From jjhaveri at gmail.com Mon Sep 6 05:30:01 2004 From: jjhaveri at gmail.com (Jinal Jhaveri) Date: Mon Mar 7 02:30:05 2005 Subject: using srs for Agrobacterium Tumefaciens c58 Message-ID: I tried downloading the protein sequences for the organism: Agrobacterium Tumefaciens C58 strain and I found that there are around 10000 entries. I remember that previously (before 1.5 months) when I tried the same query and I got only 461 genes. My suspicion is that I am doing something wrong while querying. Can you please let me know how shall I query the swissprot database so that I can obtain genes for only "Agrobacterium Tumefaciens C58" organism. thank you very much --Jinal From software at srs-user.org.uk Mon Sep 6 05:37:29 2004 From: software at srs-user.org.uk (srs-user.org.uk admin) Date: Mon Mar 7 02:30:05 2005 Subject: srs-user.org.uk Message-ID: <4a7b0e71.0409022314.73dfc892@posting.google.com> I am pleased to announce the launch of a new SRS user community site: http://www.srs-user.org.uk/ An independant community site for the popular SRS data integration software. Featuring SRS releated news, file downloads and fora for SRS users, developers and administrators. From aluciano_lion at yahoo.com Mon Sep 6 05:37:30 2004 From: aluciano_lion at yahoo.com (Anna Luciano) Date: Mon Mar 7 02:30:05 2005 Subject: LION bioscience UGMs: Agenda Announcement Message-ID: <20040902185213.52805.qmail@web60807.mail.yahoo.com> The LION bioscience User Group Meetings (UGMs) are a perfect opportunity to meet LION software users, administrators, and developers, as well as other experts in the fields of bio- and chem- informatics, and to exchange ideas about how to get the most out of LION's products. Choose one of the following meetings: - September 29-30, 2004, AstraZeneca R&D Boston, Waltham, MA - October 19-20, 2004, Reuben H. Fleet Science Center, San Diego, CA If you are a current LION user, or work at an academic or commercial R&D institution and want to learn more about LION's products, you won't want to miss these free meetings! Attendees will be able to: - Hear from leading life sciences and academic organizations about how they use, and how they have customized, LION's products to meet their needs - Learn about the new functionalities of our latest software releases and the future direction of LION products - Participate in an "SRS Tips & Tricks" round table discussion, where you can learn the latest in how to optimize your SRS installation, integrate data stored in Oracle, access SRS data via web services, and customize the SRS user interface using JSP technology - See demonstrations of new LION products and complementary solutions from LION partners in biology and chemistry The agendas are now available online! To view the agendas, register for the UGM or be added to the free mailing list, please go to www.lionbioscience.com/ugm. We look forward to seeing you there! Anna Luciano Marketing Communications Coordinator LION bioscience, Inc. (617) 245-5427 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://iubio.bio.indiana.edu/bionet/mm/bio-srs/attachments/20040906/0676b003/attachment.html From software at hpm101.gotadsl.co.uk Mon Sep 6 05:37:31 2004 From: software at hpm101.gotadsl.co.uk (Hamish McWilliam) Date: Mon Mar 7 02:30:05 2005 Subject: www.srs-user.org.uk Message-ID: I spotted the following on http://www.bioinformatik.de/, and thought it may be of interest to the group: An independant community site for the popular SRS data integration software. Featuring SRS releated news, fora and file downloads. http://www.srs-user.org.uk/ >From a quick look, while it seems to be still young and looking for contributiors, but the exiting downloads look like they could be useful. Hamish. From cjborroto at yahoo.com Tue Sep 21 12:44:42 2004 From: cjborroto at yahoo.com (Carlos Javier) Date: Mon Mar 7 02:30:05 2005 Subject: Problem indexing EMBL Message-ID: <6fae5589.0409091149.7e0241b9@posting.google.com> I found this problem indexing EMBL database: > Creating sort set for the div field of embl > Creating sort set for the acc field of embl > /gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: > Fatal internal error > Reason: "NULL lib pointer", file: "library.c", line:4838 > gmake: *** [EMBL/EMBL_sort.acc.pacc] Error 255 > /gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i -libName EMBL > -fldName 'pac' -odir /gfs/srs/srs7.1.3/srs_tmp/srs/index/ > /gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: > Fatal internal error > Reason: "NULL lib pointer", file: "library.c", line:4838 Does anyone know what is happening here?? I'm using SRS7.1.3 and EMBL Release 79. From benedict.arnold at bbsrc.ac.uk Tue Sep 21 12:44:42 2004 From: benedict.arnold at bbsrc.ac.uk ("benedict arnold JIC) Date: Mon Mar 7 02:30:05 2005 Subject: using srs for Agrobacterium Tumefaciens c58 Message-ID: <286D8A554155B54CBFB18EF26EE2F1692780DD@jie2ksrv1.jic.bbsrc.ac.uk> Hi Jinal, > I tried downloading the protein sequences for the organism: Agrobacterium > Tumefaciens C58 strain and I found that there are around 10000 entries. I > remember that previously (before 1.5 months) when I tried the same query and > I got only 461 genes. My suspicion is that I am doing something wrong while > querying. Can you please let me know how shall I query the swissprot database > so that I can obtain genes for only "Agrobacterium Tumefaciens C58" organism. I think the problem here is that if you search only in the uniprot/swissprot databank you get 482 entries for the query, if you search in the uniprot/trembl databank you find 9812 entries, as data is moved from uniprot/trembl to uniprot/swissprot, I suspect what you've been doing is searching the uniprot/swissprot databank only and missed all the entires is the uniprot/trembl data. without knowing which SRS site you have been using, it might be that the site originally had swissprot meaning just the curated version) and sptrembl as separate databanks and they now have swissprot as a virtual library where both swissprot and sptrembl are combined, so whereas before you were searching a relatively small set of all the proteins out there you are now searching the whole set hope that helps Ben ---