TheSeed - User contributions [en]

SEED People

2009-01-14T23:39:14Z

LeslieMcNeil:

The people behind SEED are the following:

* [http://www.thefig.info '''FIG''']
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs''']
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry
** Jared Wilkening

* [http://www.ci.uchicago.edu '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago''']
** Daniela Bartels
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Alex Rodriguez
** Mark D'Souza
** Rami Aziz

* [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign''']
** Gary J. Olsen
** Leslie McNeil
** Claudia Reich

* [http://www.hope.edu '''Hope College''']
** Matt DeJongh
** Aaron Best

* '''Alumni'''
** Daniel Paarmann
** Jen Zinner
** Matt Cohoon

MediaWiki:Sidebar

2009-01-10T23:27:27Z

LeslieMcNeil:

* Navigation
** Home_of_the_SEED|Home of the SEED
** Annotating_1000_genomes|Manifesto
** SEED_People| SEED People
** Contact| Contact
* SEEDs
** http://seed-viewer.theseed.org/|SEED-Viewer
** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED
* Applications
** http://www.nmpdr.org/|NMPDR
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2009-01-10T23:23:44Z

LeslieMcNeil:

* Navigation
** Home_of_the_SEED|Home of the SEED
** Annotating_1000_genomes|Manifesto
** SEED_People| SEED People
** Contact| Contact
* SEEDs
** http://seed-viewer.theseed.org/|SEED-Viewer
** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED
* Applications
** http://www.nmpdr.org/|NMPDR
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** Glossary|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2009-01-09T21:15:21Z

LeslieMcNeil:

SEED People

2009-01-08T20:14:14Z

LeslieMcNeil:

The people behind SEED are the following:

* [http://www.thefig.info '''FIG''']
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs''']
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry
** Jared Wilkening

* [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago''']
** Daniela Bartels
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Alex Rodriguez
** Mark D'Souza
** Rami Aziz

* [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign''']
** Gary J. Olsen
** Leslie McNeil
** Claudia Reich

* [http://www.hope.edu '''Hope College''']
** Matt DeJongh
** Aaron Best

* '''Alumni'''
** Daniel Paarmann
** Jen Zinner
** Matt Cohoon

SEED People

2009-01-08T18:15:34Z

LeslieMcNeil:

The people behind SEED are the following:

* [http://www.thefig.info '''FIG''']
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs''']
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry
** Jared Wilkening

* [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago''']
** Daniela Bartels
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Alex Rodriguez
** Mark D'Souza

* [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign''']
** Gary J. Olsen
** Leslie McNeil
** Claudia Reich

* [http://www.hope.edu '''Hope College''']
** Matt DeJongh
** Aaron Best

* [http://www.utmem.edu/ '''University of Tennessee Memphis Health Sciences Center''']
** Rami Aziz

* '''Alumni'''
** Daniel Paarmann
** Jen Zinner
** Matt Cohoon

SEED People

2009-01-08T18:14:30Z

LeslieMcNeil:

The people behind SEED are the following:

* [http://www.thefig.info '''FIG''']
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs''']
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry
** Jared Wilkening

* [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago''']
** Daniela Bartels
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Alex Rodriguez
** Mark D'Souza

* [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign''']
** Gary J. Olsen
** Leslie McNeil
** Claudia Reich

* [http://www.hope.edu '''Hope College''']
** Matt DeJongh
** Aaron Best

* [http://www.utmem.edu/ '''University of Memphis Tennessee''']
** Rami Aziz

* '''Alumni'''
** Daniel Paarmann
** Jen Zinner
** Matt Cohoon

Home of the SEED

2008-12-18T20:31:31Z

LeslieMcNeil:

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]

Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED].

We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.

* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures].
* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using Publications] page.

Home of the SEED

2008-12-18T20:29:44Z

LeslieMcNeil:

Home of the SEED

2008-12-18T20:26:30Z

LeslieMcNeil:

Home of the SEED

2008-12-18T20:25:29Z

LeslieMcNeil:

Home of the SEED

2008-12-18T20:22:21Z

LeslieMcNeil:

Home of the SEED

2008-12-18T20:21:59Z

LeslieMcNeil:

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]

Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED].

We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.

* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome|Standard Operating Procedures].
* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications] page.

Home of the SEED

2008-12-18T20:18:58Z

LeslieMcNeil:

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]

Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED].

We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.

* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling, etc. are outlined in a series of [[SOPs|Standard Operating Procedures]].
* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications] page.

Home of the SEED

2008-12-18T20:09:18Z

LeslieMcNeil:

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]

Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED].

We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.

* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].
* Read about how other groups have used our tools in their research on our [[http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications]] page.

Home of the SEED

2008-12-18T20:08:11Z

LeslieMcNeil:

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]

Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED].

We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.

* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].
* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications|Publications] page.

Home of the SEED

2008-12-18T20:06:01Z

LeslieMcNeil:

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]

Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED].

We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.

* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].
* Other [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications]