From vishnub at pgsolutions.com Tue Apr 3 09:51:11 2001 From: vishnub at pgsolutions.com (vishnub at pgsolutions.com) Date: Tue, 3 Apr 2001 19:21:11 +0530 Subject: [BiO BB] Re: BIO_Bulletin_Board -- confirmation of subscription -- request 618355 Message-ID: Thanks and Regards, Vishnu ________________________________________________________________________________________________________ Vishnuprasad B. Phoenix Global Solutions (I) Pvt. Ltd., No. 5, Vanivilas Road, Basavanagudi, Bangalore - 560 004 Ph: 91-080-6674516 to 19 Fax: 91-080-6674515 Extn: 2122 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. 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To confirm the request, please send a message to bio_bulletin_board-request at bioinformatics.org, and either: - maintain the subject line as is (the reply's additional "Re:" is ok), - or include the following line - and only the following line - in the message body: confirm 618355 (Simply sending a 'reply' to this message should work from most email interfaces, since that usually leaves the subject line in the right form.) If you do not wish to subscribe to this list, please simply disregard this message. Send questions to bio_bulletin_board-admin at bioinformatics.org. From jeff at bioinformatics.org Tue Apr 3 12:00:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 03 Apr 2001 16:00:38 +0000 Subject: [BiO BB] [Fwd: Need Help on Bio Informatics] Message-ID: <3AC9F3A6.B5CCA750@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Vishnu Subject: Need Help on Bio Informatics Date: Tue, 3 Apr 2001 09:28:07 -0400 Size: 1095 URL: From fnievinski at cpovo.net Tue Apr 3 16:42:10 2001 From: fnievinski at cpovo.net (Felipe G. Nievinski) Date: Tue, 03 Apr 2001 17:42:10 -0300 Subject: [BiO BB] Re: Need Help on Bio Informatics Message-ID: <200104031742100760.0066DA4B@smtp.cpovo.net> Dear Visnu, there are some good posts about 'Introducing into Bioinformatics' on the list archives: http://bioinformatics.org/pipermail/bio_bulletin_board/2001-February/ It can be a starting point. regards, Felipe Nievinski. --------------5DF4F39C2B4F0CF5EDB456E8 Content-Type: message/rfc822 X-F: Tue Apr 03 09:25:58 2001 Received: from www.bioinformatics.org [129.63.144.25] by mercury.capeonramp.com with ESMTP (SMTPD32-6.00) id AF6510B1010C; Tue, 03 Apr 2001 09:25:57 -0400 Received: (from webmaster at localhost) by www.bioinformatics.org (8.9.3/8.8.7) id JAA25902; Tue, 3 Apr 2001 09:28:07 -0400 Date: Tue, 3 Apr 2001 09:28:07 -0400 Message-Id: <200104031328.JAA25902 at www.bioinformatics.org> To: jeff at bioinformatics.org Subject: Need Help on Bio Informatics From: Vishnu X-RCPT-TO: Dear Sir, My spouse is a scientist in biotechnology company and she is MSc. BioChem., I would like to help her by gathering informatin about preparing for getting in to Bio-Informatics Field. Please let me know how should she prepare for this. What are the pre requisites for this area and as we are living in Bangalore, Where can we approach for getting training/joining courses etc. Pleas let me know in detal. Thanking you, Yours Sincerely, Vishnu Regards, Vishnu From jeff at bioinformatics.org Wed Apr 4 14:13:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 04 Apr 2001 14:13:38 -0400 Subject: [BiO BB] Fwd: Need Help on Bio Informatics Message-ID: <3ACB6452.31658E8D@bioinformatics.org> This got sent to me instead. Jeff -------------- next part -------------- An embedded message was scrubbed... From: dilip gosar Subject: Re: [[BiO BB] [Fwd: Need Help on Bio Informatics]] Date: 4 Apr 2001 11:50:32 MDT Size: 1555 URL: From gladium at terra.com.br Mon Apr 9 23:00:27 2001 From: gladium at terra.com.br (Marcos Oliveira de Carvalho) Date: Tue, 10 Apr 2001 00:00:27 -0300 Subject: [BiO BB] an idea Message-ID: Hi, In this mail I would like to send an idea... Everybody knows about the peer-to-peer technology (like Napster and Tijit)...so...why not build a software that make possible the (free) search and transfer of scientific papers (pdfs,ps,txt, etc) between users of the software? The program can create an index of the texts including the authors name, title of the article and keywords, in this manner, we can create an virtual community to share or scientific papers. If somebody can build this software, please, do it! Marcos Oliveira de Carvalho Pibic/CNPq researcher Molecular Biology Lab. - Federal University of Santa Maria - Brazil - www.ufsm.br/labdros/ From mavcunha at rbp.fmrp.usp.br Tue Apr 10 03:16:44 2001 From: mavcunha at rbp.fmrp.usp.br (Marco Aurelio Valtas Cunha) Date: Tue, 10 Apr 2001 03:16:44 -0400 Subject: [BiO BB] an idea References: Message-ID: <3AD2B35C.3000006@rbp.fmrp.usp.br> The Idea is good, but scientific papers, aren't suject to licences too? Say you have a subscription of Nature, is legal share the pdf file of the article even if others don't have the subscription? Marcos Oliveira de Carvalho wrote: > Hi, > > In this mail I would like to send an idea... > Everybody knows about the peer-to-peer technology (like Napster and > Tijit)...so...why not build a software that make possible the (free) search > and transfer of scientific papers (pdfs,ps,txt, etc) between users of the > software? The program can create an index of the texts including the authors > name, title of the article and keywords, in this manner, we can create an > virtual community to share or scientific papers. > If somebody can build this software, please, do it! > > Marcos Oliveira de Carvalho > Pibic/CNPq researcher > Molecular Biology Lab. - Federal University of Santa Maria - Brazil - > www.ufsm.br/labdros/ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Tue Apr 10 12:33:29 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 10 Apr 2001 16:33:29 +0000 Subject: [BiO BB] an idea References: <3AD2B35C.3000006@rbp.fmrp.usp.br> Message-ID: <3AD335D9.2AA98EC7@bioinformatics.org> Marco Aurelio Valtas Cunha wrote: > > The Idea is good, but scientific papers, aren't suject to licences too? > Say you have a subscription of Nature, is legal share the pdf file of > the article even if others don't have the subscription? Gnutella is a well-established P2P system capable of transferring any kind of file, not just MP3's. It would work for scientific papers in PDF or any other format. HOWEVER, as you pointed out, it is ILLEGAL to distribute (i.e., "copy") copyrighted material without the permission of the copyright holders. In this case, that would be the publishers (e.g., Nature or Macmillan). Gnutella is not a centralized system, as Napster is/was, so there wouldn't be one company for the publishers to sue. But, it is likely that they would go after individuals and anyone promoting the idea. I am strongly in favor of freely distributed scientific publications, and I am against the strict enforcement of this kind of copyright and even ownership of scientific publications by publishers (I see copyright law as something more relevant to creative works). HOWEVER, I believe that we should respect the law and put our efforts toward changing the status quo, rather than breaking the law. 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 gladium at terra.com.br Tue Apr 10 22:23:01 2001 From: gladium at terra.com.br (Marcos Oliveira de Carvalho) Date: Tue, 10 Apr 2001 23:23:01 -0300 Subject: [BiO BB] RES: BiO_Bulletin...just free papers In-Reply-To: <200104101600.MAA10175@www.bioinformatics.org> Message-ID: Well...yes...pdf files like Nature papers are subjects to licences...but others (like Genetics papers - genetics.org ) are free some time after the publication, and others text files don't have licenses . The goal of the software is provide a tool to search free pdfs among the users. I think that it is possible. best regards Marcos Oliveira de Carvalho 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. an idea (Marcos Oliveira de Carvalho) 2. Re: an idea (Marco Aurelio Valtas Cunha) --__--__-- Message: 1 From: "Marcos Oliveira de Carvalho" To: Subject: [BiO BB] an idea Date: Tue, 10 Apr 2001 00:00:27 -0300 charset="iso-8859-1" Reply-To: bio_bulletin_board at bioinformatics.org Hi, In this mail I would like to send an idea... Everybody knows about the peer-to-peer technology (like Napster and Tijit)...so...why not build a software that make possible the (free) search and transfer of scientific papers (pdfs,ps,txt, etc) between users of the software? The program can create an index of the texts including the authors name, title of the article and keywords, in this manner, we can create an virtual community to share or scientific papers. If somebody can build this software, please, do it! Marcos Oliveira de Carvalho Pibic/CNPq researcher Molecular Biology Lab. - Federal University of Santa Maria - Brazil - www.ufsm.br/labdros/ --__--__-- Message: 2 Date: Tue, 10 Apr 2001 03:16:44 -0400 From: Marco Aurelio Valtas Cunha To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] an idea Reply-To: bio_bulletin_board at bioinformatics.org The Idea is good, but scientific papers, aren't suject to licences too? Say you have a subscription of Nature, is legal share the pdf file of the article even if others don't have the subscription? _______________________________________________ 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 indraneel at indialine.org Fri Apr 13 15:15:41 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Fri, 13 Apr 2001 14:15:41 -0500 Subject: [BiO BB] an idea In-Reply-To: <3AD335D9.2AA98EC7@bioinformatics.org>; from jeff@bioinformatics.org on Tue, Apr 10, 2001 at 04:33:29PM +0000 References: <3AD2B35C.3000006@rbp.fmrp.usp.br> <3AD335D9.2AA98EC7@bioinformatics.org> Message-ID: <20010413141541.B21352@indialine.org> Hi, In addition to the hugely popular gnutella, there is also the freenet project (http://www.freenetproject.org) which aims to target exactly this aspect. It's aim is to build a free network of data where you cannot control which data is being passed through your machine. Freenet is for web pages but it's sister project espra (http://espra.net) is for any files which can pass in the same way. In any case copying nature pdf files by the so called more educated people (who read nature) might not exactly be an appealing idea to most. A more elegant solution would probably be, as Harold Varmus (ex Director of NIH) suggests, to openly publish the papers in the first place. There are a few sites (including pubmed central) which give out free copies of not-so-recent publications. I am yet to find a peer reviewed site for open free online publication of scientific papers (There was a link on google about 6 months back, but it doesn't appear now and I can't recall it :-( \Indraneel On Tue, Apr 10, 2001 at 04:33:29PM +0000, J.W. Bizzaro wrote: > Marco Aurelio Valtas Cunha wrote: > > > > The Idea is good, but scientific papers, aren't suject to licences too? > > Say you have a subscription of Nature, is legal share the pdf file of > > the article even if others don't have the subscription? > > Gnutella is a well-established P2P system capable of transferring any kind of -- http://www.indialine.org From jeff at bioinformatics.org Fri Apr 13 17:09:47 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 13 Apr 2001 17:09:47 -0400 Subject: [BiO BB] an idea References: <3AD2B35C.3000006@rbp.fmrp.usp.br> <3AD335D9.2AA98EC7@bioinformatics.org> <20010413141541.B21352@indialine.org> Message-ID: <3AD76B1B.1A6DD088@bioinformatics.org> Indraneel Majumdar wrote: > > I am yet to find a peer reviewed site for open free online > publication of scientific papers (There was a link on google > about 6 months back, but it doesn't appear now and I can't > recall it :-( I got this message from Mark Lawrence: ``BioMed Central (www.biomedcentral.com) is a company publishing peer-reviewed primary research across the biomedical sciences, including bioinformatics (see BMC Bioinformatics at www.biomedcentral.com/1471-2105/) entirely free of charge - no subscription or even registration is necessary to view published papers in full. Furthermore, copyright in these papers remains with the authors.'' Cheers. Jeff From indraneel at indialine.org Sat Apr 14 20:49:11 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sat, 14 Apr 2001 19:49:11 -0500 Subject: [BiO BB] an idea In-Reply-To: <3AD76B1B.1A6DD088@bioinformatics.org>; from jeff@bioinformatics.org on Fri, Apr 13, 2001 at 05:09:47PM -0400 References: <3AD2B35C.3000006@rbp.fmrp.usp.br> <3AD335D9.2AA98EC7@bioinformatics.org> <20010413141541.B21352@indialine.org> <3AD76B1B.1A6DD088@bioinformatics.org> Message-ID: <20010414194911.A1402@indialine.org> Thanks, guess I overlooked that one because of the .com at the end. This is good, but I'm also searching for a .org site for the same and not only limited to medicine and the life sciences. Thanks, Indraneel On Fri, Apr 13, 2001 at 05:09:47PM -0400, J.W. Bizzaro wrote: > > I got this message from Mark Lawrence: > > ``BioMed Central (www.biomedcentral.com) is a company publishing > peer-reviewed primary research across the biomedical sciences, including -- http://www.indialine.org From jeff at bioinformatics.org Mon Apr 16 10:38:40 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 16 Apr 2001 14:38:40 +0000 Subject: [BiO BB] [Fwd: Extracting helix/strand sequences from pdb:] Message-ID: <3ADB03F0.68795560@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Mathura, Venkatarajan S." Subject: Extracting helix/strand sequences from pdb: Date: Mon, 16 Apr 2001 09:32:58 -0500 Size: 1626 URL: From bioinformaticsckk at yahoo.co.in Tue Apr 17 00:09:39 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?=20?=) Date: Tue, 17 Apr 2001 05:09:39 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #21 - 1 msg In-Reply-To: <200104161600.MAA24062@www.bioinformatics.org> Message-ID: <20010417040939.46326.qmail@web8004.mail.in.yahoo.com> Dear Venkat, If you want just the amino acid sequence of the helix or a sheet, you may get that from any modelling program like rasmol wherein you have the option to see the aminoacid sequence corresponding to the structure. for nucleotide sequence, you may have to convert from protein to nucleotide sequence (different online tools are available). Regards, Kiran kumar.c --- bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body > 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific than > "Re: Contents of BiO_Bulletin_Board digest...") > > > Today's Topics: > > 1. [Fwd: Extracting helix/strand sequences from > pdb:] (J.W. Bizzaro) > > --__--__-- > > Message: 1 > Date: Mon, 16 Apr 2001 14:38:40 +0000 > From: "J.W. Bizzaro" > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] [Fwd: Extracting helix/strand > sequences from pdb:] > boundary="------------27DBC7D91E0DE1599BB4E41E" > Reply-To: bio_bulletin_board at bioinformatics.org > > This is a multi-part message in MIME format. > --------------27DBC7D91E0DE1599BB4E41E > Content-Type: text/plain; charset=us-ascii > Content-Transfer-Encoding: 7bit > > > --------------27DBC7D91E0DE1599BB4E41E > Content-Type: message/rfc822 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > X-F: Mon Apr 16 10:26:31 2001 > Received: from www.bioinformatics.org > [129.63.144.25] by mercury.capeonramp.com with ESMTP > (SMTPD32-6.00) id A1171AAC014A; Mon, 16 Apr 2001 > 10:26:31 -0400 > Received: from www.bioinformatics.org > (IDENT:mail at www.bioinformatics.org [127.0.0.1]) > by www.bioinformatics.org (8.9.3/8.8.7) with SMTP > id KAA23406; > Mon, 16 Apr 2001 10:27:34 -0400 > Received: from is1 (is1.utmb.edu [129.109.52.216]) > by www.bioinformatics.org (8.9.3/8.8.7) with ESMTP > id KAA23398 > for ; > Mon, 16 Apr 2001 10:27:33 -0400 > Received: from exchange6.utmb.edu (email.utmb.edu > [129.109.215.129]) > by is1 (PMDF V6.0-24 #38124) with ESMTP id > <0GBW005PU2UL7C at is1> for > bio_bulletin_board-admin at bioinformatics.org; Mon, > 16 Apr 2001 09:27:57 -0500 (CDT) > Received: by exchange6.utmb.edu with Internet Mail > Service (5.5.2653.19) > id ; Mon, 16 Apr 2001 09:32:15 -0500 > Content-return: allowed > Date: Mon, 16 Apr 2001 09:32:58 -0500 > From: "Mathura, Venkatarajan S." > Subject: Extracting helix/strand sequences from pdb: > To: "'bio_bulletin_board-admin at bioinformatics.org '" > > Message-id: > > MIME-version: 1.0 > X-Mailer: Internet Mail Service (5.5.2653.19) > Content-type: text/plain; charset=ISO-8859-1 > X-RCPT-TO: > > Hello, > > Do anyone have a script or know of a source where > I can obtain the > sequences of helix/sheet > from pdb file. Any help will be appreciated! > > Thanks, > > Venkat > > > --------------27DBC7D91E0DE1599BB4E41E-- > > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > --__--__---- > > End of BiO_Bulletin_Board Digest ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com From jeff at bioinformatics.org Tue Apr 17 13:52:05 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 17 Apr 2001 13:52:05 -0400 Subject: [BiO BB] [Fwd: finding sequence helix/sheet in pdb] Message-ID: <3ADC82C5.C0366AA0@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Mathura, Venkatarajan S." Subject: RE: finding sequence helix/sheet in pdb Date: Tue, 17 Apr 2001 12:51:01 -0500 Size: 7726 URL: From vsmathur at utmb.edu Tue Apr 17 15:40:56 2001 From: vsmathur at utmb.edu (Mathura, Venkatarajan S.) Date: Tue, 17 Apr 2001 14:40:56 -0500 Subject: [BiO BB] FW: finding sequence helix/sheet in pdb Message-ID: Thanks kiran. I know I can do it with RASMOl/MOLMOL but I would like to do it an very large scale. I mean the entire pdb (just for proteins) or atleast non-redundant structures. Currently I am using the pdb header HELIX or SHEET information. The script looks for starting/ending helix and sheet residue info, and reads out single letter seq for the sec structure regions using the residue number and start/end info. I have already done this for 2096 pdb files and was quiet successful. But the script doesn't handle cases where the residue numbers were numbered by 15A,16B etc (particularly in case of mutation). I am looking for someone who have already extracted all helix sequences in the pdb (I mean 12000 structures) or who have scripts that can better handle the problem mentioned above. I would like to stick to the secondary structure information from the pdb header (as supplied by authors) rather using other programs to write out sec structures from just co-ordinates alone. Any response will be appreciated, Thanks, venkat > > Hello, > > Do anyone have a script or know of a source where > I can obtain the > sequences of helix/sheet > from pdb file. Any help will be appreciated! > > Thanks, > > Venkat > > > --------------27DBC7D91E0DE1599BB4E41E-- > > > > > -- __--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- __--__-- -- > > End of BiO_Bulletin_Board Digest ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com --__--__-- _______________________________________________ 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 jeff at bioinformatics.org Tue Apr 17 17:50:31 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 17 Apr 2001 17:50:31 -0400 Subject: [BiO BB] software categories Message-ID: <3ADCBAA7.D31776D@bioinformatics.org> Greetings. You may have noticed that "Molecular Linux" has moved to Bioinformatics.org. It is a registry/repository of bioinformatics tools that run on Linux (other platforms to follow). We also have "The Open Lab", which is a project hosting system based on SourceForge. We would like to begin categorizing the software in both places for the benefit of those looking. Right now, software is just listed in alphabetical order. We have come up with a categorization scheme and have posted it below. We request comments, additions and changes to the categories as subscribers here see fit. * sequence analysis sequence viewer sequence editor/anotator sequence quantitation HMM ANN genome/chromosome viewer * phylogenetic trees parsimony neighbor joining maximum likelihood tree drawing programs * multiple alignments alignment editor alignment viewer * assembly ? * structure analysis structure viewer structure editor structure quantitation molecular dynamics simulations * biological databases biological database comparisons database querying * networking and connectivity * programming language extensions C/C++ Python Perl Java FORTRAN Lisp Ruby Tcl/Tk Cheers. Jeff From chapmanb at arches.uga.edu Tue Apr 17 17:58:00 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Tue, 17 Apr 2001 17:58:00 -0400 Subject: [BiO BB] FW: finding sequence helix/sheet in pdb In-Reply-To: References: Message-ID: <15068.48232.979585.833980@taxus.athen1.ga.home.com> [Extracting secondary structure info from pbd files] Venkat: > Thanks kiran. I know I can do it with RASMOl/MOLMOL but I would like > to do it an very large scale. Andrew Dalke has a PDB format-description in his parser generator, Martel: http://www.biopython.org/~dalke/Martel/ Martel uses a high-level regular expression description of the file format to generate XML output. The internals use python, but if you just spit out XML then you should be able to easily parse it in your language of choice. The comments on the top of the format description (in formats/PDB_2_1.py if you check it out) say it needs some work, and I've also never used this format, but it might be worth checking out. HTH, Brad From viswap_rri at 123india.com Tue Apr 17 23:56:59 2001 From: viswap_rri at 123india.com (viswap_rri at 123india.com) Date: 17 Apr 2001 20:56:59 -0700 Subject: [BiO BB] Freeware for molecular modelling !! Message-ID: <20010418035659.12481.cpmta@c001.zsm.cp.net> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From paolo at ist.unige.it Fri Apr 20 10:00:49 2001 From: paolo at ist.unige.it (Paolo Romano) Date: Fri, 20 Apr 2001 16:00:49 +0200 (DFT) Subject: [BiO BB] NETTAB: Register before May 1st at the reduced rates Message-ID: <200104201400.QAA18462@ist.unige.it> Dear list members, Register at a reduced rate before May 1st to the NETTAB Workshop on "CORBA and XML: Towards a bioinformatics integrated network environment" May 17th-18th, 2001, Advanced Biotechnology Centre, Genova May 1st is the deadline for registering to the NETTAB Workshop at a reduced fee (even lower for ISCB and TABOO members, see below). Here are the Workshop participation fees: Academic: - before May 1st: 150 EUR - after May 1st: 200 EUR Non academic: - before May 1st: 300 EUR - after May 1st: 400 EUR Participation fee includes attendance to the workshop sessions, coffee breaks, lunches, workshop's abstracts book and social dinner. Please register by filling in online the purpose form at one of the following URLs: http://www.cba.unige.it/Events/NETTAB/rform.html http://www.bioinformatics.org/NETTAB/rform.html (US mirror) --- The International Society for Computational Biology (ISCB) and the Italian Association on Object-Oriented Technologies (TABOO) have agreed to support the NETTAB Workshop. Both personal and corporate members of ISCB and TABOO are eligible a 10% discount on the registration fee. If you are not a member of these societies, please consider the chance of registering now. Information is available on-line for becoming ISCB regular and corporate members: http://www.iscb.org/ . Information is also available on-line for becoming member of TABOO (in Italian language only): http://twilight.dse.disco.unimib.it/TABOO/iscrizione/mod-ass.html --- >From MAY 19th, Genoa will host the National Meeting of Italian Alpine soldiers and it could therefore be DIFFICULT for you to find a convenient hotel later. You should book your hotel room AS SOON AS POSSIBLE! Please refer to the following URL for a list of hotels: http://www.comune.genova.it/guide/welc_alberghi.htm If you have any questions or need assistance, please contact by email the Workshop secretariat at nettab at ist.unige.it. Looking forward to seeing you in Genoa. Best regards. Paolo Romano (Workshop Chairman) -- Paolo Romano (paolo at ist.unige.it) Biotechnology Department, National Cancer Research Institute - Genova c/o Advanced Biotechnology Centre Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From jeff at bioinformatics.org Sat Apr 21 13:46:21 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 21 Apr 2001 17:46:21 +0000 Subject: [BiO BB] [Fwd: Junior Essay] Message-ID: <3AE1C76D.994EE75E@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Peter Noble Subject: [BiO Admin] Junior Essay Date: Sat, 21 Apr 2001 12:26:08 -0400 Size: 2314 URL: From jeff at bioinformatics.org Sat Apr 21 23:04:10 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 22 Apr 2001 03:04:10 +0000 Subject: [BiO BB] [Fwd: Junior Essay] References: Message-ID: <3AE24A2A.A347E6FC@bioinformatics.org> I would suggest taking a look at the THINK screensaver as well, a "fight cancer at home" project: http://members.ud.com/vypc/cancer/think.htm It too is "Internet distributed computing" and not quite traditional supercomputing. Jeff B. Jeff Ames wrote: > > Have you looked at the Fight AIDS at Home project? It uses distributed > computing, similar to the rc5 / distributed.net projects. People > contribute CPU cycles to protein modelling, supposedly to help researchers > develop new drugs to fight AIDS/HIV. I don't know of any published > results yet, though. -- 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 indraneel at indialine.org Sun Apr 22 19:29:30 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sun, 22 Apr 2001 18:29:30 -0500 Subject: [BiO BB] [Fwd: Extracting helix/strand sequences from pdb:] In-Reply-To: <3ADB03F0.68795560@bioinformatics.org>; from jeff@bioinformatics.org on Mon, Apr 16, 2001 at 02:38:40PM +0000 References: <3ADB03F0.68795560@bioinformatics.org> Message-ID: <20010422182930.A1251@indialine.org> Hi, There seems to be a lot of software for doing this. I guess you are trying to extract out the secondary structure information corresponding to each PDB file. The SHEET and HELIX headers in the PDB file itself are quite accurate as they are generated by the DSSP program. Other programs you may use to get similiar information are sstruc, jpred, predict protein. You may want to check out these pages: http://barton.ebi.ac.uk/new/software.html http://www.expasy.ch/tools/ http://biochem9.chem.ufl.edu/~cannaro/latex/appendix/appendix.html You might have to write a perl script to run the program of your choice on each PDB file and then extract out the relevant info from the output file and write it to another taking the PDB filename as the template. eg 1EMB.pdb -> 1EMB.ss I could not find any script for doing this on the net. best wishes, Indraneel PS: I am writing one such tool myself, which my employer shall release as open source, but it's still some way to go. On Mon, Apr 16, 2001 at 02:38:40PM +0000, J.W. Bizzaro wrote: > > Do anyone have a script or know of a source where I can obtain the > sequences of helix/sheet > from pdb file. Any help will be appreciated! > -- http://www.indialine.org From indraneel at indialine.org Sun Apr 22 19:31:56 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sun, 22 Apr 2001 18:31:56 -0500 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #21 - 1 msg In-Reply-To: <20010417040939.46326.qmail@web8004.mail.in.yahoo.com>; from bioinformaticsckk@yahoo.co.in on Tue, Apr 17, 2001 at 05:09:39AM +0100 References: <200104161600.MAA24062@www.bioinformatics.org> <20010417040939.46326.qmail@web8004.mail.in.yahoo.com> Message-ID: <20010422183156.B1251@indialine.org> Hi, Most of these programs, including InsightII (by MSI) actually use the DSSP generated data in the PDB file itself for coloring the molecules. It might be easier to extract the data from the PDB file itself. \Indraneel On Tue, Apr 17, 2001 at 05:09:39AM +0100, wrote: > Dear Venkat, > If you want just the amino acid sequence of the helix > or a sheet, you may get that from any modelling > program like rasmol wherein you have the option to see > the aminoacid sequence corresponding to the structure. > for nucleotide sequence, you may have to convert from > protein to nucleotide sequence (different online tools > are available). -- http://www.indialine.org From indraneel at indialine.org Sun Apr 22 19:45:28 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sun, 22 Apr 2001 18:45:28 -0500 Subject: [BiO BB] FW: finding sequence helix/sheet in pdb In-Reply-To: ; from vsmathur@utmb.edu on Tue, Apr 17, 2001 at 02:40:56PM -0500 References: Message-ID: <20010422184528.C1251@indialine.org> Hi, The PDB mostly uses the DSSP program and sometimes sstruc. You might try to look at the DSSP database (output of the DSSP program) via the SRS but it doesn't seem to be in any human readable format. As far as the PDB goes, the A,B,C etc are in the next column (the PDB was designed by Fortran programmers) after the residue number, which is otherwise left blank. So you should not have any trouble with that if you check that column too for all cases in your script. What are you using? Are you storing this in any RDBMS? If so then you might need to define two more attributes for each residue ID. (A better method would be to define your own data type for residue ID, which stores a number and a character, if the database system allows that. PostgreSQL does.) Your script would be able to directly dump the data into the database that way. IMHO this is hard work, so best wishes, Indraneel On Tue, Apr 17, 2001 at 02:40:56PM -0500, Mathura, Venkatarajan S. wrote: > > Thanks kiran. I know I can do it with RASMOl/MOLMOL but I would like > to do it an very large scale. I mean the entire pdb (just for proteins) > or atleast non-redundant structures. Currently I am using the pdb > header HELIX or SHEET information. The script looks for starting/ending > helix and sheet residue info, and reads out single letter seq for the > sec structure regions using the residue number and start/end info. I > have already done this for 2096 pdb files and was quiet successful. But > the script doesn't handle cases where the residue numbers were numbered > by 15A,16B etc (particularly in case of mutation). I am looking for > someone who have already extracted all helix sequences in the pdb (I > mean 12000 structures) or who have scripts that can better handle the > problem mentioned above. I would like to stick to the secondary > structure information from the pdb header (as supplied by authors) > rather using other programs to write out sec structures from just > co-ordinates alone. -- http://www.indialine.org From baby_lakshmi at hotmail.com Mon Apr 23 02:36:55 2001 From: baby_lakshmi at hotmail.com (baby lakshmi) Date: Mon, 23 Apr 2001 12:06:55 +0530 Subject: [BiO BB] (no subject) Message-ID: Hi all I am babylakshmi, completed my masters in Physics and has done one year diploma in bioinformatics. Glad to join in this discussion group Regards Babylakshmi _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From uysal at doctor.com Mon Apr 23 04:34:20 2001 From: uysal at doctor.com (huseyin uysal) Date: Mon, 23 Apr 2001 04:34:20 -0400 (EDT) Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #25 - 2 msgs Message-ID: <385279151.988014860179.JavaMail.root@web349-mc> Dear Peter, I advice you to look at the IBM bluegene project about the predicting tertiary structure of proteins from primary sequence means protein folding. Here is the brief description of project and you can find more info about supercomputers and aplication areas at IBM site. On December 6, 1999, IBM announced a $100 million research initiative to build the world's fastest supercomputer, "Blue Gene", to tackle fundamental problems in computational biology. The Blue Gene system will be capable of performing more than one petaop/s (1,000,000,000,000,000 operations per second). It will achieve this performance through a combination of massive parallelism (1 million processors), and new computer architecture approaches: the system will be built through the replication of a large number of identical chips, each containing multiple processors, memory and communication logic. Simultaneous multithreading will be used at each processor to hide memory latency and simplify microprocessor design. The Blue Gene project will use this computer for large scale biomolecular simulation to advance our understanding of biologically important processes, in particular our understanding of the mechanisms behind protein folding. http://www.research.ibm.com/bluegene/ Huseyin Uysal ------Original Message------ From: bio_bulletin_board-admin at bioinformatics.org To: bio_bulletin_board at bioinformatics.org Sent: April 22, 2001 4:00:03 PM GMT Subject: BiO_Bulletin_Board digest, Vol 1 #25 - 2 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. [Fwd: Junior Essay] (J.W. Bizzaro) 2. Re: [Fwd: Junior Essay] (J.W. Bizzaro) --__--__-- Message: 1 Date: Sat, 21 Apr 2001 17:46:21 +0000 From: "J.W. Bizzaro" To: bbb at bioinformatics.org Subject: [BiO BB] [Fwd: Junior Essay] boundary="------------1F7D1789ACE39FFDD76022C9" Reply-To: bio_bulletin_board at bioinformatics.org This is a multi-part message in MIME format. --------------1F7D1789ACE39FFDD76022C9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------1F7D1789ACE39FFDD76022C9 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline X-F: Sat Apr 21 12:25:30 2001 Received: from www.bioinformatics.org [129.63.144.25] by mercury.capeonramp.com with ESMTP (SMTPD32-6.00) id A4791D470100; Sat, 21 Apr 2001 12:25:29 -0400 Received: from www.bioinformatics.org (IDENT:mail at www.bioinformatics.org [127.0.0.1]) by www.bioinformatics.org (8.9.3/8.8.7) with SMTP id MAA19234; Sat, 21 Apr 2001 12:26:10 -0400 Received: (from webmaster at localhost) by www.bioinformatics.org (8.9.3/8.8.7) id MAA19211; Sat, 21 Apr 2001 12:26:08 -0400 Date: Sat, 21 Apr 2001 12:26:08 -0400 Message-Id: <200104211626.MAA19211 at www.bioinformatics.org> To: admin at bioinformatics.org Subject: [BiO Admin] Junior Essay From: Peter Noble Reply-To: tol-admin at bioinformatics.org Sender: tol-admin-admin at bioinformatics.org Errors-To: tol-admin-admin at bioinformatics.org X-Mailman-Version: 1.0b10 Precedence: bulk List-Id: Administration discussions about BiO X-BeenThere: tol-admin at bioinformatics.org X-RCPT-TO: Hello, My name is Peter Noble and I am currently attending Colville High School in Colville, WA. And as all juniors are required at this school, I am writing an essay based on a subject which has effected American history on some level, most likely something that can be argued on its importance. I chose supercomputing and its uses. As supercomputing has many uses I am able to touch on only a few sections, the medical field, nuclear research, etc. Unfortunately I have run into a small problem in regaurds to the medical field, it seems that about all I can find information on is DNA analysis, which leaves me with a small problem because not very much on a widescale level has been produced from that information yet. (Or at least not that I know of) What I was hoping was maybe a redirection of where I could find more information, say an ailment which a cure was found for through the use of supercomputing, or even an example of how I should look. Any help you can offer would be most appreciated. Thank you, Peter Noble Student _______________________________________________ tol-admin maillist - tol-admin at bioinformatics.org http://bioinformatics.org/mailman/listinfo/tol-admin --------------1F7D1789ACE39FFDD76022C9-- --__--__-- Message: 2 Date: Sun, 22 Apr 2001 03:04:10 +0000 From: "J.W. Bizzaro" To: bbb at bioinformatics.org, Peter Noble Subject: Re: [BiO BB] [Fwd: Junior Essay] Reply-To: bio_bulletin_board at bioinformatics.org I would suggest taking a look at the THINK screensaver as well, a "fight cancer at home" project: http://members.ud.com/vypc/cancer/think.htm It too is "Internet distributed computing" and not quite traditional supercomputing. Jeff B. Jeff Ames wrote: > > Have you looked at the Fight AIDS at Home project? It uses distributed > computing, similar to the rc5 / distributed.net projects. People > contribute CPU cycles to protein modelling, supposedly to help researchers > develop new drugs to fight AIDS/HIV. I don't know of any published > results yet, though. -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board --__--__---- End of BiO_Bulletin_Board Digest ______________________________________________ FREE Personalized Email at Mail.com Sign up at http://www.mail.com/?sr=signup From rahulrds at yahoo.com Mon Apr 23 04:45:26 2001 From: rahulrds at yahoo.com (sagajkar rahul) Date: Mon, 23 Apr 2001 01:45:26 -0700 (PDT) Subject: [BiO BB] (no subject) Message-ID: <20010423084526.23640.qmail@web1609.mail.yahoo.com> __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/ From micky at alum.mit.edu Tue Apr 24 01:38:41 2001 From: micky at alum.mit.edu (micky at alum.mit.edu) Date: Mon, 23 Apr 2001 22:38:41 -0700 Subject: [BiO BB] Bioinformatics companies around Boston Message-ID: <3AE51161.1A1F349A@alum.mit.edu> Hi there, I am a software engineer, and I am trying to get into the Bioinformatics field. I have four years of experience in system architecture, software design, etc., but no background in biology, or the like. I have two related questions for this group: (1) who are the players in the Boston area that might be interested in someone with my background, and (2) does anybody have strong (or weak) opinions about the companies I identified so far? Companies I intend to approach are: - Spotfire - Whitehead Institute - Xpogen - Genome Therapeutics - Lion Bioscience Thanks in advance! - Michael -- _________________________ m i c h a e l jastram mailto:micky at alum.mit.edu w w w http://jastram.de From jeff at bioinformatics.org Tue Apr 24 09:30:17 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 24 Apr 2001 13:30:17 +0000 Subject: [BiO BB] Bioinformatics companies around Boston References: <3AE51161.1A1F349A@alum.mit.edu> Message-ID: <3AE57FE9.2DFD5743@bioinformatics.org> micky at alum.mit.edu wrote: > > Companies I intend to approach are: You may also want to try Millennium Pharm. Genetics Institute Variagenics Actually, there are a bunch of them in the Cambridge area. 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 mburke at biosystemsconsulting.com Tue Apr 24 09:49:31 2001 From: mburke at biosystemsconsulting.com (mburke at biosystemsconsulting.com) Date: Tue, 24 Apr 2001 09:49:31 -0400 Subject: [BiO BB] Bioinformatics in North Carolina Message-ID: <003b01c0ccc5$639b4e40$34fea8c0@raven> Hello, I am currently working at a small startup company as a Bioinformatics Scientist \ IT Manager and will be relocating to Greensboro, North Carolina at the end of May. Does anyone have any suggestions about companies that are currently working in Bioinformatics? Thank you in advance, Mark Burke From reece at in-machina.com Tue Apr 24 12:59:42 2001 From: reece at in-machina.com (Reece Hart) Date: Tue, 24 Apr 2001 12:59:42 -0400 (EDT) Subject: [BiO BB] Bioinformatics companies around Boston In-Reply-To: <3AE51161.1A1F349A@alum.mit.edu> Message-ID: On Mon, 23 Apr 2001 micky at alum.mit.edu wrote: > I have two related questions for this group: (1) who are the players in > the Boston area that might be interested in someone with my background, > and (2) does anybody have strong (or weak) opinions about the companies > I identified so far? Michael- There are many bio companies in the Boston area from startup to monolithic pharma. I have two suggestions: 1) see www.biospace.com, especially the "jobs by region" section, and 2) keep up with breaking news to see which companies are connecting with the market. I subscribe to the www.genomeweb.com mailing lists. I have no affiliation with either of these companies. Good luck, Reece -- Reece Hart, http://www.in-machina.com/~reece/, PGP:0xD178AAF9 From jeff at bioinformatics.org Wed Apr 25 00:17:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 25 Apr 2001 04:17:38 +0000 Subject: [BiO BB] software categories References: Message-ID: <3AE64FE2.74C31CA9@bioinformatics.org> Rune Linding wrote: > > have you tried to coordinate this with the biology/chemistry section of > SAL? Have we tried to tie this into SAL, copy their entries, or work with them in some way? Nope. Have we tried using their categories for biology/chemistry apps? They don't seem to categorize at that level. Bio/chem apps are a bottom-level category, actually under "Other Scientific Fields", which I find amusing. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Wed Apr 25 00:32:10 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 25 Apr 2001 04:32:10 +0000 Subject: [BiO BB] software categories References: <3ADCBAA7.D31776D@bioinformatics.org> Message-ID: <3AE6534A.E4FE5F29@bioinformatics.org> I've extensively re-worked the categorization scheme. I think that it is much more flexible right now. Please take a look and see if the applications that you know will fit. And please let me know if not. Oh, and feel free to add anything that's missing. THANKS! Note: Words [IN CAPS WITH BRACKETS] are for organization and would not appear in category description. The hierarchy is [OBJECT] [MANIFESTATION] [PROGRAM FUNCTION] Examples using some of my own programs: "MeltSim" (http://bioinformatics.org/meltsim/) ---------------------------------------------- Nucleotide/Nucleic Acid Secondary Structure Simulating Thermodynamics "Piper" (http://bioinformatics.org/piper/) ------------------------------------------ Generic/Multiple Objects Generic/Multiple Manifestations Peripheral to Programs Networking Also... AA Sequence Alignment ------------------------------------- Amino Acid/Protein Primary Structure (sequence) Comparing Here goes: ------------------------------- [OBJECT] [MOLECULE OR MACROMOLECULE] Nucleotide/Nucleic Acid Amino Acid/Protein Fatty Acid/Lipid Sugar/Polyaccharide Other Molecule Generic/Multiple Molecules [BIOLOGICAL STRUCTURE] Tissue Organ System Organism Other Biological Structure Generic/Multiple Biological Structures Generic/Multiple Objects ------------------------------- [MANIFESTATION] [MOLECULE OR MACROMOLECULE] Primary Structure (Sequence) Secondary Structure Teriary Structure Quaternary Structre Biosynthesis Expression Other Molecule Manifestation Generic/Multiple Molecule Manifestations [BIOLOGICAL STRUCTURE] Genotype Phenotype Development Life Cycle Other Biological Structure Manifestation Generic/Multiple Biological Structure Manifestations Generic/Multiple Manifestations ------------------------------- [PROGRAM FUNCTION] Viewing Editing (Non-Annotating) Annotating Assembling Quantitating Comparing Simulating Kenetics Thermodynamics Other Generic/Multiple Genetics Punnett Square Pedigree Generic/Multiple Phylogenetics Parsimony Neighbor Joining Maximum Likelihood Tree Drawing Other Generic/Multiple Databases Comparing Querying Submitting Other Generic/Multiple Peripheral to Programs Networking Language Library Other Generic/Multiple Other Function Generic/Multiple Functions --------------------------- -- 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 bioinformaticsckk at yahoo.co.in Wed Apr 25 02:35:17 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Wed, 25 Apr 2001 07:35:17 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #27 - 3 msgs In-Reply-To: <200104241600.MAA17440@www.bioinformatics.org> Message-ID: <20010425063517.31329.qmail@web8004.mail.in.yahoo.com> Hi! Micheal, If you have experience working with GUI, i strongly suggest you for spotfire as they are working and previously worked on s/w development on GUI. Other companies like Lion Bioscience may also be intersted in Front end designers. If you are very good at database like oracle with few years of experince, I suggest you to apply to all these companies. Best of Luck, Kiran Kumar.C --- bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body > 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific than > "Re: Contents of BiO_Bulletin_Board digest...") > > > Today's Topics: > > 1. Bioinformatics companies around Boston > (michael at optimal.optimalweb.com) > 2. Re: Bioinformatics companies around Boston > (J.W. Bizzaro) > 3. Bioinformatics in North Carolina > (mburke at biosystemsconsulting.com) > > --__--__-- > > Message: 1 > From: micky at alum.mit.edu > Date: Mon, 23 Apr 2001 22:38:41 -0700 > Organization: http://jastram.de > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Bioinformatics companies around > Boston > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi there, > > I am a software engineer, and I am trying to get > into the Bioinformatics > field. I have four years of experience in system > architecture, software > design, etc., but no background in biology, or the > like. > > I have two related questions for this group: (1) who > are the players in > the Boston area that might be interested in someone > with my background, > and (2) does anybody have strong (or weak) opinions > about the companies > I identified so far? > > Companies I intend to approach are: > - Spotfire > - Whitehead Institute > - Xpogen > - Genome Therapeutics > - Lion Bioscience > > Thanks in advance! > > - Michael > > > -- > _________________________ > m i c h a e l jastram > mailto:micky at alum.mit.edu > w w w http://jastram.de > > > > > --__--__-- > > Message: 2 > Date: Tue, 24 Apr 2001 13:30:17 +0000 > From: "J.W. Bizzaro" > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Bioinformatics companies > around Boston > Reply-To: bio_bulletin_board at bioinformatics.org > > micky at alum.mit.edu wrote: > > > > Companies I intend to approach are: > > You may also want to try > > Millennium Pharm. > Genetics Institute > Variagenics > > Actually, there are a bunch of them in the Cambridge > area. > > Cheers. > Jeff > -- > J.W. Bizzaro > jeff at bioinformatics.org > Director, Bioinformatics.org > http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of > others, we > should be glad of an opportunity to serve others by > any invention > of ours; and this we should do freely and > generously." > -- Benjamin Franklin > -- > > --__--__-- > > Message: 3 > From: mburke at biosystemsconsulting.com > Reply-To: > To: > Subject: [BiO BB] Bioinformatics in North Carolina > Date: Tue, 24 Apr 2001 09:49:31 -0400 > charset="iso-8859-1" > Reply-To: bio_bulletin_board at bioinformatics.org > > Hello, > I am currently working at a small startup > company as a Bioinformatics > Scientist \ IT Manager and will be relocating to > Greensboro, North Carolina > at the end of May. Does anyone have any suggestions > about companies that > are currently working in Bioinformatics? > > Thank you in advance, > > Mark Burke > > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > --__--__---- > > End of BiO_Bulletin_Board Digest ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com From valb at vtek.com Wed Apr 25 10:30:25 2001 From: valb at vtek.com (Val Bykoski) Date: Wed, 25 Apr 2001 10:30:25 -0400 Subject: [BiO BB] software categories References: <3ADCBAA7.D31776D@bioinformatics.org> <3AE6534A.E4FE5F29@bioinformatics.org> Message-ID: <032901c0cd94$45e20c70$d2befea9@pc300> Hi Jeff/All, Yes, that adds more content and looks more convincing to me. I'd suggest also to integrate into the description the "biocontext" and "biofunction" components (meaning the description of the object' context and its biol function, respectively). cheers, /val ----- Original Message ----- From: "J.W. Bizzaro" To: Sent: Wednesday, April 25, 2001 12:32 AM Subject: Re: [BiO BB] software categories > I've extensively re-worked the categorization scheme. I think that it is much > more flexible right now. Please take a look and see if the applications that > you know will fit. And please let me know if not. > > Oh, and feel free to add anything that's missing. THANKS! > > Note: Words [IN CAPS WITH BRACKETS] are for organization and would not appear > in category description. > > The hierarchy is > > [OBJECT] > [MANIFESTATION] > [PROGRAM FUNCTION] > > Examples using some of my own programs: > > "MeltSim" (http://bioinformatics.org/meltsim/) > ---------------------------------------------- > Nucleotide/Nucleic Acid > Secondary Structure > Simulating > Thermodynamics > > "Piper" (http://bioinformatics.org/piper/) > ------------------------------------------ > Generic/Multiple Objects > Generic/Multiple Manifestations > Peripheral to Programs > Networking > > Also... > > AA Sequence Alignment > ------------------------------------- > Amino Acid/Protein > Primary Structure (sequence) > Comparing > > > Here goes: > > ------------------------------- > > [OBJECT] > > [MOLECULE OR MACROMOLECULE] > > Nucleotide/Nucleic Acid > Amino Acid/Protein > Fatty Acid/Lipid > Sugar/Polyaccharide > Other Molecule > Generic/Multiple Molecules > > [BIOLOGICAL STRUCTURE] > > Tissue > Organ > System > Organism > Other Biological Structure > Generic/Multiple Biological Structures > > Generic/Multiple Objects > > ------------------------------- > > [MANIFESTATION] > > [MOLECULE OR MACROMOLECULE] > > Primary Structure (Sequence) > Secondary Structure > Teriary Structure > Quaternary Structre > Biosynthesis > Expression > Other Molecule Manifestation > Generic/Multiple Molecule Manifestations > > [BIOLOGICAL STRUCTURE] > > Genotype > Phenotype > Development > Life Cycle > Other Biological Structure Manifestation > Generic/Multiple Biological Structure Manifestations > > Generic/Multiple Manifestations > > ------------------------------- > > [PROGRAM FUNCTION] > > Viewing > Editing (Non-Annotating) > Annotating > Assembling > Quantitating > Comparing > Simulating > > Kenetics > Thermodynamics > Other > Generic/Multiple > > Genetics > > Punnett Square > Pedigree > Generic/Multiple > > Phylogenetics > > Parsimony > Neighbor Joining > Maximum Likelihood > Tree Drawing > Other > Generic/Multiple > > Databases > > Comparing > Querying > Submitting > Other > Generic/Multiple > > Peripheral to Programs > > Networking > Language Library > Other > Generic/Multiple > > Other Function > Generic/Multiple Functions > > --------------------------- > > > > > > -- > J.W. Bizzaro jeff at bioinformatics.org > Director, Bioinformatics.org http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of others, we > should be glad of an opportunity to serve others by any invention > of ours; and this we should do freely and generously." > -- Benjamin Franklin > -- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From jeff at bioinformatics.org Wed Apr 25 11:21:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 25 Apr 2001 15:21:38 +0000 Subject: [BiO BB] [Fwd: SEEKING INFORMATION IN BIOINFORMATICS.] Message-ID: <3AE6EB82.DA700D80@bioinformatics.org> (Please don't send messages to bio_bulletin_board-admin. That just goes to the admin.) -------------- next part -------------- An embedded message was scrubbed... From: "MANOJ CHANDEL" Subject: SEEKING INFORMATION IN BIOINFORMATICS. Date: Wed, 25 Apr 2001 11:09:47 -0000 Size: 1888 URL: From jeff at bioinformatics.org Wed Apr 25 12:02:50 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 25 Apr 2001 16:02:50 +0000 Subject: [BiO BB] [Fwd: SEEKING INFORMATION IN BIOINFORMATICS.] References: <3AE6EB82.DA700D80@bioinformatics.org> Message-ID: <3AE6F52A.9C5FEA36@bioinformatics.org> > Recently ,subscribe to your organisation. Sir, i'am a student of > horticulture (post graduate). I want to know how I can persuade education in > bioinformatics. My minor subject in post graduation was plant breeding and > genetics. Mail soon. Could you tell us more about your experience and education in molecular biology and computing? Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Wed Apr 25 12:20:03 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 25 Apr 2001 16:20:03 +0000 Subject: [BiO BB] software categories References: <3ADCBAA7.D31776D@bioinformatics.org> <3AE6534A.E4FE5F29@bioinformatics.org> <032901c0cd94$45e20c70$d2befea9@pc300> Message-ID: <3AE6F933.F94E2ADC@bioinformatics.org> Val Bykoski wrote: > > Yes, that adds more content and looks more convincing to me. > I'd suggest also to integrate into the > description the "biocontext" and "biofunction" components > (meaning the description of the object' context and its biol > function, respectively). That's a good point. I hadn't considered these. But where should they go? They could be alternatives to "manifestation", e.g. [OBJECT] [BIOFUNCTION] [PROGRAM FUNCTION] Amino Acid/Protein Kinase Activity Simulation They could be in addition to manifestation: [OBJECT] [MANIFESTATION] [BIOFUNCTION] [PROGRAM FUNCTION] Amino Acid/Protein Tertiary Structure Kinase Activity Simulation Or they could be in program function: [OBJECT] [MANIFESTATION] [PROGRAM FUNCTION] Amino Acid/Protein Tertiary Structure Functional Analysis Also, could you give me an example of "biocontext"? 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 amonida.zadissa at agresearch.co.nz Wed Apr 25 19:24:35 2001 From: amonida.zadissa at agresearch.co.nz (Zadissa, Amonida) Date: Thu, 26 Apr 2001 11:24:35 +1200 Subject: [BiO BB] Free access to research articles Message-ID: <1D58E0CCBB3ED311890600508B4AAB3213F3EF@mint.agresearch.cri.nz> Hi everyone, I thought this might be interesting to you regarding a previous discussion on free access to scientific papers: http://www.scientificamerican.com/explorations/2001/042301publish/ (From Slashdot, http://slashdot.org/article.pl?sid=01/04/24/149257&mode=thread). Cheers, Amonida From valb at vtek.com Wed Apr 25 20:46:11 2001 From: valb at vtek.com (Val Bykoski) Date: Wed, 25 Apr 2001 20:46:11 -0400 Subject: [BiO BB] software categories References: <3ADCBAA7.D31776D@bioinformatics.org> <3AE6534A.E4FE5F29@bioinformatics.org> <032901c0cd94$45e20c70$d2befea9@pc300> <3AE6F933.F94E2ADC@bioinformatics.org> Message-ID: <03f001c0cdea$4b7760d0$d2befea9@pc300> A couple of points, Jeff: Within the complexity of the categorization task itself, your suggested categorization seems to me pretty good. My point with biocontext and biofunction is to _add_ (when useful) the description of the environment in which the object exists/expresses itself ("in vivo", "in vitro", or smth like that but more specifics) and of the biological function the object implements or is part of the implementation E.g.: 1. Biocontext: any (macro)molecule operates in an environment which needs to be included in the description. 2. Biofunction: any (macro)molecule (being in an env) implements some biol function (or is a part of the implementation, right?). And the whole idea here is that in bioinformatics the methods and tools need to be integrated (as much as possible) into biol "reality" which in many cases can be represented in terms of "structure-function" relationships. A structure w/out the function involved is very much a lost knowledge.. Unfortunately, this sounds too general. i'll give it another try in awhile. cheers, val ----- Original Message ----- From: "J.W. Bizzaro" To: Sent: Wednesday, April 25, 2001 12:20 PM Subject: Re: [BiO BB] software categories > Val Bykoski wrote: > > > > Yes, that adds more content and looks more convincing to me. > > I'd suggest also to integrate into the > > description the "biocontext" and "biofunction" components > > (meaning the description of the object' context and its biol > > function, respectively). > > That's a good point. I hadn't considered these. But where should they go? > They could be alternatives to "manifestation", e.g. > > [OBJECT] > [BIOFUNCTION] > [PROGRAM FUNCTION] > > Amino Acid/Protein > Kinase Activity > Simulation > > They could be in addition to manifestation: > > [OBJECT] > [MANIFESTATION] > [BIOFUNCTION] > [PROGRAM FUNCTION] > > Amino Acid/Protein > Tertiary Structure > Kinase Activity > Simulation > > Or they could be in program function: > > [OBJECT] > [MANIFESTATION] > [PROGRAM FUNCTION] > > Amino Acid/Protein > Tertiary Structure > Functional Analysis > > Also, could you give me an example of "biocontext"? > > 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 > -- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From askiran73 at hotmail.com Fri Apr 27 03:16:00 2001 From: askiran73 at hotmail.com (Kiran Ayyagari) Date: Fri, 27 Apr 2001 12:46:00 +0530 Subject: [BiO BB] Question by A.S.Kiran Message-ID: Dear all, I want to ask a general question, Seeing the significance of bioinformatics, Which among the following can be a viable and sustainable model to adopt for future companies to explore bioinformatics market? 1) Data Curators 2) Data Vendors 3) Data Compilation(Databases) and Maintenance 4) Data Visualization Please recommend any general articles published regarding this matter. Thanks in advance A.S.Kiran Bioinformatics Developer, DSQ Biotech Limited Banglare, India email: askiran73 at hotmail.com, kiran_ayyagari at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: