November 2009 - beg-bogas@psb.ugent.be

[Beg-bogas] problem with browser
by Pires da Silva, Andre 19 Nov '09

19 Nov '09

I am trying to analyze the genome structure of the gene female lethal d (Tetur03g09730) with Genome View. The problem is that when I zoom in to check the sequence, I just see a series of XXXX. Do you know what is going on? Best, Andre Andre Pires da Silva, Ph.D. Assistant Professor of Biology 501 S. Nedderman 337 Life Science Building Biology Dept (Box 19498) University of Texas at Arlington Arlington, TX 76019-0498 USA Phone: 817-272-1383 Fax: 817-272-2855 http://www3.uta.edu/faculty/Pires_daSilva/Home.html

3 2

[Beg-bogas] Pichia Pastoris Gene Ontologies - Batch Download?
by Basom, Ryan S 19 Nov '09

19 Nov '09

Hi, I have accession numbers for ~ 500 Pichia Pastoris that I'd like to retrieve gene ontologies for and would like to know if there is a way I can access this data from your site in batch mode? Thanks, Ryan -- Ryan Basom Systems Analyst\Programmer Genomics Resource Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N., DE-795 P.O. Box 19024 Seattle, WA 98109-1024 voice: (206)667-2747 fax: (206)667-2825 email: rbasom(a)fhcrc.org

1 0

[Beg-bogas] Fwd: Esi0013_0166
by Claire Gachon 18 Nov '09

18 Nov '09

Hi Lieven, screwed up again with BOGAS I am afraid. please see attached Martina's message: when you open this locus, BOGAS says it is in my workbench, but my workbench looks empty to me! Other weird things have happened recently: a number of genes appear in the list of my recent annotations, which I haven't touched at all, at least in the recent past. This is true for all the loci amended on the 16 Nov (Esi0007_0111, Esi0050_0094, Esi0307_0004), some heat shock proteins (including one called BIP) modified on the 5 Nov. I haven't given my login details to anyone, so I don't know what is going on? Your patience with me will be rewarded in Heaven! Claire Claire Gachon Scottish Association for Marine Science Dunstaffnage Marine Laboratory Dunbeg PA37 1QA Oban, UK claire.gachon(a)sams.ac.uk

2 1

[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 18 Nov '09

18 Nov '09

2009/11/18 16:40:52 An error occured connecting to the database server Error message below: DBI connect('bogas_tetur:psbsql02:3306','bogas',...) failed: Unknown database 'bogas_tetur' at /www/group/biocomp/extra/bioinformatics_prod/webtools/sandbox/liste/BOGAS/trunk/src/perl/modules/BOGAS/DB.pm line 240

1 0

[Beg-bogas] [MOBY-dev] What's up with Moby-2 --> SADI (fwd)
by Kenny Billiau 03 Nov '09

03 Nov '09

Hi, great, it looks if this will take off we will have to adapt :/ Kenny -- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau(a)ugent.be http://bioinformatics.psb.ugent.be ================================================================== "Forward Momentum" - Adm. Miles Naismith ---------- Forwarded message ---------- Date: Tue, 03 Nov 2009 09:18:37 -0800 From: Mark Wilkinson <markw(a)illuminae.com> Reply-To: Core developer announcements <moby-dev(a)lists.open-bio.org> To: "moby-l(a)biomoby.org" <moby-l(a)biomoby.org>, Core developer announcements <moby-dev(a)biomoby.org> Subject: [MOBY-dev] What's up with Moby-2 --> SADI Hi all! About every month or so, someone writes to me to ask what's up with Moby-2. Here's the update: We've finished our first pass at the specification and reference implementation of SADI - Semantic Automated Discovery and Integration. The manuscript describing the overall architecture will be presented at the IEEE Semantic Web Services meeting in Singapore in December, but the text of that paper is here: http://sadiframework.org/documentation/SADI_SWSIP09_personal.pdf The project website is: http://sadiframework.org and from there you can get to our first prototype client. Other clients are coming soon, including the SADI-Taverna plugin. The SADI equivalent to MoSeS is almost finished, and is available on CPAN - it does a pretty good job of auto-writing SADI services already, and it will get better soon! See the SADI homepage for the link. The meta-map of possible service connections is here: http://biordf.net/cardioSHARE/images/predicates.png You can already do some pretty cool SPARQL queries in our prototype interface! And finally, we are putting out a press release this week to announce that we have just received almost $1M in funding from CANARIE to deploy SADI services over Canadian (and international) bioinformatics resources, as well as provide training in semantic web and semantic web service provision. We wont be starting the training component until late next year, but if you are interested please follow our progress on the SADI homepage. That's all the news! Cheers! Mark _______________________________________________ MOBY-dev mailing list MOBY-dev(a)lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev

1 0