From gvd at penguin.pharmacy.ualberta.ca Mon Mar 5 17:16:14 2001 From: gvd at penguin.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Mon, 5 Mar 2001 15:16:14 -0700 (MST) Subject: [BiO BB] Bioperl 0.7 release. Message-ID: This message from Ewan Birney has been forwarded from the Bioperl mailing list: We are very pleased to announce the Bioperl 0.7 release. This release represents a very significant improvement to the previous 0.6 series and brings a number of important new features to bioperl. The ChangeLog is at the end of this message. The release is available at ftp://bio.perl.org/pub/DIST/bioperl-0.7.0.tar.gz and has also been uploaded to CPAN. The release will shortly be available through our web site at http://bio.perl.org/ Alongside the release a number of satellite packages are also being released being: bioperl-gui - classes for building Perl::Tk visualisation on top of bioperl bioperl-ext - C extensions for alignments to bioperl bioperl-corba-client - CORBA wrappings of the biocorba 0.2 standard for bioperl bioperl-corba-server - Wrappings of Bioperl objects compliant to the biocorba 0.2 standard Bioperl-gui has already been released on the ftp site and CPAN site. The other packages will make their way over this week. Bioperl 0.7 is predominantly the effort of Jason Staijch and Hilmar Lapp who worked to build on top of the Bioperl 0.6 effort. Lorenz Pollack and Peter Schattner also provided significant pieces of code. The effort was supported by general bioperl developers, in particular Ewan Birney and Chris Dadigidan. Many thanks also goes to our Mac (Todd Richmond) and NT (Shelly Mistry) testers. We'd also collectively like to congratulate Hilmar for the additions to his family recently (twins I believe!). I hope Hilmar can take it easy for the next couple of weeks. The Bioperl Core Group, who coordinate Bioperl, is: Ewan Birney, Chris Dadigidan, Hilmar Lapp and Jason Staijch. ChangeLog: 0.7 Large number of changes, including refactoring of the Object system, new parsers, new functionality and all round better system. Highlights are: o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI; Bio::Root::IO for I/O and file/handle capabilities. o Imported BPlite modules from Ian Korf for BLAST parsing. This is considered the supported BLAST parser; Bio::Tools::Blast.pm will eventually phase out due to lack of support. o Improved Sequence Feature model. Added complete location modelling (with fuzzy and compound locations). See Bio::LocationI and the modules under Bio/Location. Added support in Genbank/EMBL format parsing to completely parse feature tables for complex locations. o Moved special support for databanks etc to specialized modules under Bio/Seq/. One of these supports very large sequences through a temporary file as a backend. o Explicit Gene, Transcript and Exon SeqFeature objects, supporting CDS retrieval and exon shuffling. o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and DB/GDB (the latter has platform-specific limitations). o New analysis parser framework for HT sequence annotation (see Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory) o New Alignment IO framework o New Index modules (Swissprot) o New modules for running Blast within perl (Bio::Tools::Run::StandAloneBlast). Added modules for running Multiple Sequence Alignment tools ClustalW and TCoffee (Bio::Tools::Run::Alignment). o New Cookbook-style tutorial (see bptutorial.pl). Improved documentation across the package. o Much improved cross platform support. Many known incompatibilities have been fixed; however, NT and Mac do not work across the entire setup (see PLATFORMS). o Many bug fixes, code restructuring, etc. Overall stability and maintainability benefit a lot. o A total of 957 automatic tests Enjoy! ----------------------------------------------------------------- Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420 . ----------------------------------------------------------------- _______________________________________________ Bioperl-l mailing list Bioperl-l at bioperl.org http://bioperl.org/mailman/listinfo/bioperl-l From jeff at bioinformatics.org Thu Mar 8 18:59:05 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 08 Mar 2001 23:59:05 +0000 Subject: [BiO BB] [Fwd: starting a career in bioinformatics] Message-ID: <3AA81CC9.A1A5FD78@bioinformatics.org> This seems to be a recurring question. Jeff -------------- next part -------------- An embedded message was scrubbed... From: karna Subject: [tol-admin] starting a career in bioinformatics Date: Thu, 8 Mar 2001 06:51:04 -0500 Size: 1394 URL: From jeff at bioinformatics.org Thu Mar 8 18:59:39 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 08 Mar 2001 23:59:39 +0000 Subject: [BiO BB] [Fwd: DNA testing] Message-ID: <3AA81CEB.66F67228@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Bill McCarron Subject: [tol-admin] DNA testing Date: Thu, 8 Mar 2001 19:14:25 -0500 Size: 1849 URL: From lists at 123india.com Thu Mar 8 19:44:30 2001 From: lists at 123india.com (Indraneel Majumdar) Date: Thu, 8 Mar 2001 18:44:30 -0600 (CST) Subject: [BiO BB] [Fwd: starting a career in bioinformatics] In-Reply-To: <3AA81CC9.A1A5FD78@bioinformatics.org> Message-ID: Hi, Just let your C do something with biological data and you'll be neck deep in Bioinformatics in no time. At the present condition Bioinformatics as a black art and voodoo science is so nascent that it's difficult to learn it from standard textbooks. Add to that the very general definition of Bioinformatics and you have people from all sorts of streams jumping into this hot pot. If you're looking to do some work yourself, just get hold of any current problem and start working. You're lucky that you'll not be wasting time hunting. And as you work through you'll definitely pick up the good things like Perl, Python, C++ et al. and maybe even Java. This field is changing so fast that you'll never be ready enough, so probably the best is to learn on the job. Once you've done some work, companies and Bioinfo labs will be more than eager to put you to more challenging problems irrespective of what your formal qualifications (Degrees) are. This at least is a field where you're judged by what you've done and can do. And for a MSc in Life Sciences with programming skills nothing can be more satisfying than working in Bioinformatics. As a starter get yourself acquainted with these: Websites of the NCBI and EBI and all links therein If you can't locate the above: the page at google.com words like Genbank, EMBL, Pubmed, Medline, SRS Data formats of Genbank, EMBL, SWISSPROT, PDB and others Preferably an Operating system like Linux or FreeBSD (No I'm not advocating, most work gets done on these) Open source software for sequence/structure analysis/visualisation or statistical data analysis (words like BLAST, Fasta, VMD, NAMD, O etc) Websites of bioperl.org, bioxml.org, biopython.org, biojava.org Journals like Bioinformatics, PNAS, Technology Review, Computers (all this not _absolutely_ necessary) What some companies like IBM, Incyte Genomics, Structural Bioinformatics, Celera, SGI are doing (DSQ and GVK in India too have some big plans) By the time you're through maybe you'll have a project or two registered here or at sourceforge.org Best wishes, Indraneel On Thu, 8 Mar 2001, J.W. Bizzaro wrote: > This seems to be a recurring question. Jeff > I have completed m.sc(biosciences)& know Cprogramming.what > other things should i learn,as to start a career in > bioinformatics. -- http://www.indialine.org From lilyth at umich.edu Thu Mar 8 22:58:35 2001 From: lilyth at umich.edu (Deanne) Date: Thu, 8 Mar 2001 22:58:35 -0500 (EST) Subject: [BiO BB] [Fwd: starting a career in bioinformatics] In-Reply-To: Message-ID: Friend & I have just registered "bioinfotech.org" and "bioinfotech.net" Purpose is to act as a clearing house for all things bioinformatics and information tech related directly to biology (not necessarily related entirely to coding, so it's not stepping on la Open Lab). :) Articles, news, commentary, gripes, raves, rants, software and industry reviews, academic departments, etc. Maybe a who's who of the field. Something. Think slashdot for bioinformatics. It's a not-for-profit news/info site that will eventually answer questions like this one, "How do I get a job in this field." "What is there left to do?" "What do I need to know?" It'll be a good place to point people, anyway. And of course, it can host papers and articles from bioinformaticians, ala slashdot. Dunno when it'll be up. In my spare time, I suppose. Which I still owe some here and there. ...including my gengnome project and piper. Sigh. But it has to be done and no use waiting...if anyone wants to get involved, just ask..... Deanne From jacobs at genehack.org Thu Mar 8 23:08:29 2001 From: jacobs at genehack.org (John S. J. Anderson) Date: 08 Mar 2001 23:08:29 -0500 Subject: [BiO BB] [Fwd: starting a career in bioinformatics] In-Reply-To: References: Message-ID: <87itljbn42.fsf@genehack.org> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Deanne writes: > Purpose is to act as a clearing house for all things bioinformatics and > information tech related directly to biology (not necessarily related > entirely to coding, so it's not stepping on la Open Lab). :) Articles, > news, commentary, gripes, raves, rants, software and industry reviews, > academic departments, etc. Maybe a who's who of the field. Something. > Think slashdot for bioinformatics. There's already at least one '/. for bioinfo', at nodalpoint.org; I'm ostensibly a contributor, although I seem to have trouble finding time amongst all my other projects. Perhaps you folks could pool efforts? FWIW, IHMO the main problem with nodalpoint has been a lack of comment posting; the stories are there, but there's sort of a lack of discussion. Again, an area where I should be doing more... john. - -- It is by caffeine alone I set my mind in motion. It is by the beans of Java that thoughts acquire speed, the hands acquire shaking, the shaking becomes a warning, it is by caffeine alone I set my mind in motion. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.4 (GNU/Linux) Comment: Mailcrypt 3.5.5 and Gnu Privacy Guard iD8DBQE6qFc9WRJRdOm3KFARAsPkAJ0UyOxbuFskHokE1ODWaE/WO7FaXQCeIQ6d qGrTryXwmrTJAvzb5f38BBY= =GDpl -----END PGP SIGNATURE----- From lilyth at umich.edu Thu Mar 8 23:24:58 2001 From: lilyth at umich.edu (Deanne) Date: Thu, 8 Mar 2001 23:24:58 -0500 (EST) Subject: [BiO BB] [Fwd: starting a career in bioinformatics] In-Reply-To: <87itljbn42.fsf@genehack.org> Message-ID: > Perhaps you folks could pool efforts? I've seen nodal, yes, it's a very nice site, but I had something more "rooted" in mind, with more resources available, kind of a tool for kids or scientists looking for the current state of the art (and yea, nodal does a good job of the slashdotting but I want that to be secondary to the usefulness of the site). Pool efforts will be good, but first there has to be a site, and that'll take a while. :) This may never get off the ground past being an info resource, but even that will be good enough. Besides, I'm sick of mergers. Deanne at one of those merged places From paolo at ist.unige.it Fri Mar 9 05:10:45 2001 From: paolo at ist.unige.it (Paolo Romano) Date: Fri, 09 Mar 2001 11:10:45 +0100 Subject: [BiO BB] NETTAB: CFP extended to March 20th, 2001 Message-ID: <5.0.2.1.0.20010309111003.00a017d0@ist.unige.it> Dear list members, this is to inform you that the Call for Contributions (poster - oral communications - software demo) for the NETTAB Workshop on "CORBA and XML: towards a bioinformatics integrated network environment", May 17-18, 2001, Genoa, Italy, has been extended until next March 20th. For all information on the Workshop and the Call for Contributions, please refer to one of the Web sites: http://www.cba.unige.it/Events/NETTAB/ http://www.bioinformatics.org/NETTAB/ Best regards. Paolo Romano --- Ing. Paolo Romano (paolo at ist.unige.it) Applicazioni Telematiche in Biotecnologia Servizio Biotecnologie Istituto Nazionale per la Ricerca sul Cancro IST Largo Rosanna Benzi 10, I-16132, Genova Tel +39-010-5737-288, Fax +39-010-5737-295 Web: http://www.biotech.ist.unige.it/ From jeff at bioinformatics.org Fri Mar 9 06:26:45 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 09 Mar 2001 11:26:45 +0000 Subject: [BiO BB] bioinfotech (was: starting a career...) References: Message-ID: <3AA8BDF5.74F7DC4@bioinformatics.org> Hi Deanne! Deanne wrote: > > Purpose is to act as a clearing house for all things bioinformatics and > information tech related directly to biology (not necessarily related > entirely to coding, so it's not stepping on la Open Lab). :) "The Open Lab" will now refer to our project hosting system based on SourceForge. We hope to host projects there that are not directly related to coding, perhaps some research. "The Open Lab" then is really short for "The Open Collaboratory". > Articles, > news, commentary, gripes, raves, rants, software and industry reviews, > academic departments, etc. Maybe a who's who of the field. Something. > Think slashdot for bioinformatics. On the other hand, "Bioinformatics.org" is the parent organization, and we intend to provide as many free services as there are people to help provide them. There is nothing saying that BiO cannot do this or that, unless it is commercial. And we do hope to cover many things like news, commentary, gripes, raves, rants, software and industry reviews, academic departments, etc. with the BiO News service. But, like Nodalpoint, we need more contributors. Think of Bioinformatics.org as a free bioinformatics portal. > It's a not-for-profit news/info site that will eventually answer questions > like this one, "How do I get a job in this field." "What is there left to > do?" "What do I need to know?" It'll be a good place to point people, > anyway. I was thinking about a bioinformatics FAQ. "John S. J. Anderson" wrote: > > There's already at least one '/. for bioinfo', at nodalpoint.org; I'm > ostensibly a contributor, although I seem to have trouble finding time > amongst all my other projects. I consider Nodalpoint to be a Slashdot for biology, because the news topics, while of interest to all bioscientists, are always related to bioinformatics. So, its scope is a bit broader. What barrier, if any, do people find to contributing news, etc. to BiO News? Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Fri Mar 9 06:36:44 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 09 Mar 2001 11:36:44 +0000 Subject: [BiO BB] bioinfotech (was: starting a career...) References: <3AA8BDF5.74F7DC4@bioinformatics.org> Message-ID: <3AA8C04C.6FC870C@bioinformatics.org> "J.W. Bizzaro" wrote: > > I consider Nodalpoint to be a Slashdot for biology, because the news topics, > while of interest to all bioscientists, are always related to bioinformatics. Correction: ^ *NOT* Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From lilyth at umich.edu Fri Mar 9 07:50:59 2001 From: lilyth at umich.edu (Deanne) Date: Fri, 9 Mar 2001 07:50:59 -0500 (EST) Subject: [BiO BB] bioinfotech (was: starting a career...) In-Reply-To: <3AA8C04C.6FC870C@bioinformatics.org> Message-ID: Well, and it's just another domain name with information on it, anyway. :) I only "bought" the space for 6 months and the name for a year. In the end, I'd rather point the domain towards bioinformatics.org if it falls that way and just give TOL the files. it was just a way to get an information structure set up quickly and easily. I don't want it to sound so official, I'm not setting up any org on my own...it's just an experiment in trying to net the moving target that is the field and hoping it'll do someone some good in the long run. Deanne ------------ Deanne Taylor, Ph.D. Biophysics lilyth at umich.edu University of Michigan On Fri, 9 Mar 2001, J.W. Bizzaro wrote: > "J.W. Bizzaro" wrote: > > > > I consider Nodalpoint to be a Slashdot for biology, because the news topics, > > while of interest to all bioscientists, are always related to bioinformatics. > Correction: ^ *NOT* > > Jeff > -- > J.W. Bizzaro jeff at bioinformatics.org > Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff > "All those scientists--they're all alike! They say they're working for us, > but what they really want is to rule the world!" > -- Angry Villager, Young Frankenstein > -- > > _______________________________________________ > BIO_Bulletin_Board maillist - BIO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From stein at fieldmuseum.org Fri Mar 9 11:01:06 2001 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Fri, 9 Mar 2001 10:01:06 -0600 (CST) Subject: [BiO BB] Postdoc phylogenetic analyses (fwd) Message-ID: Just passing along a job posting I saw. -jennifer ---------- Forwarded message ---------- Date: Fri, 9 Mar 2001 05:26:05 -0500 (EST) From: evoldir at evol.biology.mcmaster.ca Reply-To: brian at helix.biology.mcmaster.ca To: stein at fieldmuseum.org Subject: Postdoc phylogenetic analyses Postdoctoral position for development and application of sequence analysis tools A postdoctoral position for a person interested in phylogenetic analyses of sequence data is available at the University of Bochum, Germany for a period of 5 years. If during this time a further qualitfication is obtained (the "habilitation", equivalent to junior professor) the job can be continued for another 5-6 years. We encourage applications from molecular systematists, mathematicians or related sciences (e.g., computer sciences) with a demonstrated record of successful research in the field of theory or practice of sequence analysis. Programming experience and a good mathematical background are required. This appointment is part of the department's molecular phylogenetics group, a research team focused on the study of phylogeny of invertebrates and on analyses of the information content of sequences based on new methods. We expect that the assistant will help to develop and test new tools for sequence analysis and cooperate with the group to study the phylogeny of invertebrates. It is also expected that the successful candidate participates in teaching at both the undergraduate and graduate level. Teaching may be done in English. The successful applicant will be paid according to government standard wages (BAT II, approx. 6000.- DM monthly before taxes and twice this amount in december.). Applications (including CV, list of publications and teaching experience, and a brief summary of research plans) and two letters of reference should be sent to Prof. Dr. J. W. Waegele Lehrrstuhl Spezielle Zoologie Fakultaet Biologie Ruhr-Universitaet Bochum 44780 Bochum Germany ************************ Prof. Dr. J. W. Waegele Lehrstuhl fuer Spezielle Zoologie Ruhr-Universitaet Bochum Universitaetsstr. 150 44780 Bochum Tel.: 0234/32-24563 FAX: 0234/32-14114 email: Wolfgang.Waegele at ruhr-uni-bochum.de http://134.147.236.167/spezZoologie/spezZool.htm Association of Systematists (GfBS): http://biosys-serv.biologie.uni-ulm.de/gfbs/stgfbs/stgfbs.html NEW JOURNAL FOR SYSTEMATICS: Organisms, Diversity and Evolution see http://www.urbanfischer.de/journals/ode/ From kiran_ayyagari at yahoo.com Sat Mar 10 00:13:55 2001 From: kiran_ayyagari at yahoo.com (Ayyagari Kiran) Date: Fri, 9 Mar 2001 21:13:55 -0800 (PST) Subject: [BiO BB] Linux Clustering for Bioinformatics??? Message-ID: <20010310051355.67162.qmail@web11902.mail.yahoo.com> Sir, Iam a bioinformatics programmer having my skillsets in Advanced Java programming and implementing three tier applications in bioinformatics. I worked in NT platform and have no much idea about Linux applications in Bioinformatics. Can Anyone help me understyanding the "LINUX CLUSTERING TECHNOLOGY "for Bioinformatics applications. precisely I wanted to know, 1) what sort of bioinfo applications (mention names)can run on linux clusters and why? 2) How can Linux clustering be of use to application service providers.( people who develop linux applications for Bioinfo comunity) A.S.Kiran Bioinformatics Programmer DSQ Biotech Limited Bangalore INDIA __________________________________________________ Do You Yahoo!? Yahoo! Auctions - Buy the things you want at great prices. http://auctions.yahoo.com/ From bioinformaticsckk at yahoo.co.in Sat Mar 10 00:25:43 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Sat, 10 Mar 2001 05:25:43 +0000 (GMT) Subject: [BiO BB] Re: BIO_Bulletin_Board digest, Vol 1 #6 - 10 msgs In-Reply-To: <200103091700.MAA00822@www.bioinformatics.org> Message-ID: <20010310052543.23329.qmail@web8001.mail.in.yahoo.com> (I have completed m.sc(biosciences)& know Cprogramming.what other things should i learn,as to start a career in bioinformatics.) This is in responce to the above message . The URL given below gives you sites of different bioinformatics tools. http://genamics.com/software/index.htm There is an overwhelming number of softwares present in this site. Take only one or two s/w in each topic and see what they do.Otherwise, you will be lost in that. I am working with DSQ,India. Also, i may suggest you to check this URL of my club which is good for amature bioinformaticians. http://in.clubs.yahoo.com/clubs/kiransbioinformaticsfriends Best of luck, Kiran Kuamr.C --- bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BIO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body > 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific than > "Re: Contents of BIO_Bulletin_Board digest...") > > > Today's Topics: > > 1. [Fwd: starting a career in bioinformatics] > (J.W. Bizzaro) > 2. [Fwd: DNA testing] (J.W. Bizzaro) > 3. Re: [Fwd: starting a career in bioinformatics] > (Indraneel Majumdar) > 4. Re: [Fwd: starting a career in bioinformatics] > (Deanne) > 5. Re: [Fwd: starting a career in bioinformatics] > (John S. J. Anderson) > 6. Re: [Fwd: starting a career in bioinformatics] > (Deanne) > 7. NETTAB: CFP extended to March 20th, 2001 (Paolo > Romano) > 8. bioinfotech (was: starting a career...) (J.W. > Bizzaro) > 9. Re: bioinfotech (was: starting a career...) > (J.W. Bizzaro) > 10. Re: bioinfotech (was: starting a career...) > (Deanne) > > --__--__-- > > Message: 1 > Date: Thu, 08 Mar 2001 23:59:05 +0000 > From: "J.W. Bizzaro" > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] [Fwd: starting a career in > bioinformatics] > boundary="------------A7315BAEBAEACCD5DBEA0238" > > This is a multi-part message in MIME format. > --------------A7315BAEBAEACCD5DBEA0238 > Content-Type: text/plain; charset=us-ascii > Content-Transfer-Encoding: 7bit > > This seems to be a recurring question. Jeff > --------------A7315BAEBAEACCD5DBEA0238 > Content-Type: message/rfc822 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > X-F: Thu Mar 08 > 05:41:11 2001 > Received: from www.bioinformatics.org > [129.63.144.25] by mercury.capeonramp.com with ESMTP > (SMTPD32-6.00) id A1C643570122; Thu, 08 Mar 2001 > 05:41:10 -0500 > Received: from www.bioinformatics.org > (IDENT:mail at www.bioinformatics.org [127.0.0.1]) > by www.bioinformatics.org (8.9.3/8.8.7) with SMTP > id GAA18490; > Thu, 8 Mar 2001 06:51:05 -0500 > Received: (from webmaster at localhost) > by www.bioinformatics.org (8.9.3/8.8.7) id > GAA18460; > Thu, 8 Mar 2001 06:51:04 -0500 > Date: Thu, 8 Mar 2001 06:51:04 -0500 > Message-Id: > <200103081151.GAA18460 at www.bioinformatics.org> > To: admin at bioinformatics.org > Subject: [tol-admin] starting a career in > bioinformatics > From: karna > Reply-To: tol-admin at bioinformatics.org > Sender: tol-admin-admin at bioinformatics.org > Errors-To: tol-admin-admin at bioinformatics.org > X-Mailman-Version: 1.0b10 > Precedence: bulk > List-Id: Administration discussions about TOL > > X-BeenThere: tol-admin at bioinformatics.org > X-RCPT-TO: > > I have completed m.sc(biosciences)& know > Cprogramming.what > other things should i learn,as to start a career in > bioinformatics. > > _______________________________________________ > tol-admin maillist - tol-admin at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/tol-admin > > > --------------A7315BAEBAEACCD5DBEA0238-- > > > --__--__-- > > Message: 2 > Date: Thu, 08 Mar 2001 23:59:39 +0000 > From: "J.W. Bizzaro" > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] [Fwd: DNA testing] > boundary="------------00634F4D0C3268AC94698D08" > > This is a multi-part message in MIME format. > --------------00634F4D0C3268AC94698D08 > Content-Type: text/plain; charset=us-ascii > Content-Transfer-Encoding: 7bit > > > --------------00634F4D0C3268AC94698D08 > Content-Type: message/rfc822 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > X-F: Thu Mar 08 > 18:04:44 2001 > Received: from www.bioinformatics.org > [129.63.144.25] by mercury.capeonramp.com with ESMTP > (SMTPD32-6.00) id A00A42C60130; Thu, 08 Mar 2001 > 18:04:42 -0500 > Received: from www.bioinformatics.org > (IDENT:mail at www.bioinformatics.org [127.0.0.1]) > by www.bioinformatics.org (8.9.3/8.8.7) with SMTP > id TAA23083; > Thu, 8 Mar 2001 19:14:27 -0500 > Received: (from webmaster at localhost) > by www.bioinformatics.org (8.9.3/8.8.7) id > TAA23055; > Thu, 8 Mar 2001 19:14:25 -0500 > Date: Thu, 8 Mar 2001 19:14:25 -0500 > Message-Id: > <200103090014.TAA23055 at www.bioinformatics.org> > To: admin at bioinformatics.org > Subject: [tol-admin] DNA testing > From: Bill McCarron > Reply-To: tol-admin at bioinformatics.org > Sender: tol-admin-admin at bioinformatics.org > Errors-To: tol-admin-admin at bioinformatics.org > X-Mailman-Version: 1.0b10 > Precedence: bulk > List-Id: Administration discussions about TOL > > X-BeenThere: tol-admin at bioinformatics.org > X-RCPT-TO: > > Hi > > I doing a little amateur anthropology on a group > of people known as the black irish. There is little > fact known about them. The may have come to ireland > any where from the 1700s to being the last survivors > of the pre celtic iberian tribes. They look nothing > like any mix of afro caucasion that I have ever > seen. > > A group of them imigrated to the US and settled > near a town called El Dorado in Illinois. > > Could DNA show their race? Could this be done > throgh sample of their hair? How much would this > cost? would your lab do anything like this? > > Thank You. > > Bill McCarron > > _______________________________________________ > tol-admin maillist - tol-admin at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/tol-admin > > > --------------00634F4D0C3268AC94698D08-- > > > --__--__-- > > Message: 3 > Date: Thu, 8 Mar 2001 18:44:30 -0600 (CST) > From: Indraneel Majumdar > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] [Fwd: starting a career in > bioinformatics] > > Hi, > > Just let your C do something with biological data > and you'll be neck deep > in Bioinformatics in no time. At the present > condition Bioinformatics as a > === message truncated === ____________________________________________________________ Do You Yahoo!? Get your free @yahoo.co.in address at http://mail.yahoo.co.in From lists at 123india.com Sat Mar 10 01:49:51 2001 From: lists at 123india.com (Indraneel Majumdar) Date: Sat, 10 Mar 2001 00:49:51 -0600 (CST) Subject: [BiO BB] Linux Clustering for Bioinformatics??? In-Reply-To: <20010310051355.67162.qmail@web11902.mail.yahoo.com> Message-ID: Hi, As I see it, clustering is the solution to tomorrow's computational requirements, as has aptly been demonstrated by Celera, Incyte Genomics, Google and IBM. For an introduction on Clustering and parallel processing please see the Beowulf-HOWTO Parallel-Processing-HOWTO at http://linuxdocs.org/HOWTOs/HOWTO-INDEX/howtos.html and High Availability HOWTO at http://www.ibiblio.org/pub/Linux/ALPHA/linux-ha/High-Availability-HOWTO.html If you're on a slow internet line (DSQ does have a wide channel) get hold of a Linux CD and the Howtos will be there. You might even consider installing Linux since nowadays Bioinformatics and Linux are going much hand-in-hand and it's really much simpler to work on an open platform. On Fri, 9 Mar 2001, Ayyagari Kiran wrote: > Iam a bioinformatics programmer having my skillsets in > Advanced Java programming and implementing three tier > applications in bioinformatics. I don't know Java, but probably it's threaded nature will allow some parallelisation. I don't know if the threads can communicate within themselves. This is required for true parallelisation. > I worked in NT platform and have no much idea about > Linux applications in Bioinformatics. I've not heard of many (any?) bioinfo tools on NT. Probably best will be to shift to Linux or FreeBSD and keep an Irix machine handy. > Can Anyone help me understyanding the "LINUX > CLUSTERING TECHNOLOGY "for Bioinformatics > applications. Basically Clustering is of two types: High availability: providing uninterrupted resources eg for stock markets High Processing: provides enormous processing power One of the High processing types is "Beowulf" ( www.beowulf.org )clustering which is a cluster made of off the shelf commodity parts. This allows you to join a score of PIII/Athlons to (technically) form a tiny supercomputer. For a (debatable) list of powerful supercomputers go to top500.org . A search on google.com will give you the names of many clustered supercomputers. > precisely I wanted to know, > > 1) what sort of bioinfo applications (mention > names)can run on linux clusters and why? Some of the more famous Bioinformatics applications developed for Linux clusters are: NAMD ( http://www.ks.uiuc.edu/Research/namd/ ) PMD Amber Charmm BLAST FastA (and many others) Please search on google for a more complete list and check out these pages: http://zeus.polsl.gliwice.pl/~nikodem//linux4chemistry.html http://sal.kachinatech.com/Z/2/index.shtml some software (clustered and otherwise) was discussed about 4 months back on the bionet.software newsgroup. Most of the credit for Beowulf clustering goes to Don Becker. Due to the Linux kernel's close link with the network protocols it is very easy to do things like remote installation, and booting on diskless nodes. This allows giant clusters to be installed and managed with ease. The robust and secure kernel allows running jobs for months without rebooting (which you are probably used to on NT). This is a key feature since it means that an application can never reach the kernel memory without authorisation and so the OS never fails. This helps since node failure will require other nodes to wait or reschedule the task thus delaying the job. Even if a random fraction of the nodes are continuously down, the job may never be finished (There is some maths behind this which I don't know). Essentially the different modules of a program are passed on to different nodes (as processes) and the results are collated before output. Messages between nodes are kept low to save time in network communications. Another method is to use threading (where there is more communication between different parts of a program) but this is generally better for an SMP system than for a Beowulf since data bus have to be fast. Also in a Beowulf cluster memory of each node is generally not shared. There are two popular libraries for use in coding: PVM (Parallel Virtual Machine) MPI (Message Passing Interface) though probably the MPI standards are more in use now. > 2) How can Linux clustering be of use to application > service providers.( people who develop linux > applications for Bioinfo comunity) Sooner or later all of Bioinformatics will be running on Beowulf clusters, whether in countries with huge resources like the USA or places with limited resources like INDIA. Only the type of nodes will vary. It is actually very inexpensive to set up a Beowulf cluster (such clusters exist at CDAC, very near to where you stay). Once a program has been written for a cluster it can be run on one to hundreds of nodes with no change in the code. Since the code has to be inherrently modular, it is more scaleable in terms of furthur development. And of course, you can test out your code on a supercomputer at a hundred times less cost. And for this same reason your users and customers will be setting up clusters rather than buying costly stand-alone machines. HTH, Indraneel -- http://www.indialine.org From johann at egenetics.com Mon Mar 12 10:04:55 2001 From: johann at egenetics.com (Johann Visagie) Date: Mon, 12 Mar 2001 17:04:55 +0200 Subject: [BiO BB] FreeBSD in bioinformatics Message-ID: <20010312170455.C81147@fling.sanbi.ac.za> Hi everyone, There has been some discussion on this list lately about the use of various free Unix operating systems in bioinformatics. I hope that what follows is therefore not too far off-topic. Some list members may be interested to know that there is a small but concerted effort underway by FreeBSD users in bioinformatics (and other bioscientific computing fields) to add as many applications as possible to the FreeBSD ports tree. The FreeBSD ports tree has gained some fame even outside the FreeBSD (and BSD) communities as one excellent way of integrating third party applications into a Unix-based operating system. It goes somewhat beyond a packaging system (such as RedHat's RPM) and encompasses all levels of a user's normal interaction with a package to get it up and running - from download through patching, compilation and installation. The closest equivalent in the Linux world is (I believe) Debian's apt-get system. Some of the reasons why we're doing this: - A more "bio-friendly" free Unix sounds like a good idea! :-) - End users: What can be easier than: "cd /usr/ports/biology/; make install" to install just about any bioinformatics package. - System administrators: I'm in a position where I can appreciate the pain of running a network of diverse boxes for bioinformatics research. The ports tree provides me with the tools to automate tasks such as the updating of software packages. Installing and cleanly deinstalling packages becomes trivial. Finding out which versions of the dozens of cascaded dependencies (libraries, etc.) of a large package are required - and downloading and installing them - simply isn't a problem anymore. It all happens automatically. - We found that there are already a number of FreeBSD users in bioscientific fields. We're trying to encourage them not to "hack in a vacuum" - i.e. instead of just spending days trying to get some obscure package to work on your system, do the little bit of extra work and submit a port of it. Every user of the OS will immediately benefit by being able to install said package easily, and if one of them finds a better way of doing it, the patches will be submitted back to you, making *your* life easier. The open source principle applied to mass system administration. :-) - Since the ports structure is closely integrated with the operating system, and since the operating system in question is one which ships with all the tools for building distributions, I foresee that we may eventually be able to produce a simple, free CD distribution that installs both the OS and all tools needed by a bioinformaticist. (This may or may not prove desirable - but it's an idea I have...) - There is a lot of talk about creating a unified ports structure across the various BSD-based operating systems. This will include Apple's next- generation operating system, MacOS X. And Macs are of course still entrenched in academia in many parts of the world. - Like Linux, FreeBSD supports the Compaq Alpha architecture (which is of course quite popular in this field). The ports system allows for cross-platform ports. What we need is more FreeBSD Alpha users to test the cross-platform operation of our bio ports on the Alpha. (And goodness knows, anything is better than Tru64! :-> ) Anyone who finds the above interesting, or any FreeBSD users in the field who want to share experiences, please feel free to join our mailing list: http://www.plig.net/mailman/listinfo/freebsd-bio -- Johann From uysal at doctor.com Tue Mar 13 09:57:51 2001 From: uysal at doctor.com (huseyin uysal) Date: Tue, 13 Mar 2001 09:57:51 -0500 (EST) Subject: [BiO BB] primer pairings Message-ID: <387278783.984495471120.JavaMail.root@web596-mc> Hi to everybody, I need a free software or internet site for designing primers. especially, I need a program that shows potential pairings of a primer in the given sequence. I mean, I paste the sequence into the program window and also I paste the primer then this program calculates and shows potential pairings on the pasted sequence and on its complementary sequence. Thank you very much... Huseyin Uysal ______________________________________________ FREE Personalized Email at Mail.com Sign up at http://www.mail.com/?sr=signup From btiwari at molbiol.ox.ac.uk Tue Mar 13 10:56:43 2001 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Tue, 13 Mar 2001 15:56:43 +0000 (GMT) Subject: [BiO BB] primer pairings In-Reply-To: <387278783.984495471120.JavaMail.root@web596-mc> Message-ID: >I need a free software or internet site for designing primers. >especially, I need a program that shows potential pairings of a primer in >the given sequence. I mean, I paste the sequence into the program window and >also I paste the primer then this program calculates and shows potential >pairings on the pasted sequence and on its complementary sequence. Thank >you very much... My favorite program for this (when I used to do it!) was a Mac program called Amplify. Its available, I believe, from: http://www.wisc.edu/genetics/CATG/amplify/ If you don't have access to a Mac, there is an applet at http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html which will test two primers against themselves and each other for hairpins, repeats, dimer formation, etc, etc. However, I don't think you can check for where along a sequence your primers might bind using this site. (If you do use a Mac, you probably won't be able to use this site unfortunately.) Other than that I'll just give you a couple of sites that list various primer programs that are out there (which I personally find useful references) 1) The primer list at the HGMP: http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-primer.html 2) There are reviews of various primer packages, (some free and some not) here: http://www.bbsrc.ac.uk/molbiol/reviews.html good luck. Bela .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- Dr. Bela Tiwari Bioinformatics Officer OU Bioinformatics Centre South Parks Road, 01865 (2)75507 Oxford OX1 3RE http://www.molbiol.ox.ac.uk .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- From fnievinski at cpovo.net Tue Mar 13 13:47:36 2001 From: fnievinski at cpovo.net (Felipe G. Nievinski) Date: Tue, 13 Mar 2001 15:47:36 -0300 Subject: [BiO BB] Linux Clustering for Bioinformatics??? Message-ID: <019d01c0abee$1295fec0$030110ac@felipe> Hi. It worth to keep an eye on the NCSA website, about applications. http://www.ncsa.uiuc.edu/ For example, the last published 'Cover Story' was: http://www.ncsa.uiuc.edu/access/CoverStories/phylogeny/ Gene data allow researchers to recover the evolutionary history of plants, but even the smallest dataset can require impossibly large computations. Using an Alliance Linux cluster and newly designed software, a team from the University of New Mexico and the University of Texas have increased the speed of the process millionfold for one family of plants. Best regards, Felipe Nievinski. From gvd at penguin.pharmacy.ualberta.ca Mon Mar 19 09:48:41 2001 From: gvd at penguin.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Mon, 19 Mar 2001 07:48:41 -0700 (MST) Subject: [BiO BB] Summer school on protein folding (fwd) Message-ID: Found this posting on the BioNews Email list at weizmann... Regards, g. -- -- Gary Van Domselaar Ph.D. Candidate, Associate Director, Faculty of Pharmacy, Bioinformatics.org: The Open Lab University of Alberta gary at bioinformatics.org gary at penguin.pharmacy.ualberta.ca http://bioinformatics.org/gary -- -- This message was sent via the BioNews Email List. Info & Archive: *** http://bioinfo.weizmann.ac.il/bionews.html *** Responsible: Avital Adato (bio at bioinfo.weizmann.ac.il) ---------------------------------------------------------------------- Received from > Jacques Chomilier Summer school on protein folding May 20-26, 2001 - Cargese, Corsica (France) Announcement of a summer school on the following topic : The prediction and mechanism of protein folding : from topology to intermediate states The University of Corsica, the University of Nice-Sophia Antipolis are pleased to announce this summer school, to be held in Cargese, Corsica (France) from May 20-26, 2001 and co-sponsored by the European Union, the CNRS, and Hutchinson. This school will feature about 20 invited speakers and a total of 80 participants. Courses concern as well physisists, chemists or biologists concerned (or willing to become) by the problem of protein folding, either by experimental or theoretical methods. Special attention will be paidto young scientists (under 35 years old). With the purpose to stimulate helpful discussions, attendees wille be invited to present their own research problems. Participation is limited to 60 applicants. To apply, please submit the application form at : http://psb00.snv.jussieu.fr/cargese2001/ Deadline for receiving applications is April 1, 2001. Program and practical informations are available at the following electronic adress: http://psb00.snv.jussieu.fr/cargese2001/ We would appreciate if you could diffuse this information among the members of your laboratory. The organisers : Jacques Chomilier, Laboratoire de Mineralogie-Cristallographie, Paris Gilles Labesse, Centre de Biologie Structurale, Montpellier Jean-Fran?ois Sadoc, Laboratoire de Physique des Solides, Orsay --------------------------------------------------------------------- BioNews is a discussion forum offered by the Weizmann Institute Bioinformatics Unit, see http://bioinfo.weizmann.ac.il From bioinformaticsckk at yahoo.co.in Wed Mar 21 07:37:15 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Wed, 21 Mar 2001 12:37:15 +0000 (GMT) Subject: [BiO BB] Re: BIO_Bulletin_Board digest, Vol 1 #10 - 2 msgs In-Reply-To: <200103141700.MAA21006@www.bioinformatics.org> Message-ID: <20010321123715.26431.qmail@web8002.mail.in.yahoo.com> Hi all, Can anybody tell me wether there are any Bioinformatics programs (online and downloadable) which are compatable for running parallely on linux cluster. For example are there any parallel clustalw or parallel blast available? If available, please mention the site address. with regards, Kiran Kumar.c Scientist, DSQ Biotech, India --- bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BIO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body > 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific than > "Re: Contents of BIO_Bulletin_Board digest...") > > > Today's Topics: > > 1. Re: primer pairings (Bela Tiwari) > 2. Re: Linux Clustering for Bioinformatics??? > (Felipe G. Nievinski) > > --__--__-- > > Message: 1 > Date: Tue, 13 Mar 2001 15:56:43 +0000 (GMT) > From: Bela Tiwari > To: huseyin uysal > cc: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] primer pairings > > >I need a free software or internet site for > designing primers. > >especially, I need a program that shows potential > pairings of a primer in > >the given sequence. I mean, I paste the sequence > into the program window and > >also I paste the primer then this program > calculates and shows potential > >pairings on the pasted sequence and on its > complementary sequence. Thank > >you very much... > > My favorite program for this (when I used to do it!) > was a Mac program > called Amplify. Its available, I believe, from: > > http://www.wisc.edu/genetics/CATG/amplify/ > > If you don't have access to a Mac, there is an > applet at > > http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html > > which will test two primers against themselves and > each other for > hairpins, repeats, dimer formation, etc, etc. > However, I don't think you > can check for where along a sequence your primers > might bind using this > site. (If you do use a Mac, you probably won't be > able to use this site > unfortunately.) > > > Other than that I'll just give you a couple of sites > that list various > primer programs that are out there (which I > personally find useful > references) > > 1) The primer list at the HGMP: > > http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-primer.html > > > 2) There are reviews of various primer packages, > (some free and some not) > here: > > http://www.bbsrc.ac.uk/molbiol/reviews.html > > > good luck. > > > Bela > > > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > Dr. Bela Tiwari Bioinformatics > Officer > OU Bioinformatics Centre > South Parks Road, 01865 (2)75507 > Oxford OX1 3RE > http://www.molbiol.ox.ac.uk > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > > > > --__--__-- > > Message: 2 > From: "Felipe G. Nievinski" > To: > Subject: Re: [BiO BB] Linux Clustering for > Bioinformatics??? > Date: Tue, 13 Mar 2001 15:47:36 -0300 > charset="Windows-1252" > > Hi. > > It worth to keep an eye on the NCSA website, about > applications. > http://www.ncsa.uiuc.edu/ > > For example, the last published 'Cover Story' was: > http://www.ncsa.uiuc.edu/access/CoverStories/phylogeny/ > Gene data allow researchers to recover the > evolutionary history of plants, > but even the smallest dataset can require impossibly > large computations. > Using an Alliance Linux cluster and newly designed > software, a team from the > University of New Mexico and the University of Texas > have increased the > speed of the process millionfold for one family of > plants. > > > Best regards, > Felipe Nievinski. > > > > > --__--__-- > > _______________________________________________ > BIO_Bulletin_Board maillist - > BIO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > --__--__---- > > End of BIO_Bulletin_Board Digest ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com From lists at 123india.com Wed Mar 21 09:20:55 2001 From: lists at 123india.com (lists at 123india.com) Date: Wed, 21 Mar 2001 08:20:55 -0600 Subject: [BiO BB] Re: BIO_Bulletin_Board digest, Vol 1 #10 - 2 msgs In-Reply-To: <20010321123715.26431.qmail@web8002.mail.in.yahoo.com>; from bioinformaticsckk@yahoo.co.in on Wed, Mar 21, 2001 at 12:37:15PM +0000 References: <200103141700.MAA21006@www.bioinformatics.org> <20010321123715.26431.qmail@web8002.mail.in.yahoo.com> Message-ID: <20010321082055.C1336@123india.com> Hi, clustalw does not seem to be available for parallel machines other than SGI (from sgi.com). But a perl interface for batch processing has been written by Aaron J Mackey WU-BLAST (a modification of the original NCBI BLAST) can run on parallel machines. Please see: http://blast.wustl.edu/blast/README.html \Indraneel On Wed, Mar 21, 2001 at 12:37:15PM +0000, kiran challapalli wrote: > > Can anybody tell me wether there are any > Bioinformatics programs (online and downloadable) > which are compatable for running parallely on linux > cluster. For example are there any parallel clustalw > or parallel blast available? > If available, please mention the site address. > with regards, From fnievinski at cpovo.net Thu Mar 22 14:58:06 2001 From: fnievinski at cpovo.net (Felipe G. Nievinski) Date: Thu, 22 Mar 2001 16:58:06 -0300 Subject: [BiO BB] FYI: Polymerase Precision Message-ID: <026801c0b30a$6d642b60$1800000a@felipe> FYI >From Access Online (http://access.ncsa.uiuc.edu/), March 13, 2001: COVER STORY Polymerase Precision http://access.ncsa.uiuc.edu/CoverStories/polb/ "Human DNA is complex, but errors in its replication are rare. With the help of an Alliance SGI Origin2000 supercomputer, researchers are simulating one of the enzymes important to making this replication process reliable." Best regards, Felipe Nievinski. From fnievinski at cpovo.net Thu Mar 22 18:03:16 2001 From: fnievinski at cpovo.net (Felipe G. Nievinski) Date: Thu, 22 Mar 2001 20:03:16 -0300 Subject: [BiO BB] Fw: Objects in Bio- & Chem-Informatics 2001 Call for Participation Message-ID: <03c301c0b324$47b199b0$1800000a@felipe> ----- Original Message ----- From: "OMG Public Relations" To: Sent: Thursday, March 22, 2001 3:58 PM Subject: Objects in Bio- & Chem-Informatics 2001 Call for Participation To: Industry Experts, The following press release announcing "Objects in Bio- & Chem-Informatics 2001 Call for Participation" has been issued today, Thursday, March 22, 2001 at 2:30 p.m. EST over Business Wire. FOR IMMEDIATE RELEASE Contact: Janice Gilman Object Management Group +1-781-444 0404 ext. 141 pr at omg.org Objects in Bio- & Chem-Informatics 2001 Call for Participation Needham, MA, USA March 22, 2001 --Objects In Bio- & Chem-Informatics 2001 (OiBC-2001), hosted by the Object Management Group's Life Science Research Domain Task Force (OMG LSR DTF) will be held at the Sheraton Ferncroft Hotel, Danvers, Massachusetts, USA on July 9 and 10, 2001. This two-day conference will focus on the role of object-oriented technology, reusable software components, design patterns, and distributed computing in life sciences research. The overall theme of the conference is sharing best practices for implementing object-based systems for bioinformatics, cheminformatics, and related disciplines. Conference scope includes object modeling and implementation, independent of platform or language. The OiBC Program Committee is currently seeking papers and posters reporting original research and development of object-oriented software and systems, the role of object-oriented technology, reusable software components, design patterns, and distributed computing in life sciences research. Typical but not exclusive topics of interest include: * Bioinformatics and Genomics * Cheminformatics * Combinatorial libraries and drug design * Computational chemistry * Functional genomics * Information and data management for high-throughput experimental biology * Macromolecular structure * Molecular sequence analysis * Pharmacogenomics * Proteomics * Object-Oriented Modeling, Design, and Ontologies for these disciplines * Efficient object and data stores for any of the disciplines listed above * Advantages and return on investment of object-oriented technologies * Development and application of open standards for information representation and software interoperability Demonstrations of interoperability in systems using components from two or more sources are particularly encouraged, either as posters or as platform talks. For more information about the Call for Participation and how to submit a presentation or poster proposal by May 7, 2001, see the OiBC web site at http://www.omg.org/lsr/oibc/. ### About The OMG With the support of its membership of software vendors, software developers and end users, the OMG's CORBA is "The Middleware That's EverywhereT." Since 1989, the OMG has been "Setting The Standards For Distributed ComputingT" through its mission to promote the theory and practice of object technology for the development of distributed computing systems. The goal is to provide a common architectural framework for object-oriented applications based on widely available interface specifications. The OMG is headquartered in Needham, MA, USA, with an office in Tokyo, Japan as well as international marketing offices in Bahrain, Germany, India, and the UK, along with a U.S. government representative in Washington, DC, USA. The OMG is also a major sponsor of the Integrate 2001 trade show and conference, which will be held September 19-21, 2001 in New York City. For information on joining the OMG or additional information, please contact OMG headquarters by phone at +1-781-444 0404, by fax at +1-781-444 0320, or by email at info at omg.org. The OMG provides current information and services for Distributed Object Computing through The Information Brokerage? on the World Wide Web at www.omg.org and at www.corba.org. Information about OMG Japan can be found at www.omgj.org. Note to editors: CORBA?, The Information Brokerage?, CORBA Academy?, IIOP? and the Object Management Group logo? are registered trademarks of the Object Management Group. OMGT, Object Management GroupT, the CORBA LogoT, "The Middleware That's EverywhereT" , the CORBA Academy logoT, XMIT, MOFT, CWMT, OMG Interface Definition LanguageT, IDLT, CORBAservicesT, CORBAfacilitiesT, CORBAmedT, CORBAnetT, UMLT, the UML Cube Logo, "We're Known By The Companies We ConnectT", Model Driven ArchitectureT, MDAT, OMG Model Driven ArchitectureT, OMG MDAT, "The Architecture of Choice for a Changing WorldT", and Unified Modeling LanguageT are trademarks of the Object Management Group. All other products or company names mentioned are used for identification purposes only, and may be trademarks of their respective owners.