From srilu_vidhya at yahoo.co.in Sat Jun 1 00:52:42 2002 From: srilu_vidhya at yahoo.co.in (=?iso-8859-1?q?srividhya=20arumilli?=) Date: Sat, 1 Jun 2002 05:52:42 +0100 (BST) Subject: [BiO BB] regarding the list of bio-informatics companies Message-ID: <20020601045242.70714.qmail@web8105.in.yahoo.com> I am vidya,here.I did my post graduation in bio-chemistry.now i am doing advanced diploma in bio-informatics.I will be completing it by this august.I worked with software &packages like oracle,c,c++,perl,unix,irix,java,phylip,tripos.I am doing project work on drug designing as the part of the course.I would like to know the list of bioinformatics companies preferably in india and also the job opportunities. thanking u. --------------------------------- Don't miss Yahoo India's Coverage of 2002 FIFA World Cup -------------- next part -------------- An HTML attachment was scrubbed... URL: From minniwilson at yahoo.com Sat Jun 1 01:20:23 2002 From: minniwilson at yahoo.com (minu nimmi) Date: Fri, 31 May 2002 22:20:23 -0700 (PDT) Subject: [BiO BB] regarding job Message-ID: <20020601052023.10578.qmail@web14805.mail.yahoo.com> Hi, Iam elisheba completed my Msc in biotechnology.Now doing PG diploma in bioinformatics.I would like to do job in my related field preferably in Bangalore.Can you help me in getting the up to day information regarding these jobs. __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From raju2002 at lycos.com Sat Jun 1 13:13:26 2002 From: raju2002 at lycos.com (Raju S) Date: Sat, 01 Jun 2002 10:13:26 -0700 Subject: [BiO BB] AC numbers Message-ID: Hi Wilfred, What Neeraj said is correct. After getting your fasta format you have to run it through Blast. Then you can get the best identical matching. rgds, Raju. On Fri, 31 May 2002 17:05:40 Neeraj_Tripathi wrote: >Hi Wilfred, > Please go to NCBI site (http://www.ncbi.nlm.nih.gov/entrez) and choose >"Nucleotide" as database. Submit the AC number and you get the URL for the >accession number. Go to the URL, change the 'Display' as "FASTA" in the >drop-down box and you get the sequence in FASTA format. > >rgds >Neeraj > >> ---------- >> From: Wilfred D. Stein[SMTP:wdstein at vms.huji.ac.il] >> Reply To: bio_bulletin_board at bioinformatics.org >> Sent: Friday, May 31, 2002 4:33 PM >> To: bio_bulletin_board at bioinformatics.org >> Subject: [BiO BB] AC numbers >> >> I am using a paper which has GenBank accession numbers in the form >> AC003080, for instance. How do I find the relevant sequnce from >> GenBank..GenBank does NOT accept such AC or AL numbers >> >> wds >> >> >> Yours sincerely, >> Wilfred D. Stein >> (Emeritus Professor of Biophysics) >> >> BIOLOGICAL CHEMISTRY >> SILBERMAN INSTITUTE OF LIFE SCIENCES >> HEBREW UNIVERSITY of JERUSALEM >> GIVAT RAM, JERUSALEM 91904 ISRAEL >> Tel + (+972) 2 6585679 (office) 6525649 (home) >> Cellular phone : (+972) 51 822391 >> Fax : (+972) 2 6585440 >> Email : WDSTEIN at HUJI.AC.IL >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >************************************************************************** >This email (including any attachments) is intended for the sole use of the >intended recipient/s and may contain material that is CONFIDENTIAL AND >PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or >distribution or forwarding of any or all of the contents in this message is >STRICTLY PROHIBITED. If you are not the intended recipient, please contact >the sender by email and delete all copies; your cooperation in this regard >is appreciated. >************************************************************************** >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ________________________________________________________ Outgrown your current e-mail service? Get a 25MB Inbox, POP3 Access, No Ads and No Taglines with LYCOS MAIL PLUS. http://login.mail.lycos.com/brandPage.shtml?pageId=plus From raju2002 at lycos.com Sat Jun 1 13:13:26 2002 From: raju2002 at lycos.com (Raju S) Date: Sat, 01 Jun 2002 10:13:26 -0700 Subject: [BiO BB] AC numbers Message-ID: Hi Wilfred, What Neeraj said is correct. After getting your fasta format you have to run it through Blast. Then you can get the best identical matching. rgds, Raju. On Fri, 31 May 2002 17:05:40 Neeraj_Tripathi wrote: >Hi Wilfred, > Please go to NCBI site (http://www.ncbi.nlm.nih.gov/entrez) and choose >"Nucleotide" as database. Submit the AC number and you get the URL for the >accession number. Go to the URL, change the 'Display' as "FASTA" in the >drop-down box and you get the sequence in FASTA format. > >rgds >Neeraj > >> ---------- >> From: Wilfred D. Stein[SMTP:wdstein at vms.huji.ac.il] >> Reply To: bio_bulletin_board at bioinformatics.org >> Sent: Friday, May 31, 2002 4:33 PM >> To: bio_bulletin_board at bioinformatics.org >> Subject: [BiO BB] AC numbers >> >> I am using a paper which has GenBank accession numbers in the form >> AC003080, for instance. How do I find the relevant sequnce from >> GenBank..GenBank does NOT accept such AC or AL numbers >> >> wds >> >> >> Yours sincerely, >> Wilfred D. Stein >> (Emeritus Professor of Biophysics) >> >> BIOLOGICAL CHEMISTRY >> SILBERMAN INSTITUTE OF LIFE SCIENCES >> HEBREW UNIVERSITY of JERUSALEM >> GIVAT RAM, JERUSALEM 91904 ISRAEL >> Tel + (+972) 2 6585679 (office) 6525649 (home) >> Cellular phone : (+972) 51 822391 >> Fax : (+972) 2 6585440 >> Email : WDSTEIN at HUJI.AC.IL >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >************************************************************************** >This email (including any attachments) is intended for the sole use of the >intended recipient/s and may contain material that is CONFIDENTIAL AND >PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or >distribution or forwarding of any or all of the contents in this message is >STRICTLY PROHIBITED. If you are not the intended recipient, please contact >the sender by email and delete all copies; your cooperation in this regard >is appreciated. >************************************************************************** >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ________________________________________________________ Outgrown your current e-mail service? Get a 25MB Inbox, POP3 Access, No Ads and No Taglines with LYCOS MAIL PLUS. http://login.mail.lycos.com/brandPage.shtml?pageId=plus From bioinfo at biosystemsconsulting.com Sat Jun 1 21:19:45 2002 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Sat, 1 Jun 2002 21:19:45 -0400 Subject: [BiO BB] Job postings In-Reply-To: <20020601052023.10578.qmail@web14805.mail.yahoo.com> Message-ID: <000001c209d3$94fb1eb0$befea8c0@raptor> Perhaps there is a better place to job openings. Maybe there should be a bioinformatics job email list. From landman at scientificappliance.com Sat Jun 1 21:16:47 2002 From: landman at scientificappliance.com (Joe Landman) Date: 01 Jun 2002 21:16:47 -0400 Subject: [BiO BB] Job postings In-Reply-To: <000001c209d3$94fb1eb0$befea8c0@raptor> References: <000001c209d3$94fb1eb0$befea8c0@raptor> Message-ID: <1022980608.2972.0.camel@protein.dtw.macsch.com> There is a bio-jobs list on bioinformatics.org. I wonder if it is time for a list of lists. Joe On Sat, 2002-06-01 at 21:19, bioinfo wrote: > Perhaps there is a better place to job openings. Maybe there should be > a bioinformatics job email list. > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Sat Jun 1 23:54:33 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 01 Jun 2002 23:54:33 -0400 Subject: [BiO BB] Job postings References: <000001c209d3$94fb1eb0$befea8c0@raptor> <1022980608.2972.0.camel@protein.dtw.macsch.com> Message-ID: <3CF996F9.741ACDAE@bioinformatics.org> Joe Landman wrote: > > There is a bio-jobs list on bioinformatics.org. I wonder if it is time > for a list of lists. The Jobs forum is web-based. It doesn't use Mailman, but members of Bioinformatics.Org can subscribe. The forum is at http://bioinformatics.org/jobs/ A list of Mailman mailing lists exists: http://bioinformatics.org/mailman/listinfo/ And a list of major forums (Mailman or web-based) appears on the left menubar of the website. I do think that, for the major forums, we should have some text in the descriptions pointing people to the most appropriate forums for their posts. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From prasadp77ie at yahoo.ie Tue Jun 4 06:40:46 2002 From: prasadp77ie at yahoo.ie (Prasad Phirke) Date: Tue, 4 Jun 2002 03:40:46 -0700 (PDT) Subject: [BiO BB] regarding the list of bio-informatics companies In-Reply-To: <20020601045242.70714.qmail@web8105.in.yahoo.com> Message-ID: <20020604104046.47933.qmail@web21006.mail.yahoo.com> Hi, I would suggest you to search on rediff.com for all Indian biotech companies, there are loads of them in your area, I mean south India. Good Luck Prasad --- srividhya arumilli wrote: > > I am vidya,here.I did my post graduation in > bio-chemistry.now i am doing advanced diploma in > bio-informatics.I will be completing it by this > august.I worked with software &packages like > oracle,c,c++,perl,unix,irix,java,phylip,tripos.I am > doing project work on drug designing as the part of > the course.I would like to know the list of > bioinformatics companies preferably in india and > also the job opportunities. > > thanking u. > ===== Prasad H. PhirkePost - Grad Student,Dublin City University,School Of Biotechnology,Glasnevin, Dublin - 9,IRELAND.Mobile - +353 (0)85 721 5335* __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From newgene at bigfoot.com Wed Jun 5 11:05:53 2002 From: newgene at bigfoot.com (newgene at bigfoot.com) Date: Wed, 05 Jun 2002 10:05:53 -0500 Subject: [BiO BB] Run server program remotely? Message-ID: <5.1.0.14.0.20020605094001.00b3a160@mail.uth.tmc.edu> Hi, group, I have an account to access our server equipped with many popular sequence analysis programs like GCG package, etc. I can run those tools from the terminal of server side. I am wondering if possible I can run those programs remotely just like my local programs, but using server's power. Thus, I don't need to upload my data files to server manually and then run it from server terminal. I just need send the request to server, then server will upload the needed local data file automatically and run the program ,then send me back the result. Sort of a "local program simulator". Is there a tool can do something like above? Thanks. CL From btiwari at molbiol.ox.ac.uk Wed Jun 5 11:27:32 2002 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Wed, 5 Jun 2002 16:27:32 +0100 (BST) Subject: [BiO BB] Run server program remotely? In-Reply-To: <5.1.0.14.0.20020605094001.00b3a160@mail.uth.tmc.edu> Message-ID: >popular sequence analysis programs like GCG package, etc. I can run those >tools from the terminal of server side. I am wondering if possible I can >run those programs remotely just like my local programs, but using server's >power. Thus, I don't need to upload my data files to server manually and >then run it from server terminal. I just need send the request to server, >then server will upload the needed local data file automatically and run >the program ,then send me back the result. Sort of a "local program simulator". Hello, I'm not sure this is exactly what you want, but have you looked at the Pise Bioperl modules? http://www-alt.pasteur.fr/~letondal/Pise/ If you set up Pise on your server for your programs of interest, you could probably then use the Pise Bioperl modules to run these programs from your local machine. Cheers Bela .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. Dr. Bela Tiwari Acting Manager OU Bioinformatics Centre SWD School of Pathology South Parks Road Oxford OX1 3RE 01865 (2)75507 http://www.molbiol.ox.ac.uk .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. From p.pagel at gsf.de Wed Jun 5 11:38:24 2002 From: p.pagel at gsf.de (Philipp Pagel) Date: Wed, 5 Jun 2002 17:38:24 +0200 Subject: [BiO BB] Run server program remotely? In-Reply-To: <5.1.0.14.0.20020605094001.00b3a160@mail.uth.tmc.edu> References: <5.1.0.14.0.20020605094001.00b3a160@mail.uth.tmc.edu> Message-ID: <20020605153824.GA7154@porcupine.gsf.de> On Wed, Jun 05, 2002 at 10:05:53AM -0500, newgene at bigfoot.com wrote: > Hi, group, > I have an account to access our server equipped with many > popular sequence analysis programs like GCG package, etc. I can run those > tools from the terminal of server side. I am wondering if possible I can > run those programs remotely just like my local programs, but using server's > power. Thus, I don't need to upload my data files to server manually and > then run it from server terminal. I just need send the request to server, > then server will upload the needed local data file automatically and run > the program ,then send me back the result. Sort of a "local program > simulator". > Is there a tool can do something like above? You could mount /home/ or any other data directory from an NFS server on both the server and you workstation. cu Philipp -- Dr. Philipp Pagel Tel. +49-89-3187-3640 Institute for Bioinformatics Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg Germany From newgene at bigfoot.com Wed Jun 5 12:16:33 2002 From: newgene at bigfoot.com (newgene at bigfoot.com) Date: Wed, 05 Jun 2002 11:16:33 -0500 Subject: [BiO BB] Run server program remotely? Message-ID: <5.1.0.14.0.20020605104027.00b3a370@mail.uth.tmc.edu> It's good to show by an example: Supppose I can run "clustalw INFILE" on server terminal, is there a tool allowing me to run this command locally, just like I have clustalw installed locally? In the back, this tool will upload my local INFILE onto server and run "clustalw INFILE" on the server, and then send back the output to my local computer. The uploaded data file will be deleted from server after use. "Clustalw" here is just for example. Of course, I can install it on my local computer. But for those programs available only on server or those need strong server power, this tool (if exists) will give much convenience. Thanks. CL --- Bela Tiwari wrote: > >popular sequence analysis programs like GCG > package, etc. I can run those > >tools from the terminal of server side. I am > wondering if possible I can > >run those programs remotely just like my local > programs, but using server's > >power. Thus, I don't need to upload my data files > to server manually and > >then run it from server terminal. I just need send > the request to server, > >then server will upload the needed local data file > automatically and run > >the program ,then send me back the result. Sort of > a "local program simulator". > > Hello, > > I'm not sure this is exactly what you want, but > have you looked at the Pise Bioperl modules? > > http://www-alt.pasteur.fr/~letondal/Pise/ > > If you set up Pise on your server for your programs > of interest, you could > probably then use the Pise Bioperl modules to run > these programs from your > local machine. > > > Cheers > > Bela > > > > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > Dr. Bela Tiwari > Acting Manager > > OU Bioinformatics Centre > SWD School of Pathology > South Parks Road > Oxford OX1 3RE > 01865 (2)75507 > > http://www.molbiol.ox.ac.uk > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From raj_dotcom at yahoo.com Wed Jun 5 08:29:45 2002 From: raj_dotcom at yahoo.com (narla rajinder reddy) Date: Wed, 5 Jun 2002 05:29:45 -0700 (PDT) Subject: [BiO BB] help Message-ID: <20020605122945.87773.qmail@web14806.mail.yahoo.com> my name is rajinder.i am an indian .i hold a bachelors degree in surgery and medicine.i am very much intrested in bioinformatics. i plan to move to US this fall.i have admission to georgia tech(m.s in bioinformatics).i want to make something big.could u help me by guiding me.please tell me about the software i need to learn and also any other pertinent details.u can give me a project if u wish best regards rajinder __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From Chunlei.Wu at uth.tmc.edu Wed Jun 5 11:57:14 2002 From: Chunlei.Wu at uth.tmc.edu (Chunlei Wu) Date: Wed, 05 Jun 2002 10:57:14 -0500 Subject: [BiO BB] Run server program remotely? Message-ID: <5.1.0.14.0.20020605104027.00b3a370@mail.uth.tmc.edu> It's good to show by an example: Supppose I can run "clustalw INFILE" on server terminal, is there a tool allowing me to run this command locally, just like I have clustalw installed locally? In the back, this tool will upload my local INFILE onto server and run "clustalw INFILE" on the server, and then send back the output to my local computer. The uploaded data file will be deleted from server after use. "Clustalw" here is just for example. Of course, I can install it on my local computer. But for those programs available only on server or those need strong server power, this tool (if exists) will give much convenience. Thanks. CL --- Bela Tiwari wrote: > >popular sequence analysis programs like GCG > package, etc. I can run those > >tools from the terminal of server side. I am > wondering if possible I can > >run those programs remotely just like my local > programs, but using server's > >power. Thus, I don't need to upload my data files > to server manually and > >then run it from server terminal. I just need send > the request to server, > >then server will upload the needed local data file > automatically and run > >the program ,then send me back the result. Sort of > a "local program simulator". > > Hello, > > I'm not sure this is exactly what you want, but > have you looked at the Pise Bioperl modules? > > http://www-alt.pasteur.fr/~letondal/Pise/ > > If you set up Pise on your server for your programs > of interest, you could > probably then use the Pise Bioperl modules to run > these programs from your > local machine. > > > Cheers > > Bela > > > > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > Dr. Bela Tiwari > Acting Manager > > OU Bioinformatics Centre > SWD School of Pathology > South Parks Road > Oxford OX1 3RE > 01865 (2)75507 > > http://www.molbiol.ox.ac.uk > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jprudhomme at ibcusa.com Wed Jun 5 16:44:42 2002 From: jprudhomme at ibcusa.com (Prudhomme, James) Date: Wed, 5 Jun 2002 16:44:42 -0400 Subject: [BiO BB] Post-Genomics Bioinformatics Conference, June 24-26, San Francisc o, CA Message-ID: Hello Group, I just want to inform all of you that IBC's Post-Genomics Bioinformatics conference is being held on June 24-26, 2002, Grand Hyatt San Francisco, San Francisco, CA. This conference brings together pharmaceutical, biotechnology, IT, software and hardware professionals for a 2 day conference to explore the dynamic advances in the applications of science in this new age of technology. For complete conference details and to register, visit: http://www.LifeSciencesInfo.com/2733/?source=2733-56 Distinguished Scientific Advisors: Sangtae Kim, Ph.D., Vice President and Information Officer, Eli Lilly Shankar Subramaniam, Ph.D., Professor, University of San Diego Carl Firth, M.A. (Cantab), Ph.D., Associate Director, Bioinformatics, Molecular Biology, AstraZeneca David Hodgson, Ph.D., Director of Bioinformatics, Pfizer Global Research and Development Brian Moldover, Ph.D., U.S., Head, Bioinformatics, Aventis Pharmaceuticals Here's a quick-overview of what you can expect to hear: I. Keynote Address by R&D Magazine 2001 Scientist of the Year, David Haussler, Ph.D., Director, Center for Biomolecular Science and Engineering, University of California, Santa Clara II. Developing Strategies in Information Technology III. Solving the Complexities of High-Throughput Biology To further the learning experience, IBC developed an intensive Pre-Conference Symposium on "Information Delivery - Infrastructure, Architecture and Process Integration" and a Pre-Conference Workshop on "Knowledge Management." Who will benefit by attending? This conference is designed for those working in Drug Discovery, Research & Development, Bioinformatics, Protein Informatics, Discovery Research, Computational Biology, Information Science, Information Architecture, Knowledge Management and Information Technology. Pass this message along to your colleagues, as this event is only a few weeks away! For further information or to register, contact IBC Life Sciences at (508) 616-5550 x1004 or e-mail reg at ibcusa.com You can also view complete details and register on-line: http://www.LifeSciencesInfo.com/2733/?source=2733-56 Hope to see you in San Francisco! Regards, Jim Prudhomme IBC From malcook at san.rr.com Fri Jun 7 02:07:10 2002 From: malcook at san.rr.com (Malcolm Cook) Date: Thu, 6 Jun 2002 23:07:10 -0700 Subject: [BiO BB] Run server program remotely? In-Reply-To: <5.1.0.14.0.20020605104027.00b3a370@mail.uth.tmc.edu> Message-ID: <000601c20de9$8f298840$18901e18@san.rr.com> if your programs take input on STDIN and output to STDOUT and STDERR, then you can use rsh (look it up in your unix manual pages) > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of > newgene at bigfoot.com > Sent: Wednesday, June 05, 2002 9:17 AM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Run server program remotely? > > > It's good to show by an example: > Supppose I can run "clustalw INFILE" on server terminal, is there a tool > allowing me to run this command locally, just like I have clustalw > installed locally? In the back, this tool will upload my local > INFILE onto > server and run "clustalw INFILE" on the server, and then send back the > output to my local computer. The uploaded data file will be deleted from > server after use. > > "Clustalw" here is just for example. Of course, I can install it on my > local computer. But for those programs available only on server or those > need strong server power, this tool (if exists) will give much > convenience. > > > Thanks. > > CL > > > > --- Bela Tiwari wrote: > > >popular sequence analysis programs like GCG > > package, etc. I can run those > > >tools from the terminal of server side. I am > > wondering if possible I can > > >run those programs remotely just like my local > > programs, but using server's > > >power. Thus, I don't need to upload my data files > > to server manually and > > >then run it from server terminal. I just need send > > the request to server, > > >then server will upload the needed local data file > > automatically and run > > >the program ,then send me back the result. Sort of > > a "local program simulator". > > > > Hello, > > > > I'm not sure this is exactly what you want, but > > have you looked at the Pise Bioperl modules? > > > > http://www-alt.pasteur.fr/~letondal/Pise/ > > > > If you set up Pise on your server for your programs > > of interest, you could > > probably then use the Pise Bioperl modules to run > > these programs from your > > local machine. > > > > > > Cheers > > > > Bela > > > > > > > > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > > Dr. Bela Tiwari > > Acting Manager > > > > OU Bioinformatics Centre > > SWD School of Pathology > > South Parks Road > > Oxford OX1 3RE > > 01865 (2)75507 > > > > http://www.molbiol.ox.ac.uk > > .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From bioinformaticsckk at yahoo.co.in Sun Jun 9 14:33:51 2002 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Sun, 9 Jun 2002 19:33:51 +0100 (BST) Subject: [BiO BB] perl script Message-ID: <20020609183351.76842.qmail@web8005.mail.in.yahoo.com> Hi everyone, I have text file with list of accession Ids for NcBI entries. I want to know wether any script available on the net to retieve the entries and store on my computer in text format. I want to do the same job with other databases like swissprot and embl. I know that atleast NCBI has the facility to upload the text file. But i want to make the job simpler. Any suggestions or ideas? Thanks in advance, Kiran ________________________________________________________________________ Everything you always wanted to know about cars and bikes,now at: http://in.autos.yahoo.com From pooja_jain25 at hotmail.com Mon Jun 10 02:02:22 2002 From: pooja_jain25 at hotmail.com (Pooja) Date: Mon, 10 Jun 2002 11:32:22 +0530 Subject: [BiO BB] perl script References: <20020609183351.76842.qmail@web8005.mail.in.yahoo.com> Message-ID: Hi, Find perl script following the below link. you may need to make some changes as per your requirement. http://bioinformatics.weizmann.ac.il/courses/prog2/perlBioinfo/GenBank.html Following links may be of some help to you : http://bioperl.org/Core/POD/Bio/DB/WebDBSeqI.html http://bioperl.org/Core/POD/Bio/DB/SwissProt.html Batch retrieval is provided by SwissProt http://www.expasy.org/sprot/sprot-retrieve-list.html Although EMBL doesn't provides batch retrieval but one can write a smart parser to retrieve the sequences. The accession numbers listed in a text file could be entered in search field (comma separated) at page following the below link: http://www.ebi.ac.uk/cgi-bin/emblfetch I may be missing something !! Good luck Pooja ----- Original Message ----- From: "kiran challapalli" To: Sent: Monday, June 10, 2002 12:03 AM Subject: [BiO BB] perl script > Hi everyone, > I have text file with list of accession Ids for NcBI > entries. I want to know wether any script available on > the net to retieve the entries and store on my > computer in text format. I want to do the same job > with other databases like swissprot and embl. > I know that atleast NCBI has the facility to upload > the text file. But i want to make the job simpler. > Any suggestions or ideas? > Thanks in advance, > Kiran > > ________________________________________________________________________ > Everything you always wanted to know about cars and bikes,now > at: http://in.autos.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From hz5 at njit.edu Tue Jun 11 13:35:46 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Tue, 11 Jun 2002 13:35:46 -0400 (EDT) Subject: [BiO BB] Web Based Sequence Manipulations In-Reply-To: <367404870.1022597790@spindle.bio.unc.edu> References: <367404870.1022597790@spindle.bio.unc.edu> Message-ID: <1023816946.3d0634f2144bf@mailhost.njit.edu> Hi Dale, You might want try this website: https://bioinformatics.org/sms/ It contains all basic manipulations to a DNA sequence, it is implemented by javascript, and is web based, you can also download and have a local copy on you computer, it only need unzip, no installation. Basically all html files serve the UI purpose and all javascript handle manipulations like reverse, complementary strand, translation, count GC content, codon usage, randomization, primer .... .... Hope this will help! If I could be further help, please email me at zhang at phri.org Sincerely, Haibo Zhang Quoting Dale Beach : > Hey Folks- > > I am hoping that your collective brains can help me find a web based > software suite to do some simple DNA sequence manipulations. Basically > I'd > like to find "Strider" on the web. > > I'll be teaching a "Molecular Biology for Science Wirters" class in two > > weeks. We will complete the class by cloning and sequenceing a gene, > and > we would like to do some sequence analysis with the students. Simply > looking at the sequence, translation, rev/comp sorts of things. > However, > we don't really want to install software on all of the classroom > computers. > (OK the computer support people gave us a hard time last year.) The > software should be quick and easy so that we can lead them through the > > analysis quickly as a group. > > Feel free to reply to my email address directly so that this doesn't > clutter the list. > > Thanks in advance for any helpful URLs! > dale > > PS- If you mention Pedro's Tools, please specify useful (read "not > Dead") > links. > > Dale Beach > 622 Fordham Hall CB3280 > University of North Carolina > Chapel Hill, NC 27599-3280 > > Voice- (919) 962-2363 > FAX - (919) 962-8461 > dbeach at email.unc.edu > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ================================================ Haibo Zhang Computational Biology, NJIT & Rutgers University Center for Applied Genomics http://afs13.njit.edu/~hz5 ================================================ From kishore at UDel.Edu Tue Jun 11 17:22:14 2002 From: kishore at UDel.Edu (Ravi Makkena) Date: Tue, 11 Jun 2002 17:22:14 -0400 Subject: [BiO BB] Swissprot to Genbank mapping References: <367404870.1022597790@spindle.bio.unc.edu> <1023816946.3d0634f2144bf@mailhost.njit.edu> Message-ID: <3D066A06.C6F95283@udel.edu> Hi , Could any one tell me how to map swissprot ids to genbank ids . (if there is any service which is available ) or a page which has both the swissprot and GI values would do ,,, I can parse them out thanks ravi -------------- next part -------------- A non-text attachment was scrubbed... Name: kishore.vcf Type: text/x-vcard Size: 200 bytes Desc: Card for Ravi Makkena URL: From clin at scimagix.com Tue Jun 11 17:28:04 2002 From: clin at scimagix.com (Chin Chin Lin) Date: Tue, 11 Jun 2002 14:28:04 -0700 Subject: [BiO BB] unsubscribe me to the list please Message-ID: <35C27F64C6616A44B9893A0C6F57CC561A1BB2@crawford.scimagix.com> Thanks, Chin Chin Lin Scimagix, Inc. 650-377-2375 www.scimagix.com From vinsensi at comp.nus.edu.sg Thu Jun 13 05:13:06 2002 From: vinsensi at comp.nus.edu.sg (Vinsensius Berlian Vega S N) Date: Thu, 13 Jun 2002 17:13:06 +0800 (GMT-8) Subject: [BiO BB] Docking software In-Reply-To: <3D066A06.C6F95283@udel.edu> Message-ID: Dear All, My friend and I are looking for a docking software for docking proteins and DNA. If you are aware of any, preferably the free ones, would you be so kind as to drop us an e-mail? Thanks in advance, Vega From pac at bcm.tmc.edu Thu Jun 13 11:49:45 2002 From: pac at bcm.tmc.edu (Pam Culpepper) Date: Thu, 13 Jun 2002 10:49:45 -0500 Subject: [BiO BB] ABI 3100 Format Message-ID: We have a lab that has recently purchased an ABI 3100. Unfortunately, our ABI file format reader doesn't like the new format. Does anyone have any code or links to code that they would like to share. We would appreciate Java, if possible. Thanks, Pam Culpepper Sr. Systems Programmer Biomedical Computing Facility Baylor College of Medicine Phone: 713-798-1077 Fax: 713-798-6822 From chriskim at cj.net Thu Jun 13 06:00:54 2002 From: chriskim at cj.net (=?utf-8?B?Q2hyaXMgS2ltXCjquYDssL3qsrhcKQ==?=) Date: Thu, 13 Jun 2002 11:00:54 +0100 Subject: [BiO BB] Docking software References: Message-ID: <008901c212c1$3bf6e6e0$2d3a4381@xenon> Hello Vega, What about using Autodock program? Drop by the following site : http://www.scripps.edu/pub/olson-web/doc/autodock/ Cheers, Chris. ----- Original Message ----- From: "Vinsensius Berlian Vega S N" To: Sent: Thursday, June 13, 2002 10:13 AM Subject: [BiO BB] Docking software > > Dear All, > > My friend and I are looking for a docking software for docking proteins > and DNA. If you are aware of any, preferably the free ones, would you be > so kind as to drop us an e-mail? > > Thanks in advance, > Vega > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From charles at moulinette.dyndns.org Thu Jun 13 12:51:15 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Thu, 13 Jun 2002 18:51:15 +0200 Subject: [BiO BB] ABI 3100 Format In-Reply-To: References: Message-ID: <20020613165115.GA2193@moulinette.dyndns.org> > Does anyone have any code or links to code that they would > like to share. You can have a look to abiview. It's part of EMBOSS, I think it's GPL. http://www.uk.embnet.org/Software/EMBOSS/Apps/abiview.html Charles From cmdobson at ucalgary.ca Thu Jun 13 16:07:17 2002 From: cmdobson at ucalgary.ca (C. Melissa Dobson) Date: Thu, 13 Jun 2002 14:07:17 -0600 Subject: [BiO BB] Docking software References: <008901c212c1$3bf6e6e0$2d3a4381@xenon> Message-ID: <3D08FB75.8050407@ucalgary.ca> I am wondering if there are any great programs for finding antigenicity sites - For antibody production. Many thanks Melissa From idoerg at cc.huji.ac.il Thu Jun 13 16:21:41 2002 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Thu, 13 Jun 2002 23:21:41 +0300 (GMT+0300) Subject: [BiO BB] Docking software In-Reply-To: <3D08FB75.8050407@ucalgary.ca> Message-ID: Try PreDep: http://bioinfo.md.huji.ac.il/marg/Teppred/mhc-bind/index.html On Thu, 13 Jun 2002, C. Melissa Dobson wrote: : : I am wondering if there are any great programs for finding antigenicity : sites -For antibody production. : : Many thanks : Melissa : : : _______________________________________________ : BiO_Bulletin_Board maillist- BiO_Bulletin_Board at bioinformatics.org : http://bioinformatics.org/mailman/listinfo/bio_bulletin_board : -- 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 vinsensi at comp.nus.edu.sg Thu Jun 13 20:53:32 2002 From: vinsensi at comp.nus.edu.sg (Vinsensius Berlian Vega S N) Date: Fri, 14 Jun 2002 08:53:32 +0800 (GMT-8) Subject: [BiO BB] Docking software In-Reply-To: <008901c212c1$3bf6e6e0$2d3a4381@xenon> Message-ID: Hi Chris, Thanks for the tip. We'll try it out. Regards, Vega On Thu, 13 Jun 2002, [utf-8] Chris Kim\(?????????\) wrote: > Hello Vega, > > What about using Autodock program? > Drop by the following site : > http://www.scripps.edu/pub/olson-web/doc/autodock/ > > Cheers, > > Chris. > > Dear All, > > > > My friend and I are looking for a docking software for docking proteins > > and DNA. If you are aware of any, preferably the free ones, would you be > > so kind as to drop us an e-mail? > > > > Thanks in advance, > > Vega > > From alinvr_yyoshino at hotmail.com Fri Jun 14 04:34:48 2002 From: alinvr_yyoshino at hotmail.com (=?iso-2022-jp?B?GyRCcXklLSEmJS1xeTZxJTklO248ISYlOSU5GyhCIBskQnIuJWcbKEI=?= =?iso-2022-jp?B?GyRCISYlZ247WnElOSU1ZWMlNSEmJTMbKEI=?=) Date: Fri, 14 Jun 2002 08:34:48 +0000 Subject: [BiO BB] To propose the project Message-ID: I would like to prospose the project 'AL in VR on Net'. AL -- Artificial Life VR -- Vertual Reality NET -- Internet I'm searching anyone, any company, any organization which collaborate with this project. Please see my home page 'www.geocities.com/alinvr_yyoshino'. If you have interrest, in detail, I will send mail concerning thechnical report. _________________________________________________________________ ??????????? MSN ?????????????????? http://messenger.msn.co.jp/ From whatifwhatnext at on.aibn.com Sat Jun 15 20:40:55 2002 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Sat, 15 Jun 2002 20:40:55 -0400 Subject: [BiO BB] To propose the project In-Reply-To: Message-ID: Gosh. Tell us more! Howard Oliver Principal What If What Next (TM) Consulting holiver at whatifwhatnext.com Tel: 416-638-8582 Mobile: 416-432-2764 www.whatifwhatnext.com -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of ???????????? ???????????? Sent: Friday, June 14, 2002 4:35 AM To: bbb at bioinformatics.org Subject: [BiO BB] To propose the project I would like to prospose the project 'AL in VR on Net'. AL -- Artificial Life VR -- Vertual Reality NET -- Internet I'm searching anyone, any company, any organization which collaborate with this project. Please see my home page 'www.geocities.com/alinvr_yyoshino'. If you have interrest, in detail, I will send mail concerning thechnical report. _________________________________________________________________ ??????????? MSN ?????????????????? http://messenger.msn.co.jp/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: Howard Oliver (E-mail).vcf Type: text/x-vcard Size: 530 bytes Desc: not available URL: From fernando at mail.nih.gov Sat Jun 15 15:53:38 2002 From: fernando at mail.nih.gov (Fernandez-Capetillo, Oscar (NCI)) Date: Sat, 15 Jun 2002 15:53:38 -0400 Subject: [BiO BB] Regular expressions Message-ID: <59445348FF4CD41182CF00508B6F779C0592E3F9@nihexchange11.nih.gov> Hi there, Does anybody know is there is any site that has source code for VB6 or VB.net and bioinformatics? In particular I am looking for useful classes to deal with both protein and DNA sequences. In addition, does anybody know of any good library for searching patterns with regular expressions in VB.NET? Thanks, Oskar From landman at scientificappliance.com Sat Jun 15 17:01:20 2002 From: landman at scientificappliance.com (Joe Landman) Date: 15 Jun 2002 17:01:20 -0400 Subject: [BiO BB] Re: Regular expressions Message-ID: <1024174881.2515.10.camel@protein.dtw.macsch.com> Please note that we have a biodevelopers group which might be able to help with this and any other programming type questions. I have taken the liberty of forwarding this to the list. One thing I might suggest, so as to avoid re-inventing stuff that already works, is to look at using the Bioperl system with the ActiveState Visual Perl (or Perl.NET) http://www.activestate.com/Products/Visual_Perl/, bio_bulletin_board at bioinformatics.org, create some .NET components, and utilize the existing services. Then you should be able to call these routines from VB. Has anyone done this yet? -----Forwarded Message----- From: "Fernandez-Capetillo, Oscar (NCI)" To: 'bio_bulletin_board at bioinformatics.org' Subject: [BiO BB] Regular expressions Date: 15 Jun 2002 15:53:38 -0400 Hi there, Does anybody know is there is any site that has source code for VB6 or VB.net and bioinformatics? In particular I am looking for useful classes to deal with both protein and DNA sequences. In addition, does anybody know of any good library for searching patterns with regular expressions in VB.NET? Thanks, Oskar _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joe Landman, email: landman at scientificappliance.com web : http://scientificappliance.com From Sameer_Mohta at satyam.com Sun Jun 16 23:43:01 2002 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Mon, 17 Jun 2002 09:13:01 +0530 Subject: [BiO BB] To propose the project Message-ID: <877B003B6F03D511A22E00B0D078E7A8542F2C@hst.satyam.com> It sounds exciting. Can you send some details. -----Original Message----- From: alinvr_yyoshino at hotmail.com [mailto:alinvr_yyoshino at hotmail.com] Sent: Friday, June 14, 2002 2:05 PM To: bbb at bioinformatics.org Subject: [BiO BB] To propose the project I would like to prospose the project 'AL in VR on Net'. AL -- Artificial Life VR -- Vertual Reality NET -- Internet I'm searching anyone, any company, any organization which collaborate with this project. Please see my home page 'www.geocities.com/alinvr_yyoshino'. If you have interrest, in detail, I will send mail concerning thechnical report. _________________________________________________________________ ??????????? MSN ?????????????????? http://messenger.msn.co.jp/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board ************************************************************************** This email (including any attachments) is intended for the sole use of the intended recipient/s and may contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or distribution or forwarding of any or all of the contents in this message is STRICTLY PROHIBITED. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. ************************************************************************** From Sameer_Mohta at satyam.com Mon Jun 17 00:07:57 2002 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Mon, 17 Jun 2002 09:37:57 +0530 Subject: [BiO BB] QSAR Message-ID: <877B003B6F03D511A22E00B0D078E7A8542F30@hst.satyam.com> I am looking for QSAR data that i can use in writing some algorithms on QSAR. Is there any site that provides QSAR data ? sam ************************************************************************** This email (including any attachments) is intended for the sole use of the intended recipient/s and may contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or distribution or forwarding of any or all of the contents in this message is STRICTLY PROHIBITED. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. ************************************************************************** From subba.raju at hbh.ilabsgroup.com Mon Jun 17 02:00:25 2002 From: subba.raju at hbh.ilabsgroup.com (Subba.Raju) Date: Mon, 17 Jun 2002 11:30:25 +0530 Subject: [BiO BB] clustering algo components Message-ID: <759BC7ED1B0BD6118BC400B0D0E16A1F652F85@BHILLS3NT002> hi, does any body has any idea about available data clustering algorithmic components( hierarchical clustering, k-means, self organizing maps, principal component analysis) in any open source projects. i checked with biojava, i have no idea about bioperl and other open source projects. Thanks for ur earlier attention. cheers Subba From alinvr_yyoshino at hotmail.com Mon Jun 17 07:56:31 2002 From: alinvr_yyoshino at hotmail.com (=?iso-2022-jp?B?GyRCcXklLSEmJS1xeTZxJTklO248ISYlOSU5GyhCIBskQnIuJWcbKEI=?= =?iso-2022-jp?B?GyRCISYlZ247WnElOSU1ZWMlNSEmJTMbKEI=?=) Date: Mon, 17 Jun 2002 11:56:31 +0000 Subject: [BiO BB] To propose the project Message-ID: Thank you for your mail. I think this project needs multidisciplinery knowledge Management. I will send you report concerning biological aspect. _________________________________________________________________ ??????????? MSN ?????????????????? http://messenger.msn.co.jp/ From landman at scientificappliance.com Mon Jun 17 05:43:45 2002 From: landman at scientificappliance.com (Joe Landman) Date: 17 Jun 2002 05:43:45 -0400 Subject: [BiO BB] for software development/algorithm questions please post to the biodevelopers list Message-ID: <1024307026.2241.4.camel@protein.dtw.macsch.com> Hi Folks: Just a note to everyone posting questions and responses on development issues. We have a nice email group set up specifically for this, named biodevelopers. To see the main page or archives, go to main: https://bioinformatics.org/mailman/listinfo/biodevelopers archives: https://bioinformatics.org/pipermail/biodevelopers/ The intent of this list/group is to help get you answers to these questsions. Please do consider posting your questions (or at least cross posting when appropriate), so that the message may reach its intended audience. Thanks! Joe -- Joe Landman, email: landman at scientificappliance.com web : http://scientificappliance.com From pajailwala at yahoo.com Mon Jun 17 09:14:39 2002 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Mon, 17 Jun 2002 06:14:39 -0700 (PDT) Subject: [BiO BB] clustering algo components In-Reply-To: <759BC7ED1B0BD6118BC400B0D0E16A1F652F85@BHILLS3NT002> Message-ID: <20020617131439.78458.qmail@web12306.mail.yahoo.com> Hi, Check the free analysis software called 'R'. It is open-source and the source code is also downloadable. It has most of the common clustering algorithms programmed. Parthav Jailwala --- "Subba.Raju" wrote: > hi, > does any body has any idea about available data clustering > algorithmic > components( hierarchical clustering, k-means, self organizing > maps, > principal component analysis) in any open source projects. i > checked with > biojava, i have no idea about bioperl and other open source > projects. > Thanks for ur earlier attention. > cheers > Subba > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== ---------------------------------------------------------- The trouble with being punctual is that nobody's there to appreciate it ---------------------------------------------------------- Parthav Jailwala Ph : Home : (414) 283 0403 Mobile : (414) 305 9633 __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From alinvr_yyoshino at hotmail.com Mon Jun 17 07:57:07 2002 From: alinvr_yyoshino at hotmail.com (=?iso-2022-jp?B?GyRCcXklLSEmJS1xeTZxJTklO248ISYlOSU5GyhCIBskQnIuJWcbKEI=?= =?iso-2022-jp?B?GyRCISYlZ247WnElOSU1ZWMlNSEmJTMbKEI=?=) Date: Mon, 17 Jun 2002 11:57:07 +0000 Subject: [BiO BB] To propose the project Message-ID: Thank you for your mail. I think this project needs multidisciplinery knowledge Management. I will send you report concerning biological aspect. _________________________________________________________________ ?????????????????????? MSN ??????? http://shopping.msn.co.jp/ -------------- next part -------------- A non-text attachment was scrubbed... Name: proposal.doc Type: application/msword Size: 33792 bytes Desc: not available URL: From greg at tekadence.net Tue Jun 18 19:11:41 2002 From: greg at tekadence.net (Greg Deocampo) Date: Tue, 18 Jun 2002 16:11:41 -0700 Subject: [BiO BB] To propose the project In-Reply-To: Message-ID: <006401c2171d$8f131c80$2ce8b3d1@Now> hello, "artificial life, virtual reality, and the internet"--- powerful techniques for developing medically useful predictive biosimulations, which is an area of software engineering i have been working in. i think it would be great for this group to brainjam and work on something, and would love to participate, especially from the software and visualization perspectives. I have worked on various projects exploring different approaches to using software to model and predict the behavior of complex systems, particularly the human immune system. these experiences led me to work on an enabling software technology for creating these kinds of complex software systems-- an "application authoring" technology-- something that does the kinds of things for programming that a word processor does for writing. a product goal is to enable non-software-engineering content experts, like immunologists, to be able to develop scientific quality software applications without having to supply expert level programming skills. if a user does have engineering expertise, i believe the product dramatically amplifies their efforts. there is also functionality designed to enhance group efforts. i believe this tool would be of interest to this newsgroup. i'd be happy to assist anyone interested in using the the tool in bioresearch. the tool is currently called Magik, and it's in late beta, and it's available for free here: http://www.tekadence.net. it's a good tool i think for quickly experimenting with net applications like alife and vr. another project that touches upon this thread: a relatively inexpensive system for shared virtual realities (which can be authored easily with Magik). we refer to it as a "surround cinema" system, a visual version of surround sound. there are many possible cinema configurations; most recently we have been configuring the system in geodesic domes. some useful info about it here: http://www.obscuradigital.com. i am using this system to develop a vr environment for scientific visualization-- something that does not require isolating suits, head rigs etc but instead is more of a group experience, the way going to a movie or attending a lecture is. currently, i am working on using magik to author medically useful data-driven software models and simulations with a surround cinema system as a scientific visualization engine. i'm hoping to get some of these efforts going open-source style. by way of getting back to an item in this thread...in addition to wanting to help with "AL in VR on NET", I also seek help working on an open-source virtual reality based on public genomic, proteomic etc data with a focus on the T cell response seeya-! greg /* /* Greg Deocampo Research & Development /* 3232523863 /* -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of ???L?E?L?????X?Z???E?X?X ?????E???????X?T???T?E?R Sent: Friday, June 14, 2002 1:35 AM To: bbb at bioinformatics.org Subject: [BiO BB] To propose the project I would like to prospose the project 'AL in VR on Net'. AL -- Artificial Life VR -- Vertual Reality NET -- Internet I'm searching anyone, any company, any organization which collaborate with this project. Please see my home page 'www.geocities.com/alinvr_yyoshino'. If you have interrest, in detail, I will send mail concerning thechnical report. _________________________________________________________________ ??????????? MSN ?????????????????? http://messenger.msn.co.jp/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board --- EBNMSG#32351//Incoming mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.371 / Virus Database: 206 - Release Date: 6/13/2002 --- EBNMSG#64634631//Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.371 / Virus Database: 206 - Release Date: 6/13/2002 From alexis at gambis.com Tue Jun 18 20:53:44 2002 From: alexis at gambis.com (Alexis Gambis) Date: Tue, 18 Jun 2002 17:53:44 -0700 Subject: [BiO BB] Alexis Gambis Message-ID: Hi, My name is Alexis Gambis. I am officially from paris, France but after graduating with a Scientific Baccaulaureate, I came to college in the United States. I will be a senior student majoring in bioinformatics at Bard College, which is located in upstate New York. I have already stepped foot into my senior thesis this summer. In collaboration with my advisor Doctor Rob Cutler, I am working on building up a dataset of chromosomal syntenic regions across all 64 sequenced bacterial genomes. I created syntenic unit ids for each corresponding structure ... what I mean by syntenic unit is RNA structures, non-translated genes and proteins. I couldn't narrow myself down to using the COG (cluster of orthologous groups of proteins) Ids to infer relationship b/w species because they are stringent to functionality and are only given to proteins. Eventually after doing the meticulous perl programming labor, I will use my syntenic region analysis to pinpoint the chromosomal rearrangements/splits and build a phylogenetic tree. This is a little grain of my research that I thought might interest you to give you have a sense of who I am, what I know and how that fits into what you are looking for. I can program in scheme, C, java, perl (+ bioperl modules) and I usually work on a Linux workstation. In terms of web handling, I know html, xml and cgi. I have a solid knowledge in both molecular biology and computer science. I have also delt several times with relational databases such as BerkeleyDB and know how to handle SQL to access/retrieve information from these type of databases. If you could inform me on the available scholarships/internships and any advice worthwile for a bioinformatics student (for ex: graduate school), that would be highly appreciated ... thank you in advance, Alexis Gambis From prasadp77ie at yahoo.ie Wed Jun 19 07:10:03 2002 From: prasadp77ie at yahoo.ie (Prasad Phirke) Date: Wed, 19 Jun 2002 04:10:03 -0700 (PDT) Subject: [BiO BB] Ph D Studentship Message-ID: <20020619111003.19804.qmail@web21009.mail.yahoo.com> Hi All, I am currently pursuing Masters in Biological Sciences in Dublin CIty University, Ireland. I am looking for Ph D Studentship in the project involving a blend of Bioinformatics and classical Molecular Biology in Europe. I will be thankful if anyone can suggest the universities or prof.s having such kind of studentships. I have tried to my level best but I found only one university where I found perfect 'my' kind of project but at this point of time, I am on reserved list because of my non - EU nationality status. Hope to look forward some positive replies. Thanks in advance Prasad ===== Prasad H. PhirkePost - Grad Student,Dublin City University,X1 78, School Of Biotechnology,Glasnevin, Dublin - 9,IRELAND.Mobile - +353 (0)85 721 5335Lab- +353 1 700 5908* __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From jezza_com at hotmail.com Wed Jun 19 11:54:04 2002 From: jezza_com at hotmail.com (Jeremy Smith) Date: Wed, 19 Jun 2002 16:54:04 +0100 Subject: [BiO BB] UK MRes Bioinformatician graduate seeks internships/positions globally. Message-ID: Hi there , I hold a MRes in Bioinformatics (University of York, UK), in addition I have commercial IT experience with Perl, C++, XML, Linux, and many common bioinformatics skills/software. I am confident in my programming skills. With regards to salary I am very flexible, and would be prepared to fly globally to any bioinformatics internship/positions available. I am a digilent worker. Please email me if you are interested, Regards, Jeremy Smith. _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com From niyati2212 at yahoo.co.in Thu Jun 20 02:28:41 2002 From: niyati2212 at yahoo.co.in (=?iso-8859-1?q?Niyati=20Arora?=) Date: Thu, 20 Jun 2002 07:28:41 +0100 (BST) Subject: [BiO BB] Great News For BioInformatics Aspirants!!! Message-ID: <20020620062841.33951.qmail@web8006.mail.in.yahoo.com> Great News for BioInformatics Students !!! Hello Friends, We are the Students of "Post Graduate Diploma in BioInformatics" at "BioInformatics Institute of India". This is a One yr Correspondence Course for the students both in India and Abroad. In all there are 8 papers to take up, & a student has the option of taking more papers. This course has to be completed in a maximum of 3 years. BioInformatics Institute of India(BII) has been setup as a premier Biological, Biomedical, Chemical and Informatics Institution, for the promotion, growth and prosperity of BioInformatics.The institute has been promoted as a nonprofit making scientific educational, R&D and development centre.The aim and vision of this Institute is to provide a platform for individuals, professionals, R&D organisations, Pharmaceutical & Software companies so as to utilize & harness people's potentials. Some of the main course features are: --------------------------------------------------------- Overseas Distance Education Programme Delivery Methodolgy --------------------------------------------------------- - Study Material for the courses is sent to the students in form of Books at their postal address. - Students recieve email and Internet support. - Overseas students can interact directly Programme Incharge and a Technical Support Specialist for any queries and problems. - Support is provided for software usage and applications from BII for succesful practical experience. - Final Assesment is done on the basis of an online exam. - Placement Assistance is provided Globally. Fee Structure:: Indian Applicants: - Rs.3950/-(for general candidates) - Rs.3350/-(for SC,ST,OBC, & Government Employees/physically handicapped) Foreign Applicants:: - US $400 ------------------------------------ A Brief Overview of Course Contents: ------------------------------------ -Introduction to BioInformatics [Compulsory] -BioStatistics [Compulsory] -Basics of BioComputing (Office Packages,Internet Architecture & Framework,VisualBasic6.0,Unix O/S) -BioChemistry -Molecular Genetics -MicroBiology -Virology -Immunology -BioMarkup Languages (HTML,CML,XML,BSML) -Biological Databases & their Management [Compulsory] (Database Concepts,Biological Database,Sequence Database) -BioInformatics Softwares (Clustal W,ALSCRIPT,Oligo Primer Analysis Software,Rasmol,MOLSCRIPT,Phylip,Tree View, And many more advanced softwares) -Computational Biology [Compulsory] -Genetic Engineering -Industrial Fermentation Technology -BioProgramming (C++, BioPerl, BioJava) -Metabolic Concepts & Bioenergetics Of these 4 papers are compulsory(as marked) & 4 papers are optional(from the remaining). If Anybody is interested in joining this course , then please contact us at this address as early as possible. niyati2212 at yahoo.co.in or info at bioinformaticscentre.org and plz visit: www.bioinformaticscentre.org With Regards Nitin Johri , Niyati Arora Delhi India --------------------------------- Don't miss Yahoo India's Coverage of 2002 FIFA World Cup -------------- next part -------------- An HTML attachment was scrubbed... URL: From drjohn08318 at yahoo.com Sun Jun 23 16:52:35 2002 From: drjohn08318 at yahoo.com (John Hoey) Date: Sun, 23 Jun 2002 13:52:35 -0700 (PDT) Subject: [BiO BB] Sr. Bioinformatics Scientist position: Boston area Message-ID: <20020623205235.51960.qmail@web14408.mail.yahoo.com> Hello: I am a Senior Consultant with an Executive Search firm in the Northeast. One of our clients in the Boston area has an opening for a Sr. Bioinformatics Scientist. If you or anyone you know might be interested in exploring this job opportunity, please contact me at the following address as soon as possible: drjohn08318 at yahoo.com Sincerely, John G. Hoey, Ph.D Senior Consultant AE Feldman Associates, Inc. --------------------------------- Do You Yahoo!? Sign-up for Video Highlights of 2002 FIFA World Cup -------------- next part -------------- An HTML attachment was scrubbed... URL: