From mike.fursov at gmail.com Thu Oct 2 04:04:21 2008 From: mike.fursov at gmail.com (Mikhail Fursov) Date: Thu, 2 Oct 2008 15:04:21 +0700 Subject: [BiO BB] UGENE v1.2 released Message-ID: UGENE team is glad to announce a new version of the Unipro UGENE software package: a free open-source cross-platform bioinformatics tool. The version 1.2 adds several new plugins, MacOS X platform support and dozens of performance, usability and compatibility improvements. The complete list of changes can be found here: http://ugene.unipro.ru/changelist.html Link to the project site: http://ugene.unipro.ru -- Mikhail Fursov, Unipro UGENE team. From sreebhapsyamal at gmail.com Sat Oct 18 00:09:11 2008 From: sreebhapsyamal at gmail.com (sreebha syamal) Date: Fri, 17 Oct 2008 21:09:11 -0700 Subject: [BiO BB] DNA modelling softwares Message-ID: hi , Coould any body tell me about some softwares(freewares/paid) to model nucleotide sequences. many thanks in advance spsdevi From marchywka at hotmail.com Sun Oct 19 08:13:37 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Sun, 19 Oct 2008 08:13:37 -0400 Subject: [BiO BB] DNA modelling softwares In-Reply-To: References: Message-ID: > Date: Fri, 17 Oct 2008 21:09:11 -0700 > From: sreebhapsyamal at gmail.com > To: bbb at bioinformatics.org > Subject: [BiO BB] DNA modelling softwares > > hi , > Coould any body tell me about some softwares(freewares/paid) to model > nucleotide sequences. > many thanks in advance Can you be more specific? Google on wikipedia pages could get you started but not sure where you are at or where you want to go. > spsdevi > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Stay organized with simple drag and drop from Windows Live Hotmail. http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_102008 From drjohn08318 at yahoo.com Sat Oct 18 20:37:24 2008 From: drjohn08318 at yahoo.com (drjohn08318 at yahoo.com) Date: Sun, 19 Oct 2008 00:37:24 +0000 Subject: [BiO BB] DNA modelling softwares Message-ID: <1224988153-1224376734-cardhu_decombobulator_blackberry.rim.net-258080340-@bxe244.bisx.prod.on.blackberry> What type of modeling do you want to do? ------Original Message------ From: sreebha syamal Sender: To: bbb at bioinformatics.org ReplyTo: General Forum at Bioinformatics.Org Sent: Oct 18, 2008 00:09 Subject: [BiO BB] DNA modelling softwares hi , Coould any body tell me about some softwares(freewares/paid) to model nucleotide sequences. many thanks in advance spsdevi _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb Sent via BlackBerry by AT&T From kailsen at yahoo.com Sun Oct 19 01:27:51 2008 From: kailsen at yahoo.com (senthil kumar) Date: Sun, 19 Oct 2008 10:57:51 +0530 (IST) Subject: [BiO BB] DNA modelling softwares Message-ID: <511205.74173.qm@web94809.mail.in2.yahoo.com> hi what exactly ur looking for, modelling double stranded DNA from a given sequence ??? if so u can use NUCGEN a program developed in our lab and published. detail ur requirments to be of more use... regards, DKS kumar ________________________________ From: sreebha syamal To: bbb at bioinformatics.org Sent: Saturday, 18 October, 2008 9:39:11 AM Subject: [BiO BB] DNA modelling softwares hi , Coould any body tell me about some softwares(freewares/paid) to model nucleotide sequences. many thanks in advance spsdevi _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php From mike.fursov at gmail.com Sun Oct 19 03:31:43 2008 From: mike.fursov at gmail.com (Mikhail Fursov) Date: Sun, 19 Oct 2008 14:31:43 +0700 Subject: [BiO BB] DNA modelling softwares In-Reply-To: References: Message-ID: What kind of modeling do you need? For example, you can use ChromaView plugin for UGENE (it's free, http://ugene.unipro.ru/plugin_chromaview.html) to adjust DNA sequences from chromatograms. Or, may be, you need new sequence generation tool by some model? On Sat, Oct 18, 2008 at 11:09 AM, sreebha syamal wrote: > hi , > Coould any body tell me about some softwares(freewares/paid) to model > nucleotide sequences. > many thanks in advance > spsdevi > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Mikhail Fursov From jeff at bioinformatics.org Thu Oct 23 20:47:13 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 23 Oct 2008 20:47:13 -0400 Subject: [BiO BB] survey of how scientists use computers Message-ID: <49011B11.2020007@bioinformatics.org> -------- Original Message -------- Subject: survey of how scientists use computers Date: Thu, 16 Oct 2008 08:14:19 -0400 From: Greg Wilson Hi, A group of us are running a survey to find out how scientists actually use computers in their day-to-day work. The blurb we're sending out is included below, and I'd be happy to provide more information. We've promised first crack at the results to "American Scientist", but will be making the data generally available. We'd be very grateful if you could spread the word through mailing lists, your blog, your web site, or whatever --- we'd like to get as many people to respond as possible. Thanks, Greg ----------------------------------------------------------------- Computers are as important to modern scientists as test tubes, but we know surprisingly little about how scientists develop and use software in their research. To find out, the University of Toronto, Simula Research Laboratory, and the National Research Council of Canada have launched an online survey in conjunction with "American Scientist" magazine. If you have 20 minutes to take part, please go to: http://softwareresearch.ca/seg/SCS/scientific-computing-survey.html Thanks in advance for your help! Jo Hannay (Simula Research Laboratory) Hans Petter Langtangen (Simula Research Laboratory) Dietmar Pfahl (Simula Research Laboratory) Janice Singer (National Research Council of Canada) Greg Wilson (University of Toronto) From jprudhomme at healthtech.com Fri Oct 24 07:48:39 2008 From: jprudhomme at healthtech.com (Jim Prudhomme) Date: Fri, 24 Oct 2008 07:48:39 -0400 Subject: [BiO BB] Adopting Integrated R&D Informatics Systems Message-ID: <000001c935ce$75699a80$603ccf80$@com> Conference Preliminary Details ADOPTING INTEGRATED R&D INFORMATICS SYSTEMS Data Management & Integration - How Far Have We Come? February 25-27, 2009, San Francisco, CA http://tri-conference.com/09_ird.asp Topics of Discussion: Integrated R&D - Driving Productivity, Innovation & Managing Resources & Costs Translational Research Informatics Integrating Genomic Data Data Integration and Management for Early and Late Chemistry Data Integration and Management Confirmed Presenters, as of 10/24/08: Scientific Workflows as Productivity Tools for Drug Discovery Juergen Hammer, Ph.D., M.Sc., MBA, Global Research Informatics Director, Group Research Information- Global Head In Silico Sciences - Center Head - Liaison to Pharma Research, Hoffmann-La Roche Inc. The Role of Informatics and Genomics to Drive Innovation in Pharma Jakob DeVlieg, Ph.D., Global Head, Molecular Design & Informatics, Molecular Design & Informatics, Schering-Plough Resource Management Strategies Impacting Systems Integration in R&D David M. Sedlock, Ph.D., Senior Director, R&D Systems, Millennium Pharmaceuticals The TAKEDA Oncology Company Evolution of an Innovation Model to Support Pharma R&D Martin D. Leach, Ph.D., Executive Director, MRL IT Basic Research & Biomarkers, Merck & Co., Inc. Executive Panel: Integrated R&D, How Far Have We Come? Moderator: Joseph A. Cerro, President & Founder, Schooner Group LLC Enterprise Information Integration to Inform Biomarker Discovery and Development: Clinical Patient, Biosample and Omics Data Gary Mallow, Ph.D., Director, Biomarker Programs, Information Services for Basic Research, Merck & Co., Inc. Integrated Informatics - Are We There Yet? Sandor Szalma, Ph.D., Director, R&D Informatics, Centocor R&D Inc. The Genomic Data Pipeline: Collecting, Cleaning, Analyzing, Integrating, Sharing Jeanette Papp, Ph.D., Associate Professor, Human Genetics, University of California, Los Angeles Platform for the FDA Genetic Data Submission and Review Process Weida Tong, Ph.D., Director, Center for Toxicoinformatics, National Center for Toxicological Research, U.S. Food and Drug Administration Tales from the Edge: Advanced Approaches to Knowledge Integration & Search David M. Hodgson, Site Head, Global Research Informatics & Global Head, Group Knowledge Exchange, Roche A Strategy for Internal-External Data and Information Integration Jason M. Johnson, Ph.D., Senior Director, Molecular Informatics, Merck & Co., Inc. Advancing Research Through Information Exploitation Chris Waller, Ph.D., Senior Director, Chemistry Informations, Research and Development Informatics, Worldwide Technology, Pfizer, Inc. Panel: Effective Knowledge Management Novel Insights Into the Kinase Gene Family Stephan Schurer, Ph.D., Group Leader Chemoinformatics, Scientific Computing, The Scripps Research Institute Lilly's Transition from Paper to Electronic Lab Notebooks Keith DeVries, Ph.D., Director, Chemical Product, R&D, Eli Lilly and Company, Lilly Research Labs Closing Panel: Integrated R&D Informatics - Take Home Messages Moderator: Joseph A. Cerro, President & Founder, Schooner Group LLC Regards, James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Direct: 781-972-5486 Fax: 781-972-5425 www.healthtech.com From tdmlwilo at yahoo.com Fri Oct 24 00:54:32 2008 From: tdmlwilo at yahoo.com (Twaha Daudi) Date: Thu, 23 Oct 2008 21:54:32 -0700 (PDT) Subject: [BiO BB] setting simple bioinformatic Message-ID: <374653.30266.qm@web37105.mail.mud.yahoo.com> hello all, greetings My institute would like to set up simple bioinformatic unit for drug resistance checking/testing and other activities.Please can anyone help me to point out the hardware and software tools needed?. Any help is appreciated! Thanks From marty.gollery at gmail.com Tue Oct 28 13:47:33 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Tue, 28 Oct 2008 10:47:33 -0700 Subject: [BiO BB] setting simple bioinformatic In-Reply-To: <374653.30266.qm@web37105.mail.mud.yahoo.com> References: <374653.30266.qm@web37105.mail.mud.yahoo.com> Message-ID: What sort of Bioinformatics do you want to do? -Marty On Thu, Oct 23, 2008 at 9:54 PM, Twaha Daudi wrote: > hello all, > greetings > > My institute would like to set up simple bioinformatic unit for drug resistance checking/testing and other activities.Please can anyone help me to point out the hardware and software tools needed?. > > Any help is appreciated! > Thanks > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif North America Toll Free (877) 222-9543 ext. 6 Direct (760) 431-1263 ext. 6 From marchywka at hotmail.com Tue Oct 28 19:29:41 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 28 Oct 2008 19:29:41 -0400 Subject: [BiO BB] setting simple bioinformatic In-Reply-To: References: <374653.30266.qm@web37105.mail.mud.yahoo.com> Message-ID: > Date: Tue, 28 Oct 2008 10:47:33 -0700 > From: marty.gollery at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] setting simple bioinformatic > > What sort of Bioinformatics do you want to do? > -Marty > > On Thu, Oct 23, 2008 at 9:54 PM, Twaha Daudi wrote: >> hello all, >> greetings >> >> My institute would like to set up simple bioinformatic unit for drug resistance checking/testing and other activities.Please can anyone help me to point out the hardware and software tools needed?. >> Yes, it would help if you could be a little more specific and phrase your question in terms of an informatics problem ( to paraphase the US TV show Jeopardy, LOL). This is a pretty large area and I could offer a couple of ideas depending on exactly what you are trying to do. I happen to be more familiar with things like resistance evolution in controlled conditions ( things like testing hepatitis drug candidates for evolution of resistant strains ), this was the first google hit for example, http://www.natap.org/2006/AASLD/AASLD_17.htm but there are a variety of organizations that deal with emerging pathogen reports and follow up. For example, I'm on this mailing list, and there are probably many people here that the moderator could put you in touch with, http://www.promedmail.org/pls/otn/f?p=2400:1000: certainly the US CDC comes to mind also, http://www.cdc.gov/ncidod/EID/vol11no10/05-0644.htm If you are interested in stuff like this, there is a link to a group at mit at the bottom, http://www.sciencedaily.com/releases/2007/11/071121094524.htm "These data can be accessed through the Broad Institute website, at http://www.broad.mit.edu/XDR_TB. " If you had more details on what exactly your group is trying to do, that would help narrow down things a bit. >> Any help is appreciated! >> Thanks >> >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > -- > Martin Gollery > Senior Bioinformatics Scientist > TimeLogic- a Division of Active Motif > North America Toll Free (877) 222-9543 ext. 6 > Direct (760) 431-1263 ext. 6 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: hotmail is getting cumbersom, try also marchywka at yahoo.com _________________________________________________________________ Store, manage and share up to 5GB with Windows Live SkyDrive. http://skydrive.live.com/welcome.aspx?provision=1?ocid=TXT_TAGLM_WL_skydrive_102008 From imitra at myezconnect.com Wed Oct 29 02:20:44 2008 From: imitra at myezconnect.com (Indranil Mitra) Date: Wed, 29 Oct 2008 11:50:44 +0530 Subject: [BiO BB] setting simple bioinformatic In-Reply-To: References: <374653.30266.qm@web37105.mail.mud.yahoo.com> Message-ID: <023e01c9398e$7b056460$71102d20$@com> Hi This is Neil, Do let me know what is the kind of WET/DRY lab setup you are looking for? What kind of work you will do in there and I can suggest something after that. Best, -Indranil -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Mike Marchywka Sent: 29 October 2008 05:00 To: bbb at bioinformatics.org Subject: Re: [BiO BB] setting simple bioinformatic > Date: Tue, 28 Oct 2008 10:47:33 -0700 > From: marty.gollery at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] setting simple bioinformatic > > What sort of Bioinformatics do you want to do? > -Marty > > On Thu, Oct 23, 2008 at 9:54 PM, Twaha Daudi wrote: >> hello all, >> greetings >> >> My institute would like to set up simple bioinformatic unit for drug resistance checking/testing and other activities.Please can anyone help me to point out the hardware and software tools needed?. >> Yes, it would help if you could be a little more specific and phrase your question in terms of an informatics problem ( to paraphase the US TV show Jeopardy, LOL). This is a pretty large area and I could offer a couple of ideas depending on exactly what you are trying to do. I happen to be more familiar with things like resistance evolution in controlled conditions ( things like testing hepatitis drug candidates for evolution of resistant strains ), this was the first google hit for example, http://www.natap.org/2006/AASLD/AASLD_17.htm but there are a variety of organizations that deal with emerging pathogen reports and follow up. For example, I'm on this mailing list, and there are probably many people here that the moderator could put you in touch with, http://www.promedmail.org/pls/otn/f?p=2400:1000: certainly the US CDC comes to mind also, http://www.cdc.gov/ncidod/EID/vol11no10/05-0644.htm If you are interested in stuff like this, there is a link to a group at mit at the bottom, http://www.sciencedaily.com/releases/2007/11/071121094524.htm "These data can be accessed through the Broad Institute website, at http://www.broad.mit.edu/XDR_TB. " If you had more details on what exactly your group is trying to do, that would help narrow down things a bit. >> Any help is appreciated! >> Thanks >> >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > -- > Martin Gollery > Senior Bioinformatics Scientist > TimeLogic- a Division of Active Motif > North America Toll Free (877) 222-9543 ext. 6 > Direct (760) 431-1263 ext. 6 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: hotmail is getting cumbersom, try also marchywka at yahoo.com _________________________________________________________________ Store, manage and share up to 5GB with Windows Live SkyDrive. http://skydrive.live.com/welcome.aspx?provision=1?ocid=TXT_TAGLM_WL_skydrive _102008 _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb