TheSeed - User contributions [en]

Home of the SEED

2008-02-14T19:44:34Z

WilliamMihalo:

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 [[papers that use the SEED]]

Home of the SEED

2007-09-18T20:45:41Z

WilliamMihalo:

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.

We 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]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time.

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 make all our software and data available for download and use on our [[DownloadPage]] page.

* When using the SEED, please 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 Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].

Home of the SEED

2007-07-04T15:13:14Z

WilliamMihalo:

Home of the SEED

2007-05-21T17:48:51Z

WilliamMihalo:

SEED People

2007-04-13T14:26:04Z

WilliamMihalo:

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

* [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago]
** Daniela Bartels
** Matt Cohoon
** Michael Kubal
** William Mihalo
** Daniel Paarmann
** Tobias Paczian
** Andreas Wilke
** Jen Zinner

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

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

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

File:Listeria.png

2006-12-04T21:39:34Z

WilliamMihalo: listeria

listeria

File:CentOS 4.2.pdf

2006-12-04T21:28:49Z

WilliamMihalo: A description of CentOS

A description of CentOS

File:Jed.pdf

2006-12-04T21:17:40Z

WilliamMihalo:

SEED People

2006-12-01T14:01:55Z

WilliamMihalo:

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
** ...

* [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago]
** Daniela Bartels
** Matt Cohoon
** Kaitlyn Hwang
** Michael Kubal
** William Mihalo
** Daniel Paarmann
** Tobias Paczian
** Andreas Wilke
** Jen Zinner
** ...

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

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

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

Home of the SEED

2006-08-23T21:20:48Z

WilliamMihalo:

With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time.

We make all our software and data available for download and use on our [[DownloadPage]] page.

* When using the SEED, please 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 Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].

Home of the SEED

2006-08-23T21:19:59Z

WilliamMihalo:

With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://seedviewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time.

We make all our software and data available for download and use on our [[DownloadPage]] page.

* When using the SEED, please 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 Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].

MediaWiki:Sidebar

2006-08-23T21:05:23Z

WilliamMihalo:

SEED People

2006-08-11T18:40:25Z

WilliamMihalo:

The people behind SEED are the following:

* [http://www.thefig.info FIG]
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parello
** Rob Edwards
** Andrei Ostermann
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** ...

* [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs]
** Rick Stevens
** Terry Disz
** Robert Olson
** Kaitlyn Hwang
** Folker Meyer
** ...

* [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago]
** Michael Kubal
** Matt Cohoon
** Jen Zinner
** Daniela Bartels
** Tobias Paczian
** William Mihalo
** ...

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

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

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

Home of the SEED

2006-08-01T21:07:44Z

WilliamMihalo: /* '''Home of the SEED''' */

== '''Home of the SEED''' ==

With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations.

The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations.
For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED].

The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time.

* You can download software and data from our [[Download]] page.
* We provide a list [[Glossary]] of terms used.
* When using the SEED, please 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 Acids Res 33(17)], 2005
* Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes.
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].