From jeff at bioinformatics.org Mon Oct 1 12:31:26 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 01 Oct 2001 12:31:26 -0400 Subject: [BiO BB] connectivity problems References: <200109302014.QAA02788@www.bioinformatics.org> Message-ID: <3BB89A5E.6F277C5A@bioinformatics.org> Okay, the problem has been resolved. It is now safe to resume activities. Cheers. Jeff "J.W. Bizzaro" wrote: > > Greetings. > > This message is for people using our primary server. > > We noticed some access problems over the weekend, particularly disconnections > and access denials. Some administrators worked from late Saturday night until > Sunday afternoon trying to hunt down the problem, which seemed to evade us. > The problem did not appear to be internal, as no programs were being > executed during outage times, and there were no signs of a break-in. > > It turns out that someone else on the local network decided to "borrow" > our static IP address, and this is causing some "confusion" on the network. > > We're going to work with the IT department on Monday to find the offenders, > and when we do, we will kill and eat them with ketchup and a side order of > fries. > > Anyway, we apologize for the inconvenience. > > -- The Lab Rats From omi_80 at rediffmail.com Fri Oct 5 05:39:48 2001 From: omi_80 at rediffmail.com (Omica Jain) Date: 5 Oct 2001 09:39:48 -0000 Subject: [BiO BB] Re: Re: [BiO BB] How to write Algorithm Message-ID: <20011005093948.30975.qmail@mailweb33.rediffmail.com> Hi there, Thanks to everybody who responded regarding my query about writing algorithms. I got a number of responses suggesting a variety of books can somebody suggest me some online resource to get start???? Omi On Wed, 26 Sep 2001 Philipp Pagel wrote : > Hi! > > > > There is a very nice O'reilly book: Developing > Bioinformatics Computer Skills > > I bought it and don't like it at all. I think it's just > a compilation of tools > found on the Web. None of the concepts is really > introduced, no algorithms etc. > I don't think you can really learn anything from this > book. > > > My recommendations: > > 1) David Mount > Bioinformatics: Sequence and Genome Analysis > Cold Spring Harbour Lab. Press > > Very nice if you are coming from the biology side. > Very understandable but > not to shallow. This book really teaches you about > some of the ideas that > are used for e.g. sequence alignment etc. > > > 2) Dan Gusfield > Algorithms on Strings, Trees, and Sequences: Computer > Science and > Computational Biology > > Great for Computer scientists or as a more in depth > reading after 1) > > > > 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 > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > From pkerrwall at yahoo.com Fri Oct 5 09:36:31 2001 From: pkerrwall at yahoo.com (pkerrwall at yahoo.com) Date: Fri, 5 Oct 2001 06:36:31 -0700 (PDT) Subject: [BiO BB] Career Advice Message-ID: <20011005133631.24544.qmail@web13508.mail.yahoo.com> Hello all, I've been a member of this list for nearly 6 months and would like to thank everyone for letting me pick at your brains during this time. I need help with a career question. I graduated from college with undergraduate degrees in Chemical Engineering and Zoology. After graduation, I got a job as a software developer and have been working with the same company for the last year and a half doing java server-side development, DB Administration, and GUI Development. My company is about to go under and I've been looking for a job in bioinformatics with no luck. I usuall get the same responses - need graduate degree, need more IT experience, need Biotech experience, or local candidates only (I would live in Louisiana). I currently have 2 career opportunities: 1) I can get a job with an IT company doing EJB Development or 2) I can get a job with an Energy company doing controls (there will be software/web development associated with the work). I'm interested in the EJB development b/c i've never developed in a 3-tier architecture and I'm interested in the controls job b/c I miss the math, statistics, and flow charts. If I take one of these jobs, I definetely want my next job to be in a bioinformatics discipline. Any suggestions on which would be better for my carrer are appreciated. Thanks, Kerr Wall __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From philipp.pagel at cmp.yale.edu Fri Oct 5 09:42:53 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Fri, 5 Oct 2001 09:42:53 -0400 Subject: [BiO BB] Online resources In-Reply-To: <20011005093948.30975.qmail@mailweb33.rediffmail.com> References: <20011005093948.30975.qmail@mailweb33.rediffmail.com> Message-ID: <20011005094253.A826@merlin> On Fri, Oct 05, 2001 at 09:39:48AM -0000, Omica Jain wrote: > > Hi there, > > Thanks to everybody who responded regarding my query about writing > algorithms. I got a number of responses suggesting a variety of books > can somebody suggest me some online resource to get start???? Algorithms in Molecular Biology at the Tel Aviv University School of Computer Science: http://www.math.tau.ac.il/~rshamir/algmb/algmb00.html BioComputing Hypertext Coursebook at the University of Bielefeld: http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html Some links at the same institute: http://www.techfak.uni-bielefeld.de/bcd/ Computational Biology (Computer Science, Washington): http://www.cs.washington.edu/education/courses/527/00wi/ 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 bioinfo_india at yahoo.com Fri Oct 5 12:02:09 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Fri, 5 Oct 2001 09:02:09 -0700 (PDT) Subject: [BiO BB] Single-domain proteins Message-ID: <20011005160209.28162.qmail@web14510.mail.yahoo.com> hi group, what are the advantages of single-domain proteins ? thanks SP ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From Joel.Dudley at DevelopOnline.com Fri Oct 5 12:29:21 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Fri, 5 Oct 2001 09:29:21 -0700 Subject: [BiO BB] Career Advice Message-ID: I am in almost the exact same predicament as yourself. I have a degree in microbiology but was hired as a Unix programmer out of school. Since I work for a .com the future is always uncertain and hiring guidelines for the good Bioinformatics jobs are strict. As a result I am taking on some consulting jobs so I can work locally and go back for my masters in Computational Biosciences at Arizona State. This will on ly take me 2 years and put me in the postion I want to be in. IT/Programming jobs will always be available and will always provide a good wage. However, if you truly have a passion for bioinformatics I suggest you take the time to go back for a masters or PhD in computational biology because the payoff is a lifetime doing something that you really want to do. Just my 2 cents. - Joel -----Original Message----- From: pkerrwall at yahoo.com [mailto:pkerrwall at yahoo.com] Sent: Friday, October 05, 2001 6:37 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Career Advice Hello all, I've been a member of this list for nearly 6 months and would like to thank everyone for letting me pick at your brains during this time. I need help with a career question. I graduated from college with undergraduate degrees in Chemical Engineering and Zoology. After graduation, I got a job as a software developer and have been working with the same company for the last year and a half doing java server-side development, DB Administration, and GUI Development. My company is about to go under and I've been looking for a job in bioinformatics with no luck. I usuall get the same responses - need graduate degree, need more IT experience, need Biotech experience, or local candidates only (I would live in Louisiana). I currently have 2 career opportunities: 1) I can get a job with an IT company doing EJB Development or 2) I can get a job with an Energy company doing controls (there will be software/web development associated with the work). I'm interested in the EJB development b/c i've never developed in a 3-tier architecture and I'm interested in the controls job b/c I miss the math, statistics, and flow charts. If I take one of these jobs, I definetely want my next job to be in a bioinformatics discipline. Any suggestions on which would be better for my carrer are appreciated. Thanks, Kerr Wall __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jfreeman at variagenics.com Fri Oct 5 13:08:04 2001 From: jfreeman at variagenics.com (jfreeman) Date: Fri, 05 Oct 2001 13:08:04 -0400 Subject: [BiO BB] Single-domain proteins References: <20011005160209.28162.qmail@web14510.mail.yahoo.com> Message-ID: <3BBDE8F4.7DF49DE1@variagenics.com> Hi Dr. Suraj, et al. On the bioinformatics end of things: If a protein has two or more domains, but it is only annotated with a single domains function, and a simple homology from that proteins domain to another protein will give transitive false annotation assignments. For example: 1. A-- 2. A--B 3. B--C 4. C-- Given that: 1, 2, 3, and 4 are different proteins. and domains A, B, C, and D have different functions, but you only know A and C's functions, what you annotate protein 2 and 3 depends on what you start with 1 or 4. If you use simple homology to assign a function to 2 from 1, and then use this functional assignment on 2 to annotate by simple homology protein 3, the annotation for 3 will be function A and be completely false. Finding single domain proteins, or important motifs, therefore becomes a very important annotation tool. For more information see: http://bmerc-www.bu.edu/bmerc_info/temple.html http://bmerc-www.bu.edu/bioinformatics/profile_list.shtml http://www.expasy.ch/prosite/ http://pfam.wustl.edu/ http://www.geneontology.org/ Happy Hunting, Jim Freeman Peri Suraj wrote: > > hi group, > what are the advantages of single-domain proteins ? > > thanks > SP > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. > http://geocities.yahoo.com/ps/info1 > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From clarisca at cwpanama.net Sat Oct 6 11:08:31 2001 From: clarisca at cwpanama.net (Claris Castillo T.) Date: Sat, 6 Oct 2001 10:08:31 -0500 Subject: [BiO BB] Hoe many days consume a commong problem in genetic and protemic field. Message-ID: <000e01c14e78$c37ee580$481861ce@cwpanama.net> I am working ona research paper about bioinformatics and I need to collect information about the time consumed by typical genetic calculations. COuld some one give me a hint? Thanks, Claris -------------- next part -------------- An HTML attachment was scrubbed... URL: From balarji at rediffmail.com Sat Oct 6 15:05:46 2001 From: balarji at rediffmail.com (balaji r) Date: 6 Oct 2001 19:05:46 -0000 Subject: [BiO BB] dual protein Message-ID: <20011006190546.4252.qmail@mailweb34.rediffmail.com> hi, can any one tell me a list of proteins that show dual nature in their secondary structure..i think prion is one of them..can any one know from where can i download these kind of sequences.. balaji From thriotus at yahoo.com Mon Oct 8 17:36:44 2001 From: thriotus at yahoo.com (nabula easter) Date: Mon, 8 Oct 2001 14:36:44 -0700 (PDT) Subject: [BiO BB] BLAST vs SW searches Message-ID: <20011008213644.56459.qmail@web21003.mail.yahoo.com> hi group, what is the difference between BLAST searches and Smith and waterman searches ? i understood in a way that BLAST is used for limited set of sequences and Smith and waterman searches are used for bulk searches ? is this so ? please help me ! thank you regards thrio __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From thriotus at yahoo.com Tue Oct 9 03:04:27 2001 From: thriotus at yahoo.com (nabula easter) Date: Tue, 9 Oct 2001 00:04:27 -0700 (PDT) Subject: [BiO BB] Domain recognition In-Reply-To: <20011008213644.56459.qmail@web21003.mail.yahoo.com> Message-ID: <20011009070427.7413.qmail@web21006.mail.yahoo.com> hi, how easy is to find a domain in protein. is there any protocol in identifying protein. i have a protein which is related to dolichyl - transferase,which do not have any domain , now when i do PSI-BLAST i find some other proteins which has some identical and similar areas ? does this mean that there is a domain in these proteins. would you please help me pointing any protocol to finalise any putative domain. IF i am looking at a novel domain how to validate that domain ? please suggest any publications where the rules are mentioned thank you Easter __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From ngadewal at yahoo.com Tue Oct 9 05:04:17 2001 From: ngadewal at yahoo.com (nikhil gadewal) Date: Tue, 9 Oct 2001 02:04:17 -0700 (PDT) Subject: [BiO BB] BLAST vs SW searches In-Reply-To: <20011008213644.56459.qmail@web21003.mail.yahoo.com> Message-ID: <20011009090417.68105.qmail@web9506.mail.yahoo.com> hi thrio, I think you are little bit confused. The smith waterman algorithm is a dynamic programming algorithm used for homology search without loss of specificity. In contrast BLAST is a heuristic progrmming algorithm for homology search to increase the speed of search with a minimal sacrifice of specificity. Hence BLAST is used for large database search. SOme algorithm modified SW algorith to increase the speed of search. Therefore I don't think set of sequences are important. Hope you understood NIKHIL __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From bioinfo_india at yahoo.com Tue Oct 9 06:06:07 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Tue, 9 Oct 2001 03:06:07 -0700 (PDT) Subject: [BiO BB] interaction domain In-Reply-To: <20011009070427.7413.qmail@web21006.mail.yahoo.com> Message-ID: <20011009100607.47803.qmail@web14501.mail.yahoo.com> hi , is there any difference between coiled-coil regions of proteins localized to nucleus and cytoplasm ? if so, would you please discuss that ! thank you SP ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From tsucheta at hotmail.com Tue Oct 9 11:06:13 2001 From: tsucheta at hotmail.com (Sucheta Tripathi) Date: Tue, 09 Oct 2001 11:06:13 Subject: [BiO BB] (no subject) Message-ID: An HTML attachment was scrubbed... URL: From jacobs at genehack.org Tue Oct 9 07:32:03 2001 From: jacobs at genehack.org (John S. J. Anderson) Date: 09 Oct 2001 07:32:03 -0400 Subject: [BiO BB] (no subject) In-Reply-To: References: Message-ID: <87het9kq18.fsf@mendel.genehack.org> "Sucheta Tripathi" writes: > I was writing a small program of DNA-> protein translation in C, but > when substituting 3 letter codons by an amino acid I can't think of > any other option than for if ..elseif statements, which makes me > wild. Can anyone suggest me any other way to go about it. Switch statement? john. -- Before we polish that "diamond", we should probably ask ourselves if it's brown and stinks. -- Larry Wall in <199911061942.LAA29314 at kiev.wall.org> From shafi at sfc.keio.ac.jp Tue Oct 9 10:05:59 2001 From: shafi at sfc.keio.ac.jp (Kouichi Takahashi) Date: Tue, 09 Oct 2001 23:05:59 +0900 Subject: [BiO BB] (no subject) In-Reply-To: <87het9kq18.fsf@mendel.genehack.org> References: <87het9kq18.fsf@mendel.genehack.org> Message-ID: <200110091406.XAA24338@mail.sfc.keio.ac.jp> > "Sucheta Tripathi" writes: > > > I was writing a small program of DNA-> protein translation in C, but > > when substituting 3 letter codons by an amino acid I can't think of > > any other option than for if ..elseif statements, which makes me > > wild. Can anyone suggest me any other way to go about it. > > Switch statement? Table lookup. const int CodonTable[4][4][4] = { { /* AA? */ {Lys,Asn,Lys,Asn}, /* AC? */ {Thr,Thr,Thr,Thr}, /* AG? */ {Arg,Ser,Arg,Ser}, /* AT? */ {Ile,Ile,Met,Ile} }, { /* CA? */ {Gln,His,Gln,His}, /* CC? */ {Pro,Pro,Pro,Pro}, /* CG? */ {Arg,Arg,Arg,Arg}, /* CT? */ {Leu,Leu,Leu,Leu} }, { /* GA? */ {Glu,Asp,Glu,Asp}, /* GC? */ {Ala,Ala,Ala,Ala}, /* GG? */ {Gly,Gly,Gly,Gly}, /* GT? */ {Val,Val,gVal,Val} }, { /* TA? */ {Term,Tyr,Term,Tyr}, /* TC? */ {Ser,Ser,Ser,Ser}, /* TG? */ {Term,Cys,Trp,Cys}, /* TT? */ {Leu,Phe,Leu,Phe} }, }; ----- Kouichi Takahashi E-CELL Project, email: shafi at sfc.keio.ac.jp Institute for Advanced Biosciences shafi at e-cell.org Keio Univ. SFC From balarji at rediffmail.com Tue Oct 9 11:36:59 2001 From: balarji at rediffmail.com (balaji r) Date: 9 Oct 2001 15:36:59 -0000 Subject: [BiO BB] Re: Re: [BiO BB] Domain recognition Message-ID: <20011009153659.21437.qmail@mailweb16.rediffmail.com> you can use..prosite,emotif,....programs like this that exclusively are used to search the domains in a particular protein seqences.. On Tue, 09 Oct 2001 nabula easter wrote : > hi, > how easy is to find a domain in protein. > is there any protocol in identifying protein. i have a > protein which is related to dolichyl - > transferase,which do not have any domain , now when i > do PSI-BLAST i find some other proteins which has some > identical and similar areas ? does this mean that > there is a domain in these proteins. > would you please help me pointing any protocol to > finalise any putative domain. IF i am looking at a > novel domain how to validate that domain ? > please suggest any publications where the rules are > mentioned > thank you > Easter > > __________________________________________________ > Do You Yahoo!? > NEW from Yahoo! GeoCities - quick and easy web site > hosting, just $8.95/month. > http://geocities.yahoo.com/ps/info1 > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > From charles at moulinette.dyndns.org Tue Oct 9 13:03:41 2001 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Tue, 9 Oct 2001 19:03:41 +0200 (CEST) Subject: [BiO BB] (no subject) In-Reply-To: Message-ID: > I was writing a small program of DNA-> protein translation in C, but when > substituting 3 letter codons by an amino acid I can't think of any other > option than for if ..elseif statements, which makes me wild. Can anyone > suggest me any other way to go about it. In perl I used a hash. I don't know anything of C but this structure may exist... Charles From clin at scimagix.com Tue Oct 9 19:05:59 2001 From: clin at scimagix.com (Chin Chin Lin) Date: Tue, 9 Oct 2001 16:05:59 -0700 Subject: [BiO BB] need some senior people Message-ID: <01a901c15116$f5f48e20$579afa18@C296924B> Hi there! I know that this is probably not the best place to be recruiting people, but if any of you are interested in making a move, check out our website. I am attaching our latest press release. Take a look and browse the site for our most up to date openings in the dynamic field of IMAGE INFORMATICS! We are growing when others are closing! Please reply to me directly if you are interested. Scimagix Secures $25 Million Funding Company Strengthens Leadership in Image Informatics REDWOOD SHORES, Calif. - July 18, 2001 - ScimagixT Inc., the leading provider of image informatics solutions for pharmaceutical research and discovery, today announced that it has secured $25 million in its third round of funding. Led by Dresdner Kleinwort Capital and EuclidSR Partners, this oversubscribed private placement was also backed by previous investor Tullis-Dickerson & Co. Inc., and new investors INVESCO, Future Capital and IngleWood Ventures. Both Daniel Green, director, Dresdner Kleinwort Capital, and Barbara Dalton, Ph.D., partner at EuclidSR Partners, will take seats on Scimagix's board of directors. According to Robert Dunkle, president and CEO of Scimagix, this round of funding will enable the company to expand capabilities and applications for its SIMST (Scientific Image Management System) platform and strengthen its market position as the preferred provider of image informatics solutions. "Our technology offers a breakthrough for pharmaceutical and biotechnology research in the analytical use of images at every stage of the drug discovery R&D process," said Dunkle. "We are the only company capable of quantifying the content of digital images and providing research scientists with automated access to legacy and new images - an enormous productivity boon in the decision-making process where images are currently an underutilized corporate asset." Advances in functional genomics, proteomics, tissue microarrays and high-throughput screening have resulted in an explosion of data in pharmaceutical and life science research. Estimates are that as much as 70 percent of experimental data is image-based, rather than numbers or text, presenting research enterprises with the challenge of managing these valuable assets effectively. An innovator in the category of image informatics, Scimagix is the first to provide research scientists with a domain-specific, data management system for storage, annotation, retrieval and mining of images from all types of experiments. Building on SIMS, its infrastructure platform, Scimagix is developing a suite of specialized applications for in-depth analysis and mining of various types of images according to visual criteria. ProteinMineT, the first commercially available application in this suite, is designed to analyze and search protein patterns in 2-dimensional (2D) electrophoresis gels according to visual criteria and was jointly developed with Pfizer Global R&D (formerly Parke-Davis). "The overwhelmingly positive response we received during this round of financing validates our company mission and the market potential for our products," Dunkle continued. "From the beginning, our customers have been enthusiastic, and now we have generated the same excitement in the investor community. We intend to sustain our leadership position by introducing new image-mining applications with specific capabilities to a wider range of drug discovery research and development and by developing further processes that fully optimize our open architecture." "The SIMS platform and ProteinMine have transformed our proteomics studies, bringing speed and efficiency to the process of recognizing and evaluating potential new drugs," said James Bristol, Ph.D., head of discovery at Pfizer. "Scimagix gives us the unprecedented ability to search and analyze an archive of thousands of images to evaluate elements such as biological mechanisms, toxicity profiles and drug metabolism." "Life sciences is an image-based, information-driven industry," said Barbara Dalton, Ph.D., partner at EuclidSR Partners. "Scimagix is the only company that brings image analysis and mining applications into a single data management system that can store, search and mine life science data." Added Daniel Green, director, Dresdner Kleinwort Capital, "The Scimagix team has demonstrated that it understands what the pharmaceuticals industry wants and that it can deliver. Scimagix's infrastructure and tools vastly improve the efficiency of researching new life-saving medicines. Clearly, this oversubscribed round of funding demonstrates that the global investment community has recognized the rapidly growing demand for such a solution." Scimagix will continue to work closely with its customers to develop specialized applications that allow easy access to a multitude of images at all stages of pharmaceutical research and development. About Scimagix Inc. ScimagixT Inc., based in Redwood Shores, Calif., is the leading provider of image informatics solutions for pharmaceutical research and development. Its flagship SIMST (Scientific Image Management System) platform is the first data management system designed to optimize the use of images generated during drug discovery research and development. The Oracle?/Web-based software system enables enterprise-wide image management, providing researchers with a comprehensive and searchable corporate database of image data. Researchers can easily retrieve image sets from diverse experiments based on specific search parameters to identify correlations between images and functional data and derive added value from images. Scimagix serves six of the top 15 pharmaceutical companies including Pfizer Global R&D and Eli Lilly & Co. For additional information, please visit Scimagix's corporate Web site at www.scimagix.com Thanks, Chin Chin Lin Scimagix, Inc. 650-508-2115 www.scimagix.com From Joel.Dudley at DevelopOnline.com Tue Oct 9 19:43:06 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Tue, 9 Oct 2001 16:43:06 -0700 Subject: [BiO BB] need some senior people Message-ID: Looks great, but it seems like (according to the job listings on the site) you are looking for pure computer scientists in the feild of computer imaging and graphics. What about the computational biology aspect of the job, are there any positons that are a mix of advanced computing and biology? Thank you. - Joel Dudley -----Original Message----- From: Chin Chin Lin [mailto:clin at scimagix.com] Sent: Tuesday, October 09, 2001 4:06 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] need some senior people Importance: High Hi there! I know that this is probably not the best place to be recruiting people, but if any of you are interested in making a move, check out our website. I am attaching our latest press release. Take a look and browse the site for our most up to date openings in the dynamic field of IMAGE INFORMATICS! We are growing when others are closing! Please reply to me directly if you are interested. Scimagix Secures $25 Million Funding Company Strengthens Leadership in Image Informatics REDWOOD SHORES, Calif. - July 18, 2001 - ScimagixT Inc., the leading provider of image informatics solutions for pharmaceutical research and discovery, today announced that it has secured $25 million in its third round of funding. Led by Dresdner Kleinwort Capital and EuclidSR Partners, this oversubscribed private placement was also backed by previous investor Tullis-Dickerson & Co. Inc., and new investors INVESCO, Future Capital and IngleWood Ventures. Both Daniel Green, director, Dresdner Kleinwort Capital, and Barbara Dalton, Ph.D., partner at EuclidSR Partners, will take seats on Scimagix's board of directors. According to Robert Dunkle, president and CEO of Scimagix, this round of funding will enable the company to expand capabilities and applications for its SIMST (Scientific Image Management System) platform and strengthen its market position as the preferred provider of image informatics solutions. "Our technology offers a breakthrough for pharmaceutical and biotechnology research in the analytical use of images at every stage of the drug discovery R&D process," said Dunkle. "We are the only company capable of quantifying the content of digital images and providing research scientists with automated access to legacy and new images - an enormous productivity boon in the decision-making process where images are currently an underutilized corporate asset." Advances in functional genomics, proteomics, tissue microarrays and high-throughput screening have resulted in an explosion of data in pharmaceutical and life science research. Estimates are that as much as 70 percent of experimental data is image-based, rather than numbers or text, presenting research enterprises with the challenge of managing these valuable assets effectively. An innovator in the category of image informatics, Scimagix is the first to provide research scientists with a domain-specific, data management system for storage, annotation, retrieval and mining of images from all types of experiments. Building on SIMS, its infrastructure platform, Scimagix is developing a suite of specialized applications for in-depth analysis and mining of various types of images according to visual criteria. ProteinMineT, the first commercially available application in this suite, is designed to analyze and search protein patterns in 2-dimensional (2D) electrophoresis gels according to visual criteria and was jointly developed with Pfizer Global R&D (formerly Parke-Davis). "The overwhelmingly positive response we received during this round of financing validates our company mission and the market potential for our products," Dunkle continued. "From the beginning, our customers have been enthusiastic, and now we have generated the same excitement in the investor community. We intend to sustain our leadership position by introducing new image-mining applications with specific capabilities to a wider range of drug discovery research and development and by developing further processes that fully optimize our open architecture." "The SIMS platform and ProteinMine have transformed our proteomics studies, bringing speed and efficiency to the process of recognizing and evaluating potential new drugs," said James Bristol, Ph.D., head of discovery at Pfizer. "Scimagix gives us the unprecedented ability to search and analyze an archive of thousands of images to evaluate elements such as biological mechanisms, toxicity profiles and drug metabolism." "Life sciences is an image-based, information-driven industry," said Barbara Dalton, Ph.D., partner at EuclidSR Partners. "Scimagix is the only company that brings image analysis and mining applications into a single data management system that can store, search and mine life science data." Added Daniel Green, director, Dresdner Kleinwort Capital, "The Scimagix team has demonstrated that it understands what the pharmaceuticals industry wants and that it can deliver. Scimagix's infrastructure and tools vastly improve the efficiency of researching new life-saving medicines. Clearly, this oversubscribed round of funding demonstrates that the global investment community has recognized the rapidly growing demand for such a solution." Scimagix will continue to work closely with its customers to develop specialized applications that allow easy access to a multitude of images at all stages of pharmaceutical research and development. About Scimagix Inc. ScimagixT Inc., based in Redwood Shores, Calif., is the leading provider of image informatics solutions for pharmaceutical research and development. Its flagship SIMST (Scientific Image Management System) platform is the first data management system designed to optimize the use of images generated during drug discovery research and development. The Oracle?/Web-based software system enables enterprise-wide image management, providing researchers with a comprehensive and searchable corporate database of image data. Researchers can easily retrieve image sets from diverse experiments based on specific search parameters to identify correlations between images and functional data and derive added value from images. Scimagix serves six of the top 15 pharmaceutical companies including Pfizer Global R&D and Eli Lilly & Co. For additional information, please visit Scimagix's corporate Web site at www.scimagix.com Thanks, Chin Chin Lin Scimagix, Inc. 650-508-2115 www.scimagix.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From bniknar at yahoo.com Wed Oct 10 02:36:52 2001 From: bniknar at yahoo.com (Brian Rankin) Date: Tue, 9 Oct 2001 23:36:52 -0700 Subject: [BiO BB] Career Question Message-ID: <000e01c15155$f31b30c0$0b00a8c0@yahoo.com> Hello, I'm interested in moving into the field of bioinformatics. My background is pure Information Technology; I've been working with and managing large systems (Solaris/Oracle/networking/security) for over 12 years. I've always had a strong interest in science and biology, and it seems logical that bioinformatics may be the place for me. However: I don't have any formal training or degree in a biological field (I have an MBA). Is there any way I can move into bioinformatics, using my current skillset? All advice greatly appreciated. Sincerely, Brian Rankin From yadhukumar at hotmail.com Wed Oct 10 08:08:05 2001 From: yadhukumar at hotmail.com (yadhu kumar) Date: Wed, 10 Oct 2001 17:38:05 +0530 Subject: [BiO BB] Career Question Message-ID: Hello brian , Having said that you are a pure information tech guy and have an experience of more than a decade, its not wise to take up any biological science degree/diploma to strengthen your biology knowledge. I think better way to enter bioinformatics is to look out some sites on the web (use google.com with keyword search - bioinformatics) and you will know what exactly is bioinformatics and the probable ways to fit in. See also faq about bioinformatics in bioinformatics.org. you may use yadhu at mikro.biologie.tu-muenchen.de for personal contacts. best regards yadhu Mr.Yadhukumar Bioinformatics Unit Department of Microbiology Technical Univeristy of Munich Munich , Germany Phone : 0049 89 2892 2370 (O) 0049 89 3603 4718 (R) >From: "Brian Rankin" >Reply-To: bio_bulletin_board at bioinformatics.org >To: >Subject: [BiO BB] Career Question >Date: Tue, 9 Oct 2001 23:36:52 -0700 > >Hello, > >I'm interested in moving into the field of bioinformatics. My background >is >pure Information Technology; I've been working with and managing large >systems (Solaris/Oracle/networking/security) for over 12 years. I've >always >had a strong interest in science and biology, and it seems logical that >bioinformatics may be the place for me. However: I don't have any formal >training or degree in a biological field (I have an MBA). > >Is there any way I can move into bioinformatics, using my current skillset? >All advice greatly appreciated. > >Sincerely, Brian Rankin > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From jfreeman at variagenics.com Wed Oct 10 10:50:26 2001 From: jfreeman at variagenics.com (jfreeman) Date: Wed, 10 Oct 2001 10:50:26 -0400 Subject: [BiO BB] Career Question References: <000e01c15155$f31b30c0$0b00a8c0@yahoo.com> Message-ID: <3BC46032.7E34D85C@variagenics.com> Dear Brian et al., The best approach, if you are willing to take the temporary pay cut, is to work as the IT guy in a prominent lab for a few years. Your skill in IT will be welcome, if you are willing to work at academic rates, but after a few years you will have enough exposure to go out into the pharmaceutical market. Finding the right lab to work for is a difficult part of your due diligence, a suggestion is to go to a bioinformatics conference and see who is presenting and ask them if they need your skill set. A good book to start with: Developing Bioinformatics Computer Skills http://www.half.com/cat/buy/prod.cgi?cpid=1056094268&domain_id=1856&meta_id=1 Good luck, Jim Freeman Senior Scientist Variagenics, Inc. Brian Rankin wrote: > > Hello, > > I'm interested in moving into the field of bioinformatics. My background is > pure Information Technology; I've been working with and managing large > systems (Solaris/Oracle/networking/security) for over 12 years. I've always > had a strong interest in science and biology, and it seems logical that > bioinformatics may be the place for me. However: I don't have any formal > training or degree in a biological field (I have an MBA). > > Is there any way I can move into bioinformatics, using my current skillset? > All advice greatly appreciated. > > Sincerely, Brian Rankin > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Wed Oct 10 17:14:27 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 10 Oct 2001 17:14:27 -0400 Subject: [BiO BB] ANNOUNCE: THE SECOND ANNUAL MEETING OF BIOINFORMATICS.ORG Message-ID: <3BC4BA33.D94A4BEC@bioinformatics.org> INITIAL ANNOUNCEMENT THE SECOND ANNUAL MEETING OF BIOINFORMATICS.ORG TUSCON, ARIZONA, USA JANUARY 28-31, 2002 Bioinformatics.Org is a non-profit organization that promotes freedom and openness in bioinformatics by providing resources to support software development and information sharing in the bioinformatics community. Currently, Bioinformatics.Org has almost 1,200 registered members and hosts over 45 resources and projects on its web site. Each year, the organization holds a meeting, often as an adjunct event to a larger bioinformatics conference. In the past, this meeting has occurred as part of the ISMB meeting, and we are proud to announce that in 2002 it will occur during one day of the O'Reilly Bioinformatics Technology Conference in Tucson, Arizona. The meeting's program will include the following: * An introduction to the origins and goals of Bioinformatics.Org, and the resources the organization provides to members * Moderated panel discussions addressing topics of wide relevance to the bioinformatics community, such as the following: * Intellectual property rights in the context of biological information and scientific processes * The relationship of Free and Open Source software to intellectual property in the biotech arena * The movement to obtain unfettered electronic access to the scientific literature * The commercialization of academic research * An overview of the web-based project management software tools provided by Bioinfomatics.Org * Several oral and poster presentations on the research of Bioinformatics.Org members * Presentation of the first annual "Benjamin Franklin Award" for work promoting freedom and openness in bioinformatics * "Birds of a feather" (BoF) meetings and other social events will occur in the evening of the same day The annual Trustees meeting will also occur during the O'Reilly Bioinformatics Technology Conference. A press conference will also be held to announce members of the Advisory Committee, Board of Trustees, and the Systems Administrators, plus plans for the upcoming 2002 year. If you are unable to join us during the one-day meeting, Bioinformatics.org will have a presence in the exhibit hall during the whole O'Reilly Conference. Please stop by and meet some of the Bioinformatics.org staff, and become a member! ---------------------------------- If you are involved in a project hosted at Bioinformatics.Org and would like to present at the annual meeting, please contact us at bof at bioinformatics.org (No deadlines have been set yet.) From ahmed.rebai at cbs.rnrt.tn Fri Oct 12 02:57:49 2001 From: ahmed.rebai at cbs.rnrt.tn (Ahmed Rebai) Date: Fri, 12 Oct 2001 08:57:49 +0200 Subject: [BiO BB] (no subject) In-Reply-To: <3BC4BA33.D94A4BEC@bioinformatics.org> Message-ID: Hi all, I am currently writing a general paper (for a widely read national tunisian scientific newpaper) on bioinformatics and need some examples to illustrate practical sucesses for example in drug design. Does anyone know about a drug (already commercialized) which has benefit in its design from the tools of bioinformatics ? Other examples from practical achievments of bioinformatics in human health are welcome. Thanks Dr Ahmed Rebai Associate Professor Unit of Statistical genomics and bioinformatics Centre de Biotechnologie de Sfax B.P. 'K', 3038 Sfax, Tunisia Tel: +216.4.274.110, Fax: +216.4.275.970 Email: Ahmed.Rebai at cbs.rnrt.tn -----Message d'origine----- De : jeff at oln-127.olney.uml.edu [mailto:jeff at oln-127.olney.uml.edu]De la part de J.W. Bizzaro Envoye : mercredi 10 octobre 2001 23:14 A : bbb at bioinformatics.org Objet : [BiO BB] ANNOUNCE: THE SECOND ANNUAL MEETING OF BIOINFORMATICS.ORG INITIAL ANNOUNCEMENT THE SECOND ANNUAL MEETING OF BIOINFORMATICS.ORG TUSCON, ARIZONA, USA JANUARY 28-31, 2002 Bioinformatics.Org is a non-profit organization that promotes freedom and openness in bioinformatics by providing resources to support software development and information sharing in the bioinformatics community. Currently, Bioinformatics.Org has almost 1,200 registered members and hosts over 45 resources and projects on its web site. Each year, the organization holds a meeting, often as an adjunct event to a larger bioinformatics conference. In the past, this meeting has occurred as part of the ISMB meeting, and we are proud to announce that in 2002 it will occur during one day of the O'Reilly Bioinformatics Technology Conference in Tucson, Arizona. The meeting's program will include the following: * An introduction to the origins and goals of Bioinformatics.Org, and the resources the organization provides to members * Moderated panel discussions addressing topics of wide relevance to the bioinformatics community, such as the following: * Intellectual property rights in the context of biological information and scientific processes * The relationship of Free and Open Source software to intellectual property in the biotech arena * The movement to obtain unfettered electronic access to the scientific literature * The commercialization of academic research * An overview of the web-based project management software tools provided by Bioinfomatics.Org * Several oral and poster presentations on the research of Bioinformatics.Org members * Presentation of the first annual "Benjamin Franklin Award" for work promoting freedom and openness in bioinformatics * "Birds of a feather" (BoF) meetings and other social events will occur in the evening of the same day The annual Trustees meeting will also occur during the O'Reilly Bioinformatics Technology Conference. A press conference will also be held to announce members of the Advisory Committee, Board of Trustees, and the Systems Administrators, plus plans for the upcoming 2002 year. If you are unable to join us during the one-day meeting, Bioinformatics.org will have a presence in the exhibit hall during the whole O'Reilly Conference. Please stop by and meet some of the Bioinformatics.org staff, and become a member! ---------------------------------- If you are involved in a project hosted at Bioinformatics.Org and would like to present at the annual meeting, please contact us at bof at bioinformatics.org (No deadlines have been set yet.) _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From idoerg at cc.huji.ac.il Fri Oct 12 07:15:47 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Fri, 12 Oct 2001 13:15:47 +0200 (GMT+0200) Subject: [BiO BB] (no subject) In-Reply-To: Message-ID: On Fri, 12 Oct 2001, Ahmed Rebai wrote: : Hi all, : I am currently writing a general paper (for a widely read national tunisian : scientific : newpaper) onbioinformatics and need some examples to illustrate practical : sucesses for example in drug design. Does anyone know about a drug (already : commercialized) which has benefit in its design from the tools of : bioinformatics ? Two cases I know of are are nelfinavir (trade name Viracept) from Agouron and amprenavir (Agenerase) from Vertex. Both HIV protease inhibitors. Iddo -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From saneie at hpi.uni-hamburg.de Fri Oct 12 14:08:39 2001 From: saneie at hpi.uni-hamburg.de (Sanei Moghadam, Ehsan) Date: Fri, 12 Oct 2001 18:09:39 +1 Subject: [BiO BB] Re:Subscribtion Request Message-ID: From balarji at rediffmail.com Sat Oct 13 15:19:30 2001 From: balarji at rediffmail.com (balaji r) Date: 13 Oct 2001 19:19:30 -0000 Subject: [BiO BB] drug Message-ID: <20011013191930.1849.qmail@mailFA3.rediffmail.com> i think there is one more drug by name vitravene not sure if u can chek it out... balaji From saneie at hpi.uni-hamburg.de Sun Oct 14 06:57:11 2001 From: saneie at hpi.uni-hamburg.de (Sanei Moghadam, Ehsan) Date: Sun, 14 Oct 2001 10:58:11 +1 Subject: [BiO BB] Re:Subscribtion Request Message-ID: From vidya_dhote at yahoo.com Sun Oct 14 23:35:52 2001 From: vidya_dhote at yahoo.com (Vidya Dhote) Date: Sun, 14 Oct 2001 20:35:52 -0700 (PDT) Subject: [BiO BB] drug from bioinfo tools In-Reply-To: <200110121600.MAA27682@www.bioinformatics.org> Message-ID: <20011015033552.19671.qmail@web11001.mail.yahoo.com> Dear Dr Ahmed Rebai, This may be one of the examples you can use. There might be more... --- (From Scientific American) An early example of the utility of bioinformatics is cathepsin K, an enzyme that might turn out to be an important target for treating osteoporosis, a crippling disease caused by the breakdown of bone. In 1993 researchers at SmithKline Beecham, based in Philadelphia, asked scientists at Human Genome Sciences to help them analyze some genetic material they had isolated from the osteoclast cells of people with bone tumors. (Osteoclasts are cells that break down bone in the normal course of bone replenishment; they are thought to be overactive in individuals with osteoporosis.) Human Genome Sciences scientists sequenced the sample and conducted database homology searches to look for matches would give them a clue to the proteins that the sample's gene sequences encoded. Once they found near-matches for the sequences, they carried out further analyses and discovered that one sequence in particular was overexpressed by the osteoclast cells and that it matched those of a previously identified class of molecules: cathepsins. For SmithKline Beecham, that exercise in bioinformatics yielded in just weeks a promising drug target that standard laboratory experiments could not have found without years and a pinch of luck. Company researchers are now trying to find a potential drug that blocks the cathepsin K target. ---- __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From Shashank_Singh at satyam.com Mon Oct 15 07:28:03 2001 From: Shashank_Singh at satyam.com (Shashank_Singh) Date: Mon, 15 Oct 2001 16:58:03 +0530 Subject: [BiO BB] Just enrolled into this forum Message-ID: <877B003B6F03D511A22E00B0D078E7A8055556A7@hst.satyam.com> Hi All, I've just enrolled into this mailing-list. I'm a new-bee into Biotech area as I've only IT background. Recently, I was attracted towards this area, and wanted to map the IT skills with Biotechnology. Can anyone guide me how to start and what are good references to follow ? Pls brief on: * Bioinformatics and related IT background(how biotechnology be best served with IT) * What are the tools which can help me in learning * Related hyperlinks Help of any sort will be highly appreciated. Thanks, Shashank From jkwaran at rediffmail.com Mon Oct 15 08:44:41 2001 From: jkwaran at rediffmail.com (j kamesh) Date: 15 Oct 2001 12:44:41 -0000 Subject: [BiO BB] Just enrolled into this forum Message-ID: <20011015124441.17327.qmail@mailweb12.rediffmail.com> Hi this is kamesh i work for mi bio world, where do you stay if its chennai pls contact me at these numbers i shall tell u more on bioinformatics. the no's are mascom infology 4362855, 4339436. bye Regs J.Kamesh On Mon, 15 Oct 2001 Shashank_Singh wrote : > Hi All, > I've just enrolled into this mailing-list. I'm a > new-bee into > Biotech area as I've only IT background. Recently, I > was attracted towards > this area, and wanted to map the IT skills with > Biotechnology. Can anyone > guide me how to start and what are good references to > follow ? Pls brief on: > * Bioinformatics and related IT background(how > biotechnology be best > served with IT) > * What are the tools which can help me in learning > * Related hyperlinks > > Help of any sort will be highly appreciated. > > Thanks, > Shashank > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > From virenbio at yahoo.com Mon Oct 15 08:54:36 2001 From: virenbio at yahoo.com (Viren Konde) Date: Mon, 15 Oct 2001 05:54:36 -0700 (PDT) Subject: [BiO BB] JBuilder and WINDOWS Message-ID: <20011015125436.8342.qmail@web20902.mail.yahoo.com> Dear List Members: Which version of Borland JBuilder is compatible (works) with WINDOWS Millenium edition ? Thanks. Sincerely, Viren __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From sapna at resource-logistics.com Mon Oct 15 15:57:21 2001 From: sapna at resource-logistics.com (Sapna Goswami) Date: Mon, 15 Oct 2001 12:57:21 -0700 Subject: [BiO BB] Clinical Trial Consultants In-Reply-To: <200110151600.MAA28521@www.bioinformatics.org> Message-ID: We are a firm based in the Northern US and are actively seeking IT consultants with the following skills- - Clinical Trials background. Experience with any software such as ClinSoft, Oracle Clinical, SAS(with Clinical Trials) a big plus. - CRA For more details, please see http://www.resource-logistics.com/ClinicalJobs.htm Consultants with all levels of experience are invited to apply. Thanks S. Goswami sapna at resource-logistics.com -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] Sent: Monday, October 15, 2001 9:00 AM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #113 - 4 msgs Send BiO_Bulletin_Board maillist submissions to bio_bulletin_board at bioinformatics.org To subscribe or unsubscribe via the web, visit http://bioinformatics.org/mailman/listinfo/bio_bulletin_board or, via email, send a message with subject or body 'help' to bio_bulletin_board-request at bioinformatics.org You can reach the person managing the list at bio_bulletin_board-admin at bioinformatics.org When replying, please edit your Subject line so it is more specific than "Re: Contents of BiO_Bulletin_Board digest...") Today's Topics: 1. drug from bioinfo tools (Vidya Dhote) 2. Just enrolled into this forum (Shashank_Singh) 3. Re: Just enrolled into this forum (j kamesh) 4. JBuilder and WINDOWS (Viren Konde) --__--__-- Message: 1 Date: Sun, 14 Oct 2001 20:35:52 -0700 (PDT) From: Vidya Dhote Subject: [BiO BB] drug from bioinfo tools To: bio_bulletin_board at bioinformatics.org Reply-To: bio_bulletin_board at bioinformatics.org Dear Dr Ahmed Rebai, This may be one of the examples you can use. There might be more... --- (From Scientific American) An early example of the utility of bioinformatics is cathepsin K, an enzyme that might turn out to be an important target for treating osteoporosis, a crippling disease caused by the breakdown of bone. In 1993 researchers at SmithKline Beecham, based in Philadelphia, asked scientists at Human Genome Sciences to help them analyze some genetic material they had isolated from the osteoclast cells of people with bone tumors. (Osteoclasts are cells that break down bone in the normal course of bone replenishment; they are thought to be overactive in individuals with osteoporosis.) Human Genome Sciences scientists sequenced the sample and conducted database homology searches to look for matches would give them a clue to the proteins that the sample's gene sequences encoded. Once they found near-matches for the sequences, they carried out further analyses and discovered that one sequence in particular was overexpressed by the osteoclast cells and that it matched those of a previously identified class of molecules: cathepsins. For SmithKline Beecham, that exercise in bioinformatics yielded in just weeks a promising drug target that standard laboratory experiments could not have found without years and a pinch of luck. Company researchers are now trying to find a potential drug that blocks the cathepsin K target. ---- __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com --__--__-- Message: 2 From: Shashank_Singh To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Just enrolled into this forum Date: Mon, 15 Oct 2001 16:58:03 +0530 Reply-To: bio_bulletin_board at bioinformatics.org Hi All, I've just enrolled into this mailing-list. I'm a new-bee into Biotech area as I've only IT background. Recently, I was attracted towards this area, and wanted to map the IT skills with Biotechnology. Can anyone guide me how to start and what are good references to follow ? Pls brief on: * Bioinformatics and related IT background(how biotechnology be best served with IT) * What are the tools which can help me in learning * Related hyperlinks Help of any sort will be highly appreciated. Thanks, Shashank --__--__-- Message: 3 Date: 15 Oct 2001 12:44:41 -0000 From: "j kamesh" Reply-To: "j kamesh" To: Subject: Re: [BiO BB] Just enrolled into this forum charset=iso-8859-1 Reply-To: bio_bulletin_board at bioinformatics.org Hi this is kamesh i work for mi bio world, where do you stay if its chennai pls contact me at these numbers i shall tell u more on bioinformatics. the no's are mascom infology 4362855, 4339436. bye Regs J.Kamesh On Mon, 15 Oct 2001 Shashank_Singh wrote : > Hi All, > I've just enrolled into this mailing-list. I'm a > new-bee into > Biotech area as I've only IT background. Recently, I > was attracted towards > this area, and wanted to map the IT skills with > Biotechnology. Can anyone > guide me how to start and what are good references to > follow ? Pls brief on: > * Bioinformatics and related IT background(how > biotechnology be best > served with IT) > * What are the tools which can help me in learning > * Related hyperlinks > > Help of any sort will be highly appreciated. > > Thanks, > Shashank > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > --__--__-- Message: 4 Date: Mon, 15 Oct 2001 05:54:36 -0700 (PDT) From: Viren Konde Subject: [BiO BB] JBuilder and WINDOWS To: bio_bulletin_board at bioinformatics.org Reply-To: bio_bulletin_board at bioinformatics.org Dear List Members: Which version of Borland JBuilder is compatible (works) with WINDOWS Millenium edition ? Thanks. Sincerely, Viren __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.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 From ngadewal at yahoo.com Tue Oct 16 06:21:57 2001 From: ngadewal at yahoo.com (nikhil gadewal) Date: Tue, 16 Oct 2001 03:21:57 -0700 (PDT) Subject: [BiO BB] GCG problem Message-ID: <20011016102157.15325.qmail@web9502.mail.yahoo.com> Hi all, How to can connect the online sequence data from swissprot to the GCG package 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!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From idoerg at cc.huji.ac.il Tue Oct 16 07:05:33 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Tue, 16 Oct 2001 13:05:33 +0200 (GMT+0200) Subject: [BiO BB] GCG problem In-Reply-To: <20011016102157.15325.qmail@web9502.mail.yahoo.com> Message-ID: On Tue, 16 Oct 2001, nikhil gadewal wrote: : Hi all, : : How to can connect the online sequence data : from swissprot to the GCG package 1) Save the data as text, NOT from the NiceProt page, but rather from the text page. (When you get an online entry from SwissProt, you usually get a fancy web page. Hit the link at the bottom to get the text entry). 2) In the text file you have just created, substitute all consecutive dots (..) with dashes or underscores. This is because GCG treats consecutive dots as a documentation/sequence seperator. On a UNIX system just do: sed 's/\.\./-/g' swissentry.txt > gcgentry.sw 3) Now, using your favorite editor, just before the sequence, add a ".." in a seperate line. This functions as the seperator between documentation and the sequence. 4) Use GCG's REFORMAT on your file, to add all those weird unprintables GCG likes in its files. 5) In the first couple of times you are doing this, check the resulting file with your favorite editor. Just to make sure no documentation entered the sequence area, or vice-versa. Hope this helps. Feel free to email me if problems occur. Iddo -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From ngadewal at yahoo.com Wed Oct 17 04:28:36 2001 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 17 Oct 2001 01:28:36 -0700 (PDT) Subject: [BiO BB] citation index Message-ID: <20011017082836.60565.qmail@web9505.mail.yahoo.com> Hi all, How to find a citation index of a particular artical. 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!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From thriotus at yahoo.com Mon Oct 22 16:42:08 2001 From: thriotus at yahoo.com (nabula easter) Date: Mon, 22 Oct 2001 13:42:08 -0700 (PDT) Subject: [BiO BB] protein identity In-Reply-To: <877B003B6F03D511A22E00B0D078E7A8055556A7@hst.satyam.com> Message-ID: <20011022204208.70213.qmail@web21004.mail.yahoo.com> Hi Group. When two proteins are 98-99% identical, what is the relationship associated between them. Can we call those proteins as very close homologues ! or that 2% difference between then is due to sequence errors at Nucleic acid level. At nucleic acid level they would be 94% identical and we can say a sequnce error! I have this confusion ! could any one please explain this and help me out of this confusion Thanks Cheers Thrio __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From philipp.pagel at cmp.yale.edu Mon Oct 22 17:49:43 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Mon, 22 Oct 2001 17:49:43 -0400 Subject: [BiO BB] protein identity In-Reply-To: <20011022204208.70213.qmail@web21004.mail.yahoo.com> References: <877B003B6F03D511A22E00B0D078E7A8055556A7@hst.satyam.com> <20011022204208.70213.qmail@web21004.mail.yahoo.com> Message-ID: <20011022174943.A5692@merlin> Hi! On Mon, Oct 22, 2001 at 01:42:08PM -0700, nabula easter wrote: > When two proteins are 98-99% identical, what is the > relationship associated between them. > Can we call those proteins as very close homologues ! > or that 2% difference between then is due to sequence > errors at Nucleic acid level. > At nucleic acid level they would be 94% identical and > we can say a sequnce error! That depends on how reliable your sequence is. If your sequence data is reliable you have a close homologue. What exactly that means depends on the source of the DNA and functional data: - In the same species you might be looking at different isoforms - maybe with functional differences. - If it's from different species it is likely that they are functionally the same thing. - The proteins might also have significantly different functions although you would expect less identity. So they could be orthologs, paralogs, isoforms or just sequencing errors. Was this a hypothetical question or are you talking about something you are working on right now? If it's a real-world question you may want to tell us where the sequence data came from and we can narrow it down some more. cu and hope it helps 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 ramakris at trinetra.cs.vt.edu Mon Oct 22 21:26:05 2001 From: ramakris at trinetra.cs.vt.edu (Naren Ramakrishnan) Date: Mon, 22 Oct 2001 21:26:05 -0400 (EDT) Subject: [BiO BB] IEEE Computer special issue; Call for Papers Message-ID: IEEE Computer Special Issue on Bioinformatics Software Systems Scheduled Date of Publication: July 2002 Bioinformatics and the information-centric revolution in biology constitute one of the most exciting and challenging application areas for computational science. The data-driven emphasis in experimental biology has ushered in a veritable revolution involving technologies such as DNA sequencing, data mining, microarrays, and nano-robotics. The recent completion of a draft of the entire human genome and the complete sequencing of the Arabidopsis genome signify major milestones in data acquisition. The success of these endeavors hinges on the design and implementation of high-thoroughput software systems and tools. Further analysis of the biological data flowing from these endeavors presents unique challenges to computational science. We invite wide-ranging articles on bioinformatics software systems appropriate to IEEE Computer's readership. Topics include: sequence comparison, alignment, and annotation tools; new metrics for effective data analysis; microarray expression analysis systems; methodologies for incorporating biological knowledge into analysis (in the form of graphical, declarative, and continually arriving streams of data); software for phylogenetic tree reconstruction; semi-structured and mediated databases for information integration; web-based tools for bioinformatics research; integrated problem-solving environments for targeted applications; and dedicated resources for various biological domains. Emphasis is placed on novelty of software system design and integration of multiple modes of investigation, rather than on any particular algorithmic or computational approach. Articles should also motivate the biological questions influencing software system design and implementation. ------------------------------------------------------------------------ Guest Editors Lenwood S. Heath Department of Computer Science Virginia Tech, VA 24061 Tel: (540) 231-4352 Fax: (540) 231-6075 Email: heath at cs.vt.edu Web: http://www.cs.vt.edu/~heath Naren Ramakrishnan Department of Computer Science Virginia Tech, VA 24061 Tel: (540) 231-8451 Fax: (540) 231-6075 Email: naren at cs.vt.edu Web: http://www.cs.vt.edu/~ramakris ------------------------------------------------------------------------ Submissions, which would be six to seven pages in the final magazine format, are limited to 6,000 words with each figure or table counted as 300 words. In terms of manuscript pages, this is about 20 double-spaced, typewritten pages, with each illustration counted as one-half to one full page of text, depending on its complexity. References are limited to the most relevant 12. Interested authors should submit their manuscript by November 30, 2001 to either of the guest editors. Email submissions in Postscript or PDF are preferred. Authors should also keep in mind IEEE Computer's wide audience; Articles covering real-world applications and approaches are of more interest than those that concentrate purely on generic solution techniques and concepts. ------------------------------------------------------------------------ From thriotus at yahoo.com Tue Oct 23 03:33:17 2001 From: thriotus at yahoo.com (nabula easter) Date: Tue, 23 Oct 2001 00:33:17 -0700 (PDT) Subject: [BiO BB] protein identity In-Reply-To: <20011022174943.A5692@merlin> Message-ID: <20011023073317.78271.qmail@web21001.mail.yahoo.com> Hi Philipp, many thanks for your mail. this is not a hypothetical question. Many times i confront this type of situation where in my BLAST report one hit is 99% identical and when i look carefully, i find replacement of some residues not by a similar residue but by a totally different residue. However, as these hits( proteins) are hypothetical, its difficult to assess this difference is in some functional site or presumably a key domain ( putative) of this protein. I am dealing with cDNA sequences, i i BLAST the ORF of these cDNAs. So when i do BLASTN with cDNA , i see these two DNA sequences are 94% identical. So its difficult to say that these two cDNAs are identical. I hope now my problem is clear, please suggest more . In my analysis , i consider these sometimes as homologs, because i see a different UNIGENE patter for these two sequences. Cheers Thrio __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From ngadewal at yahoo.com Wed Oct 24 05:34:29 2001 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 24 Oct 2001 02:34:29 -0700 (PDT) Subject: [BiO BB] STR Message-ID: <20011024093429.95355.qmail@web9506.mail.yahoo.com> Hi all, I want to find out the STR(short tandem repeat) from COL2A1 (collagen gene) which are polymorphic in nature. thank you in advance 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!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From erwin.lamping at dent.otago.ac.nz Thu Oct 25 00:14:22 2001 From: erwin.lamping at dent.otago.ac.nz (Erwin Lamping) Date: Thu, 25 Oct 2001 17:14:22 +1300 Subject: [BiO BB] Free Software for MacIntosh Message-ID: Dear bioinformatics members. I am a MacIntosh user and looking for easy to use software to edit and analyse sequencing data. Also I would be very interested in a system which allows me to draw Plasmid maps and all the necessary features that go with it. I am not sure whether this is the place to ask these questions but I thought I might just try. Thank you Erwin Lamping email. erwin.lamping at dent.otago.ac.nz From philipp.pagel at cmp.yale.edu Thu Oct 25 10:14:27 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Thu, 25 Oct 2001 10:14:27 -0400 Subject: [BiO BB] Free Software for MacIntosh In-Reply-To: References: Message-ID: <20011025101427.A1107@merlin> Hi! > Dear bioinformatics members. I am a MacIntosh user and looking for > easy to use software to edit and analyse sequencing data. Also I > would be very interested in a system which allows me to draw Plasmid > maps and all the necessary features that go with it. There is a nice little tool called JellyFish. It is available for Windoze, Mac and UNIX/LINUX for free from: http://www.biowire.com/bw_jsp/j_welcome_top.jsp If you are interested in buying something you may want to look at Lasergene (DNA Star), Vector NTI, biotools, MacVector: http://www.dnastar.com/products/products.html http://www.informaxinc.com/ http://www.biotools.com/ http://www.accelrys.com/products/macvector/ I'm sure there are many others that I'm not aware of.. 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 ssotero at mail.com Thu Oct 25 18:04:25 2001 From: ssotero at mail.com (Steven Sotero) Date: Thu, 25 Oct 2001 16:04:25 -0600 Subject: [BiO BB] Graduate School Advice Message-ID: <20011025220425.2908.qmail@mail.com> Greetings all, I have recently found out about Bioinformatics and I am very interested in getting into the field. I've been scouring and I was able to find several schools that have or are starting Bioinformatics programs in the US. My problem now is trying to decide on which schools I can apply to. I have a Bachelor's in CS and I have been working at a Financial company. I was premed during my undergraduate studies as well, so I do have exposure to the Biological Sciences, however, I don't have any experience in research. I?m also not sure if I should be trying for a Master?s or a PhD. From the various information I?ve gathered and from what I?ve been told, Master?s is geared towards a career in industry whereas a PhD is usually for people who want to do research, teach, or become a ?scientist.? Due to my lack of experience in research, I?m not sure if I would make a good scientist, but I do know that I am currently unhappy with my desk job and I was hoping to move away from cubicle oriented work and get some lab experience. I'm really interested in pursuing a PhD in the field, but I'm afraid that my lack of experience may prevent me from being a qualified candidate for these highly competitive programs. I've noticed that a lot of the universities that offer degrees in Bioinformatics are top notch and I'm wary of how difficult it may be to gain acceptance. I was wondering if any of you out there in the field or in academia might have some helpful advice in what schools you think I might have a chance. Should I focus on a PhD or Master?s programs? I was also wondering what qualities or skills that one needs to be good at independent research or to be a ?good scientist.? How can I turn my experience as a programmer (behind a desk in a cubicle) into qualifications that match the criteria of a ?good scientist?? I have spoken to grad advisors at my undergrad school and I have been in contact with the directors of some of the programs I?m interested in and some students. But I?m still unsure about which schools to apply to. The advice and experience that other students have shared often doesn?t seem to apply to my situation because they often came from a biologically intensive background and have had plenty of research experience. I do have a tentative list of schools that I want to apply to: Washington University in St. Louis ? Ph.D in Computational Molecular Biology Boston University ? Ph.D in Bioinformatics Rensselear Polytechnic Institute ? Master?s in Applied Science with a concentration in Bioinformatics RICE ? Master?s in Computer Science with a concentration in Bioinformatics Rutgers ? Ph.D in Computational Biology Carnegie Mellon University - Master?s in Computational Biology Keck Graduate Institute ? Master?s in BioScience I chose a mix of programs, although I would like to get into a good PhD program, primarily for the degree but tuition remission doesn?t hurt, I also plan to apply to Master?s programs. I am still fearful about my chances, and I at least want to get in somewhere. I would appreciate any comments or advice, even (and especially) if you think I would be wasting my time applying to a certain school, or if you have any suggestions for other programs or schools. I apologize for my garrulousness, but I am running out of avenues to explore and I am trying to exhaust all resources available to me. I hope that I have not taken up too much of your time. - Ste -- _______________________________________________ Sign-up for your own FREE Personalized E-mail at Mail.com http://www.mail.com/?sr=signup Have you downloaded the latest calling software from Net2Phone? Click here to get it now! http://www.net2phone.com/cgi-bin/link.cgi?157 From Joel.Dudley at DevelopOnline.com Thu Oct 25 18:54:32 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Thu, 25 Oct 2001 15:54:32 -0700 Subject: [BiO BB] Graduate School Advice Message-ID: You forgot a school! Arizona State University will be starting a Computational Biology Masters next semester. It is a Sloan foundation program. They will not be offering a PhD because they feel that a masters is more practical for individuals who want to work in the bioinformatics industry. Part of the masters requires that you intern at a company so thay are building great relationships with local companies doing bioinformatics work (Motorola Life Sceinces division for example). The program is very flexible and offers several pathways. The program is geared towards biologists and computer scientists, but they are welcoming people from various backgrounds. I am already taking classes towards this degree, but it will not be oficially available until next semester. There are some great professors working in computational biology at ASU including Sudhir Kumar who is the author of MEGA (www.megasoftware.net). Oh yeah, there is sunshine over 300 days out of the year here too! :-) Hope this helps. - Joel -----Original Message----- From: Steven Sotero [mailto:ssotero at mail.com] Sent: Thursday, October 25, 2001 3:04 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Graduate School Advice Greetings all, I have recently found out about Bioinformatics and I am very interested in getting into the field. I've been scouring and I was able to find several schools that have or are starting Bioinformatics programs in the US. My problem now is trying to decide on which schools I can apply to. I have a Bachelor's in CS and I have been working at a Financial company. I was premed during my undergraduate studies as well, so I do have exposure to the Biological Sciences, however, I don't have any experience in research. I'm also not sure if I should be trying for a Master's or a PhD. From the various information I've gathered and from what I've been told, Master's is geared towards a career in industry whereas a PhD is usually for people who want to do research, teach, or become a "scientist." Due to my lack of experience in research, I'm not sure if I would make a good scientist, but I do know that I am currently unhappy with my desk job and I was hoping to move away from cubicle oriented work and get some lab experience. I'm really interested in pursuing a PhD in the field, but I'm afraid that my lack of experience may prevent me from being a qualified candidate for these highly competitive programs. I've noticed that a lot of the universities that offer degrees in Bioinformatics are top notch and I'm wary of how difficult it may be to gain acceptance. I was wondering if any of you out there in the field or in academia might have some helpful advice in what schools you think I might have a chance. Should I focus on a PhD or Master's programs? I was also wondering what qualities or skills that one needs to be good at independent research or to be a "good scientist." How can I turn my experience as a programmer (behind a desk in a cubicle) into qualifications that match the criteria of a "good scientist?" I have spoken to grad advisors at my undergrad school and I have been in contact with the directors of some of the programs I'm interested in and some students. But I'm still unsure about which schools to apply to. The advice and experience that other students have shared often doesn't seem to apply to my situation because they often came from a biologically intensive background and have had plenty of research experience. I do have a tentative list of schools that I want to apply to: Washington University in St. Louis - Ph.D in Computational Molecular Biology Boston University - Ph.D in Bioinformatics Rensselear Polytechnic Institute - Master's in Applied Science with a concentration in Bioinformatics RICE - Master's in Computer Science with a concentration in Bioinformatics Rutgers - Ph.D in Computational Biology Carnegie Mellon University - Master's in Computational Biology Keck Graduate Institute - Master's in BioScience I chose a mix of programs, although I would like to get into a good PhD program, primarily for the degree but tuition remission doesn't hurt, I also plan to apply to Master's programs. I am still fearful about my chances, and I at least want to get in somewhere. I would appreciate any comments or advice, even (and especially) if you think I would be wasting my time applying to a certain school, or if you have any suggestions for other programs or schools. I apologize for my garrulousness, but I am running out of avenues to explore and I am trying to exhaust all resources available to me. I hope that I have not taken up too much of your time. - Ste -- _______________________________________________ Sign-up for your own FREE Personalized E-mail at Mail.com http://www.mail.com/?sr=signup Have you downloaded the latest calling software from Net2Phone? Click here to get it now! http://www.net2phone.com/cgi-bin/link.cgi?157 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From thriotus at yahoo.com Mon Oct 29 13:42:47 2001 From: thriotus at yahoo.com (nabula easter) Date: Mon, 29 Oct 2001 10:42:47 -0800 (PST) Subject: [BiO BB] Src of Drosophila In-Reply-To: <20011025220425.2908.qmail@mail.com> Message-ID: <20011029184247.26559.qmail@web21004.mail.yahoo.com> Hi group, Would any one please help me ( sp. Drosophila biologist). Which is more related to c-src ( a high identity orthlog of c-src) , is this Drosohpila src 42A or Drosophila Src 64B? Its so confusing to read that in Fly homepage. Please help me ASAP. thanks regards thrio __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From charles at moulinette.dyndns.org Mon Oct 29 15:08:28 2001 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Mon, 29 Oct 2001 21:08:28 +0100 Subject: [BiO BB] Src of Drosophila In-Reply-To: <20011029184247.26559.qmail@web21004.mail.yahoo.com> References: <20011025220425.2908.qmail@mail.com> <20011029184247.26559.qmail@web21004.mail.yahoo.com> Message-ID: <20011029210828.B15005@moulinette.dyndns.org> > Its so confusing to read that in Fly homepage. I don't have the answer, but did you try the "interactive fly" weblink in flybase's page of src? It's a summary of publications, and has sometimes a "evolutionary homologs" section. Charles From thriotus at yahoo.com Mon Oct 29 16:35:22 2001 From: thriotus at yahoo.com (nabula easter) Date: Mon, 29 Oct 2001 13:35:22 -0800 (PST) Subject: [BiO BB] Src of Drosophila In-Reply-To: <20011029210828.B15005@moulinette.dyndns.org> Message-ID: <20011029213522.93938.qmail@web21003.mail.yahoo.com> hi , thanks for your mail. i did read that section. according to that DmSrc64B was considered previously as strong ortholog to vertebrate c-src. however after characterizing another kinase at 42A position on the same locus, it was conculded that this src kinase show strong evidence to be called as a strong ortholog of vertebrate c-src. i consider that a fly biologist and biologist working in vertebrate systems understand the same biological concept in different ways. so final conclusion what exactly reality is unknown through that section. niether a reference was cited nor a description was mentioned which led to that concusion. So my request to any drosophila biologist is to clarify me over my question ( generic rather silly) . thanks in advance thrio __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From Sameer_Mohta at satyam.com Tue Oct 30 01:08:29 2001 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Tue, 30 Oct 2001 11:38:29 +0530 Subject: [BiO BB] HMM Message-ID: <877B003B6F03D511A22E00B0D078E7A85428EE@hst.satyam.com> Hi, Can anybody suggest me a good book on HMM. thanks, sam From charles at moulinette.dyndns.org Tue Oct 30 02:24:14 2001 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Tue, 30 Oct 2001 08:24:14 +0100 Subject: [BiO BB] Src of Drosophila In-Reply-To: <20011029213522.93938.qmail@web21003.mail.yahoo.com> References: <20011029210828.B15005@moulinette.dyndns.org> <20011029213522.93938.qmail@web21003.mail.yahoo.com> Message-ID: <20011030082414.A16091@moulinette.dyndns.org> > so final conclusion what exactly reality is unknown > through that section. niether a reference was cited > nor a description was mentioned which led to that > concusion. You read crude bibliographic extracts, all paragraphs being terminated by (Author, date). The reference section is in the same list as "evolutionary homologs". If you vant bioinformatical evidences, follow the GadFly link of src42A's Flybase page. Charles From idoerg at cc.huji.ac.il Tue Oct 30 04:49:56 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Tue, 30 Oct 2001 11:49:56 +0200 (GMT+0200) Subject: [BiO BB] HMM In-Reply-To: <877B003B6F03D511A22E00B0D078E7A85428EE@hst.satyam.com> Message-ID: On Tue, 30 Oct 2001, Sameer_Mohta wrote: : Hi, : : Can anybody suggest me a good book on HMM. : : thanks, : sam For Bioinformatics, I would suggest the relevant chapters from: 1) Bioinformatics: a Machine Learning Approach / Pierre Baldi & Soren Brunak 2) Biological Sequence Analysis / R. Durbin, S. Eddy, A. Krogh, G. Mitchison Iddo -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From karthaton at yahoo.co.uk Tue Oct 30 05:41:19 2001 From: karthaton at yahoo.co.uk (=?iso-8859-1?q?Keith=20arthaton?=) Date: Tue, 30 Oct 2001 10:41:19 +0000 (GMT) Subject: [BiO BB] (no subject) Message-ID: <20011030104119.87026.qmail@web20805.mail.yahoo.com> Hi, I found out how I can manually send multiple protein sequences in a batch file for Blast search to Husar server (which takes the file only in FASTA format)which also uses GCG. But is there a way I can do it directly through perl? I mean is there any algorithm in perl which can do these cross platform evaluations and give me bak the results so that i can run this perl script on my protein batch file and get the blast results. ===== ____________________________________________________________ Nokia Game is on again. Go to http://uk.yahoo.com/nokiagame/ and join the new all media adventure before November 3rd. From Ingrid.Marchal at univ-lille1.fr Tue Oct 30 12:36:11 2001 From: Ingrid.Marchal at univ-lille1.fr (Ingrid Marchal) Date: Tue, 30 Oct 2001 18:36:11 +0100 Subject: [BiO BB] introduction to bioinfo In-Reply-To: <200110301700.MAA14095@www.bioinformatics.org> Message-ID: <5.1.0.14.0.20011030183110.009e98e0@pop.univ-lille1.fr> Hi, I am a biochemist and don't know much on bioinformatics... Can anyone suggest me a good introductory book? Thanks Ingrid From john_scheiderer at msn.com Tue Oct 30 13:27:08 2001 From: john_scheiderer at msn.com (John Scheiderer) Date: Tue, 30 Oct 2001 13:27:08 -0500 Subject: [BiO BB] introduction to bioinfo Message-ID: Hi, O'Reilly has a book titled "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck. http://shop.barnesandnoble.com/booksearch/isbnInquiry.asp?userid=6BTGGYL97D&mscssid=33705MEPMAFM8LGDCLUUAG1B1X0A78LA&isbn=1565926641 Hope this helps. Thanks, John ----- Original Message ----- From: Ingrid Marchal Sent: Tuesday, October 30, 2001 1:23 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] introduction to bioinfo Hi, I am a biochemist and don't know much on bioinformatics... Can anyone suggest me a good introductory book? Thanks Ingrid _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_boardGet more from the Web. FREE MSN Explorer download : http://explorer.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From sag46 at columbia.edu Tue Oct 30 13:32:58 2001 From: sag46 at columbia.edu (Seth Gale) Date: Tue, 30 Oct 2001 13:32:58 -0500 Subject: [BiO BB] introduction to bioinfo References: Message-ID: <011a01c16171$4c74b440$78c227a0@columbia.edu> This book is no good at all in my opinion. It has a lot of websites really, that's it. It tlaks about the very basics of databases, etc. and it doesn't really go into any concrete understanding needed for bioinformatics. I, personally, would avoid this book. Seth ----- Original Message ----- From: John Scheiderer To: bio_bulletin_board at bioinformatics.org Sent: Tuesday, October 30, 2001 1:27 PM Subject: Re: [BiO BB] introduction to bioinfo Hi, O'Reilly has a book titled "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck. http://shop.barnesandnoble.com/booksearch/isbnInquiry.asp?userid=6BTGGYL97D&mscssid=33705MEPMAFM8LGDCLUUAG1B1X0A78LA&isbn=1565926641 Hope this helps. Thanks, John ----- Original Message ----- From: Ingrid Marchal Sent: Tuesday, October 30, 2001 1:23 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] introduction to bioinfo Hi, I am a biochemist and don't know much on bioinformatics... Can anyone suggest me a good introductory book? Thanks Ingrid _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board ------------------------------------------------------------------------------ Get more from the Web. FREE MSN Explorer download : http://explorer.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From john_scheiderer at msn.com Tue Oct 30 14:25:24 2001 From: john_scheiderer at msn.com (John Scheiderer) Date: Tue, 30 Oct 2001 14:25:24 -0500 Subject: [BiO BB] introduction to bioinfo Message-ID: So, what would you recommend? Would love to know so I can order the book(s). ----- Original Message ----- From: Seth Gale Sent: Tuesday, October 30, 2001 2:16 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] introduction to bioinfo This book is no good at all in my opinion. It has a lot of websites really, that's it. It tlaks about the very basics of databases, etc. and it doesn't really go into any concrete understanding needed for bioinformatics. I, personally, would avoid this book. Seth ----- Original Message ----- From: John Scheiderer To: bio_bulletin_board at bioinformatics.org Sent: Tuesday, October 30, 2001 1:27 PM Subject: Re: [BiO BB] introduction to bioinfo Hi, O'Reilly has a book titled "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck. http://shop.barnesandnoble.com/booksearch/isbnInquiry.asp?userid=6BTGGYL97D&mscssid=33705MEPMAFM8LGDCLUUAG1B1X0A78LA&isbn=1565926641 Hope this helps. Thanks, John ----- Original Message ----- From: Ingrid Marchal Sent: Tuesday, October 30, 2001 1:23 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] introduction to bioinfo Hi, I am a biochemist and don't know much on bioinformatics... Can anyone suggest me a good introductory book? Thanks Ingrid _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get more from the Web. FREE MSN Explorer download : http://explorer.msn.comGet more from the Web. FREE MSN Explorer download : http://explorer.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioinfo_india at yahoo.com Tue Oct 30 14:26:01 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Tue, 30 Oct 2001 11:26:01 -0800 (PST) Subject: [BiO BB] introduction to bioinfo In-Reply-To: <011a01c16171$4c74b440$78c227a0@columbia.edu> Message-ID: <20011030192601.33731.qmail@web14508.mail.yahoo.com> This book is not that informative and thought provoking. this would certainly help as a jumpstart for novice. however if you need a good start consider braxevanis second edition. to me , i personally feel there is no good book like Lehninger in Bioinfomratics..... best SP --- Seth Gale wrote: > This book is no good at all in my opinion. It has a > lot of websites really, that's it. It tlaks about > the very basics of databases, etc. and it doesn't > really go into any concrete understanding needed for > bioinformatics. I, personally, would avoid this > book. > > Seth > ----- Original Message ----- > From: John Scheiderer > To: bio_bulletin_board at bioinformatics.org > Sent: Tuesday, October 30, 2001 1:27 PM > Subject: Re: [BiO BB] introduction to bioinfo > > > Hi, > > O'Reilly has a book titled "Developing > Bioinformatics Computer Skills" by Cynthia Gibas and > Per Jambeck. > > > http://shop.barnesandnoble.com/booksearch/isbnInquiry.asp?userid=6BTGGYL97D&mscssid=33705MEPMAFM8LGDCLUUAG1B1X0A78LA&isbn=1565926641 > > Hope this helps. > > Thanks, > John > > ----- Original Message ----- > From: Ingrid Marchal > Sent: Tuesday, October 30, 2001 1:23 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] introduction to bioinfo > > Hi, > I am a biochemist and don't know much on > bioinformatics... Can anyone > suggest me a good introductory book? > Thanks > Ingrid > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > ------------------------------------------------------------------------------ > Get more from the Web. FREE MSN Explorer download > : http://explorer.msn.com > > > ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From philipp.pagel at cmp.yale.edu Tue Oct 30 14:33:54 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Tue, 30 Oct 2001 14:33:54 -0500 Subject: [BiO BB] introduction to bioinfo In-Reply-To: <5.1.0.14.0.20011030183110.009e98e0@pop.univ-lille1.fr> References: <200110301700.MAA14095@www.bioinformatics.org> <5.1.0.14.0.20011030183110.009e98e0@pop.univ-lille1.fr> Message-ID: <20011030143354.A2157@merlin> Hi! On Tue, Oct 30, 2001 at 06:36:11PM +0100, Ingrid Marchal wrote: > I am a biochemist and don't know much on bioinformatics... Can anyone > suggest me a good introductory book? Although not exactly cheap I would recommend "Bioinformatics" by David W. Mount. In my opinion the author succeeded in hitting the right level: You can understand the text without beeing a computer scientist but it is not shallow at all - you really learn how things are done. Up to now the best book on the subject I have found. One book I would not recommend although it has gotten a lot of attention is "Developing bioinformatics computer skills" by Gibas and Jambeck. This book is nice to flip through if you are looking for interesting things on the web but you will certainly not learn anything - it is quite shallow. 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 danag at bioinformatics.weizmann.ac.il Wed Oct 31 01:45:00 2001 From: danag at bioinformatics.weizmann.ac.il (Dana Gerber) Date: Wed, 31 Oct 2001 08:45:00 +0200 Subject: [BiO BB] introduction to bioinfo References: <5.1.0.14.0.20011030183110.009e98e0@pop.univ-lille1.fr> Message-ID: <3BDF9DEB.106D219A@bioinfo.weizmann.ac.il> Try book of D. Heggins and W. Taylor "Bioinformatics: sequences, structure and database" , OXFORD university press. enjoy, Dana Ingrid Marchal wrote: > Hi, > I am a biochemist and don't know much on bioinformatics... Can anyone > suggest me a good introductory book? > Thanks > Ingrid > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Dana Gerber Dep. of Molecular Genetics The Weizmann Institute of Science POB 26, Rehovot, 76100, Israel Tel.: 972-8-9344427 (lab.) 972-53-856992 (cellular) Fax.: 972-8-9344108 (dep.) email: danag at bioinfo.weizmann.ac.il From idoerg at cc.huji.ac.il Wed Oct 31 02:12:11 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Wed, 31 Oct 2001 09:12:11 +0200 (GMT+0200) Subject: [BiO BB] introduction to bioinfo In-Reply-To: Message-ID: On Tue, 30 Oct 2001, John Scheiderer wrote: : So, what would you recommend?Would love to know so I can order the book(s). David Mount's "Bioinformatics". Good introductory text for biologists, and it goes in-depth enough for you to be able to move to more specific/advanced materials. Based on a course, it has a "coursebook feel" which I like in introcuctory texts. Also, if you buy it, you can register to a site on the web which has problems and supplementary material. http://www.bioinformaticsonline.org Iddo -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From Sameer_Mohta at satyam.com Wed Oct 31 23:36:01 2001 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Thu, 1 Nov 2001 10:06:01 +0530 Subject: [BiO BB] Blast Message-ID: <877B003B6F03D511A22E00B0D078E7A85428FA@hst.satyam.com> Hi All, can we schedule a batch BLAST job on NCBI server. I mean i want to run BLAST for 100 sequences. But i don't want to do it manually. i want to submit all these sequences in a single shot. is there any facility available ? sam