https:/// /w/api.php?action=feedcontributions&feedformat=atom&user=TerryDisz 2026-05-26T06:21:01Z User contributions MediaWiki 1.35.6 /w/index.php?title=MediaWiki:Sidebar&diff=2497 2010-11-15T22:35:46Z

<p>TerryDisz: </p> <hr /> <div>* Navigation<br /> ** Home_of_the_SEED|Home of the SEED<br /> ** Annotating_1000_genomes|Manifesto<br /> ** SEED_People| SEED People<br /> ** Contact| Contact<br /> * SEEDs<br /> ** http://seed-viewer.theseed.org/|SEED-Viewer<br /> ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED<br /> ** http://pseed.theseed.org/|PATRIC SEED<br /> ** http://seed-viewer.theseed.org/models|Model SEED<br /> * Applications<br /> ** http://blog.theseed.org/servers/|Servers Blog<br /> ** http://blog.theseed.org/model_seed/|Model SEED Blog<br /> ** http://rast.nmpdr.org/|RAST Annotation Server<br /> ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server<br /> ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)<br /> * Documentation<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial<br /> ** SEED_Viewer_Tutorial|SEED Viewer Tutorial<br /> * Miscellaneous<br /> ** DownloadPage|Download Page<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions<br /> ** Glossary|Glossary<br /> ** SOPs|SOPs<br /> ** SpecialPurposeDBs|Special Purpose DBs</div>

TerryDisz /w/index.php?title=MediaWiki:Sidebar&diff=2496 2010-11-15T22:34:08Z

<p>TerryDisz: </p> <hr /> <div>* Navigation<br /> ** Home_of_the_SEED|Home of the SEED<br /> ** Annotating_1000_genomes|Manifesto<br /> ** SEED_People| SEED People<br /> ** Contact| Contact<br /> * SEEDs<br /> ** http://seed-viewer.theseed.org/|SEED-Viewer<br /> ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED<br /> ** http://pseed.theseed.org/|PATRIC SEED<br /> * Applications<br /> ** http://blog.theseed.org/servers/|Servers Blog<br /> ** http://blog.theseed.org/model_seed/|Model SEED Blog<br /> ** http://seed-viewer.theseed.org/models|Model SEED Viewer<br /> ** http://rast.nmpdr.org/|RAST Annotation Server<br /> ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server<br /> ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)<br /> * Documentation<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial<br /> ** SEED_Viewer_Tutorial|SEED Viewer Tutorial<br /> * Miscellaneous<br /> ** DownloadPage|Download Page<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions<br /> ** Glossary|Glossary<br /> ** SOPs|SOPs<br /> ** SpecialPurposeDBs|Special Purpose DBs</div>

TerryDisz /w/index.php?title=MediaWiki:Sidebar&diff=2495 2010-11-15T22:31:37Z

<p>TerryDisz: </p> <hr /> <div>* Navigation<br /> ** Home_of_the_SEED|Home of the SEED<br /> ** Annotating_1000_genomes|Manifesto<br /> ** SEED_People| SEED People<br /> ** Contact| Contact<br /> * SEEDs<br /> ** http://seed-viewer.theseed.org/|SEED-Viewer<br /> ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED<br /> ** http://pseed.theseed.org/|PATRIC SEED<br /> * Applications<br /> ** http://blog.theseed.org/servers/|Servers Blog<br /> ** http://blog.theseed.org/model_seed/|Model SEED Blog<br /> ** http://seed-viewer.theseed.org/models| Model SEED-Viewer<br /> ** http://rast.nmpdr.org/|RAST Annotation Server<br /> ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server<br /> ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)<br /> * Documentation<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial<br /> ** SEED_Viewer_Tutorial|SEED Viewer Tutorial<br /> * Miscellaneous<br /> ** DownloadPage|Download Page<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions<br /> ** Glossary|Glossary<br /> ** SOPs|SOPs<br /> ** SpecialPurposeDBs|Special Purpose DBs</div>

TerryDisz /w/index.php?title=MediaWiki:Sidebar&diff=2494 2010-11-15T22:31:01Z

<p>TerryDisz: </p> <hr /> <div>* Navigation<br /> ** Home_of_the_SEED|Home of the SEED<br /> ** Annotating_1000_genomes|Manifesto<br /> ** SEED_People| SEED People<br /> ** Contact| Contact<br /> * SEEDs<br /> ** http://seed-viewer.theseed.org/|SEED-Viewer<br /> ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED<br /> ** http://pseed.theseed.org/|PATRIC SEED<br /> * Applications<br /> ** http://blog.theseed.org/servers/|Servers Blog<br /> ** http://blog.theseed.org/model_seed/|Model SEED Blog<br /> ** http://seed-viewer.theseed.org/models| SEED<br /> ** http://rast.nmpdr.org/|RAST Annotation Server<br /> ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server<br /> ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)<br /> * Documentation<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial<br /> ** SEED_Viewer_Tutorial|SEED Viewer Tutorial<br /> * Miscellaneous<br /> ** DownloadPage|Download Page<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions<br /> ** Glossary|Glossary<br /> ** SOPs|SOPs<br /> ** SpecialPurposeDBs|Special Purpose DBs</div>

TerryDisz /w/index.php?title=MediaWiki:Sidebar&diff=2493 2010-11-15T22:29:31Z

<p>TerryDisz: </p> <hr /> <div>* Navigation<br /> ** Home_of_the_SEED|Home of the SEED<br /> ** Annotating_1000_genomes|Manifesto<br /> ** SEED_People| SEED People<br /> ** Contact| Contact<br /> * SEEDs<br /> ** http://seed-viewer.theseed.org/|SEED-Viewer<br /> ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED<br /> ** http://pseed.theseed.org/|PATRIC SEED<br /> * Applications<br /> ** http://blog.theseed.org/servers/|Servers Blog<br /> ** http://blog.theseed.org/model_seed/|Model SEED Blog<br /> ** http://seed-viewer.theseed.org/models SEED<br /> ** http://rast.nmpdr.org/|RAST Annotation Server<br /> ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server<br /> ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)<br /> * Documentation<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial<br /> ** SEED_Viewer_Tutorial|SEED Viewer Tutorial<br /> * Miscellaneous<br /> ** DownloadPage|Download Page<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions<br /> ** Glossary|Glossary<br /> ** SOPs|SOPs<br /> ** SpecialPurposeDBs|Special Purpose DBs</div>

TerryDisz /w/index.php?title=MediaWiki:Sidebar&diff=2492 2010-11-15T22:27:43Z

<p>TerryDisz: </p> <hr /> <div>* Navigation<br /> ** Home_of_the_SEED|Home of the SEED<br /> ** Annotating_1000_genomes|Manifesto<br /> ** SEED_People| SEED People<br /> ** Contact| Contact<br /> * SEEDs<br /> ** http://seed-viewer.theseed.org/|SEED-Viewer<br /> ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED<br /> ** http://pseed.theseed.org/|PATRIC SEED<br /> * Applications<br /> ** http://blog.theseed.org/servers/|Servers Blog<br /> ** http://blog.theseed.org/model_seed/|Model SEED Blog<br /> ** http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView Model SEED<br /> ** http://rast.nmpdr.org/|RAST Annotation Server<br /> ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server<br /> ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)<br /> * Documentation<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial<br /> ** SEED_Viewer_Tutorial|SEED Viewer Tutorial<br /> * Miscellaneous<br /> ** DownloadPage|Download Page<br /> ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions<br /> ** Glossary|Glossary<br /> ** SOPs|SOPs<br /> ** SpecialPurposeDBs|Special Purpose DBs</div>

TerryDisz /w/index.php?title=Home_of_the_SEED&diff=2485 2010-06-11T20:52:03Z

<p>TerryDisz: </p> <hr /> <div>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. <br /> <br /> [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]<br /> <br /> Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not on 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 ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology.<br /> <br /> <br /> 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]. <br /> <br /> We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.<br /> <br /> * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=16214803&amp;query_hl=2&amp;itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br /> * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])<br /> * 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].<br /> * 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.</div>

TerryDisz /w/index.php?title=MediaWiki:Sidebar&diff=2484 2010-06-11T19:49:42Z

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

TerryDisz /w/index.php?title=Home_of_the_SEED&diff=1623 2006-12-11T17:11:11Z

<p>TerryDisz: fixed seed viewer link in body</p> <hr /> <div>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 Lab 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 comperative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br /> <br /> 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. <br /> <br /> <br /> We make all our software and data available for download and use on our [[DownloadPage]] page.<br /> <br /> <br /> * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=16214803&amp;query_hl=2&amp;itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br /> * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].</div>

TerryDisz /w/index.php?title=SOPs&diff=1622 2006-12-06T15:27:30Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** Annotation Codes (NMPDR|SOP010) [[Image:Annotation sop.pdf]]<br /> ** Annotating a genome with the 48-hour service (NMPDR|SOP005) [[Image:The48hrserver.pdf]]<br /> ** Creation of GO-terms (NMPDR|SOP004) [[Image:GO AND PFAM SOP.pdf|thumb|Description]] <br /> *BRC<br /> **Releasing GFF3 files(NMPDR|SOP006) [[Image:brc upload sop.pdf]]<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** Adding Genomes to the NMPDR (NMPDR|SOP003) [[Image:New_genome_sop.pdf]]</div>

TerryDisz /w/index.php?title=File:Annotation_sop.pdf&diff=1621 2006-12-06T15:25:11Z

<p>TerryDisz: </p> <hr /> <div></div>

TerryDisz /w/index.php?title=SOPs&diff=1620 2006-12-06T15:10:35Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** Annotating a genome with the 48-hour service (NMPDR|SOP005) [[Image:The48hrserver.pdf]]<br /> ** Creation of GO-terms (NMPDR|SOP004) [[Image:GO AND PFAM SOP.pdf|thumb|Description]] <br /> *BRC<br /> **Releasing GFF3 files(NMPDR|SOP006) [[Image:brc upload sop.pdf]]<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** Adding Genomes to the NMPDR (NMPDR|SOP003) [[Image:New_genome_sop.pdf]]</div>

TerryDisz /w/index.php?title=SOPs&diff=1619 2006-12-06T14:46:04Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** [[Image:The48hrserver.pdf]] Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** [[Image:GO AND PFAM SOP.pdf|thumb|Description]] Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:brc upload sop.pdf]] Releasing GFF3 files(NMPDR|SOP006)<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf]] Adding Genomes to the NMPDR (NMPDR|SOP003)</div>

TerryDisz /w/index.php?title=File:GO_AND_PFAM_SOP.pdf&diff=1618 2006-12-06T14:44:10Z

<p>TerryDisz: </p> <hr /> <div></div>

TerryDisz /w/index.php?title=SOPs&diff=1617 2006-12-06T14:38:42Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** [[Image:The48hrserver.pdf]] Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:brc upload sop.pdf]] Releasing GFF3 files(NMPDR|SOP006)<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf]] Adding Genomes to the NMPDR (NMPDR|SOP003)</div>

TerryDisz /w/index.php?title=SOPs&diff=1616 2006-12-06T14:38:15Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** [[Image:The48hrserver.pdf]]Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:brc upload sop.pdf]]Releasing GFF3 files(NMPDR|SOP006)<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf]]Adding Genomes to the NMPDR (NMPDR|SOP003)</div>

TerryDisz /w/index.php?title=SOPs&diff=1615 2006-12-06T14:34:10Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** [[Image:The48hrserver.pdf|Annotating a genome with the 48-hour service (NMPDR|SOP005)]] Using the 48 hour server.<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]]<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]]</div>

TerryDisz /w/index.php?title=SOPs&diff=1614 2006-12-06T14:31:33Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** [[Image:The48hrserver.pdf|Annotating a genome with the 48-hour service (NMPDR|SOP005)]]<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]]<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]]</div>

TerryDisz /w/index.php?title=File:The48hrserver.pdf&diff=1613 2006-12-06T14:30:38Z

<p>TerryDisz: </p> <hr /> <div></div>

TerryDisz /w/index.php?title=SOPs&diff=1612 2006-12-06T14:29:34Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** [[Image:48hrserver.pdf|Annotating a genome with the 48-hour service (NMPDR|SOP005)]]<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]]<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]]</div>

TerryDisz /w/index.php?title=File:48hrserver.pdf&diff=1611 2006-12-06T14:20:23Z

<p>TerryDisz: </p> <hr /> <div></div>

TerryDisz /w/index.php?title=SOPs&diff=1610 2006-12-04T21:56:04Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:Brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] -- Creating and uploading GFF3 files<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]]</div>

TerryDisz /w/index.php?title=File:New_genome_sop.pdf&diff=1609 2006-12-04T21:49:43Z

<p>TerryDisz: </p> <hr /> <div></div>

TerryDisz /w/index.php?title=File:brc_upload_sop.pdf&diff=1608 2006-12-04T21:44:41Z

<p>TerryDisz: New Version</p> <hr /> <div>New Version</div>

TerryDisz /w/index.php?title=File:Brc_upload_sop.pdf&diff=1607 2006-12-04T21:43:22Z

<p>TerryDisz: </p> <hr /> <div></div>

TerryDisz /w/index.php?title=SOPs&diff=1602 2006-12-04T20:54:14Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Image:Brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] -- Creating and uploading GFF3 files<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Adding Genomes|Adding Genomes to the NMPDR (NMPDR|SOP003)]]</div>

TerryDisz /w/index.php?title=SOPs&diff=1598 2006-12-04T20:21:31Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Release_to_BRC|Releasing GFF3 files(NMPDR|SOP006)]] -- Creating and uploading GFF3 files<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]<br /> ** [[Adding Genomes to the NMPDR (NMPDR|SOP003)]]</div>

TerryDisz /w/index.php?title=SOPs&diff=1597 2006-12-04T20:13:56Z

<p>TerryDisz: </p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures.<br /> <br /> <br /> * Annotation<br /> ** Annotating a genome with the 48-hour service (NMPDR|SOP005)<br /> ** Creation of GO-terms (NMPDR|SOP004)<br /> *BRC<br /> **[[Release_to_BRC|Releasing GFF3 files(NMPDR|SOP003)]] -- Creating and uploading GFF3 files<br /> <br /> <br /> * Obsolete SOPs<br /> ** [[GeneCalling|Gene calling (NMPDR|SOP001)]]<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]]</div>

TerryDisz /w/index.php?title=SOPs&diff=1590 2006-11-15T21:11:34Z

<p>TerryDisz: /* SEED standard operating procedures */</p> <hr /> <div>== SEED standard operating procedures ==<br /> <br /> To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures.<br /> <br /> * [[GeneCalling|Gene calling]]<br /> * Annotation<br /> ** [[Annotation_of_close_strain_sets|Annotation of close strain sets]]<br /> ** Annotation of diverse genomes.<br /> *BRC<br /> **[[Release_to_BRC|Releasing GFF3 files]] -- Creating and uploading GFF3 files</div>

TerryDisz