From paul.reiners from gmail.com Wed Mar 12 20:18:42 2008 From: paul.reiners from gmail.com (Paul Reiners) Date: Wed Mar 12 20:25:27 2008 Subject: [Bio-software] Dynamic programming and sequence alignment Message-ID: A tutorial about dynamic programming and sequence alignment: http://www.ibm.com/developerworks/java/library/j-seqalign/index.html From stevet from bio.fsu.edu Fri Mar 21 07:45:03 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Fri Mar 21 11:42:18 2008 Subject: [Bio-software] GCG/SeqLab petition Message-ID: <20080321083045.G1788@epsilon.bio.fsu.edu> Hi all - I apologize for my multiple cross-group postings but I feel the importance and urgency of this message warrant it. As many of you are aware, last summer Accelrys announced that they would be discontinuing support for GCG and SeqLab this upcoming June. That situation dismayed me and others and I wanted to do something about it. I contacted Steven Smith, one of the original authors of SeqLab, and discussed the situation with him. He volunteered to contact Accelrys in an attempt to minimally get SeqLab's license and code released to him. I gave Steve several months to try to persuade the company. Accelrys was not very cooperative. Therefore, I set about creating a petition in an attempt to add some leverage. I've contacted a few of you earlier regarding this initiative and appreciate your support. Anyway, I have created and posted that petition. It's at: http://www.petitiononline.com/gcg/petition.html And a nicely formatted PDF version is available in my own Web space: http://bio.fsu.edu/~stevet/Accelrys_petition.pdf I would very much appreciate you adding your name to this petition, if you agree with our sentiment. Thank you for your time! Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From clements from nescent.org Mon Mar 24 15:32:48 2008 From: clements from nescent.org (Dave Clements) Date: Mon Mar 24 15:58:06 2008 Subject: [Bio-software] GMOD Summer School, July 11-13, 2008, Durham, NC, USA Message-ID: GMOD Summer School 11-13 July, 2008 National Evolutionary Synthesis Center (NESCent) Durham, North Carolina, USA The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will be held July 11-13, 2008 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina, USA. GMOD is a collection of interoperable open source software components for managing genomic data. GMOD components are used in diverse contexts, with both emerging and established model organisms. The course will provide an overview of GMOD and cover these popular components in detail: * Chado - a modular and extensible database schema * Apollo - genome annotation editor * GBrowse - genome viewer * CMap - comparative map viewer * Community Annotation System - GMOD's most popular components in a single system This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to use GMOD. The National Evolutionary Synthesis Center (NESCent, http://nescent.org) has joined the GMOD project with the goal of lowering the barrier to entry for research communities focused on emerging model organisms. The GMOD Summer School is a part of this effort. NESCent is also extending GMOD components, particularly Chado, to better support comparative and evolutionary data. If you are interested in attending the GMOD Summer School please submit a Statement of Interest before April 15, 2008. The course is free but enrollment is limited. For application information and a tentative program see: http://gmod.org/GMOD_Summer_School Please let me know if you have any questions, comments, or requests. Thanks, Dave Clements GMOD Help Desk help@gmod.org ------------------------ NESCent offers various courses and workshops, as well as funding post-doctoral and sabbatical positions, working groups and other meetings. For more information about research and training opportunities at NESCent, visit our website at www.nescent.org. Sign up for our quarterly electronic newsletter at http://www.nescent.org/about/contact.php to automatically receive information about events at NESCent. From fretwell192 from yahoo.com Thu Mar 27 15:11:34 2008 From: fretwell192 from yahoo.com (jonathan fretwell) Date: Thu Mar 27 18:52:32 2008 Subject: [Bio-software] Need software for Cytofluor Series 4000 Message-ID: <463323.87967.qm@web45110.mail.sp1.yahoo.com> I also need the software for the cytofluor 4000. Could you please share. From martin.burkert from gmail.com Mon Mar 31 10:49:55 2008 From: martin.burkert from gmail.com (martin.burkert@gmail.com) Date: Mon Mar 31 13:04:27 2008 Subject: [Bio-software] blast command - one hit is sufficient Message-ID: <0429f550-1685-4079-bb97-f87a4c68ec97@n58g2000hsf.googlegroups.com> Hello NG, i'm using command line blast for searching multiple nucleotide queries against a protein database. For each query I get a detailed output with hits on the database surviving my cutoff value. There can be a lot of hits for one single query. For my task it would be sufficient to know if there is any hit (below the cutoff) in the database for my query at all. Once the blast search was able to determine a hit which e-value is lower than my cutoff value it could print this hit to the output, stop searching and continue with the next query. Is some one out there, who can provide me with a simple solution using custom command line parameters for my blastall binary? That's my command until now: /blastall -p blastx -d /path/to/swissprot -e 1e-10 -i input.fas -m 9 > output.bla (using blastall 2.2.15) Thank you :-) Martin