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From: Scott C. <ca...@cs...> - 2003-10-07 14:07:32
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Hello, I am pleased to announce the release of the Restriction Graph Viewer (RestGraph) contributed by developers at SGD at Stanford. It can be downloaded via the GMOD website (http://www.gmod.org/). Below is the README for RestGraph. Please contact Shuai Weng <sh...@ge...> and the GMOD-devel list (gmo...@li...) with questions. Scott ------------------- The RestGraph is a simple web-based restriction analysis tool. It is a component of the Generic Model Organism Systems Database project (GMOD.sourceforge.net). - For a demo, go to http://seq.yeastgenome.org/cgi-bin/GMOD/RestGraph.pl - To set your own parameters for the map display, please see the configuration module lib/Bio/GMOD/Tools/RestGraphDefs.pm. - The RestGraph.pl is a simple cgi program which you can copy to any subdirectory under your cgi-bin directory and change the $tmpDir and $htmlTmp to your own tmp directory and make it world writable. - To install this module on your own system, type perl Makefile.PL make make install - Prerequisites: it runs on top of several software packages. These packages must be installed before you can use this module. A) Apache Web Server -- http://www.apache.org The Apache web server is the industry standard open source web server for Unix and Windows systems. B) Perl 5.005 or higher-- http://www.cpan.org The Perl language is widely used for web applications. C) Standard Perl modules -- http://www.cpan.org The following Perl modules must be installed for the Blast Graphic Viewer to work. They can be found on CPAN: GD CGI D) Bioperl modules -- http://www.bioperl.org The following Bioperl modules must be installed for this viewer to work. Bio::Root::IO Bio::PrimarySeq Bio::Seq Bio::Tools::RestrictionEnzyme This is a free software. You can use it under the same terms as perl itself. Please see DISCLAIMER for limitations of warranty... Support is available from the discussion groups and mailing lists at www.gmod.org Shuai Weng & SGD team sh...@ge... www.yeastgenome.org Sept 9, 2003 -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-09-29 20:27:36
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Version 0.09 of CMap has been released. Changes include:
- Fixed problems in "cache_dir" method where temp dir wasn't being
created
- Fixed bug in name-based correspondences where extra feature types
weren't being correctly included in checks
- Significantly increased speed of making name-based correspondences
- Fixed bugs in admin feature search
- Added "accession_id" to map type table
- Added restriction by species and map type to map set info page
- Added expanded ability to indicate number selections in
cmap_admin.pl
- Added order by species/map type on map viewer "Ref. Map" selection
- Fixed errors in map detail page
- Added map set names to top of matrix
- Added "View All Maps" link to map set info template
- Added "description" field to feature type and "feature_type_info"
handler for displaying details on feature types
- Added reference map set info to map viewer page when only the
reference map set has been chosen
- Changed installation to use Module::Build instead of
ExtUtils::MakeMaker
- Added SIGNATURE to verify tarball
The tarball is available from Sourceforge:
http://sourceforge.net/project/showfiles.php?group_id=27707
I'm hoping the new installation procedure proves to be smoother than
past releases. If you have any problems or comments, please drop a
line to the CMap mailing list (gmo...@li...).
--
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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From: Scott C. <ca...@cs...> - 2003-09-22 18:30:08
|
I am please to announce the initial public release of seqdb_engine, contributed by the developers at Mouse Genome Informatics and the Jackson Lab. Seqdb_engine is a framework for building customized blastable sequence databases from sources such as GenBank, SwissProt, TIGR, etc. Seqdb_engine includes an extensible Java class framework for defining sequence filtering and routing pipelines, combined with an efficient makefile-based approach to execution. Seqdb_engine includes a large set of working examples, including code for building 14 different databases GenBank and 7 from SwissProt. It is available for download at http://prdownloads.sourceforge.net/gmod/seqdb_engine-2-1-4.tar.gz?download Please address questions about the use of this software to Joel Richardson (je...@in...) and Sharon Cousins (sc...@in...). Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-09-22 17:31:47
|
Thanks to the contribution by Nathan Siemers and Donald Jackson at the Applied Genomics group of Bristol-Myers Squib, I am pleased to announce the release of a set of cross genome comparison data. This data was collected by TBLASTXing the genomic sequences of human, mouse, fly, worm, yeast and zebrafish and then performing considerable post processing to get the data into GFF format. These data are now available at http://prdownloads.sourceforge.net/gmod/Refseq_Genome_TBLASTX.tar.gz?download In addition to the raw data are files to create a GadFly-based GFF database suitable for use with GBrowse. Please direct questions about these files to Nathan Siemers (Nat...@bm...) as well as to the GBrowse discussion list at gmo...@li.... Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-09-10 18:14:38
|
Hello, This email is to cover several of the details for the GMOD meeting next week at LBNL. First, because it is a government run lab, they do have some security measures in place. The names of the attendees will be given to gate guards to insure that you get in. For directions to the lab, see http://www.lbl.gov/Workplace/Transportation.html which will get you close to the lab. Here is a map of the campus: http://www.lbl.gov/Workplace/lab-site-map.html. For those staying at a hotel near LBNL, there is a shuttle that stops in front of the Bancroft hotel. The Bancroft bus stops near the hotel at about :18 and :48 past the hour and then loops around campus and back up the hill. Here is the shuttle map and schedule: http://www.lbl.gov/Workplace/Facilities/Support/Busses/off-site.html They've gotten kind of picky about letting non-LBNL people board the LBNL shuttle bus, but if you explain that you're attending this meeting at LBNL, it should be ok. They will probably make you get out of the bus at the gate, and then you can walk to the cafeteria. Walk up the hill from the bus stop. At the first intersection, stay right. Keep walking up hill until you see a parking lot right next to the road; turn right after the parking lot into a sort of diagonal road. This leads to the cafeteria (building 54). Perseverance Hall (where the meeting will take place) is in building 54 (dining hall). Walk past the cashiers (they'll be on your left), walk down the corridor with the big windows, and go through a door--you'll be in Perseverance Hall. The final agenda (that is, it is final until somebody else makes me change it), is below. I look forward to seeing you at the meeting. If you have any problems or questions, please email me, or if it is after Saturday, call me at 216-392-3087. That is my cell phone and I will have it with me (and probably even have it turned on :-) Thanks, Scott --------------------------- GMOD Workshop September 15-16 2003 Lawrence Berkeley National Laboratory September 15 9:00-11:00 Updates: SGD tools MGI tools SMD tools Pathway Tools Apollo GBrowse Cmap Chado 11:00-11:15 break 11:15-12:00 Website design discussion part I (Allen Day/Bradley Marshall) brief (20 minute each) intros to technologies 12:00-1:00 Lunch 1:00-2:15 Website design discussion part II head to head comparison on specified gene pages 2:15-3:00 GDS/Argos/Lucegene (Don Gilbert) 3:00-3:15 break 3:15-4:00 GBrowse with Artemis as a editor (Sheldon McKay) 4:00-4:30 Sequence Ontology (Karen Eilbeck) 4:30-5:00 TIGR tools update (Owen White) September 16 9:00-9:45 Pub* from a curator's perspective (TAIR/RDB) 9:45-10:30 Textpresso (Eimear Kenny) 10:30-11:00 break 11:00-11:45 Biopipe (Kiran Kumar) 11:45-1:00 Lunch 1:00-3:30 Breakout groups: Curators - Developing a MOD: Create a table of contents for SOPs Developers - Topics to be addressed: * release pathway * chado development 3:30-3:45 break 3:45-5:00 Discussion & action plan (Scott Cain) -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-08-22 17:37:24
|
Hello, Version 1.53 of the Generic Genome Browser (GBrowse) was released today. A PPM version for Windows should be available sometime next week. As it fixes a security hole in previous versions of GBrowse, I strong advise all users to upgrade to it at their earliest convenience. Since version 1.53 requires BioPerl 1.2.2, I realize some users may be reluctant to immediately update, so as a secondary recommendation, I suggest you look at the bug report for the security hole and my fix at: http://sourceforge.net/tracker/index.php?func=detail&aid=783035&group_id=27707&atid=511474 Here is the Change log for this version: 1.53 Thu Aug 21 14:40:54 EDT 2003 * Security hole that allowed the display of /etc/passwd and other files fixed * Documentation reworked as pod and which is converted to html on install. That documentation is then available at http://localhost/gbrowse * Added an extensive tutorial, also available at http://localhost/gbrowse * Added tools for making it easier to create a PPM package for Windows * Added a 'nascent' synteny browser. * Added gbrowse_details, a CGI that gives skeletal details on each feature * Added an optional 'flip mode' to flip the orientation of the display * Added a multiple alignment plugin * Added a GeneFinder plugin * Added support for the chado database schema * Added support for the PostgreSQL database server * Added a script for converting UCSC genome data to GFF3 * Added a script for loading Genbank/EMBL files to a GFF database Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-08-13 14:47:20
|
Hello, This is a reminder that the quarterly GMOD meeting is being held at Lawrence Berkeley Lab on September 15-16. The Bancroft Hotel is holding rooms and giving a group discount for the 14-16th, but they are going to release that hold 30 days prior, which is tomorrow. So if you haven't booked a room and plan on attending from out of town, now is the time! Contact the hotel at 510-549-1000 and mention the GMOD meeting to receive the discount. Also, if you have topics in mind that you would like to see added to the agenda, please let me know, as I am formulating it now. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-07-28 16:30:15
|
Hello, I have somewhat of a conundrum: how to announce the creation of an announcements mailing list? Since there is no good way to do it, I'll just have to spam everyone I can think of. So, if you get this message three or four times, my apologies. Anyway, I've created a gmod-announce mailing list. This is a low traffic, completely spam-free, moderated mailing list for the announcement of software releases and meetings. Please subscribe at http://sourceforge.net/mail/?group_id=27707 . Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Scott C. <ca...@cs...> - 2003-07-25 15:45:41
|
test -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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