From jezza_com at hotmail.com Wed Jan 2 09:32:49 2002 From: jezza_com at hotmail.com (Jeremy Smith) Date: Wed, 02 Jan 2002 14:32:49 +0000 Subject: [BiO BB] Bioinformatics project suggestions Message-ID: Hello, I am free for ~6 months to code Bioinformatics software (C++, QT3) I wish to write some software under the GPL specifically addressing: 1. Microarrays (clustering/visualisation/processing/probe design) or perhaps 2. XML applications to Bioinformatics (esp. MAML) 3. Or anything else of use. Any suggestions would be appreciated. Regards, Jeremy Smith. MRes Bioinformatics (York). _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From longli at itsa.ucsf.edu Thu Jan 3 02:25:05 2002 From: longli at itsa.ucsf.edu (Li, LC) Date: Wed, 2 Jan 2002 23:25:05 -0800 Subject: [BiO BB] CpG island prediction Message-ID: <000a01c19427$c5750320$01f7da80@long> Hi All, Where can I find the source code (in perl or C ) of a program which can do CpG island prediction? There are some web interfaces for predicting CpG island, but it's hard to get the source code. Thanks in advance. Long Li -------------- next part -------------- An HTML attachment was scrubbed... URL: From vvp at ibmh.msk.su Thu Jan 3 10:26:34 2002 From: vvp at ibmh.msk.su (Vladimir Poroikov) Date: Thu, 03 Jan 2002 18:26:34 +0300 Subject: [BiO BB] International Conference "Genomics, Proteomics and Bioinformatics for Medicine" Message-ID: <3C34782A.B93@ibmh.msk.su> Dear Colleagues, Best wishes for 2002! I would like to inform you that the International Conference "Genomics, Proteomics and Bioinformatics for Medicine" will be held in Moscow - St.Petersburg, Russia, on 22-29 June 2002. The Conference will take place aboard the comfortable ship going down the channels and the greatest Russian Volga river from Moscow to St. Petersburg. The participants will get a unique chance to enjoy the picturesque nature landscapes and the historical monuments of Russia. The Conference is organized by: International Union of Biochemistry and Molecular Biology (IUBMB) The Human Proteome Organization (HUPO) Russian Ministry of Industry, Science and Technology Russian Ministry of Health Russian Academy of Medical Sciences Russian Foundation for Basic Research Moscow Committee on Science and Technology Institute of Biomedical Chemistry of Russian Academy of Medical Sciences Institute of Physico-Chemical Medicine of Russian Ministry of Health The scientific part of the conference will be composed of three major topics: 1. Genomics 1.1. Human genome 1.2. Genomes of microorganisms and plants 1.3. Genomics in medical researches 2. Proteomics. 2.1. Human Proteome Index 2.2. Proteomics of microorganisms and plants 2.3. Proteome diagnostics of widespread human diseases 3. Bioinformatics. 3.1. Analysis of genomes: what can be derived from the genetic texts 3.2. Structural genomics: high throughoutput 3D - modelling 3.3. Computer-aided drug discovery In the framework of the Conference two Symposia will be held concerning applications of genomics, bioinformatics and proteomics for the analysis of: 4.1. Immunoglobulines 4.2. Cytochromes P450 More information is available on the Conference web-site: http://www.ibmh.msk.su/gpbm2002 Your colleagues and you are welcome to take part in the Conference. Kind regards, Vladimir Poroikov, Prof.Dr. Chairman of the Local Organizing Committee From Greg at tekadence.net Thu Jan 3 12:33:11 2002 From: Greg at tekadence.net (Greg Deocampo) Date: Thu, 3 Jan 2002 12:33:11 -0500 Subject: [BiO BB] CpG island prediction In-Reply-To: <000a01c19427$c5750320$01f7da80@long> Message-ID: Hello, I believe you can get the GPL open source for the functionality you seek here: http://www-bio.unizh.ch/docu/emboss_zi/docu/pdf/emboss_qg.pdf. Curious about what you are up to, let me know if you can! Thanks. G /* /* Greg Deocampo <> CEO /* Applied Biocomputing, Incorporated -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Li, LC Sent: Thursday, January 03, 2002 2:25 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] CpG island prediction Hi All, Where can I find the source code (in perl or C ) of a program which can do CpG island prediction? There are some web interfaces for predicting CpG island, but it's hard to get the source code. Thanks in advance. Long Li -------------- next part -------------- An HTML attachment was scrubbed... URL: From franciswyeung at yahoo.com Sat Jan 5 15:12:23 2002 From: franciswyeung at yahoo.com (Francis Yeung) Date: Sat, 5 Jan 2002 12:12:23 -0800 (PST) Subject: [BiO BB] Bioinformatics project suggestions In-Reply-To: Message-ID: <20020105201223.91611.qmail@web14306.mail.yahoo.com> Is BioXML still alive ? Francis --- Jeremy Smith wrote: > Hello, > > I am free for ~6 months to code Bioinformatics > software (C++, QT3) > > I wish to write some software under the GPL > specifically addressing: > > 1. Microarrays > (clustering/visualisation/processing/probe design) > > or perhaps > > 2. XML applications to Bioinformatics (esp. MAML) > 3. Or anything else of use. > > Any suggestions would be appreciated. > > Regards, Jeremy Smith. > MRes Bioinformatics (York). > > > _________________________________________________________________ > MSN Photos is the easiest way to share and print > your photos: > http://photos.msn.com/support/worldwide.aspx > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From reshmi_renu at hotmail.com Sun Jan 6 23:23:57 2002 From: reshmi_renu at hotmail.com (renu nair) Date: Mon, 07 Jan 2002 09:53:57 +0530 Subject: [BiO BB] looking for people Message-ID: An HTML attachment was scrubbed... URL: From ngadewal at yahoo.com Tue Jan 8 05:01:14 2002 From: ngadewal at yahoo.com (nikhil gadewal) Date: Tue, 8 Jan 2002 02:01:14 -0800 (PST) Subject: [BiO BB] Gene Expression Message-ID: <20020108100114.61171.qmail@web9504.mail.yahoo.com> Hello all members, Whether a program is available to sort data from expression libraries into different categories based on function or subcellular localization of molecules. Thankyou in advance. with regards, NIKHIL ===== NIKHIL. S. GADEWAL * HOME ADDRESS * # 22, subhshree apts, Bioinformatics center, * near vijan hospital, Cancer Research Institute, * college road, Parel, Mumbai-12. * nashik-422005 cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 Phone no. 4123803 etx. 242 * __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From innomedical at home.com Tue Jan 8 13:31:55 2002 From: innomedical at home.com (Innovative Medical Recruiting) Date: Tue, 8 Jan 2002 12:31:55 -0600 Subject: [BiO BB] Job Posting - Bioinformatics VP of Business Message-ID: <005501c19872$c01ffca0$1fa20b41@stbrnrd1.la.home.com> Company is a leading Bioinformatics Solution Provider located in the Northeast U.S. They are seeking an individual to lead their U.S. Sales, Marketing and Business Development teams, with up to 20 direct reports. Company will relocate the right candidate to the company headquarters. This newly created position is an ideal opportunity for a dynamic individual who has a proven track record of leadership and who is effective at developing and inspiring a growing sales team. Through collaboration with the company's Global Business Management team, this key position will assist in the development of the global business strategy. Further, the VP of Business, U.S. will create and implement a marketing and sales strategy to expand business opportunities for the company in the U.S., with an active role in the U.S. Senior Management Team. The base for the position is $150,000+ (depending on experience), with a total income package in the $300,000 range. In order to qualify, candidates MUST have over 10 years experience in sales & sales management of information technology solutions, with the bulk of the experience in the Life Sciences industry. A PhD, Life Sciences, Natural Sciences, or IT is highly desired. Company will also consider Master's degrees in a similar field. Successful candidates must possess strong leadership ability and a proven sales record. Knowledge of Research & Development in the Life Science industry is strongly preferred. Travel is required. Relocation package available. Please submit qualified CVs/resumes as an MS Word (.doc) attachment to dale at innomedical.com. Thanks, Dale Busbee, Owner Innovative Medical Recruiting, LLC www.innomedical.com (504) 281-0117 - Phone (419) 791-8747 - Fax -------------- next part -------------- An HTML attachment was scrubbed... URL: From renator at global-2.com Wed Jan 9 14:01:09 2002 From: renator at global-2.com (RenatoR) Date: Wed, 09 Jan 2002 11:01:09 -0800 Subject: [BiO BB] Bioinformatics Career Opportunity in USA/CA. Message-ID: Hello. My name is Renato Rivera and my background is in the Biotech Research/Genomics. I?ve recently made a career move as a Researcher Recruiter for G2 Sciences. G2 Sciences is in the business of shaping the careers of talented and skilled individuals in the areas of Biotechnology and Bioinformatics. If you consider yourself one of those individuals I would like to talk to you. One of our current hottest needs from a prestigious technology leader in the Science market place is for a Bioinformatics Programmer USA/CA. This would be a great career move. I can be reached at 1-800-503-1921 ext. 203 Voice Mail, 1-707-265-1800 Corporate number, or renator at global-2.com e-mail. Look forward to hearing from you. Renato F. Rivera, Jr. Researcher Recruiter G2 Sciences- A Division of Global 2, Inc. 421 Walnut Street, Suite 212 Napa, CA 94559 Tel: 1-800-503-1921 Tel: 707-426-9553 Fax: 707-257-7675 www.global-2.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Global 2 Logo.gif Type: image/gif Size: 7099 bytes Desc: not available URL: From vishwa at atc.tcs.co.in Thu Jan 10 02:35:11 2002 From: vishwa at atc.tcs.co.in (Vishwanath Alevoor) Date: Thu, 10 Jan 2002 18:35:11 +1100 Subject: [BiO BB] (no subject) Message-ID: <000a01c199a9$58cc6ec0$822813ac@ATCVISHWA> Hi, I would like to know whether any patents are involved in using algorithms and methods that are being used in Bioinformatics. Thanks. Vishwanath Alevoor -------------- next part -------------- An HTML attachment was scrubbed... URL: From zola at k2.pcz.czest.pl Fri Jan 11 14:50:55 2002 From: zola at k2.pcz.czest.pl (Jaroslaw Zola) Date: Fri, 11 Jan 2002 20:50:55 +0100 (MET) Subject: [BiO BB] parallel BLAST In-Reply-To: <200112101423.JAA26017@www.bioinformatics.org> Message-ID: Hi, I would like to know if there exists parallel implementation of BLAST algorithms. J.Z. From Joel.Dudley at DevelopOnline.com Fri Jan 11 15:13:47 2002 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Fri, 11 Jan 2002 13:13:47 -0700 Subject: [BiO BB] parallel BLAST Message-ID: Such an implementation exists indeed. check out http://www.turbogenomics.com/about/ - Joel Dudley -----Original Message----- From: Jaroslaw Zola [mailto:zola at k2.pcz.czest.pl] Sent: Friday, January 11, 2002 12:51 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] parallel BLAST Hi, I would like to know if there exists parallel implementation of BLAST algorithms. J.Z. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From philipp.pagel at cmp.yale.edu Fri Jan 11 15:57:22 2002 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Fri, 11 Jan 2002 15:57:22 -0500 Subject: [BiO BB] parallel BLAST In-Reply-To: References: Message-ID: <20020111205721.GA5286@merlin.med.yale.edu> On Fri, Jan 11, 2002 at 01:13:47PM -0700, Joel Dudley wrote: > Such an implementation exists indeed. check out > http://www.turbogenomics.com/about/ > > - Joel Dudley >> I would like to know if there exists parallel implementation of BLAST >> algorithms. I'm not sure this is really a paralellized version of the algorithm. I just heard a talk by the head of Turbo Genomics and he emphasized the advantage of sticking to the original BLAST program and run multiple instances of it on a bunch of machines instead of modifying the algorithm because that way you don't have to keep up with improvements to the original algorithm yourself. cu Philipp -- Dr. Philipp Pagel Department of Cellular and Molecular Physiology phone: (203) 785-6835 SHM, B117 fax: (203) 785-4951 Yale University 333 Cedar ST New Haven, CT 06520 USA From gary.bader at utoronto.ca Fri Jan 11 16:45:34 2002 From: gary.bader at utoronto.ca (Gary Bader) Date: Fri, 11 Jan 2002 16:45:34 -0500 Subject: [BiO BB] parallel BLAST In-Reply-To: References: <200112101423.JAA26017@www.bioinformatics.org> Message-ID: <3.0.5.32.20020111164534.01a1f9b0@mailbox96.utcc.utoronto.ca> Hi, Parallel does not necessarily mean distributed across more than one machine. NCBI's version of BLAST is parallelized nicely using threads and can be run on multiprocessor machines. The default is set to run using 4 CPUs if they are available because the performance/CPU ratio decreases when running on more than 4 (last I heard). Gary At 08:50 PM 01/11/2002 +0100, Jaroslaw Zola wrote: >Hi, > >I would like to know if there exists parallel implementation of BLAST >algorithms. > >J.Z. > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ---------------------------------------------------------- Gary Bader (gary.bader at utoronto.ca), Ph.D. student Biochemistry Department University of Toronto/Samuel Lunenfeld Research Institute http://bioinfo.mshri.on.ca/people/gbader From jdasilva at ncsc.org Fri Jan 11 16:54:21 2002 From: jdasilva at ncsc.org (Jack da Silva) Date: Fri, 11 Jan 2002 16:54:21 -0500 Subject: [BiO BB] parallel BLAST References: Message-ID: <3C3F5F0D.DF16BBC4@ncsc.org> Jaroslaw Zola wrote: > > Hi, > > I would like to know if there exists parallel implementation of BLAST > algorithms. > > J.Z. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board The current version of NCBI BLAST is multithreaded, so it will run in parallel on a multiprocessor machine (use the -a option to specify the number of processors). -- Jack da Silva, PhD Bioinformatics Project Leader North Carolina Supercomputing Center www.ncsc.org/academics/bio_web/ From bioash at hotmail.com Fri Jan 11 22:08:08 2002 From: bioash at hotmail.com (Ashwin Sivakumar) Date: Sat, 12 Jan 2002 03:08:08 +0000 Subject: [BiO BB] patenting-algorithms Message-ID: hi, I am pretty sure of reading that a few bioinfo patents do cover algorithms of the underlying software.So I guess it does apply. regards. Ashwin Sivakumar _________________________________________________________ Ashwin Sivakumar. Research Student, School of Biochemisty and Molecular Biology, University of Leeds _________________________________________________________ >Today's Topics: > >1. (no subject) (Vishwanath Alevoor) >From: "Vishwanath Alevoor" > >Hi, I would like to know whether any patents are involved in using = >algorithms and methods that are being used in Bioinformatics. > >Thanks. Vishwanath Alevoor _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From RHLAUSTIN at aol.com Sat Jan 12 10:36:34 2002 From: RHLAUSTIN at aol.com (RHLAUSTIN at aol.com) Date: Sat, 12 Jan 2002 10:36:34 EST Subject: [BiO BB] patenting-algorithms Message-ID: <163.7037b65.2971b202@aol.com> Hi Yes there do seem to be a few patents/applications out there on the subject. For example, a recent PCT ("World") application entitled: "MULTIPLE SEQUENCE ALIGNMENT", WO0169508, was published on September 20th last year. Derwent Information does a slightly better job of writing a meaningful title than the author, for its World Patents Index database: L6 ANSWER 12 OF 127 WPIX COPYRIGHT 2002 DERWENT INFORMATION LTD TI Computer-implemented method of aligning protein or nucleic acid sequences involves alignment of a query sequence to target sequence using dynamic programming algorithm. However I am not an expert, so you'd really have to pay a patent lawyer or a qualified search broker service to get a full answer. Rob ====================================== Robert Austin Regional Sales Manager USA FIZ Karlsruhe 376 Carter Road Princeton, NJ 08540 Tel: 1 609 333 1466 mailto:robert.austin at fiz-k.com ====================================== www.fiz-k.com ====================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From roumieu at genops.com Sat Jan 12 12:32:15 2002 From: roumieu at genops.com (jordan) Date: Sat, 12 Jan 2002 09:32:15 -0800 Subject: [BiO BB] parallel BLAST Message-ID: <001201c19b8f$145aad00$7efab440@bc.hsia.telus.net> Jaroslaw, You could also try www.genops.com for a distributed version of BLAST. You can try it out for free. By downloading the Ngene software located there you will have access to BLAST running on multiple nodes of a Linux cluster. Jordan -------------- next part -------------- An HTML attachment was scrubbed... URL: From prion at jhu.edu Mon Jan 14 14:57:43 2002 From: prion at jhu.edu (FREDERICK TAN) Date: Mon, 14 Jan 2002 14:57:43 -0500 Subject: [BiO BB] Macintosh In-Reply-To: Message-ID: Good afternoon, . I was wondering how many people out there were using Macintosh as a supplementary computing platform. I am considering the purchase of a Macintosh (in addition to the Win32/Linux/SGI machines) for the purposes of: - presentation machine - part-time mobile computational analysis - light administrative tasks (MS Office essentially) . My questions lie along four major questions: 1) How to compare the performance of the PowerPC G3/G4 chips with that of the Intel based 80x86 chips 2) The basis of Mac OS X/Darwin (is this a true Unix flavored implementation, able to compile and run existing Unix applications); on the same lines a) will this machine be able to run basic sequence analysis packages (phylip, clustalx, etc) and molecular modeling software (RasMol, Chime, etc) and b) how much support does Mac OS X have for emulating a Win32VM? 3) Interoperatability with existing networks-- how much trouble will I have trying to interface with two SGI Octanes and a host of other Windows XP systems (as well as a non postscript HP laser printer) 4) Any suggested configurations for the iBook/PowerBook? . Thank you in advance. Sincerely, Frederick Tan From crasmen at magic.fr Tue Jan 15 03:59:20 2002 From: crasmen at magic.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Tue, 15 Jan 2002 09:59:20 +0100 Subject: [BiO BB] Macintosh In-Reply-To: References: Message-ID: At 14:57 -0500 14/01/02, FREDERICK TAN wrote: >Good afternoon, > >. I was wondering how many people out there were using Macintosh as a >supplementary computing platform. I am considering the purchase of a >Macintosh (in addition to the Win32/Linux/SGI machines) for the purposes >of: I am. >- presentation machine >- part-time mobile computational analysis >- light administrative tasks (MS Office essentially) > >. My questions lie along four major questions: > >1) How to compare the performance of the PowerPC G3/G4 chips with that of >the Intel based 80x86 chips I am delighted with my G4. It is very hard to compare processors as performances greatly vary depending on the application you use. I only have one thing to say, people using wintel machines in my lab envy my TiBook :-) >2) The basis of Mac OS X/Darwin (is this a true Unix flavored >implementation, able to compile and run existing Unix applications); Yes. No doubt about this. ClustalW is faster that ever in the terminal. I run Unix and Perl programs al the time. > on >the same lines a) will this machine be able to run basic sequence analysis >packages (phylip, clustalx, etc) Yep. >and molecular modeling software (RasMol, >Chime, etc) I never tried these so I couldn't tell. > and b) how much support does Mac OS X have for emulating a >Win32VM? VirtualPC 5 is supposed to be MacOS X native (carbon) but I don't use it. I've used previous releases under MacOS 9. It worked just fine but I had no real use of it since all the application I needed exist as native MacOS Applications. >3) Interoperatability with existing networks-- how much trouble will I >have trying to interface with two SGI Octanes and a host of other Windows >XP systems (as well as a non postscript HP laser printer) MacOS X can use NFS and Samba. The implementation is not as "obvious" as AppleTalk but it works just fine. If you need better networking support (and Windows based printers and so on) I'd recommend Dave from Thursby software. Vist their web site, it says it all. http://www.thursby.com/products/dave.html >4) Any suggested configurations for the iBook/PowerBook? It depends on how much you are willing to spend and what applications you'll use. I'd recommend tons of RAM. >. Thank you in advance. > >Sincerely, >Frederick Tan > Corentin From biopolak at yahoo.co.uk Tue Jan 15 08:30:15 2002 From: biopolak at yahoo.co.uk (=?iso-8859-1?q?Peter=20oledzki?=) Date: Tue, 15 Jan 2002 13:30:15 +0000 (GMT) Subject: [BiO BB] Bioinformatics SME's In-Reply-To: Message-ID: <20020115133015.49942.qmail@web12205.mail.yahoo.com> Sorry for not being in contact sooner but i broke my leg on holiday in Switzerland and i just got back a few days ago. Right i'm writing an essay (1500 Words)on SME's in Bioinformatics ANY help will be good as i'm already behind and i have only researched the field by using google with the words SME's and bioinformatics. Pointing me to the source will be a great help Any help would be a great help.... Cheers Peter --- Howard Oliver wrote: > HI All: > > > I had a thought. What if we collectively, using this > board created a check > list for BI SME's? I propose to start with something > simple: > > (SWOT- Broad Analysis) > Strengths > Weaknesses > Opportunities > Threats > > (PEST - Drivers) > Political > Economic > Societal > Technological > > > We can see how it goes from there. I'd be willing to > post our results on my > website and edit it if that is cool with everybody. > Hey something to do > while drinking holiday punch! > > > Happy Holidays: > > > > Howard Oliver > Principal > What If What Next (TM) Consulting > holiver at whatifwhatnext.com > Tel: 416-638-8582 > Mobile: 416-432-2764 > www.whatifwhatnext.com > > > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > Behalf Of balaji > r > Sent: Friday, December 21, 2001 9:25 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Bioinformatics SME's > > > > > > Hi Peter Im interested in the SME's as well > would try to give some suggestions. > balaji > > > > -----Original Message----- > > From: bio_bulletin_board-admin at bioinformatics.org > > > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > > Behalf Of Peter > > Oledzki > > Sent: Sunday, December 09, 2001 12:47 PM > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Bioinformatics SME's > > > > > > I'm writing a review on Bioinformatics SME's > > (small-medium > > enterprises)and was wondering if anyone out there > has > > material on such a > > subject ie examples of small bioinformatics > companies, > > how easy it is to > > set up, competitiveness and sucess rates.... etc > etc > > you get the idea. > > Any help would be much appreciated. > > Thank you > > Pete Oledzki > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > BEGIN:VCARD > VERSION:2.1 > N:Oliver;Howard > FN:Howard Oliver (E-mail) > ORG:What If What Next (TM) Consulting > TITLE:Principal > TEL;WORK;VOICE:(416) 638-8582 > TEL;CELL;VOICE:(416) 432-2764 > TEL;VOICE:+1 (800) 799-2486 > ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;100 Canyon, > Suite 801=0D=0AToronto, Ontario;M3h;5T9;;United > States of Amer= > ica > LABEL;WORK;ENCODING=QUOTED-PRINTABLE:100 Canyon, > Suite 801=0D=0AToronto, Ontario=0D=0AM3h, > 5T9=0D=0AUnited States= > of America > EMAIL;PREF;INTERNET:holiver at whatifwhatnext.com > REV:20000630T111501Z > END:VCARD > __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From RMayreddy at NBME.org Tue Jan 15 10:07:02 2002 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Tue, 15 Jan 2002 10:07:02 -0500 Subject: [BiO BB] Bioinformatics SME's Message-ID: Hi: I need some help from you guys. I am teaching database management and data mining concepts for a group of biologists who are interested in bioinformatics. I am IT person with little knowledge of biology applications of Databases. I need some pointers that will be able to help me to teach the database concepts elegantly with biology db examples. If I can borrow a small bio db schema with some data in it, would be immensely helpful. Also, any data/info on data maining is appreciated!! Thanks In Advance. -Ravi -----Original Message----- From: Peter oledzki [mailto:biopolak at yahoo.co.uk] Sent: Tuesday, January 15, 2002 8:30 AM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] Bioinformatics SME's Sorry for not being in contact sooner but i broke my leg on holiday in Switzerland and i just got back a few days ago. Right i'm writing an essay (1500 Words)on SME's in Bioinformatics ANY help will be good as i'm already behind and i have only researched the field by using google with the words SME's and bioinformatics. Pointing me to the source will be a great help Any help would be a great help.... Cheers Peter --- Howard Oliver wrote: > HI All: > > > I had a thought. What if we collectively, using this > board created a check > list for BI SME's? I propose to start with something > simple: > > (SWOT- Broad Analysis) > Strengths > Weaknesses > Opportunities > Threats > > (PEST - Drivers) > Political > Economic > Societal > Technological > > > We can see how it goes from there. I'd be willing to > post our results on my > website and edit it if that is cool with everybody. > Hey something to do > while drinking holiday punch! > > > Happy Holidays: > > > > Howard Oliver > Principal > What If What Next (TM) Consulting > holiver at whatifwhatnext.com > Tel: 416-638-8582 > Mobile: 416-432-2764 > www.whatifwhatnext.com > > > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > Behalf Of balaji > r > Sent: Friday, December 21, 2001 9:25 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Bioinformatics SME's > > > > > > Hi Peter Im interested in the SME's as well > would try to give some suggestions. > balaji > > > > -----Original Message----- > > From: bio_bulletin_board-admin at bioinformatics.org > > > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > > Behalf Of Peter > > Oledzki > > Sent: Sunday, December 09, 2001 12:47 PM > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Bioinformatics SME's > > > > > > I'm writing a review on Bioinformatics SME's > > (small-medium > > enterprises)and was wondering if anyone out there > has > > material on such a > > subject ie examples of small bioinformatics > companies, > > how easy it is to > > set up, competitiveness and sucess rates.... etc > etc > > you get the idea. > > Any help would be much appreciated. > > Thank you > > Pete Oledzki > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > BEGIN:VCARD > VERSION:2.1 > N:Oliver;Howard > FN:Howard Oliver (E-mail) > ORG:What If What Next (TM) Consulting > TITLE:Principal > TEL;WORK;VOICE:(416) 638-8582 > TEL;CELL;VOICE:(416) 432-2764 > TEL;VOICE:+1 (800) 799-2486 > ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;100 Canyon, > Suite 801=0D=0AToronto, Ontario;M3h;5T9;;United > States of Amer= > ica > LABEL;WORK;ENCODING=QUOTED-PRINTABLE:100 Canyon, > Suite 801=0D=0AToronto, Ontario=0D=0AM3h, > 5T9=0D=0AUnited States= > of America > EMAIL;PREF;INTERNET:holiver at whatifwhatnext.com > REV:20000630T111501Z > END:VCARD > __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jfreeman at variagenics.com Tue Jan 15 10:54:20 2002 From: jfreeman at variagenics.com (jfreeman) Date: Tue, 15 Jan 2002 10:54:20 -0500 Subject: [BiO BB] Bioinformatics SME's References: Message-ID: <3C4450AC.D5E6F542@variagenics.com> Hi Ravi, Take a look at the ensembl website: http://www.ensembl.org/ and http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CurrentEnsemblSchema.html Ensembl is the world open source standard for curating Human sequence data, and you can download it yourself. Tons of other documentation is available which would help. Happy Hunting, Jim Ravi Mayreddy wrote: > > Hi: > > I need some help from you guys. I am teaching database management and data > mining concepts for a group of biologists who are interested in > bioinformatics. I am IT person with little knowledge of biology applications > of Databases. I need some pointers that will be able to help me to teach the > database concepts elegantly with biology db examples. If I can borrow a > small bio db schema with some data in it, would be immensely helpful. > > Also, any data/info on data maining is appreciated!! > > Thanks In Advance. > > -Ravi > > -----Original Message----- > From: Peter oledzki [mailto:biopolak at yahoo.co.uk] > Sent: Tuesday, January 15, 2002 8:30 AM > To: bio_bulletin_board at bioinformatics.org > Subject: RE: [BiO BB] Bioinformatics SME's > > Sorry for not being in contact sooner but i broke my > leg on holiday in Switzerland and i just got back a > few days ago. > > Right i'm writing an essay (1500 Words)on SME's in > Bioinformatics ANY help will be good as i'm already > behind and i have only researched the field by using > google with the words SME's and bioinformatics. > > Pointing me to the source will be a great help > > Any help would be a great help.... > > Cheers Peter > > --- Howard Oliver wrote: > > HI All: > > > > > > I had a thought. What if we collectively, using this > > board created a check > > list for BI SME's? I propose to start with something > > simple: > > > > (SWOT- Broad Analysis) > > Strengths > > Weaknesses > > Opportunities > > Threats > > > > (PEST - Drivers) > > Political > > Economic > > Societal > > Technological > > > > > > We can see how it goes from there. I'd be willing to > > post our results on my > > website and edit it if that is cool with everybody. > > Hey something to do > > while drinking holiday punch! > > > > > > Happy Holidays: > > > > > > > > Howard Oliver > > Principal > > What If What Next (TM) Consulting > > holiver at whatifwhatnext.com > > Tel: 416-638-8582 > > Mobile: 416-432-2764 > > www.whatifwhatnext.com > > > > > > > > -----Original Message----- > > From: bio_bulletin_board-admin at bioinformatics.org > > > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > > Behalf Of balaji > > r > > Sent: Friday, December 21, 2001 9:25 AM > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Bioinformatics SME's > > > > > > > > > > > > Hi Peter Im interested in the SME's as well > > would try to give some suggestions. > > balaji > > > > > > > -----Original Message----- > > > From: bio_bulletin_board-admin at bioinformatics.org > > > > > > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > > > Behalf Of Peter > > > Oledzki > > > Sent: Sunday, December 09, 2001 12:47 PM > > > To: bio_bulletin_board at bioinformatics.org > > > Subject: [BiO BB] Bioinformatics SME's > > > > > > > > > I'm writing a review on Bioinformatics SME's > > > (small-medium > > > enterprises)and was wondering if anyone out there > > has > > > material on such a > > > subject ie examples of small bioinformatics > > companies, > > > how easy it is to > > > set up, competitiveness and sucess rates.... etc > > etc > > > you get the idea. > > > Any help would be much appreciated. > > > Thank you > > > Pete Oledzki > > > > > > > > > _______________________________________________ > > > BiO_Bulletin_Board maillist - > > > BiO_Bulletin_Board at bioinformatics.org > > > > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > > board > > > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > BEGIN:VCARD > > VERSION:2.1 > > N:Oliver;Howard > > FN:Howard Oliver (E-mail) > > ORG:What If What Next (TM) Consulting > > TITLE:Principal > > TEL;WORK;VOICE:(416) 638-8582 > > TEL;CELL;VOICE:(416) 432-2764 > > TEL;VOICE:+1 (800) 799-2486 > > ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;100 Canyon, > > Suite 801=0D=0AToronto, Ontario;M3h;5T9;;United > > States of Amer= > > ica > > LABEL;WORK;ENCODING=QUOTED-PRINTABLE:100 Canyon, > > Suite 801=0D=0AToronto, Ontario=0D=0AM3h, > > 5T9=0D=0AUnited States= > > of America > > EMAIL;PREF;INTERNET:holiver at whatifwhatnext.com > > REV:20000630T111501Z > > END:VCARD > > > > __________________________________________________ > Do You Yahoo!? > Everything you'll ever need on one web page > from News and Sport to Email and Music Charts > http://uk.my.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From bioash at hotmail.com Tue Jan 15 13:46:02 2002 From: bioash at hotmail.com (Ashwin Sivakumar) Date: Tue, 15 Jan 2002 18:46:02 +0000 Subject: [BiO BB] SME's Message-ID: Hi Pete! I can suggest you one thing... ISMB 2001 workshop had a session which dealt with topics on similar lines.If u visit the ISMB web site and mail accross the person who hosted that session..u could be helped. http://ismb01.cbs.dtu.dk/workshop.html Catch u soon here! cheers! Ash _______________________________________ Ashwin Sivakumar, Leeds university,UK _______________________________________ _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From gabeeichler at yahoo.com Tue Jan 15 15:09:09 2002 From: gabeeichler at yahoo.com (Gabriel Eichler) Date: Tue, 15 Jan 2002 15:09:09 -0500 Subject: [BiO BB] Bioinformatics Research Seeker Message-ID: <00fd01c19e00$7fe3aae0$6401a8c0@brain> I am currently applying to Ph.D. programs in Bioinformatics and in the mean time I would like to gain some good hands on experience with bioinformatics. My background is a BSE in Computer Science Engineering from the University of Pennsylvania and I am willing to perform any sort of lab/computer work that is available. I am eager to learn and be a part of exciting research. If you have any positions or ideas of how I may find some work, please email me directly. Thanks so much, Gabriel Eichler -------------- next part -------------- An HTML attachment was scrubbed... URL: From btiwari at molbiol.ox.ac.uk Wed Jan 16 04:54:18 2002 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Wed, 16 Jan 2002 09:54:18 +0000 (GMT) Subject: [BiO BB] Bioinformatics - biology db examples In-Reply-To: Message-ID: >I need some help from you guys. I am teaching database management and data >mining concepts for a group of biologists who are interested in >bioinformatics. I am IT person with little knowledge of biology applications >of Databases. I need some pointers that will be able to help me to teach the >database concepts elegantly with biology db examples. If I can borrow a >small bio db schema with some data in it, would be immensely helpful. Hello, I'm not sure if this is the type of thing you are looking for or not, but have you tried looking at Interpro: http://www.ebi.ac.uk/interpro/ I attended a course on interpro last year where they showed us the relational model they used. I couldn't find this kind of documentation on their site, but they do have an email address you could contact to see if their models/schemas are available. interhelp at ebi.ac.uk The reference for Interpro is Nucleic Acids Research vol 29(1):37-40 (2001). I hope this helps, 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 asen.nenov at metalife.de Wed Jan 16 09:17:56 2002 From: asen.nenov at metalife.de (Asen Nenov) Date: Wed, 16 Jan 2002 15:17:56 +0100 Subject: [BiO BB] New BIOINFORMATICS Resource launched! Message-ID: <001d01c19e98$988b05f0$e401a8c0@metagen.bg> Dear Coleagues, In the beginning of the year 2002 a team of biologists and programmers launched new FREE bioinformatics resource. This site offers: - collected information in searchable databases [incl. GBK, SPRT, PIR and many of major databases available]; - Algorithms [Blast, ClustlW, 3D modeler, 2D Prediction and many others] - User can save their files generated by algorithms and search processes. Servers are placed in Bulgaria, at the following address: http://metalife.online.bg Feel free to contact any member of METALIFE team. Best Regards Asen Nenov METALIFE -------------- next part -------------- An HTML attachment was scrubbed... URL: From crasmen at magic.fr Wed Jan 16 11:41:36 2002 From: crasmen at magic.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Wed, 16 Jan 2002 17:41:36 +0100 Subject: [BiO BB] Macintosh In-Reply-To: References: Message-ID: At 17:57 -0500 15/01/02, FREDERICK TAN wrote: >. As a beginning graduate student, I have been contemplating the >price/performance of the G3 and G4 systems (in reality, the iBook vs the >TiBook). So that's sort of the situation I am in, examining the merits of >the respective laptop series. If you are a student, maybe you should consider subscribing the the Apple ADC Student program (Apple Developer Connection - 100$). Among other things (developer tools, systems, other software), it will allow you to buy a machine with 20 % off????? See http://www.apple.com/developer/ >. In general, how much better do you feel the G4 chip performs on pure >number crunching operations. For instance, if I was attempting to run a >molecular dynamics simulation for seven days on an SGI, and then I ran it >on a G4 machine and came away with X days, how close would the G3 machine >perform? I realize that this may be a very loaded question dependent on >the system memory and bus speed, but "all other things being equal".... All other things being equal, there's not much difference between the G4 and G3 in term of calculation power. You have some other things to take into account though : The system and other applications use the velocity engine so it makes day to day use a lot smoother (especially in MacOS X) The Screen is soooooooo great !!! >. My understanding (which could very well be wrong) is that the *only* >difference between the G3 and the G4 is the AltiVec unit. Is that true? >If that is the case, then for the calculations to perform better (setting >aside clock speed), the algorithm would have to be optimized to take >advantage of that unit? Yep. > > > I'd recommend tons of RAM. > >. Probably a given that I'll try and get as much as possible :) Wise decision :-) >. It seems that in my price range, that the 133Mhz bus in the TiBook is >out of reach, and that it would be a worthy investment to upgrade from the >66Mhz of the iBook. Memory at 128 seems standard, with options for >upgrade now/later through Apple/3rd party. I'll put myself in the >position of saying "hard drive size and optical drive option is >irrelevant". So my dilemma comes down to: is the G4 chip and the 15.2 >inch display worth the extra $700? Consider the discount you may have as an ADC student? >. Thanks again for all of your help. My pleasure :-)) Corentin From ozelensky at yahoo.ca Thu Jan 17 11:29:08 2002 From: ozelensky at yahoo.ca (olga zelensky) Date: Thu, 17 Jan 2002 11:29:08 -0500 (EST) Subject: [BiO BB] opinion of specialists Message-ID: <20020117162908.7092.qmail@web12805.mail.yahoo.com> Bioinformatics - a new direction in biology for me. I'l be very appreciate to everybody for it's centences about this plan. With the best wishes OLGA Plan of bioinformatics analysis of genes responsible for basement membrane formation 1. Provide a Data Bases retrieval to determine promoter structure of genes responsible for laminin and collagen IV formation (human, mouse and puffer fish). 2. Analysis of individual nucleotide sequences of analyzed objects. 3. Multiple alignments of sequences at different biological objects to determine homology between them. 4. Statistical analysis of bases in analyzed regulatory regions (frequency analysis and distribution of every base, dinucleotide frequencies and distribution, correlations within nucleotides for the selected region of the sequence) to determine their similarities and difference, and possible connection between them. The correlation analysis for analysis of aligned data sets for different groups of genes in attempts to understand long-range correlations in DNA sequences potentially associated with specific in vivo structures during development and differentiation. 5. Investigation of regulatory regions of analyzed genes. Analysis of specific sequence motifs in a set of different genes to examine particular genomic loci in depth, focusing on regions sharing synteny with human chromosomes 6. Genes mapping to analyze their spatial location and it?s influence on regulatory function. 7. Comparative analysis of regulatory regions of different genes to determine logic of their activity. Analysis of specificity in bases sequences (repetitions, periodicity etc.) 8. Statistics of codons responsible for laminin and collagen formation (base compositional bias between codon positions, periodicity in base occurrence) for testing of hypothesis about genes concerted regulation and for explanation their regulatory activity. Frequency of usage of each codon (per thousand) in human coding regions and the relative frequency of each codon among synonymous codons. By comparing the frequency of codons in a region of an species genome read in a given frame with the typical frequency of codons in the species genes, it is possible to estimate a likelihood of the region coding. 9. Analysis of genes mutations in thickened basement membranes. 10. Sequence analysis of regulatory regions of genes from health cells and those with thickened basement membranes. Involved Data Bases : BLAST, Compugen, EMBL, Ensemble, Fasta, Gbase, GDB, GenBank, HUGEN, SWISS-PROT, The Fugu Genomics Project, Mouse Gene, Statistical Packages: StatGraph, Costat, Statistica, Jump ______________________________________________________________________ Web-hosting solutions for home and business! http://website.yahoo.ca From shure at mail.ru Fri Jan 18 15:14:55 2002 From: shure at mail.ru (shure) Date: Fri, 18 Jan 2002 21:14:55 +0100 Subject: [BiO BB] opinion of specialists In-Reply-To: <20020117162908.7092.qmail@web12805.mail.yahoo.com> References: <20020117162908.7092.qmail@web12805.mail.yahoo.com> Message-ID: <3885.020118@mail.ru> ??????... ?????? ?? ?????????, ?? ?????????? ????... *?? ??? ??????, ???????) ?? ?????? ??? ? oz> I'l be very appreciate to everybody for it's centences oz> about this plan. ???????...:) Thursday, January 17, 2002, 5:29:08 PM, you wrote: oz> Bioinformatics - a new direction in biology for me. oz> I'l be very appreciate to everybody for it's centences oz> about this plan. oz> With the best wishes oz> OLGA oz> Plan of bioinformatics analysis of oz> genes responsible for basement membrane formation oz> 1. Provide a Data Bases retrieval to determine oz> promoter structure of genes responsible for laminin oz> and collagen IV formation (human, mouse and puffer oz> fish). oz> 2. Analysis of individual nucleotide sequences of oz> analyzed objects. oz> 3. Multiple alignments of sequences at different oz> biological objects to determine homology between them. oz> 4. Statistical analysis of bases in analyzed oz> regulatory regions (frequency analysis and oz> distribution of every base, dinucleotide frequencies oz> and distribution, correlations within nucleotides for oz> the selected region of the sequence) to determine oz> their similarities and difference, and possible oz> connection between them. The correlation analysis for oz> analysis of aligned data sets for different groups of oz> genes in attempts to understand long-range oz> correlations in DNA sequences potentially associated oz> with specific in vivo structures during development oz> and differentiation. oz> 5. Investigation of regulatory regions of analyzed oz> genes. Analysis of specific sequence motifs in a set oz> of different genes to examine particular genomic loci oz> in depth, focusing on regions sharing synteny with oz> human chromosomes oz> 6. Genes mapping to analyze their spatial location and oz> it?s influence on regulatory function. oz> 7. Comparative analysis of regulatory regions of oz> different genes to determine logic of their activity. oz> Analysis of specificity in bases sequences oz> (repetitions, periodicity etc.) oz> 8. Statistics of codons responsible for laminin and oz> collagen formation (base compositional bias between oz> codon positions, periodicity in base occurrence) for oz> testing of hypothesis about genes concerted regulation oz> and for explanation their regulatory activity. oz> Frequency of usage of each codon (per thousand) in oz> human coding regions and the relative frequency of oz> each codon among synonymous codons. By comparing the oz> frequency of codons in a region of an species genome oz> read in a given frame with the typical frequency of oz> codons in the species genes, it is possible to oz> estimate a likelihood of the region coding. oz> 9. Analysis of genes mutations in thickened basement oz> membranes. oz> 10. Sequence analysis of regulatory regions of genes oz> from health cells and those with thickened basement oz> membranes. oz> Involved Data Bases : BLAST, Compugen, EMBL, Ensemble, oz> Fasta, Gbase, GDB, GenBank, HUGEN, SWISS-PROT, The oz> Fugu Genomics Project, Mouse Gene, oz> Statistical Packages: StatGraph, Costat, Statistica, Jump oz> ______________________________________________________________________ oz> Web-hosting solutions for home and business! http://website.yahoo.ca oz> _______________________________________________ oz> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org oz> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Best regards, shure mailto:shure at mail.ru From mail at c-jet.com Mon Jan 21 10:08:58 2002 From: mail at c-jet.com (webmaster) Date: Mon, 21 Jan 2002 10:08:58 -0500 Subject: [BiO BB] 200M 空间 + 国际域名 = 150元/年 Message-ID: <200201211508.g0LF8sT20824@www.bioinformatics.org> ????????????????????! ??????????????????????????????Imail 7.04????????????SMTP?????????? ????????????????????????????SMTP????????????"??POP3??????????"???????? ?????????????????????????????????????????????????????????????????????? ????,?????????????????????????????????????????????????? 200M HTML???? + 1?????????? = 150??/?? 200M????(????ASP)+200M????????+30M Access??????+1???????????? ????350??/?? ????????????????????????????????????????????????????! ???????????????????????????????????????????? 40M ?????????? ???????? http://www.c-jet.com ???????????????????????????? ?????????????? QQ??93753765 ?????????????????????????????? --------------------------------------------------------------- ????????????,??????????????????(http://www.21cmm.com) ??CMM????(http://www.21cmm.com)???????????????? From ozelensky at yahoo.ca Mon Jan 21 12:44:02 2002 From: ozelensky at yahoo.ca (olga zelensky) Date: Mon, 21 Jan 2002 12:44:02 -0500 (EST) Subject: [BiO BB] Win-1251 In-Reply-To: <200201211703.g0LH3AT22721@www.bioinformatics.org> Message-ID: <20020121174402.3305.qmail@web12803.mail.yahoo.com> I can't read this message on my comp. Please, send again in code Win-1251 Sincerely Yours - Olga --- bio_bulletin_board-request at bioinformatics.org wrote: > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide 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. 200M ???? + ???????? = 150??/?? (webmaster) > > --__--__-- > > Message: 1 > Date: Mon, 21 Jan 2002 10:08:58 -0500 > From: webmaster > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] 200M ???? + ???????? = 150??/?? > Reply-To: bio_bulletin_board at bioinformatics.org > > > ????????????????????! > > ??????????????????????????????Imail > 7.04????????????SMTP?????????? > > ????????????????????????????SMTP????????????"??POP3??????????"???????? > > ?????????????????????????????????????????????????????????????????????? > > ????,?????????????????????????????????????????????????? > > > 200M HTML???? + 1?????????? = 150??/?? > > 200M????(????ASP)+200M????????+30M > Access??????+1???????????? > > ????350??/?? > > > > ????????????????????????????????????????????????????! > > ???????????????????????????????????????????? 40M > ?????????? > > ???????? http://www.c-jet.com > > > > ???????????????????????????? > > ?????????????? > QQ??93753765 > > > ?????????????????????????????? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --------------------------------------------------------------- > ????????????,??????????????????(http://www.21cmm.com) > > ??CMM????(http://www.21cmm.com)???????????????? > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest ______________________________________________________________________ Web-hosting solutions for home and business! http://website.yahoo.ca From jeff at bioinformatics.org Mon Jan 21 15:19:32 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 21 Jan 2002 15:19:32 -0500 Subject: [BiO BB] website login temporarily offline Message-ID: <3C4C77D4.43C9201A@bioinformatics.org> Greetings. Due to recent software upgrades, members have been unable to log in via the web interface. We expect to have the problem resolved within the next day or two, and we appreciate your understanding. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Tue Jan 22 09:16:11 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 22 Jan 2002 09:16:11 -0500 Subject: [BiO BB] website login temporarily offline References: <3C4C77D4.43C9201A@bioinformatics.org> Message-ID: <3C4D742B.4BDED8A9@bioinformatics.org> The problem has been fixed. Enjoy. Cheers. Jeff "J.W. Bizzaro" wrote: > > Due to recent software upgrades, members have been unable to log in via the > web interface. We expect to have the problem resolved within the next day or > two, and we appreciate your understanding. -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From fanfuhao at yahoo.com Tue Jan 22 23:45:08 2002 From: fanfuhao at yahoo.com (FRANK FAN) Date: Wed, 23 Jan 2002 12:45:08 +0800 Subject: [BiO BB] Re: Contents of BiO_Bulletin_Board digest... References: <200201221701.g0MH12T15277@www.bioinformatics.org> Message-ID: <002601c1a3c8$bdf63320$ca6c8c3d@oemcomputer> ----- Original Message ----- From: To: Sent: Wednesday, January 23, 2002 1:01 AM Subject: BiO_Bulletin_Board digest, Vol 1 #179 - 3 msgs > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide 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. Win-1251 (olga zelensky) > 2. website login temporarily offline (J.W. Bizzaro) > 3. Re: website login temporarily offline (J.W. Bizzaro) > > --__--__-- > > Message: 1 > Date: Mon, 21 Jan 2002 12:44:02 -0500 (EST) > From: olga zelensky > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Win-1251 > Reply-To: bio_bulletin_board at bioinformatics.org > > I can't read this message on my comp. Please, send > again in code Win-1251 > Sincerely Yours - Olga > --- bio_bulletin_board-request at bioinformatics.org > wrote: > > Send BiO_Bulletin_Board mailing list submissions to > > bio_bulletin_board at bioinformatics.org > > > > To subscribe or unsubscribe via the World Wide 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. 200M ???? + ???????? = 150??/?? (webmaster) > > > > -- __--__-- > > > > Message: 1 > > Date: Mon, 21 Jan 2002 10:08:58 -0500 > > From: webmaster > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] 200M ???? + ???????? = 150??/?? > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > > > ????????????????????! > > > > ??????????????????????????????Imail > > 7.04????????????SMTP?????????? > > > > > ????????????????????????????SMTP????????????"??POP3??????????"???????? > > > > > ?????????????????????????????????????????????????????????????????????? > > > > > ????,?????????????????????????????????????????????????? > > > > > > 200M HTML???? + 1?????????? = 150??/?? > > > > 200M????(????ASP)+200M????????+30M > > Access??????+1???????????? > > > > ????350??/?? > > > > > > > > > ????????????????????????????????????????????????????! > > > > ???????????????????????????????????????????? 40M > > ?????????? > > > > ???????? http://www.c-jet.com > > > > > > > > ???????????????????????????? > > > > ?????????????? > > QQ??93753765 > > > > > > ?????????????????????????????? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --------------------------------------------------------------- > > > ????????????,??????????????????(http://www.21cmm.com) > > > > ??CMM????(http://www.21cmm.com)???????????????? > > > > > > -- __--__-- > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > End of BiO_Bulletin_Board Digest > > > ______________________________________________________________________ > Web-hosting solutions for home and business! http://website.yahoo.ca > > --__--__-- > > Message: 2 > Date: Mon, 21 Jan 2002 15:19:32 -0500 > From: "J.W. Bizzaro" > To: bbb at bioinformatics.org > Subject: [BiO BB] website login temporarily offline > Reply-To: bio_bulletin_board at bioinformatics.org > > Greetings. > > Due to recent software upgrades, members have been unable to log in via the > web interface. We expect to have the problem resolved within the next day or > two, and we appreciate your understanding. > > Cheers. > Jeff > -- > J.W. Bizzaro jeff at bioinformatics.org > Director, Bioinformatics.Org http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of others, we > should be glad of an opportunity to serve others by any invention > of ours; and this we should do freely and generously." > -- Benjamin Franklin > -- > > --__--__-- > > Message: 3 > Date: Tue, 22 Jan 2002 09:16:11 -0500 > From: "J.W. Bizzaro" > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] website login temporarily offline > Reply-To: bio_bulletin_board at bioinformatics.org > > The problem has been fixed. Enjoy. > > Cheers. > Jeff > > "J.W. Bizzaro" wrote: > > > > Due to recent software upgrades, members have been unable to log in via the > > web interface. We expect to have the problem resolved within the next day or > > two, and we appreciate your understanding. > > > -- > J.W. Bizzaro jeff at bioinformatics.org > Director, Bioinformatics.Org http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of others, we > should be glad of an opportunity to serve others by any invention > of ours; and this we should do freely and generously." > -- Benjamin Franklin > -- > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest ???????????????????????????????????????????:??????g????~???&?????f?v????a???????_?j(??& From bioinfo_india at yahoo.com Thu Jan 24 07:17:40 2002 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Thu, 24 Jan 2002 04:17:40 -0800 (PST) Subject: [BiO BB] how to fetch sequences from web In-Reply-To: <3C34782A.B93@ibmh.msk.su> Message-ID: <20020124121740.18561.qmail@web14510.mail.yahoo.com> Hi group, Do you know if there is any tool which can fetch fasta formated sequences based on the accession numbers list what i have with me. I know that we can do this in GCG and EMBOSS. I want a web based facility, because i do not have access to EMBOSS or GCG. Please reply soon ! Thank you in advance Suraj Peri ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Great stuff seeking new owners in Yahoo! Auctions! http://auctions.yahoo.com From jfreeman at variagenics.com Thu Jan 24 09:10:59 2002 From: jfreeman at variagenics.com (jfreeman) Date: Thu, 24 Jan 2002 09:10:59 -0500 Subject: [BiO BB] how to fetch sequences from web References: <20020124121740.18561.qmail@web14510.mail.yahoo.com> Message-ID: <3C5015F3.AF632B09@variagenics.com> If you are a programmer, or have one in your employ, try bioperl: http://www.bioperl.org/ or, try batch entrez: http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Nucleotide Regards, Jim Freeman Peri Suraj wrote: > > Hi group, > Do you know if there is any tool which can fetch > fasta formated sequences based on the accession > numbers list what i have with me. > I know that we can do this in GCG and EMBOSS. > I want a web based facility, because i do not have > access to EMBOSS or GCG. > Please reply soon ! > Thank you in advance > Suraj Peri > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > Great stuff seeking new owners in Yahoo! Auctions! > http://auctions.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From danag at bioinformatics.weizmann.ac.il Thu Jan 24 09:20:38 2002 From: danag at bioinformatics.weizmann.ac.il (Dana Gerber) Date: Thu, 24 Jan 2002 16:20:38 +0200 Subject: [BiO BB] how to fetch sequences from web References: <20020124121740.18561.qmail@web14510.mail.yahoo.com> Message-ID: <3C501835.BB203BAF@bioinfo.weizmann.ac.il> Hi, Try use service of NCBI,Batch Entrez: http://www3.ncbi.nlm.nih.gov/entrez/batchentrez.cgi Create a file with the accession numbers and run it in this program. good luck, Dana Peri Suraj wrote: > Hi group, > Do you know if there is any tool which can fetch > fasta formated sequences based on the accession > numbers list what i have with me. > I know that we can do this in GCG and EMBOSS. > I want a web based facility, because i do not have > access to EMBOSS or GCG. > Please reply soon ! > Thank you in advance > Suraj Peri > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > Great stuff seeking new owners in Yahoo! Auctions! > http://auctions.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ozelensky at yahoo.ca Thu Jan 24 12:28:01 2002 From: ozelensky at yahoo.ca (olga zelensky) Date: Thu, 24 Jan 2002 12:28:01 -0500 (EST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #181 - 3 msgs In-Reply-To: <200201241703.g0OH3dT27805@www.bioinformatics.org> Message-ID: <20020124172801.75931.qmail@web12808.mail.yahoo.com> http://www.gdb.org/gdb-bin/genera/genera/hgd/ExternalDB?!action=query http://www.acedb.org/ http://www.accelrys.com/products/gcg_wisconsin_package/ http://www.expasy.ch/ http://www.dkfz-heidelberg.de/GeneCards/ http://www.genome.ad.jp/kegg/ http://www.ncbi.nlm.nih.gov/gorf/gorf.html http://www.ebi.ac.uk/ ______________________________________________________________________ Web-hosting solutions for home and business! http://website.yahoo.ca From sales at thephonedome.com Fri Jan 25 06:30:48 2002 From: sales at thephonedome.com (The Phone Dome) Date: Fri, 25 Jan 2002 11:30:48 -0000 Subject: [BiO BB] Protect Yourself from mobile/cell phone radiation Message-ID: <2002125113048884BOXNLHTSPUKR@M5Mailer> ARE YOU BURNING YOUR BRAIN? GET THE PHONE DOME - ABSORBS 99% OF HARMFUL RADIATION www.thephonedome.com Mobile / Cell phones are bad for you - everyone knows it and research has proven links with several forms of cancer. The world's leading phone makers have even agreed to start publishing information about the levels of radiation emitted by their phones. Recently launched the PHONE DOME, a tiny anti-radiation safety accessory made up of micro crystals that neutralise and change the negative effects of all mobile/cell phones reducing harmful radiation by over 99% without any adverse effects on the phone's functionality. Acting as an energy cell the PHONE DOME creates a positive energy cell alteration within the radiation fields emitted from the mobile/cell phones. The PHONE DOME weighs less than a paperclip and simply sticks onto the back of a phone. "The PHONE DOME is a Bio-Radiation shield the size of a button easily attached to a mobile phone for transforming the negative emissions and thereby helping to protect you." John G Walker. H.F Rad. A.I.C.R. S.Hom. RADIONICS Expert. From e115918 at metu.edu.tr Sat Jan 26 11:34:28 2002 From: e115918 at metu.edu.tr (bilal) Date: Sat, 26 Jan 2002 18:34:28 +0200 Subject: [BiO BB] bioinf. and electronics eng. Message-ID: <200201261634.g0QGYUv12784@myra.cc.metu.edu.tr> Hello, my name is Bilal. I am from Turkey. I am attending METU Electrical& Electronics Engineering, as a senior student. I need some information over bioinformatics so I got involved in this mail group. I want to know that what bioinformatics maily concern with and where do professionals work. Also some ideas which may explain how an electronics eng. may get involved in this area. That's all for now. I will be very glad to hear from you soon. thank you for your attention. Bilal Catakoglu METU Electrical Electronics Eng. 4th year student From kiran_ayyagari at yahoo.com Sun Jan 27 23:54:26 2002 From: kiran_ayyagari at yahoo.com (Ayyagari Kiran) Date: Sun, 27 Jan 2002 20:54:26 -0800 (PST) Subject: [BiO BB] doubt in protein modeling step Message-ID: <20020128045426.10441.qmail@web11901.mail.yahoo.com> Hi all, In protein modeling,at first we look for protein sequence similarity and doing Multiple Seq alignment. Supposing I take 5 protein sequences hits (after doing Blastp),assuming that there are no pdb structures for any of them but still i have to model my protein sequence. the next step is to go for Multiple sequence alignment where in we can find out which are the regions exactly conserved and find whether those regions have any structural similarity also!!! But here the input for Multiple Sequence alignment is our query sequence + the 5 similar sequences having highest hits (from BLAST) my question is whether we can/should build a consensus sequence by multiple alignment taking into consideration our query sequence also?? or build a consensus sequence by Multiple alignment taking only those 5 sequences (excluding our query seq) and then align that consensus sequence with our query sequence both at sequence level and structure level. I shall refine my doubt if am not clear in my subsequent discussions.Thanks in advance Ayyagari Kiran __________________________________________________ Do You Yahoo!? Great stuff seeking new owners in Yahoo! Auctions! http://auctions.yahoo.com From jtrynak at scigenium.com Tue Jan 29 00:16:56 2002 From: jtrynak at scigenium.com (John Rynak) Date: Tue, 29 Jan 2002 00:16:56 -0500 Subject: [BiO BB] SciGenium - Opening in Europe Message-ID: <00b601c1a884$2be8a1a0$ca00fea9@computer> Informatics Scientist (Collaborator Liaison) The person in this position serves as a liaison between SciGenium and a specific collaborating client, with primary responsibility for European operations. The liaison provides full-time on-site consulting including demonstration and support for data visualization and mining software, understanding the collaborator's needs and conveying those to the home office, defining software requirements to support the collaborator, participating in prototype development, and performing data analysis. The European liaison is part of a two-person team to support the collaborator's needs. Along with the other liaison, who has primary responsibility for North American operations, this two-person team must act in a unified fashion to best represent, unify, and integrate the needs of this client under a single client director. Effective and frequent communication is an important aspect of success in this position. The Informatics Scientist needs to have an understanding of information visualization, in general. In addition, knowledge of the technical areas being addressed by the client is needed. The candidate should have some familiarity with exploratory data analysis, bioinformatics, and cheminformatics and be willing to learn more in these areas. Familiarity with existing informatics software and Windows and UNIX platforms is desired. Experience with programming languages such as JAVA would be advantageous. Training and experience equivalent to a Ph.D. in mathematics/statistics, biochemistry/molecular biology, chemistry, or computer science or an M.D. Experience with informatics and excellent interpersonal skills required. Interested candidates should forward their resumes to jtrynak at scigenium.com or FAX 208.567.3995 or send to: SciGenium P.O Box 380916 Cambridge, MA 02238 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zola at k2.pcz.czest.pl Tue Jan 29 16:40:34 2002 From: zola at k2.pcz.czest.pl (Jaroslaw Zola) Date: Tue, 29 Jan 2002 22:40:34 +0100 (MET) Subject: [BiO BB] bio-cluster Message-ID: Dear Colleagues, Our Institute of Mathematics and Computer Science of the Technical University of Czestochowa (Poland) is specialized in parallel computing and its applications. This year we finished building of our own ACCORD cluster, with 34 processors -- 18 Pentiums III and 16 Athlons connected with very fast Myrinet network (please visit http://eltoro.imi.pcz.czest.pl for more information). We start also some research in application of parallel processing in bioinformatics. This cluster has fast Internet connection. Since we have still "free time" on our machine we can provide accounts for users who are interested in using this cluster for bioinformatics research. At the moment we work mainly with MPI and we have started to adapt the ACCORD machine to work as a bio-cluster. We are very opened for any suggestions about free software you would like to use in your research. If you are interested in our offer please contact Jaroslaw Zola for details of obtaining and using account on the ACCORD cluster. With best regards, Jaroslaw Zola -- ............................................................................... Jaroslaw Zola Institute of Mathematics & Computer Science Technical University of Czestochowa Dabrowskiego 73 42-200 Czestochowa, Poland mail: zola at k2.pcz.czest.pl www: www.k2.pcz.czest.pl/~zola tel: +48(0)503685896 ............................................................................... From wnussbau at speakeasy.net Tue Jan 29 21:24:45 2002 From: wnussbau at speakeasy.net (Bill Nussbaumer) Date: Tue, 29 Jan 2002 21:24:45 -0500 Subject: [BiO BB] Pharmacogenomics Course Message-ID: <4.3.2.7.2.20020129212227.01dedee8@mail.speakeasy.net> Back in November Ravi Mayreddy made reference to a developing course in Pharmacogenomics to be help in Philadelphia. Is there any more available information on this course at this time? - Bill Nussbaumer From ngadewal at yahoo.com Wed Jan 30 04:49:01 2002 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 30 Jan 2002 01:49:01 -0800 (PST) Subject: [BiO BB] doubt in protein modeling step In-Reply-To: <20020128045426.10441.qmail@web11901.mail.yahoo.com> Message-ID: <20020130094901.41704.qmail@web9501.mail.yahoo.com> Hi kiran, Both your doubt can be solved. But it is better to go with first one. You can build consensus sequence by multiple alignment taking into consideration of query sequence also by using Bio-edit program which is freeware. regards, NIKHIL --- Ayyagari Kiran wrote: > Hi all, > In protein modeling,at first we look for protein > sequence similarity and doing Multiple Seq > alignment. > Supposing I take 5 protein sequences hits (after > doing > Blastp),assuming that there are no pdb structures > for > any of them but still i have to model my protein > sequence. > the next step is to go for Multiple sequence > alignment > where in we can find out which are the regions > exactly > conserved and find whether those regions have any > structural similarity also!!! > > But here the input for Multiple Sequence alignment > is > our query sequence + the 5 similar > sequences having highest hits (from BLAST) > > my question is whether we can/should build a > consensus > sequence by multiple alignment taking into > consideration our query sequence also?? > > or build a consensus sequence by Multiple alignment > taking only those 5 sequences (excluding our query > seq) and then align that consensus sequence with our > query sequence both at sequence level and structure > level. > I shall refine my doubt if am not clear in my > subsequent discussions.Thanks in advance > > Ayyagari Kiran > > > __________________________________________________ > Do You Yahoo!? > Great stuff seeking new owners in Yahoo! Auctions! > http://auctions.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== NIKHIL. S. GADEWAL * HOME ADDRESS * # 22, subhshree apts, Bioinformatics center, * near vijan hospital, Cancer Research Institute, * college road, Parel, Mumbai-12. * nashik-422005 cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 Phone no. 4123803 etx. 242 * __________________________________________________ Do You Yahoo!? Great stuff seeking new owners in Yahoo! Auctions! http://auctions.yahoo.com From RMayreddy at NBME.org Wed Jan 30 10:53:18 2002 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Wed, 30 Jan 2002 10:53:18 -0500 Subject: [BiO BB] Pharmacogenomics Course Message-ID: Yes, we are organizing a series of bioinformatics training modules in Philly. So far, we have done Perl and Bioperl module. Database management and data mining module will be done by next week. Our next module on 'Microarray Analysis' will be held in first and second saturdays (March, 2 and 9) of March. Pls send me mail for more info. Thanks for your interest. -Ravi -----Original Message----- From: Bill Nussbaumer [mailto:wnussbau at speakeasy.net] Sent: Tuesday, January 29, 2002 9:25 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Pharmacogenomics Course Back in November Ravi Mayreddy made reference to a developing course in Pharmacogenomics to be help in Philadelphia. Is there any more available information on this course at this time? - Bill Nussbaumer _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From prion at jhu.edu Wed Jan 30 02:06:29 2002 From: prion at jhu.edu (FREDERICK TAN) Date: Wed, 30 Jan 2002 02:06:29 -0500 Subject: [BiO BB] Vector NTI In-Reply-To: <4.3.2.7.2.20020129212227.01dedee8@mail.speakeasy.net> Message-ID: Good evening, . Does anyone have any comments to share about the Vector NTI suite offered by InforMax (http://www.informaxinc.com/solutions/)? In particular, how does it fare in comparison to GCG? . I am wondering if the main selling part of this program is the integration between the various analysis tools (which I realize becomes a great time saver in a certain situations), which it appears to do a good job at. However I am more interested in the performance of the algorithms more than anything. . Thanks! Sincerely, Frederick Tan From philipp.pagel at cmp.yale.edu Wed Jan 30 12:26:14 2002 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Wed, 30 Jan 2002 12:26:14 -0500 Subject: [BiO BB] Vector NTI In-Reply-To: References: <4.3.2.7.2.20020129212227.01dedee8@mail.speakeasy.net> Message-ID: <20020130172613.GA4722@merlin.med.yale.edu> On Wed, Jan 30, 2002 at 02:06:29AM -0500, FREDERICK TAN wrote: > . Does anyone have any comments to share about the Vector NTI suite > offered by InforMax (http://www.informaxinc.com/solutions/)? In > particular, how does it fare in comparison to GCG? > > . I am wondering if the main selling part of this program is the > integration between the various analysis tools (which I realize becomes a > great time saver in a certain situations), which it appears to do a > good job at. However I am more interested in the performance of the > algorithms more than anything. Hi! We are using VectorNTI in our lab. It is a nice piece of software for everyday lab work and due to its graphical user interface people like it much better than GCG. But the two are hard to compare. First of all you can not compare performance directly since VectorNT runs exclusivly on Mac and Windows while GCG (to my knowledge) runs on UNIX and VMS. I do not have much first hand experience with GCG - so take this with a grain of salt ... Both products have an very different philosophy and user interface. If you are more on the bioinformatics side and want to do batch analysis of sequences VectorNTI is not the way to go since it lacks scripting capabilities. GCG or EMBOSS are much better for that. If you are a bench scientist and want to analyse smaller numbers of sequences, design constructs etc. Vector NTI is much more convenient and performance of the algorithms is not a real issue anyway. If you are not decided, I suggest you download the demo version of VectorNTI. You can not import your own sequences or export stuff but its good enough to get an idea. If you think you need more testing just contact them an they will provide you with a free trieal period of something like 10 user hours or so during which you can use all functions without restrictions. Another player in this field would be lasergene (DNA Star) which I have tested also. Its a good piece of software aswell but has less integration than VectorNTI. If you have more questions feel free to contact me. cu Philipp -- Dr. Philipp Pagel Department of Cellular and Molecular Physiology phone: (203) 785-6835 SHM, B117 fax: (203) 785-4951 Yale University 333 Cedar ST New Haven, CT 06520 USA From westerman at purdue.edu Wed Jan 30 12:56:31 2002 From: westerman at purdue.edu (Rick Westerman) Date: Wed, 30 Jan 2002 12:56:31 -0500 Subject: [BiO BB] Re: VectorNTI [BiO_Bulletin_Board digest, Vol 1 #186] In-Reply-To: <200201301703.g0UH36T16482@www.bioinformatics.org> Message-ID: <5.1.0.14.2.20020130123027.00ae86d0@postoffice.purdue.edu> >. Does anyone have any comments to share about the Vector NTI suite >offered by InforMax (http://www.informaxinc.com/solutions/)? In >particular, how does it fare in comparison to GCG? > >. I am wondering if the main selling part of this program is the >integration between the various analysis tools (which I realize becomes a >great time saver in a certain situations), which it appears to do a >good job at. However I am more interested in the performance of the >algorithms more than anything. The algorithms are, of course, hidden from us but they seem to be standard ones. There are only so many ways that a program can do enzyme cutting, multiple sequence alignment, etc. and generally these methods are published and, if coded properly, robust. VNTI will also send your sequence to web sites if the site contains a unique algorithm. As for performance, I suspect my GHz PC running VNTI outperforms my Sun server at 400 MHz for most applications. Of course I do not have the Genbank database on PC and so can't do local Blast searches. VNTI simply sends your sequence to NCBI in order to do a Blast search. And that brings up the major limitation of VNTI: it generally works with one sequence at a time. If a person wants to work with 100s of sequences then GCG (or other command-line oriented package) is the way to go. Please note that VNTI's support for the Mac is rather old. The current PC version is 7; the Macs are stuck at version 5.3 until (if and when) Informax decides to develop for OS-10. VNTI is also expensive. As an academic site we can purchase a site-wide GCG license for less than the price of two VNTI single-lab licenses. There is a test copy of VNTI available so that you can try it out yourself. In summary we use both packages. Some people really love VNTI -- it looks nice and helps visualize single sequencing processing -- while other people avoid it and get along with GCG and other server-based tools. -- Rick Rick Westerman westerman at purdue.edu Phone: (765) 494-0505 FAX: (765) 496-7255 S049 WSLR bldg. Purdue Univ. W. Lafayette, IN 47907-1153 Bioinformatics specialist at the Genomics Initiative. Part time system manager of Biochemistry department. href="http://www.biochem.purdue.edu/~westerm" From ngadewal at yahoo.com Thu Jan 31 05:07:59 2002 From: ngadewal at yahoo.com (nikhil gadewal) Date: Thu, 31 Jan 2002 02:07:59 -0800 (PST) Subject: [BiO BB] microarray Message-ID: <20020131100759.23019.qmail@web9501.mail.yahoo.com> Hello all members, Is their any freeware software to design primers for microarray. Thanks in advance. with regards, NIKHIL ===== NIKHIL. S. GADEWAL * HOME ADDRESS * # 22, subhshree apts, Bioinformatics center, * near vijan hospital, Cancer Research Institute, * college road, Parel, Mumbai-12. * nashik-422005 cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 Phone no. 4123803 etx. 242 * __________________________________________________ Do You Yahoo!? Great stuff seeking new owners in Yahoo! Auctions! http://auctions.yahoo.com From roumieu at genops.com Thu Jan 31 12:23:48 2002 From: roumieu at genops.com (jordan) Date: Thu, 31 Jan 2002 09:23:48 -0800 Subject: [BiO BB] Re: VectorNTI [BiO_Bulletin_Board digest, Vol 1 #186] Message-ID: <003601c1aa7c$10e82340$7efab440@bc.hsia.telus.net> If you are wanting both high throughput capability and a nice GUI, you should try downloading Ngene. The beta-version is on the site: http://www.genops.com/download/default.htm Ngene distributes jobs over a Linux cluster, and permits you to do local BLAST searching vs Swiss Prot, public databases, etc. The the much more responsive commercial version should be available in 2 - 3 weeks in PC/Windows then Mac not far behind. Ngene is also very affordable starting at ~$3000 for an academic license (1-5 accounts). From delmar_brat at hotmail.com Thu Jan 31 15:24:51 2002 From: delmar_brat at hotmail.com (Brat) Date: Thu, 31 Jan 2002 12:24:51 -0800 Subject: [BiO BB] Iobion Message-ID: Hi, Does anyone know anything about Iobion? -------------- next part -------------- An HTML attachment was scrubbed... URL: From Greg at tekadence.net Thu Jan 31 16:16:03 2002 From: Greg at tekadence.net (Greg Deocampo) Date: Thu, 31 Jan 2002 13:16:03 -0800 Subject: [BiO BB] Iobion References: Message-ID: <00a201c1aa9c$82163c80$cba0b2d1@tekadence> do you mean the company? http://www.iobion.com/ G ----- Original Message ----- From: Brat To: bio_bulletin_board at bioinformatics.org Sent: Thursday, January 31, 2002 12:24 PM Subject: [BiO BB] Iobion Hi, Does anyone know anything about Iobion? -------------- next part -------------- An HTML attachment was scrubbed... URL: From benjaminelsy at hotmail.com Thu Jan 31 06:26:27 2002 From: benjaminelsy at hotmail.com (Elsy Benjamin) Date: Thu, 31 Jan 2002 16:56:27 +0530 Subject: [BiO BB] What is Pharmacogenomics ? Message-ID: Hello Board Members, Could someone please explain the term pharmacogenomics and share their knowledge about the field? How can the modern information technology serve the pharmacogenomics? I would appreciate your views. Thank you. Regards Elsy -------------- next part -------------- An HTML attachment was scrubbed... URL: