: 11px;color: #333333;font-style: italic;">above image © 2007, Dennis Kunkel</div>

	'''References'''		'''References'''

Steven Green: /* Proposed research areas */

Steven Green — Tue, 11 Nov 2008 20:56:14 GMT

Proposed research areas

←Older revision		Revision as of 20:56, 11 November 2008
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	## Metagenomic analysis of community phylogenetic structure		## Metagenomic analysis of community phylogenetic structure
	## Estimating biodiversity from metagenomic samples		## Estimating biodiversity from metagenomic samples
		+	<span style="float: right;border: 2px solid #666666;margin-left: 20px;margin-bottom: 10px;">[[Image:dk2.jpg]]</span>
	#'''Metagenomic studies of microbial evolutionary dynamics'''		#'''Metagenomic studies of microbial evolutionary dynamics'''
	##Molecular evolutionary dynamics of gene families		##Molecular evolutionary dynamics of gene families
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-	~~<span style="float: right;border: 2px solid #666666;margin-left: 30px;margin-bottom: 10px;">[[Image:dk2.jpg]]</span>~~Though each of these projects can be considered separate activities, they are highly interdependent and the interdisciplinary nature of the labs involved is critical for the success of the project. For example, we propose to use phylogenetic analysis to search for new types of organisms and genes (project 1.2 led by Eisen). The results of this phylogenetic analysis will also be used to assess the phylogenetic structure of communities (project 1.3 led by Green) and to study evolution of gene families across environments (project 2.2 led by Pollard). Similarly, the statistical methods developed for comparative metagenomics (project 3 led by Pollard) will be used in the population genomic studies (project 2.1 led by Eisen) as well as in the development of biodiversity estimators (project 1.4 led by Green). To achieve this integration we plan to have active feedback between each of the PIs and each of the projects. To do this we propose a management plan that will help guide these interactions. We believe that by taking this integrated approach – both in terms of the research topics and by combining separate fields of study, we will not only make important scientific discoveries about microbial communities but we will also build and develop novel methods and approaches of great utility to the metagenomics community.	+	Though each of these projects can be considered separate activities, they are highly interdependent and the interdisciplinary nature of the labs involved is critical for the success of the project. For example, we propose to use phylogenetic analysis to search for new types of organisms and genes (project 1.2 led by Eisen). The results of this phylogenetic analysis will also be used to assess the phylogenetic structure of communities (project 1.3 led by Green) and to study evolution of gene families across environments (project 2.2 led by Pollard). Similarly, the statistical methods developed for comparative metagenomics (project 3 led by Pollard) will be used in the population genomic studies (project 2.1 led by Eisen) as well as in the development of biodiversity estimators (project 1.4 led by Green). To achieve this integration we plan to have active feedback between each of the PIs and each of the projects. To do this we propose a management plan that will help guide these interactions. We believe that by taking this integrated approach – both in terms of the research topics and by combining separate fields of study, we will not only make important scientific discoveries about microbial communities but we will also build and develop novel methods and approaches of great utility to the metagenomics community.
		+

	'''References'''		'''References'''

Steven Green: /* Proposed research areas */

Steven Green — Tue, 11 Nov 2008 20:52:08 GMT

Proposed research areas

←Older revision		Revision as of 20:52, 11 November 2008
Line 51:		Line 51:


-	Though each of these projects can be considered separate activities, they are highly interdependent and the interdisciplinary nature of the labs involved is critical for the success of the project. For example, we propose to use phylogenetic analysis to search for new types of organisms and genes (project 1.2 led by Eisen). The results of this phylogenetic analysis will also be used to assess the phylogenetic structure of communities (project 1.3 led by Green) and to study evolution of gene families across environments (project 2.2 led by Pollard). Similarly, the statistical methods developed for comparative metagenomics (project 3 led by Pollard) will be used in the population genomic studies (project 2.1 led by Eisen) as well as in the development of biodiversity estimators (project 1.4 led by Green). To achieve this integration we plan to have active feedback between each of the PIs and each of the projects. To do this we propose a management plan that will help guide these interactions. We believe that by taking this integrated approach – both in terms of the research topics and by combining separate fields of study, we will not only make important scientific discoveries about microbial communities but we will also build and develop novel methods and approaches of great utility to the metagenomics community.	+	<span style="float: right;border: 2px solid #666666;margin-left: 30px;margin-bottom: 10px;">[[Image:dk2.jpg]]</span>Though each of these projects can be considered separate activities, they are highly interdependent and the interdisciplinary nature of the labs involved is critical for the success of the project. For example, we propose to use phylogenetic analysis to search for new types of organisms and genes (project 1.2 led by Eisen). The results of this phylogenetic analysis will also be used to assess the phylogenetic structure of communities (project 1.3 led by Green) and to study evolution of gene families across environments (project 2.2 led by Pollard). Similarly, the statistical methods developed for comparative metagenomics (project 3 led by Pollard) will be used in the population genomic studies (project 2.1 led by Eisen) as well as in the development of biodiversity estimators (project 1.4 led by Green). To achieve this integration we plan to have active feedback between each of the PIs and each of the projects. To do this we propose a management plan that will help guide these interactions. We believe that by taking this integrated approach – both in terms of the research topics and by combining separate fields of study, we will not only make important scientific discoveries about microbial communities but we will also build and develop novel methods and approaches of great utility to the metagenomics community.

	'''References'''		'''References'''

Steven Green: /* Introduction */

Steven Green — Tue, 11 Nov 2008 18:51:25 GMT

Introduction

←Older revision		Revision as of 18:51, 11 November 2008
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	<span style="font-size:9px;vertical-align: super;display: inline;">3</span> In the NAS report they identify four key questions: how can we find new functions; how diverse is life; how do microbes evolve; and what role do microbes play in the health of their hosts.		<span style="font-size:9px;vertical-align: super;display: inline;">3</span> In the NAS report they identify four key questions: how can we find new functions; how diverse is life; how do microbes evolve; and what role do microbes play in the health of their hosts.
		+
		+	<div style="width: 720px;border-bottom-width: 2px;;border-bottom-style: solid;border-bottom-color: #333333;font-family: Arial, Helvetica, sans-serif;font-size: 11px;color: #333333;font-style: italic;">above image © 2007, Dennis Kunkel</div>

	==Principal investigators==		==Principal investigators==