FAQ - Revision history

FolkerMeyer at 15:20, 1 November 2006

2006-11-01T15:20:13Z

FolkerMeyer at 15:19, 1 November 2006

2006-11-01T15:19:26Z

VeronikaVonstein at 00:52, 1 November 2006

2006-11-01T00:52:52Z

VeronikaVonstein at 00:50, 1 November 2006

2006-11-01T00:50:02Z

VeronikaVonstein at 00:49, 1 November 2006

2006-11-01T00:49:20Z

FolkerMeyer at 22:05, 31 October 2006

2006-10-31T22:05:36Z

FolkerMeyer at 21:37, 31 October 2006

2006-10-31T21:37:44Z

FolkerMeyer at 21:36, 31 October 2006

2006-10-31T21:36:22Z

FolkerMeyer at 21:34, 31 October 2006

2006-10-31T21:34:44Z

FolkerMeyer at 21:28, 31 October 2006

2006-10-31T21:28:41Z

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 * Are the annotations in the SEED computer generated?
 The [[Glossary#Subsystems|subsystems]] based annotations in the SEED are created by a human expert, in contrast to many existing annotation approaches, the SEED annotation approach is to annotated a [[Glossary#Subsystems|subsystems]] across many genomes at a time by an expert curator. Genes not in subsystems are annotated using an automatic decision procedure.
 * Is the SEED available?
 Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]].
 * What genomes are included in the SEED data set?
 ''This is a placeholder for a PAGE that has a pointer to our genomelist.''
 * How often is the SEED updated?
 The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank.
 * What is the difference between SEED, SEED-Viewer and Trail-SEED?
@@ Line 17: / Line 21: @@
 The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets.
 The [http://theseed.uchicago.edu/FIG/index.cgi/ Trail-SEED], a publicly writable copy of the SEED is available for testing purposes.
 * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED.
 While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes.
 * What data is available inside the SEED-Viewer?
 All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server.
 * Can I link my web site to the SEED?
@@ Line 33: / Line 40: @@
   Example:
    http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2
 * On what platforms do you run SEED?
 Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC).
 * Can I annotate my genome with the SEED?
 Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email.
 However we are planning to make available a genome annotation service based on SEED technology.
 * Are there other similar efforts out there?
 Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]).
 * What is the difference between SEED and other annotation approaches?
 Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]].

@@ Line 1: / Line 1: @@
 == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. ==
 * Is the SEED available?
@@ Line 17: / Line 20: @@
 * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED.
 While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes.
 * What data is available inside the SEED-Viewer?

@@ Line 13: / Line 13: @@
 The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing  [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED.
 The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets.
-The Trail-SEED, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi] copy of the SEED is available for testing purposes.
+The [http://theseed.uchicago.edu/FIG/index.cgi/ Trail-SEED], a publicly writable copy of the SEED is available for testing purposes.
 * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED.

@@ Line 11: / Line 11: @@
 * What is the difference between SEED, SEED-Viewer and Trail-SEED?
-The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the annotation [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing  [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED.
+The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing  [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED.
 The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets.
 The Trail-SEED, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi] copy of the SEED is available for testing purposes.

@@ Line 1: / Line 1: @@
-== '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. ==
+== '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. ==
 * Is the SEED available?
-Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]].
+Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]].
 * What genomes are included in the SEED data set?
@@ Line 10: / Line 10: @@
 The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank.
-* What is the difference between SEED and the SEED-Viewer?
+* What is the difference between SEED, SEED-Viewer and Trail-SEED?
-The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the
+The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the annotation [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing  [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED.
-[[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems.
+The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets.
 * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED.
@@ Line 22: / Line 23: @@
 * Can I link my web site to the SEED?
-YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks.
+YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks.
 The base URL:
@@ Line 38: / Line 39: @@
 However we are planning to make available a genome annotation service based on SEED technology.
-* Are there other similar efforts our there?
+* Are there other similar efforts out there?
 Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]).
 * What is the difference between SEED and other annotation approaches?
 Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]].

@@ Line 27: / Line 27: @@
    http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2
-* What platforms do you run SEED on?
+* On what platforms do you run SEED?
-Our main platforms are MacOSX (Intel and PPC) and Linux (Intel and PPC), there is no reason the SEED should not run on other platforms, we do however not perform testing etc.
+Our platforms are MacOSX (Intel and PPC) and Linux (Debian/ReHat/Fedora on Intel and PPC).
 * Can I annotate my genome with the SEED?