From martin.goodson at iconmedialab.co.uk Sat Sep 1 06:02:11 2001 From: martin.goodson at iconmedialab.co.uk (Martin Goodson) Date: Sat, 1 Sep 2001 11:02:11 +0100 Subject: [BiO BB] Basic Bioinformatics question Message-ID: <78F62F91ABC1D41198E6009027B11CA28586D2@QUENTIN> i'd add www.s-star.org to that. Also the, often overlooked but excellent, trends guides, at http://journals.bmn.com/supp. Start with the bioinformatics guide and move on to the genomics and proteomics guides. for a list of books please feel free to email me. martin goodson -----Original Message----- From: J.W. Bizzaro [mailto:jeff at bioinformatics.org] Sent: 01 September 2001 01:06 To: bio_bulletin_board at bioinformatics.org; atprelease at yahoo.com Subject: Re: [BiO BB] Basic Bioinformatics question Hi Ross. The first thing I suggest whenever asked this question is to look at the FAQ: http://bioinformatics.org/faq/ Damian has done a great deal of work on it, and it is now very comprehensive. Cheers. Jeff Ross Corriden wrote: > > I recently graduated from college with a degree in > Biochemistry and I am searching for resources on the > internet that provide a basic overview of > bioinformatics. If anyone knows about a site that > contains this kind of information, I would greatly > appreciate it if they would send the address of the > page to my e-mail: -- 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 The information contained in this e-mail is intended solely for the use of the person to whom it is addressed and others authorized to receive it. It may contain confidential or legally privileged information and, if you are not the intended recipient, any disclosure, copying, distribution or taking any action regarding the contents of this information is strictly prohibited and may be unlawful. If you received this e-mail in error, please notify us immediately by replying to this e-mail and then delete it from your system. From roumieu at genops.com Wed Sep 5 00:42:17 2001 From: roumieu at genops.com (jordan) Date: Tue, 4 Sep 2001 21:42:17 -0700 Subject: [BiO BB] Ngene integrated sequence analysis Message-ID: Hi All, Genops Bioinformatics Inc., a Vancouver BC based company has released an evaluation version integrated sequence analysis package. It is very easy to use and adds impressive performance and productivity increasing features to essential bioinformatics applications and data. We would be pleased to hear your feedback about the work in progress. Please see www.genops.com to register for a free download of Ngene v1.07. Jordan Roumieu Business Development Associate Genops Bioinformatics, Inc. www.genops.com 245-4259 Canada Way Burnaby BC, V5G 1H1 Phone: (604) 451-2441 Fax: (604) 451-2445 From liza at egenetics.com Thu Sep 6 06:37:40 2001 From: liza at egenetics.com (Liza Groenewald) Date: Thu, 06 Sep 2001 12:37:40 +0200 Subject: [BiO BB] New release of STACKdb, in relational database format Message-ID: <3B9751F4.21D727E8@egenetics.com> Major revamp of the STACKdb Human Gene Expression Index, provided free to academics, incorporates mRNA sequences and visualization software. ---------------------------------------- The latest version of the STACK database of reconstructed human expressed transcripts, STACKdb v3.0, has been released by The South African National Bioinformatics Institute (SANBI), in collaboration with Electric Genetics. The STACK human gene expression index is unique in that it is the only gene expression index that is availabe with the tools that are used in its manufacture. In addition, it contains verified, clone-linked cluster assemblies. The index is processed into hierarchically organized human transcript consensus sequences that reflect gene expression forms and, in particular, alternate expression variants, within several tissue-based and one disease expression category. STACKdb v3.0 is created from 2,524,209 EST sequences and 51,638 partially redundant mRNA sequences, distributed according to tissue expression, and represents an increase of 569,014 new EST sequences and 51,638 mRNA sequences as compared to the previous release, STACKdb v2.4. STACKdb v3.0 contains 241,258 clusters and 12,943 clonelinks in total. What's New --------------------------------------- STACKdb 3.0 has been produced with the latest generation stackPACK transcript reconstruction and variation analysis management tools, and therefore has several fundamental improvements: * Inclusion of mRNA sequences in clusters. * The database is now distributed in two forms: - Relational database tables, for use with the web-based viewing software. - FastA files containing non-redundant sets of linked clusters, clusters and singletons for each tissue type, for use with external programs. * Web-based viewing software, equivalent to that found in stackPACK v2.1.1, which: - highlights variation. - allows the viewing of cluster, linked cluster and alternate consensus sequences. - displays initial (PHRAP) alignments, alignment analyses (CRAW output), as well as alignments for each potential alternate expression form. * Various web-based and command line reports to extract data for use in other programs. Availability ------------------------------- The database is available free of charge to academic and non-profit institutions. Interested users who wish to download STACKdb 3.0 may register at www.sanbi.ac.za/CODES. The Swiss Institute of Bioinformatics collaborates with SANBI and serves SANBI's STACKdb download from the Swiss Institute of Bioinformatics web site to ensure faster download times. The database may also be searched on-line by comparing a query sequence to any of the STACKdb categories. WebBLAST is available at: http://juju.egenetics.com/stackpack/webblast.html The stackPACK tools, used to create STACKdb, are also available free of charge to academics. Interested users may register at www.sanbi.ac.za/CODES to download the stackPACK tools for COMPAQ, Linux, Silicon Graphics or Sun platforms. Interested in transcript reconstruction? ----------------------------------------------- The STACKers mailing list is for information on EST clustering and transcript reconstruction. Please point your browser to the following URL in order to subscribe to STACKers: http://fling.sanbi.ac.za/mailman/listinfo/stackers Scientific Publications ------------------------------------------- StackPACK has been described in several publications. * The method employed and assessment of quality of the resource is fully described in: STACK: sequence tag alignment and consensus knowledgebase. Christoffels A, Gelder Av, Greyling G, Miller R, Hide T, Hide W. Nucleic Acids Res. 2001 Jan 1;29(1):234-8. and A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge Base Robert T. Miller, Alan G. Christoffels, Chella Gopalakrishnan, John Burke, Andrey A. Ptitsyn, Tania R. Broveak, and Winston A. Hide. November 1999: Genome Research: 9:1143-1155 * The clustering algorithm employed in stackPACK is described in: d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences. John Burke, Dan Davison, and Winston Hide. November 1999: Genome Research: 9:1135-1142 Additionally, stackPACK has been instrumental in several discoveries. A listing of scientific publications and posters involving stackPACK can be found at: http://www.egenetics.com/?Section=publications&Parent=science Contact Details ---------------------------- STACKdb is managed and distributed by Electric Genetics who also provides free support for academic users. Please contact support at egenetics.com for support, feedback or any queries. For further information on STACKdb, please refer to the Electric Genetics website: http://www.egenetics.com/?Section=STACKdb&Parent=products For further information on research at the South African National Bioinformatics Institute, please visit: http://www.sanbi.ac.za/Research.html From nirubala at yahoo.com Sat Sep 8 13:19:26 2001 From: nirubala at yahoo.com (Nirupama Bala) Date: Sat, 8 Sep 2001 10:19:26 -0700 (PDT) Subject: [BiO BB] (no subject) Message-ID: <20010908171926.32045.qmail@web14008.mail.yahoo.com> Subscribing to the list --------------------------------- Do You Yahoo!? Get email alerts & NEW webcam video instant messaging with Yahoo! Messenger. -------------- next part -------------- An HTML attachment was scrubbed... URL: From WilsonE02 at darden.virginia.edu Tue Sep 11 07:43:58 2001 From: WilsonE02 at darden.virginia.edu (Wilson, Edmund) Date: Tue, 11 Sep 2001 07:43:58 -0400 Subject: [BiO BB] Question to the Board Message-ID: <576DF5639F8CD311999600508B5A2356088D0FA6@DARDENMAIL> All: I'm currently involved in a project that is assessing the feasibility of distributed computing within the realm of bioinformatics. While I'm familiar with the existence of some commercial products out there (eg. United Devices has a BLAST tool), I would be very interested in hearing more from members of this discussion group on this topic. If you would be interested in answering a few additional questions and providing insight on pros and cons of distributed bioinformatics applications and tools, please send an email directly to me: WilsonE02 at darden.virginia.edu. Thank you for the help. Edmund Wilson From dfield at molbiol.ox.ac.uk Tue Sep 11 08:12:44 2001 From: dfield at molbiol.ox.ac.uk (Dawn Field) Date: Tue, 11 Sep 2001 12:12:44 +0000 Subject: [BiO BB] Question to the Board In-Reply-To: <576DF5639F8CD311999600508B5A2356088D0FA6@DARDENMAIL> References: <576DF5639F8CD311999600508B5A2356088D0FA6@DARDENMAIL> Message-ID: >Hello, Ed, I would be very interested in hearing more about your project, and if possible seeing the results of your 'poll' of this group if it occurs off-list. Out of interest, when you talk about distributed computing in bioinformatics do you mean GRID enabled resources (e.g. using Globus or similar GRID enabling software toolkits) or distributed computing like clusters and complex scheduling between UNIX machines (or PC's along the lines of a 'seti-like' :-) approach)? Dawn >All: > >I'm currently involved in a project that is assessing the feasibility of >distributed computing within the realm of bioinformatics. While I'm >familiar with the existence of some commercial products out there (eg. >United Devices has a BLAST tool), I would be very interested in hearing more >from members of this discussion group on this topic. > >If you would be interested in answering a few additional questions and >providing insight on pros and cons of distributed bioinformatics >applications and tools, please send an email directly to me: >WilsonE02 at darden.virginia.edu. > >Thank you for the help. > >Edmund Wilson > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Dawn Field Molecular Evolution and Bioinformatics CEH, Oxford Mansfield Road Oxford OX1 3SR Tel: *-44-(0)1865-281659 (direct) Tel: *-44-(0)1865-281630 (reception to leave a message) Fax: *-44-(0)1865-281696 http://www.nox.ac.uk/ From indraneel at indialine.org Tue Sep 11 11:18:28 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 11 Sep 2001 10:18:28 -0500 Subject: [BiO BB] Question to the Board In-Reply-To: References: <576DF5639F8CD311999600508B5A2356088D0FA6@DARDENMAIL> Message-ID: <20010911101828.A18341@indialine.org> I believe it would be somewhat difficult to use distributed computing (in it's true sense, a seti like approach) for Bioinformatics. Right now all our computation is IO limited (as someone pointed out in an earlier post), by having to move large datasets all the time. PVFS might be an answer, but it is probably not fast enough (speed limiting factor being metadata lookups). (Probably if we can find out the encryption technology in biological data, things would be simpler ;-) \Indraneel On Tue, Sep 11, 2001 at 12:12:44PM +0000, Dawn Field wrote: > >Hello, > distributed computing like clusters and complex scheduling between > UNIX machines (or PC's along the lines of a 'seti-like' :-) approach)? > Dawn > -- http://www.indialine.org/indraneel/ From cmdobson at ucalgary.ca Tue Sep 11 12:23:49 2001 From: cmdobson at ucalgary.ca (C. Melissa Dobson) Date: Tue, 11 Sep 2001 10:23:49 -0600 Subject: [BiO BB] Question to the Board References: <576DF5639F8CD311999600508B5A2356088D0FA6@DARDENMAIL> Message-ID: <3B9E3A95.5D9D51DE@ucalgary.ca> > Hello all, I am very much enjoying the commentary which is going on with this board. I would like to ask a thought povoking question - Where do you feel the area of bioinformatics is going? Thanks in advance for any commentary you give. C. M. Dobson From Sameer_Mohta at satyam.com Wed Sep 12 01:05:29 2001 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Wed, 12 Sep 2001 10:35:29 +0530 Subject: [BiO BB] Question to the Board Message-ID: <877B003B6F03D511A22E00B0D078E7A85426E4@hst.satyam.com> Hi All, what exactly you mean by encryption technology in Biological data. Do you mean to say adding one layer of security in data handling ? moreover i would like to know what efforts are going on related to Distributed Programming in BioInformatics. hey friends if we want to make a small prototyoe software in Bioinformatics, then what topics can you suggest and how to proceed. sam -----Original Message----- From: Indraneel Majumdar [mailto:indraneel at indialine.org] Sent: Tuesday, September 11, 2001 8:48 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Question to the Board I believe it would be somewhat difficult to use distributed computing (in it's true sense, a seti like approach) for Bioinformatics. Right now all our computation is IO limited (as someone pointed out in an earlier post), by having to move large datasets all the time. PVFS might be an answer, but it is probably not fast enough (speed limiting factor being metadata lookups). (Probably if we can find out the encryption technology in biological data, things would be simpler ;-) \Indraneel On Tue, Sep 11, 2001 at 12:12:44PM +0000, Dawn Field wrote: > >Hello, > distributed computing like clusters and complex scheduling between > UNIX machines (or PC's along the lines of a 'seti-like' :-) approach)? > Dawn > -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Nancy_Kozlowski at ncbiotech.org Wed Sep 12 12:16:10 2001 From: Nancy_Kozlowski at ncbiotech.org (Nancy Kozlowski) Date: Wed, 12 Sep 2001 12:16:10 -0400 Subject: [BiO BB] unsubscribe Message-ID: <5A2CDD9303F2D41199C200B0D078C6912A461E@www.ncbiotechmail.org> Nancy G. Kozlowski, Director Library & Information Services North Carolina Biotechnology Center POB 13547 * 15 Alexander Dr. * RTP, NC 27709-3547 phone: (919) 541-9366 * fax: (919) 990-9521 reference email: xlibrary at ncbiotech.org -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] Sent: September 12, 2001 12:00 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #87 - 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. Re: Question to the Board (C. Melissa Dobson) 2. RE: Question to the Board (Sameer_Mohta) --__--__-- Message: 1 Date: Tue, 11 Sep 2001 10:23:49 -0600 From: "C. Melissa Dobson" Organization: University of Calgary To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Question to the Board Reply-To: bio_bulletin_board at bioinformatics.org > Hello all, I am very much enjoying the commentary which is going on with this board. I would like to ask a thought povoking question - Where do you feel the area of bioinformatics is going? Thanks in advance for any commentary you give. C. M. Dobson --__--__-- Message: 2 From: Sameer_Mohta To: "'bio_bulletin_board at bioinformatics.org'" Subject: RE: [BiO BB] Question to the Board Date: Wed, 12 Sep 2001 10:35:29 +0530 charset="iso-8859-1" Reply-To: bio_bulletin_board at bioinformatics.org Hi All, what exactly you mean by encryption technology in Biological data. Do you mean to say adding one layer of security in data handling ? moreover i would like to know what efforts are going on related to Distributed Programming in BioInformatics. hey friends if we want to make a small prototyoe software in Bioinformatics, then what topics can you suggest and how to proceed. sam -----Original Message----- From: Indraneel Majumdar [mailto:indraneel at indialine.org] Sent: Tuesday, September 11, 2001 8:48 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Question to the Board I believe it would be somewhat difficult to use distributed computing (in it's true sense, a seti like approach) for Bioinformatics. Right now all our computation is IO limited (as someone pointed out in an earlier post), by having to move large datasets all the time. PVFS might be an answer, but it is probably not fast enough (speed limiting factor being metadata lookups). (Probably if we can find out the encryption technology in biological data, things would be simpler ;-) \Indraneel On Tue, Sep 11, 2001 at 12:12:44PM +0000, Dawn Field wrote: > >Hello, > distributed computing like clusters and complex scheduling between > UNIX machines (or PC's along the lines of a 'seti-like' :-) approach)? > Dawn > -- http://www.indialine.org/indraneel/ _______________________________________________ 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 --__--__---- End of BiO_Bulletin_Board Digest From indraneel at indialine.org Thu Sep 13 15:41:34 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Thu, 13 Sep 2001 14:41:34 -0500 Subject: [BiO BB] Question to the Board In-Reply-To: <877B003B6F03D511A22E00B0D078E7A85426E4@hst.satyam.com> References: <877B003B6F03D511A22E00B0D078E7A85426E4@hst.satyam.com> Message-ID: <20010913144134.A28809@indialine.org> No, no, I was just joking. Biological information itself seems to be encrypted by a code known only to the Gods. How else will you explain that identical twins are in many ways not exactly identical. I was simply referring to the fact that in today's encryption/decryption technology one does not move around large datasets, but use computational methods. There are examples of number crunching in bioinformatics too (molecular dynamics comes to mind), but probably the vast majority of software stumbles around within huge files. \Indraneel On Wed, Sep 12, 2001 at 10:35:29AM +0530, Sameer_Mohta wrote: > Hi All, > > what exactly you mean by encryption technology in Biological data. Do you > mean to say adding one layer of security in data handling ? > moreover i would like to know what efforts are going on related to > Distributed Programming in BioInformatics. > hey friends if we want to make a small prototyoe software in Bioinformatics, > then what topics can you suggest and how to proceed. > > sam -- http://www.indialine.org/indraneel/ From mike at biotools.com Thu Sep 13 18:32:54 2001 From: mike at biotools.com (Mike Fedeyko) Date: Thu, 13 Sep 2001 16:32:54 -0600 Subject: [BiO BB] (no subject) Message-ID: <3BA13416.50CF7624@biotools.com> Hey Melissa, Just thought I'd answer a fellow Albertan's query. I think the questions "where is bioinformatics going" would engender a different response from whomever you ask. I think the next big problem to solve however is data integration. How to get all of these disparate sources of data to interact with each other. In regards to specific applications, I imagine the development of an automated and dependable "drug discovery tool" would cause quite a stir. -------------- next part -------------- A non-text attachment was scrubbed... Name: mike.vcf Type: text/x-vcard Size: 331 bytes Desc: Card for Mike Fedeyko URL: From cmdobson at ucalgary.ca Thu Sep 13 19:01:31 2001 From: cmdobson at ucalgary.ca (C. Melissa Dobson) Date: Thu, 13 Sep 2001 17:01:31 -0600 Subject: [BiO BB] (no subject) References: <3BA13416.50CF7624@biotools.com> Message-ID: <3BA13ACB.EC11B110@ucalgary.ca> Thank--you for the response Mike Fedeyko wrote: > Hey Melissa, > > Just thought I'd answer a fellow Albertan's query. I think the > questions "where is bioinformatics going" would engender a different > response from whomever you ask. I think the next big problem to solve > however is data integration. How to get all of these disparate sources > of data to interact with each other. In regards to specific > applications, I imagine the development of an automated and dependable > "drug discovery tool" would cause quite a stir. From valb at vtek.com Thu Sep 13 22:34:18 2001 From: valb at vtek.com (Val Bykoski) Date: Thu, 13 Sep 2001 22:34:18 -0400 Subject: [BiO BB] (no subject) References: <3BA13416.50CF7624@biotools.com> Message-ID: <03d801c13cc5$c15595c0$d2befea9@pc300> Mike, To me, data integration is part of more serious problem how to build a realistic cell model. Without cell model, there is no (computational) framework to integrate the data around. Data needs to be integrated into smth biologically significant - otherwise the data is very much useless... my best, val ----- Original Message ----- From: "Mike Fedeyko" To: Sent: Thursday, September 13, 2001 6:32 PM Subject: [BiO BB] (no subject) > Hey Melissa, > > Just thought I'd answer a fellow Albertan's query. I think the > questions "where is bioinformatics going" would engender a different > response from whomever you ask. I think the next big problem to solve > however is data integration. How to get all of these disparate sources > of data to interact with each other. In regards to specific > applications, I imagine the development of an automated and dependable > "drug discovery tool" would cause quite a stir. > From rick at bioinformatics.org Fri Sep 14 13:25:20 2001 From: rick at bioinformatics.org (Rick Ree) Date: 14 Sep 2001 10:25:20 -0700 Subject: [BiO BB] Python bindings for the Nexus Class Library Message-ID: <1000488320.2538.23.camel@pedic> I've (finally) put together some python bindings to Paul Lewis' Nexus Class Library. Nexus is a data format widely used in phylogenetics, and these bindings allow Nexus files to be parsed, and expose an object-oriented framework for accessing the data. It uses the Boost::Python C++ library. The package can be obtained from: Any comments and suggestions are welcome. regards, Rick -- Section of Evolution and Ecology University of California Davis, CA 95616 From risea at cecalc.ula.ve Fri Sep 14 17:38:20 2001 From: risea at cecalc.ula.ve (Raul Isea) Date: Fri, 14 Sep 2001 17:38:20 -0400 Subject: [BiO BB] Second Latin-American Course in Merida, Venezuela References: <576DF5639F8CD311999600508B5A2356088D0FA6@DARDENMAIL> <20010911101828.A18341@indialine.org> Message-ID: <3BA278CC.E25B779A@cecalc.ula.ve> Dear Everyone The Center for Scientific Research of Universidad de Los Andes (CeCalCULA, http://www.cecalc.ula.ve) announces the Second Latin-American Course on Parallel and High Performance Computing, to be held in M?rida, Venezuela, from December 3 to 7, 2001. This course is aimed to undergraduated, postdoctoral, Ph.D. students and junior research faculty working in computational areas related to Chemistry, Physics, Mathematics, Biology, surface science, catalysis and other related sciences. Participants are expected to have basic theoretical knowledge on computational sciences. This year, Grid Computing, a novel paradigm aiming to exploit a large number of resources geographically distributed through the Internet, will be the main focus of the course. Professors: John Boisseau - Texas Advanced Computing Center, USA Jack Dongarra - University of Tennessee & Oak Ridge National Lab, USA Barton Miller - University of Wisconsin Henry Casanova - University of California, USA Ben Segal - CERN, Switzerland. Antonio Redondo - Los Alamos, USA Z. Hong Zhou - University of Texas - Health Science Center, USA Gustavo Scuseria - Rice University, USA Alfonso Mu?oz - Universidad de la Laguna, Spain Reinaldo Pis Diez - La Plata, Argentina Victor Pereyra - Weidlinger Associates, USA Jos? Castillo - San Diego State University, USA Registration The registration fee, US$500, covers lecture notes and social events. More information can be found at http://www.cecalc.ula.ve/elpcar2/planilla00.html Scholarships A reduced number of scholarships covering the registration fee will be available. Overseas participants are encouraged to apply. Applications should include a curriculum vitae and a letter of recommendation written by the supervisor. Exhibits Booths are available to sponsors of this event. Companies offering services and/or products related to high performance computing, distributed computing, database integration, bioinformatics, and other technologies, that could benefit from exhibiting, are encouraged to contact us at elpcar2 at cecalc.ula.ve. Posters Poster presentations will be chosen from abstracts received and approved. Each participant is encouraged to submit one abstract. You MUST submit your abstract by E-mail (elpcar2 at cecalc.ula.ve). For further information please send your inquiries to elpcar2 at cecalc.ula.ve or http://www.cecalc.ula.ve/elpcar2/abstracts.html Deadlines - Application form: October 30th 2001 Notification: November 5th 2001 Registration Fee Payment: October 30th 2001 Poster submission: October 30th 2001 Sponsors CONICIT FUNDACITE-M?rida SUN de VENEZUELA SILICON GRAPHICS de VENEZUELA IBM de VENEZUELA Additional information can be found at the Course's web site, at http://www.cecalc.ula.ve/elpcar2/ -- Dr. Raul Isea Ph. D. in Chemistry Email: risea at cecalc.ula.ve; lrisea at yahoo.com http://www.cecalc.ula.ve/~risea -------------- next part -------------- An HTML attachment was scrubbed... URL: From indraneel at indialine.org Sat Sep 15 18:35:06 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sat, 15 Sep 2001 17:35:06 -0500 Subject: [BiO BB] (no subject) In-Reply-To: <03d801c13cc5$c15595c0$d2befea9@pc300> References: <3BA13416.50CF7624@biotools.com> <03d801c13cc5$c15595c0$d2befea9@pc300> Message-ID: <20010915173506.A16277@indialine.org> Hi, I'm sorry I didn't understand properly. Do you refer to the cell as a biological cell, or as a unit of useful data? In case of the former probably that's what we are trying to find out, together with the broader perspective of all cells working together. In case of the latter, we probably already have the units of data, sometimes related and sometimes not. Now is the time to seggregate them to it's smallest units and link them up using relations (yes, I'm implying relational database systems). We do however need to know what to expect out of this database, and also account for the fact that we can never know how to scale it when new types of data come along (but then this applies to every field). From my personal work, I have found that simply being able to group and ungroup data shows up hidden facts, and also generates ideas for new studies. (If you're curious, I use PostgreSQL :) \Indraneel On Thu, Sep 13, 2001 at 10:34:18PM -0400, Val Bykoski wrote: > Mike, > To me, data integration is part of more serious problem > how to build a realistic cell model. Without cell model, > there is no (computational) framework to integrate the > data around. Data needs to be integrated into smth biologically > significant - otherwise the data is very much useless... > my best, val -- http://www.indialine.org/indraneel/ From valb at vtek.com Sat Sep 15 21:41:34 2001 From: valb at vtek.com (Val Bykoski) Date: Sat, 15 Sep 2001 21:41:34 -0400 Subject: [BiO BB] (no subject) References: <3BA13416.50CF7624@biotools.com> <03d801c13cc5$c15595c0$d2befea9@pc300> <20010915173506.A16277@indialine.org> Message-ID: <052201c13e55$016e4270$d2befea9@pc300> Hi Indraneel, Thanx for your comments. I refer to the cell as a biological cell, and my point, to put it a little differently, was that data has to work inside a (realistic) cell model, not to sit passively in databases. Data grouping, visualization, etc. is better than nothing, but still there is a huge gap between data (nicely grouped, visualized, etc) and their biological significance or context. I guess my point is that if you integrate data into a realistic cell model, the model is both a predictive framework and a (bio)context-sensitive database for the data. Then, data is hidden and work inside the model for predictions, and does not require grouping, visualization, etc. Sure, the "realistic cell model" is a hard nut...but may be worth of efforts, in particular, for a data-driven model. cheers, val val at vtek.com ----- Original Message ----- From: "Indraneel Majumdar" To: Sent: Saturday, September 15, 2001 6:35 PM Subject: Re: [BiO BB] (no subject) > Hi, > I'm sorry I didn't understand properly. Do you refer to the cell as a > biological cell, or as a unit of useful data? > > In case of the former probably that's what we are trying to find out, > together with the broader perspective of all cells working together. > > In case of the latter, we probably already have the units of data, > sometimes related and sometimes not. Now is the time to seggregate them > to it's smallest units and link them up using relations (yes, I'm > implying relational database systems). We do however need to know what > to expect out of this database, and also account for the fact that we > can never know how to scale it when new types of data come along (but > then this applies to every field). From my personal work, I have found > that simply being able to group and ungroup data shows up hidden facts, > and also generates ideas for new studies. (If you're curious, I use > PostgreSQL :) > > \Indraneel > > On Thu, Sep 13, 2001 at 10:34:18PM -0400, Val Bykoski wrote: > > Mike, > > To me, data integration is part of more serious problem > > how to build a realistic cell model. Without cell model, > > there is no (computational) framework to integrate the > > data around. Data needs to be integrated into smth biologically > > significant - otherwise the data is very much useless... > > my best, val > > -- > http://www.indialine.org/indraneel/ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Sameer_Mohta at satyam.com Mon Sep 17 03:48:27 2001 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Mon, 17 Sep 2001 13:18:27 +0530 Subject: [BiO BB] prototyping Message-ID: <877B003B6F03D511A22E00B0D078E7A854271A@hst.satyam.com> hi all, i have one question. if a IT person wants to do a quick and dirty prototyping in a weeks time or two weeks time, where can he put effort. I have seen alignment tools, structure prediction and so on. But what can be the new area in Bioinformatics where this prototyping can be done in this short span of time, considering the limitation of in depth scientific knowledge of a IT person. r/sam -----Original Message----- From: Val Bykoski [mailto:valb at vtek.com] Sent: Sunday, September 16, 2001 7:12 AM To: bio_bulletin_board at bioinformatics.org Cc: Val Bykoski - valb Subject: Re: [BiO BB] (no subject) Hi Indraneel, Thanx for your comments. I refer to the cell as a biological cell, and my point, to put it a little differently, was that data has to work inside a (realistic) cell model, not to sit passively in databases. Data grouping, visualization, etc. is better than nothing, but still there is a huge gap between data (nicely grouped, visualized, etc) and their biological significance or context. I guess my point is that if you integrate data into a realistic cell model, the model is both a predictive framework and a (bio)context-sensitive database for the data. Then, data is hidden and work inside the model for predictions, and does not require grouping, visualization, etc. Sure, the "realistic cell model" is a hard nut...but may be worth of efforts, in particular, for a data-driven model. cheers, val val at vtek.com ----- Original Message ----- From: "Indraneel Majumdar" To: Sent: Saturday, September 15, 2001 6:35 PM Subject: Re: [BiO BB] (no subject) > Hi, > I'm sorry I didn't understand properly. Do you refer to the cell as a > biological cell, or as a unit of useful data? > > In case of the former probably that's what we are trying to find out, > together with the broader perspective of all cells working together. > > In case of the latter, we probably already have the units of data, > sometimes related and sometimes not. Now is the time to seggregate them > to it's smallest units and link them up using relations (yes, I'm > implying relational database systems). We do however need to know what > to expect out of this database, and also account for the fact that we > can never know how to scale it when new types of data come along (but > then this applies to every field). From my personal work, I have found > that simply being able to group and ungroup data shows up hidden facts, > and also generates ideas for new studies. (If you're curious, I use > PostgreSQL :) > > \Indraneel > > On Thu, Sep 13, 2001 at 10:34:18PM -0400, Val Bykoski wrote: > > Mike, > > To me, data integration is part of more serious problem > > how to build a realistic cell model. Without cell model, > > there is no (computational) framework to integrate the > > data around. Data needs to be integrated into smth biologically > > significant - otherwise the data is very much useless... > > my best, val > > -- > http://www.indialine.org/indraneel/ > > _______________________________________________ > 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 jwester at sgi1.chemie.uni-hamburg.de Mon Sep 17 05:34:49 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Mon, 17 Sep 2001 11:34:49 +0200 Subject: [BiO BB] prototyping References: <877B003B6F03D511A22E00B0D078E7A854271A@hst.satyam.com> Message-ID: <3BA5C3B9.CB9E7746@sgi1.chemie.uni-hamburg.de> Sameer_Mohta wrote: > > hi all, > > i have one question. if a IT person wants to do a quick and dirty > prototyping in a weeks time or two weeks time, where can he put effort. I > have seen alignment tools, structure prediction and so on. But what can be > the new area in Bioinformatics where this prototyping can be done in this > short span of time, considering the limitation of in depth scientific > knowledge of a IT person. I'm not shure if I got your Question right but I'll try an answer. The prototyping itself could be done by a non IT-person (scientist for example) who tries to work out and solve the problem on scale of 'proof of concept' (not fast). This ist mostly done in a skript langauges (Perl, Python) wich are easy to learn. The ITpro would then turn the concept into an application that does the work faster. HTH, jcw From cc at cormack.uct.ac.za Mon Sep 17 12:45:00 2001 From: cc at cormack.uct.ac.za (Cupido,Cinda-Lee,Ms) Date: Mon, 17 Sep 2001 18:45:00 +0200 Subject: [BiO BB] Biostatistics Message-ID: Hi All Does anyone have information on upcoming training courses/ workshops on the non-parametric analysis of complex genetic disorders? Regards *************************************** Ms Cinda-Lee Cupido ( BSc, Hons(Med) ) Department of Human Genetics University of Cape Town Medical School Anatomy building, Room 1127 Penzance Road Observatory 7925 Ph: +27 21 4066456 Fax: +27 21 4480906 e-mail: cc at cormack.uct.ac.za *************************************** From clarisca at cwpanama.net Mon Sep 17 18:13:52 2001 From: clarisca at cwpanama.net (Claris Castillo T.) Date: Mon, 17 Sep 2001 17:13:52 -0500 Subject: [BiO BB] Statistics like how many operations needed by Rasmol? Message-ID: <00b001c13fc6$093aaf80$481861ce@cwpanama.net> Hi. I am working in a research project for the Smithsonian Tropical Research Institute about Bioinformatics. I am wondering where can I find some information like Number of operations needed by RASMOL to display a protein of X length. I have not found any statistics like this one. Thanks in advance, Claris -------------- next part -------------- An HTML attachment was scrubbed... URL: From michikami at yahoo.com Mon Sep 17 18:35:55 2001 From: michikami at yahoo.com (Michi Kami) Date: Mon, 17 Sep 2001 15:35:55 -0700 (PDT) Subject: [BiO BB] Biostatistics In-Reply-To: Message-ID: <20010917223555.25035.qmail@web20010.mail.yahoo.com> --- "Cupido,Cinda-Lee,Ms" wrote: > Hi All > > Does anyone have information on upcoming training courses/ workshops > on the non-parametric analysis of complex genetic disorders? > > Regards > > *************************************** > Ms Cinda-Lee Cupido ( BSc, Hons(Med) ) > Department of Human Genetics > University of Cape Town > Medical School > Anatomy building, Room 1127 > Penzance Road > Observatory > 7925 > Ph: +27 21 4066456 > Fax: +27 21 4480906 > e-mail: cc at cormack.uct.ac.za > *************************************** > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________________________ Terrorist Attacks on U.S. - How can you help? Donate cash, emergency relief information http://dailynews.yahoo.com/fc/US/Emergency_Information/ From hema at hakkinen.com Thu Sep 20 07:04:37 2001 From: hema at hakkinen.com (hemavathy douraiswami) Date: Thu, 20 Sep 2001 04:04:37 -0700 (PDT) Subject: [BiO BB] (no subject) Message-ID: <20010920110438.1CB242755@sitemail.everyone.net> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From krishna_p_reddy at indiatimes.com Thu Sep 20 06:56:44 2001 From: krishna_p_reddy at indiatimes.com (krishna_p_reddy) Date: Thu, 20 Sep 2001 16:26:44 +0530 Subject: [BiO BB] (no subject) Message-ID: <200109201050.QAA18326@WS0005.indiatimes.com> sir, I would like to take the course in protein structure from ur institute , will u give the placement if so please give futher details my number is 98482 61660 thank u Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From hema at hakkinen.com Fri Sep 21 00:55:27 2001 From: hema at hakkinen.com (hemavathy douraiswami) Date: Thu, 20 Sep 2001 21:55:27 -0700 (PDT) Subject: [BiO BB] (no subject) Message-ID: <20010921045527.B1DD63ECC@sitemail.everyone.net> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From reshmi_renu at hotmail.com Fri Sep 21 01:34:08 2001 From: reshmi_renu at hotmail.com (renu nair) Date: Fri, 21 Sep 2001 11:04:08 +0530 Subject: [BiO BB] enquiry Message-ID: An HTML attachment was scrubbed... URL: From helge.tippmann at risoe.dk Fri Sep 21 06:57:20 2001 From: helge.tippmann at risoe.dk (helge.tippmann at risoe.dk) Date: Fri, 21 Sep 2001 12:57:20 +0200 Subject: [BiO BB] Biological Database designing Message-ID: <7F6BCF6B9307D311980C0090273C746C03DEDAD2@cssrv1> I would like to know if anybody has an idea how to create a small database i.e. for plant microbe interactions and involved genes respectively? The thought behind it is to create a small dataset to get results with higher statistical relevance & faster searching through? How could one start off ? best regards Helge ---------------------------------------------------------------------------- ------------- Dipl-Ing. Helge Tippmann Risoe National Laboratory Plant Research Department (PRD) Resistance Biology Programme (PLR) Building 330 Fredriksborgvej 399, P.O. Box 49 DK-4000 Roskilde http://www.risoe.dk/pbk/research_uk/plr/Defence/Arabidopsis.htm From dfield at molbiol.ox.ac.uk Fri Sep 21 07:33:56 2001 From: dfield at molbiol.ox.ac.uk (Dawn Field) Date: Fri, 21 Sep 2001 11:33:56 +0000 Subject: [BiO BB] Biological Database designing In-Reply-To: <7F6BCF6B9307D311980C0090273C746C03DEDAD2@cssrv1> References: <7F6BCF6B9307D311980C0090273C746C03DEDAD2@cssrv1> Message-ID: >Hello, It would help if you told the list exactly what kind of data you hope to store, how much curation you'll need to do once you sent up your database, and a bit about how you hope to search it. This would help people evaluate whether there are existing options or whether you need to start from scratch... Also, what's your computing background and what platform do you what to develop for - will it be web based? Dawn >I would like to know if anybody has an idea how to create a small database >i.e. for plant microbe interactions and involved genes respectively? The >thought behind it is to create a small dataset to get results with higher >statistical relevance & faster searching through? How could one start off ? > >best regards > >Helge > >---------------------------------------------------------------------------- >------------- >Dipl-Ing. Helge Tippmann >Risoe National Laboratory >Plant Research Department (PRD) >Resistance Biology Programme (PLR) >Building 330 >Fredriksborgvej 399, P.O. Box 49 >DK-4000 Roskilde > >http://www.risoe.dk/pbk/research_uk/plr/Defence/Arabidopsis.htm > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Dawn Field Molecular Evolution and Bioinformatics CEH, Oxford Mansfield Road Oxford OX1 3SR Tel: *-44-(0)1865-281659 (direct) Tel: *-44-(0)1865-281630 (reception to leave a message) Fax: *-44-(0)1865-281696 http://www.nox.ac.uk/ From balarji at rediffmail.com Sat Sep 22 03:06:50 2001 From: balarji at rediffmail.com (balaji r) Date: 22 Sep 2001 07:06:50 -0000 Subject: [BiO BB] Biological Database designing Message-ID: <20010922070650.24945.qmail@mailweb34.rediffmail.com> hi there i just want to ask you .. few questions? what have you planned for your database i mean who are your users?? >>is it going to be put on web / CD if you are going for web.. the front end will be either html / java script/ vb script /cgi script... and the back end will be oracle /MySQL/flat files any database as such will do.. but in your case i think you will need some RDBMS as you can split up data and help the user to find what he wants easily.. to start with i feel you identify your fields, then design your tables and relation betwen them ..once you identify to what extent you are going to put your data then your database designing will harldly take time .. and data is very imp... if you have any more queries you can get back to my personal email..balajior at rediffmail.com Balaji Bioinformatics-Programmer On Fri, 21 Sep 2001 helge.tippmann at risoe.dk wrote : >I would like to know if anybody has an idea how to >create a small database >i.e. for plant microbe interactions and involved genes >respectively? The >thought behind it is to create a small dataset to get >results with higher >statistical relevance & faster searching through? How >could one start off ? > >best regards > >Helge > >--------------------------------------------------------- >-------------------- >------------- >Dipl-Ing. Helge Tippmann >Risoe National Laboratory >Plant Research Department (PRD) >Resistance Biology Programme (PLR) >Building 330 >Fredriksborgvej 399, P.O. Box 49 >DK-4000 Roskilde > >http://www.risoe.dk/pbk/research_uk/plr/Defence/Arabidop- >sis.htm > > >_______________________________________________ >BiO_Bulletin_Board maillist - >BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >board > From omi_80 at rediffmail.com Sat Sep 22 04:14:13 2001 From: omi_80 at rediffmail.com (Omica Jain) Date: 22 Sep 2001 08:14:13 -0000 Subject: [BiO BB] How to write Algorithm Message-ID: <20010922081413.31204.qmail@mailFA9.rediffmail.com> Hi there, I?m very new to the field of bioinformatics. I wanted to become an algorithm expert. Can anybody suggest how should I start from skretch? BTW what is neural network algorithm? Any suggestion will be highly appreciated. Thanks in advance. From jeff at bioinformatics.org Sat Sep 22 22:45:20 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 22 Sep 2001 22:45:20 -0400 Subject: [BiO BB] (no subject) References: <200109201050.QAA18326@WS0005.indiatimes.com> Message-ID: <3BAD4CC0.55C54D52@bioinformatics.org> krishna_p_reddy wrote: > > I would like to take the course in protein structure from ur institute , > will u give the placement Bioinformatics.org doesn't have a course in protein structure, although we may someday. I'm curious as to why you think we are offering a course. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Sun Sep 23 18:39:12 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 23 Sep 2001 18:39:12 -0400 Subject: [BiO BB] [Fwd: fragments of structurally equivalent regions!] Message-ID: <3BAE6490.670D9131@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Mathura, Venkatarajan S." Subject: fragments of structurally equivalent regions! Date: Sun, 23 Sep 2001 12:39:35 -0500 Size: 1676 URL: From kiran_ayyagari at yahoo.com Mon Sep 24 00:24:33 2001 From: kiran_ayyagari at yahoo.com (Kiran Ayyagari) Date: Mon, 24 Sep 2001 09:54:33 +0530 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #96 - 2 msgs References: <200109221600.MAA23655@www.bioinformatics.org> Message-ID: <00ba01c144b9$00717a80$c901a8c0@dsqbiotech.co.in> Hi Omica Jain, The best book for finding some of the algos ur intersted in is " the introduction to computational biology" by Watermann, I dont know ur academic bkg but if ur perfect in maths and probability and statistics, your the perfect person to become an algo expert.. All the Best A.S.Kiran Scientist- Bioinformatics email: kiran_ayyagari at yahoo.com ----- Original Message ----- From: To: Sent: Saturday, September 22, 2001 9:30 PM Subject: BiO_Bulletin_Board digest, Vol 1 #96 - 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. Re: Biological Database designing (balaji r) > 2. How to write Algorithm (Omica Jain) > > --__--__-- > > Message: 1 > Date: 22 Sep 2001 07:06:50 -0000 > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Biological Database designing > CC: helge.tippmann at risoe.dk > From: "balaji r" > Reply-To: bio_bulletin_board at bioinformatics.org > > hi there > i just want to ask you .. few questions? > what have you planned for your database i mean who are your users?? > >>is it going to be put on web / CD = > > if you are going for web.. the front end will be either html / java scrip= > t/ vb script /cgi script... > and the back end will be oracle /MySQL/flat files any database as such wi= > ll do.. > but in your case i think you will need some RDBMS as you can split up dat= > a and help the user to find what he wants easily.. > > to start with i feel you identify your fields, then design your tables an= > d relation betwen them ..once you identify to what extent you are going t= > o put your data then your database designing will harldly take time .. an= > d data is very imp... > > if you have any more queries you can get back to my personal email..balaj= > ior at rediffmail.com > > > Balaji > Bioinformatics-Programmer > > > On Fri, 21 Sep 2001 helge.tippmann at risoe.dk wrote : > >I would like to know if anybody has an idea how to = > > >create a small database > >i.e. for plant microbe interactions and involved genes = > > >respectively? The > >thought behind it is to create a small dataset to get = > > >results with higher > >statistical relevance & faster searching through? How = > > >could one start off ? = > > > > >best regards = > > > > >Helge > > > >--------------------------------------------------------- > >-------------------- > >------------- > >Dipl-Ing. Helge Tippmann > >Risoe National Laboratory > >Plant Research Department (PRD) > >Resistance Biology Programme (PLR) > >Building 330 > >Fredriksborgvej 399, P.O. Box 49 > >DK-4000 Roskilde > > > >http://www.risoe.dk/pbk/research_uk/plr/Defence/Arabidop- > >sis.htm > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - = > > >BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >board > > > > > = > > > > > > --__--__-- > > Message: 2 > Date: 22 Sep 2001 08:14:13 -0000 > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] How to write Algorithm > From: "Omica Jain" > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi there, > > I=92m very new to the field of bioinformatics. I wanted to become an algo= > rithm expert. Can anybody suggest how should I start from skretch? = > > BTW what is neural network algorithm? = > > Any suggestion will be highly appreciated. > > Thanks in advance. > > > = > > > > > > > > --__--__-- > > _______________________________________________ > 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!? Get your free @yahoo.com address at http://mail.yahoo.com From jwester at sgi1.chemie.uni-hamburg.de Mon Sep 24 05:22:39 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Mon, 24 Sep 2001 11:22:39 +0200 Subject: [BiO BB] How to write Algorithm References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> Message-ID: <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> Omica Jain wrote: > > Hi there, > > I?m very new to the field of bioinformatics. I wanted to become an algorithm expert. Can anybody > suggest how should I start from skretch? What should that algorithm do? Try these books: Algorithms in C (O'Reilly) Numerical Recipies in C (Cambridge University Press, available free in the www) > BTW what is neural network algorithm? Depends on the type of the artificial neural network you want/need (Kohonen, ABAM, back-propagation, counter-propagation...). Litrature: Neural Networks for Chemists, J. Zupan, J. Gasteiger, VCH or the book from Susan Dayhof (haven't got the title...) > Any suggestion will be highly appreciated. > > Thanks in advance. HTH jcw -- Ungef?hr so gemein wie tote Schafe treten. Unsportm?nnisch, aber angenehm wolig-warm im Tritt. Tobias Wolter in dagh-l From jacobs at genehack.org Mon Sep 24 06:47:16 2001 From: jacobs at genehack.org (John S. J. Anderson) Date: 24 Sep 2001 06:47:16 -0400 Subject: [BiO BB] How to write Algorithm In-Reply-To: <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> Message-ID: <87k7youaq3.fsf@mendel.genehack.org> Jan-Christoph Westermann writes: > > I'm very new to the field of bioinformatics. I wanted to become an > > algorithm expert. Can anybody suggest how should I start from > > skretch? > > What should that algorithm do? > Try these books: > Algorithms in C (O'Reilly) IIRC, that's _Mastering Algorithms with C_; there's also a _Mastering Algoritms with Perl_. > Numerical Recipies in C (Cambridge University Press, available free > in the www) The canonical "algorithm book" is Knuth's multi-volume _The Art of Programming_. If you want to become an "algorithm expert", you should acquire these books (currently three of them), read them cover to cover, and understand them. This is very non-trivial. Good luck, john. -- genehack.org * weblog == ( bioinfo / linux / opinion / stuff ) * daily * "Acquire the habit of reading specs and talking to your peers." - Per Cederqvist, _Version Management with CVS_ From jwester at sgi1.chemie.uni-hamburg.de Mon Sep 24 08:11:34 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Mon, 24 Sep 2001 14:11:34 +0200 Subject: [BiO BB] How to write Algorithm References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> <87k7youaq3.fsf@mendel.genehack.org> Message-ID: <3BAF22F6.792FBB8B@sgi1.chemie.uni-hamburg.de> "John S. J. Anderson" wrote: >>> I'm very new to the field of bioinformatics. I wanted to become an >>> algorithm expert. Can anybody suggest how should I start from >>> skretch? >> >> What should that algorithm do? >> Try these books: >> Algorithms in C (O'Reilly) > > IIRC, that's _Mastering Algorithms with C_; there's also a _Mastering > Algoritms with Perl_. 'Algorithms in C' is from Addison-Wesley, sorry for the confusion. jcw -- Ungef?hr so gemein wie tote Schafe treten. Unsportm?nnisch, aber angenehm wolig-warm im Tritt. Tobias Wolter in dagh-l From beoneel at bluewin.ch Tue Sep 25 08:20:50 2001 From: beoneel at bluewin.ch (Bruce ONeel) Date: Tue, 25 Sep 2001 14:20:50 +0200 Subject: [BiO BB] How to write Algorithm Message-ID: <3BA6DA0A003760B6@mta1n.bluewin.ch> (added by postmaster@bluewin.ch) Very worthwhile also: Introduction to Algorithms by Cormen, Leiserson, Rivest, et al. ISBN 0262032937 Also, Algorithms on Strings, Trees, and Sequences by Gusfield ISBN 0521585198 cheers bruce jacobs at genehack.org (John S. J. Anderson) wrote: > Jan-Christoph Westermann writes: > > > > I'm very new to the field of bioinformatics. I wanted to become an > > > algorithm expert. Can anybody suggest how should I start from > > > skretch? > > > > What should that algorithm do? > > Try these books: > > Algorithms in C (O'Reilly) > > IIRC, that's _Mastering Algorithms with C_; there's also a _Mastering > Algoritms with Perl_. > > > Numerical Recipies in C (Cambridge University Press, available free > > in the www) > > The canonical "algorithm book" is Knuth's multi-volume _The Art of > Programming_. If you want to become an "algorithm expert", you should > acquire these books (currently three of them), read them cover to > cover, and understand them. This is very non-trivial. > > Good luck, > > > john. > -- > genehack.org * weblog == ( bioinfo / linux / opinion / stuff ) * daily * > > "Acquire the habit of reading specs and talking to your peers." > - Per Cederqvist, _Version Management with CVS_ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From indraneel at indialine.org Tue Sep 25 23:58:02 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 25 Sep 2001 22:58:02 -0500 Subject: [BiO BB] (no subject) In-Reply-To: <052201c13e55$016e4270$d2befea9@pc300> References: <3BA13416.50CF7624@biotools.com> <03d801c13cc5$c15595c0$d2befea9@pc300> <20010915173506.A16277@indialine.org> <052201c13e55$016e4270$d2befea9@pc300> Message-ID: <20010925225802.A6601@indialine.org> Hi Val, Sorry for the very late followup. After your mail I realised that truly we are basing most of our bioinfo ideas on things like homology/analogy rather than in terms of biochemical pathways, protein function prediction in terms of cellular requirements and such things (something that I wanted to do when I first entered this field, but lost sight of and forgot very soon). I believe the concepts you point out are at present fairly complicated to represent and visualise using current software. Remember that most of current software was generated not to study the unknown diversity but to store man made discrete units (eg financial data). Possibly a giant step is required to produce such things and since I cannot at present see any necessity for it in the commercial world (since a .com will always want quick results), such a system will most probably be an open source development. Coming to the development issue, such software would require highly experienced biologists to develop (maybe not highly, but at least a person interested in Biology). Most people I have come across interested in bioinformatics are from a non Biology background (there is nothing wrong in that, this is a field where all need to contribute from the viewpoint of his/her own specialisation). Thus the diversity is either missed completely, or avoided because it's too complex. The few biologists on this bandwagon do their best to forget (or as in my case have already forgot) things like the evolution of the endocrine hormone system, development of the inner ear, functioning of the lambda genome (and such things). The "parts" (that we study now) indeed make up the "whole", but we also need to remember, maybe according to "chaos" (or the gaia hypothesis?), that the whole is something more than just the parts. On Sat, Sep 15, 2001 at 09:41:34PM -0400, Val Bykoski wrote: > Hi Indraneel, > Thanx for your comments. > I refer to the cell as a biological cell, and my point, > to put it a little differently, was that data has to work > inside a (realistic) cell model, not to sit passively in databases. > Data grouping, visualization, etc. is better than nothing, > but still there is a huge gap between data (nicely grouped, > visualized, etc) and their biological significance or context. > I guess my point is that if you integrate data into a realistic > cell model, the model is both a predictive framework and > a (bio)context-sensitive database for the data. Then, > data is hidden and work inside the model for predictions, > and does not require grouping, visualization, etc. > Sure, the "realistic cell model" is a hard nut...but may be > worth of efforts, in particular, for a data-driven model. > cheers, val > val at vtek.com > -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Wed Sep 26 00:09:06 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 25 Sep 2001 23:09:06 -0500 Subject: [BiO BB] Biological Database designing In-Reply-To: <7F6BCF6B9307D311980C0090273C746C03DEDAD2@cssrv1> References: <7F6BCF6B9307D311980C0090273C746C03DEDAD2@cssrv1> Message-ID: <20010925230906.B6601@indialine.org> Hi, Probably all you need are three tables, but I may be mistaken. The best way to start off is a visit to: http://www.postgresql.org and read the book: An Introduction to Relational Database Systems - by - C.J.Date And then the most complex datasets will seem real easy to implement (except of course the cell model discussed earlier in this list ;-) HTH, Indraneel On Fri, Sep 21, 2001 at 12:57:20PM +0200, helge.tippmann at risoe.dk wrote: > I would like to know if anybody has an idea how to create a small database > i.e. for plant microbe interactions and involved genes respectively? The > thought behind it is to create a small dataset to get results with higher > statistical relevance & faster searching through? How could one start off ? -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Wed Sep 26 00:23:12 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 25 Sep 2001 23:23:12 -0500 Subject: [BiO BB] How to write Algorithm In-Reply-To: <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> Message-ID: <20010925232312.C6601@indialine.org> On Mon, Sep 24, 2001 at 11:22:39AM +0200, Jan-Christoph Westermann wrote: > > What should that algorithm do? > Try these books: > Algorithms in C (O'Reilly) > Numerical Recipies in C (Cambridge University Press, > available free in the www) (Undoubtedly the best for a beginner in the same order) And what about Donald Knuth's books? The Art Of Computer Programming (TAOCP)? There is a very nice O'reilly book: Developing Bioinformatics Computer Skills And talking about algorithms, I think data structures come first. One can try this: Algorithms + Data Structures = Programs by Nicklaus Wirth \Indraneel -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Wed Sep 26 00:31:49 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 25 Sep 2001 23:31:49 -0500 Subject: [BiO BB] How to write Algorithm In-Reply-To: <87k7youaq3.fsf@mendel.genehack.org> References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> <87k7youaq3.fsf@mendel.genehack.org> Message-ID: <20010925233149.D6601@indialine.org> On Mon, Sep 24, 2001 at 06:47:16AM -0400, John S. J. Anderson wrote: > > IIRC, that's _Mastering Algorithms with C_; there's also a _Mastering > Algoritms with Perl_. Yep, and there's also a new perl-bioinfo book > > Numerical Recipies in C (Cambridge University Press, available free > > in the www) > > The canonical "algorithm book" is Knuth's multi-volume _The Art of > Programming_. If you want to become an "algorithm expert", you should > acquire these books (currently three of them), read them cover to > cover, and understand them. This is very non-trivial. oops, i just posted this :( One should also add that supposedly the satan of the other world (BG of M$) has asked for the resume of anyone who has read all the volumes ;) \Indraneel -- http://www.indialine.org/indraneel/ From jacobs at genehack.org Wed Sep 26 08:35:30 2001 From: jacobs at genehack.org (John S. J. Anderson) Date: 26 Sep 2001 08:35:30 -0400 Subject: [BiO BB] How to write Algorithm In-Reply-To: <20010925232312.C6601@indialine.org> References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> <20010925232312.C6601@indialine.org> Message-ID: <878zf2t9il.fsf@mendel.genehack.org> Indraneel Majumdar writes: > And what about Donald Knuth's books? The Art Of Computer Programming > (TAOCP)? Great minds think alike. 8^)= > There is a very nice O'reilly book: Developing Bioinformatics > Computer Skills I wouldn't really recommend this for reading about algorithms -- there wasn't really any in-depth stuff in this book IIRC. (The book is still good for what it is -- it's just not a book about bioinfo algorithms.) > And talking about algorithms, I think data structures come first. One > can try this: > Algorithms + Data Structures = Programs > by Nicklaus Wirth If you're a Perl programmer, especially a Perl programmer of the "I used to be a biologist but now I do Perl even though I never had a programming class in my life" variety, you should read chapters two and three of the ORA _Mastering Algorithms with Perl_ book, which discuss the implementation of some of the classic data structures (heaps, B trees, stack/queues/deques, etc.) in Perl. You will learn a staggering amount. john. -- Unix is like a toll road on which you have to stop every 50 feet to pay another nickel. But hey! You only feel 5 cents poorer each time. -- Larry Wall in <1992Aug13.192357.15731 at netlabs.com> From indraneel at indialine.org Wed Sep 26 10:03:37 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Wed, 26 Sep 2001 09:03:37 -0500 Subject: [BiO BB] How to write Algorithm In-Reply-To: <878zf2t9il.fsf@mendel.genehack.org> References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> <20010925232312.C6601@indialine.org> <878zf2t9il.fsf@mendel.genehack.org> Message-ID: <20010926090336.A9369@indialine.org> On Wed, Sep 26, 2001 at 08:35:30AM -0400, John S. J. Anderson wrote: > Indraneel Majumdar writes: > > > There is a very nice O'reilly book: Developing Bioinformatics > > Computer Skills > > I wouldn't really recommend this for reading about algorithms -- there > wasn't really any in-depth stuff in this book IIRC. (The book is still > good for what it is -- it's just not a book about bioinfo algorithms.) yes, you're right. It's a good book, but not specially about algorithms > If you're a Perl programmer, especially a Perl programmer of the "I > used to be a biologist but now I do Perl even though I never had a > programming class in my life" variety, you should read chapters two > and three of the ORA _Mastering Algorithms with Perl_ book, which > discuss the implementation of some of the classic data structures > (heaps, B trees, stack/queues/deques, etc.) in Perl. You will learn a > staggering amount. Thanks for this great piece of information. I am a bioprogrammer of the variety you described (which couldn't have been put better ;-) "Mastering Algorithms with C" does have some of the heaps, trees, queues etc. I'll get the perl book too to see how it's easier. Thanks a lot, Indraneel > -- > Unix is like a toll road on which you have to stop every 50 feet to > pay another nickel. But hey! You only feel 5 cents poorer each time. > -- Larry Wall in <1992Aug13.192357.15731 at netlabs.com> ^^^^^^^ Didn't Linux appear a year before that? -- http://www.indialine.org/indraneel/ From JATP at Lundbeck.com Wed Sep 26 10:21:49 2001 From: JATP at Lundbeck.com (Jan Torleif Pedersen) Date: Wed, 26 Sep 2001 16:21:49 +0200 Subject: [BiO BB] How to write Algorithms Message-ID: Greetings, I have have as a byline been following this thread and I am deeply puzzled about the whole concept. An algorithm is the embodyment of a piece of mathematics, which in turn is the embodyment of a theoretical experiment. In my mind you need to be able to understand scientific problems and how to explain and describe these in terms of mathematics. Once this is done one can consider numerical solutions to a given problem. Just being able to implement an amoeba minimizer, reverse heap sort, binary trees etc etc does in my mind have limited to no value. The analogy I would like to draw is having all the tools for building a car, without ever having seen a car - what is the point ? Finally, I think all the books suggested are great and I have myself used them extensively, so please do not misunderstand my point, which is - Find a problem first and then start thinking about how you want to solve it. --- Jan Dr. Jan T. Pedersen Dep of Computational Chemistry H. Lundbeck A/S Ottiliavej 9, 2500 Valby email: jatp at lundbeck.com phone: +45 36 30 13 11 FAX : +45 36 30 13 85 -----Original Message----- From: Indraneel Majumdar [mailto:indraneel at indialine.org] Sent: Wednesday, September 26, 2001 4:04 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] How to write Algorithm On Wed, Sep 26, 2001 at 08:35:30AM -0400, John S. J. Anderson wrote: > Indraneel Majumdar writes: > > > There is a very nice O'reilly book: Developing Bioinformatics > > Computer Skills > > I wouldn't really recommend this for reading about algorithms -- there > wasn't really any in-depth stuff in this book IIRC. (The book is still > good for what it is -- it's just not a book about bioinfo algorithms.) yes, you're right. It's a good book, but not specially about algorithms > If you're a Perl programmer, especially a Perl programmer of the "I > used to be a biologist but now I do Perl even though I never had a > programming class in my life" variety, you should read chapters two > and three of the ORA _Mastering Algorithms with Perl_ book, which > discuss the implementation of some of the classic data structures > (heaps, B trees, stack/queues/deques, etc.) in Perl. You will learn a > staggering amount. Thanks for this great piece of information. I am a bioprogrammer of the variety you described (which couldn't have been put better ;-) "Mastering Algorithms with C" does have some of the heaps, trees, queues etc. I'll get the perl book too to see how it's easier. Thanks a lot, Indraneel > -- > Unix is like a toll road on which you have to stop every 50 feet to > pay another nickel. But hey! You only feel 5 cents poorer each time. > -- Larry Wall in <1992Aug13.192357.15731 at netlabs.com> ^^^^^^^ Didn't Linux appear a year before that? -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From philipp.pagel at cmp.yale.edu Wed Sep 26 10:53:33 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Wed, 26 Sep 2001 10:53:33 -0400 Subject: [BiO BB] How to write Algorithm In-Reply-To: <20010925232312.C6601@indialine.org> References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> <20010925232312.C6601@indialine.org> Message-ID: <20010926105332.A847@merlin> Hi! > There is a very nice O'reilly book: Developing Bioinformatics Computer Skills I bought it and don't like it at all. I think it's just a compilation of tools found on the Web. None of the concepts is really introduced, no algorithms etc. I don't think you can really learn anything from this book. My recommendations: 1) David Mount Bioinformatics: Sequence and Genome Analysis Cold Spring Harbour Lab. Press Very nice if you are coming from the biology side. Very understandable but not to shallow. This book really teaches you about some of the ideas that are used for e.g. sequence alignment etc. 2) Dan Gusfield Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology Great for Computer scientists or as a more in depth reading after 1) cu Philipp -- Dr. Philipp Pagel Department of Cellular and Molecular Physiology phone: (203) 785-6835 SHM, B117 fax: (203) 785-4951 Yale University 333 Cedar ST New Haven, CT 06520 USA From philipp.pagel at cmp.yale.edu Wed Sep 26 11:40:55 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Wed, 26 Sep 2001 11:40:55 -0400 Subject: [BiO BB] How to write Algorithms In-Reply-To: References: Message-ID: <20010926114055.A6519@merlin> Hi! > The analogy I would like to draw is having all the tools for building a car, > without ever having seen a car - what is the point ? > > Finally, I think all the books suggested are great and I have myself used > them extensively, so please do not misunderstand my point, which is - Find a > problem first and then start thinking about how you want to solve it. Sure - in order to solve a real world problem you want to understand the problem first (and see the big picture). But I think it's a rather bad idea to find a computational problem and then start thinking about learning how to programm. Picking up your car analogy: I wouldn't ask a designer to actually build a car - i'd much prefer a mechanical engineer to do that job. Also most computational problems are not entirely novel and it helps a lot to have reasonable background in common algorithms and techniques in the relevant field. What I like about bioinformatics is that a lot of knowledge from both biology and computerscience is required to tackle real problems. Neither of those sciences alone is up to the task... cu Philipp -- Dr. Philipp Pagel Department of Cellular and Molecular Physiology phone: (203) 785-6835 SHM, B117 fax: (203) 785-4951 Yale University 333 Cedar ST New Haven, CT 06520 USA From jeff at bioinformatics.org Wed Sep 26 12:30:50 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 26 Sep 2001 12:30:50 -0400 Subject: [BiO BB] reviews and feature articles Message-ID: <3BB202BA.B4AC5457@bioinformatics.org> Greetings. If anyone at all would like to write a review article on a book or computer program of interest to the community, please contact me (jeff at bioinformatics.org). The review should be fairly detailed and comprehensive, perhaps 5 or more paragraphs in length. Also, please contact me if you have written, or would like to write, a feature article of general interest to the community. All articles will be announced on BiO News and kept permanently on the Bioinformatics.org website. And the offer is open indefinitely. Cheers. Jeff From valb at vtek.com Wed Sep 26 15:19:40 2001 From: valb at vtek.com (Val Bykoski) Date: Wed, 26 Sep 2001 15:19:40 -0400 Subject: [BiO BB] (no subject) References: <3BA13416.50CF7624@biotools.com> <03d801c13cc5$c15595c0$d2befea9@pc300> <20010915173506.A16277@indialine.org> <052201c13e55$016e4270$d2befea9@pc300> <20010925225802.A6601@indialine.org> Message-ID: <079601c146c0$3281b130$d2befea9@pc300> Hi Indraneel, Thanx for very informative comments and ideas. You say: >I believe the concepts you point out are at present fairly complicated > to represent and visualise using current software. Remember that most of > current software was generated not to study the unknown diversity but to > store man made discrete units (eg financial data). Possibly a giant step > is required to produce such things and since I cannot at present see any > necessity for it in the commercial world (since a .com will always want > quick results), such a system will most probably be an open source > development. Agree. Very much so... Still, with the increasingly available (expression) data, the homology/analogy data/text processing is simply not enough, it creates an ever increasing gap between the data and the biology context, and thus makes drug discovery ineffective/unreliable. Molecular details of cell mechanisms are indeed a highly complex stuff, and it will take time to clarify the details. Meanwhile, the coarse-grain cell models with the rich (sequence-based) stimulus-response logic and infrastructure might be a really good starting point in designing the next-generation data-driven (and biochemistry/pathway-driven) cell models that incrementally refine cell structure and functions as soon as more and more data is available. With huge computational power and storage available and powerful OO languages (eg, Python), design and implementation of data-driven cell models seems to be quite practical now. > The "parts" (that we study now) indeed make up the "whole", but we also > need to remember, maybe according to "chaos" (or the gaia hypothesis?), > that the whole is something more than just the parts. Totally agree. That's what i call the cell infrastructure, and i believe that existing kinetic cell models need to be complemented with an infrastructure borrowed from physics and chemistry of (soft) condensed state such as "aperiodic" crystals (with space-variant subunits) that allows for cell-wide signaling, update, genome restructuring, etc Open source approach sounds great to me... i think, though, that NIH/NSF would certainly be interested in this kind of explorative research and development, and with enough interest/input from the bioinformatics community i'd be willing to explore the proposal writing opportunities... my best, /val vbykosky at galileo.eng.uml.edu val at vtek.com ----- Original Message ----- From: "Indraneel Majumdar" To: Sent: Tuesday, September 25, 2001 11:58 PM Subject: Re: [BiO BB] (no subject) > Hi Val, > > Sorry for the very late followup. After your mail I realised that truly > we are basing most of our bioinfo ideas on things like homology/analogy > rather than in terms of biochemical pathways, protein function prediction > in terms of cellular requirements and such things (something that I > wanted to do when I first entered this field, but lost sight of and > forgot very soon). > ... skipped > > On Sat, Sep 15, 2001 at 09:41:34PM -0400, Val Bykoski wrote: > > Hi Indraneel, > > Thanx for your comments. > > I refer to the cell as a biological cell, and my point, > > to put it a little differently, was that data has to work > > inside a (realistic) cell model, not to sit passively in databases. > > Data grouping, visualization, etc. is better than nothing, > > but still there is a huge gap between data (nicely grouped, > > visualized, etc) and their biological significance or context. > > I guess my point is that if you integrate data into a realistic > > cell model, the model is both a predictive framework and > > a (bio)context-sensitive database for the data. Then, > > data is hidden and work inside the model for predictions, > > and does not require grouping, visualization, etc. > > Sure, the "realistic cell model" is a hard nut...but may be > > worth of efforts, in particular, for a data-driven model. > > cheers, val > > val at vtek.com > > > > -- > http://www.indialine.org/indraneel/ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From haylic at hotmail.com Thu Sep 27 00:26:11 2001 From: haylic at hotmail.com (Hayli Chwang) Date: Thu, 27 Sep 2001 00:26:11 Subject: [BiO BB] review on bioinformatic developments in pharmacogenomics Message-ID: An HTML attachment was scrubbed... URL: From hzi at uol.com.br Wed Sep 26 23:15:50 2001 From: hzi at uol.com.br (hzi at uol.com.br) Date: Thu, 27 Sep 2001 00:15:50 -0300 Subject: [BiO BB] How to write Algorithm In-Reply-To: <20010926090336.A9369@indialine.org>; from indraneel@indialine.org on Wed, Sep 26, 2001 at 09:03:37AM -0500 References: <20010922081413.31204.qmail@mailFA9.rediffmail.com> <3BAEFB5F.EDD1757E@sgi1.chemie.uni-hamburg.de> <20010925232312.C6601@indialine.org> <878zf2t9il.fsf@mendel.genehack.org> <20010926090336.A9369@indialine.org> Message-ID: <20010927001550.A2732@siddhi.samsara.org> On Wed, Sep 26, 2001 at 09:03:37AM -0500, Indraneel Majumdar wrote: > On Wed, Sep 26, 2001 at 08:35:30AM -0400, John S. J. Anderson wrote: > > Indraneel Majumdar writes: > > > > > There is a very nice O'reilly book: Developing Bioinformatics > > > Computer Skills > > > > I wouldn't really recommend this for reading about algorithms -- there > > wasn't really any in-depth stuff in this book IIRC. (The book is still > > good for what it is -- it's just not a book about bioinfo algorithms.) > > yes, you're right. It's a good book, but not specially about algorithms Isn't this book a little too basic? I mean, I'm only reading it now, and it's my first book on Bioinformatics (I'm a medical student-Brazil), but I feel it's too basic: - if you already know your way around a GNU/Linux box (we debianers say "GNU/Linux"...so sue me... :-) ) In fact, if you use GNU/Linux or Unix, you can skip half of the book... - if you're familiar with genetics Would anyone reccomend another one? > > If you're a Perl programmer, especially a Perl programmer of the "I > > used to be a biologist but now I do Perl even though I never had a > > programming class in my life" variety, you should read chapters two > > and three of the ORA _Mastering Algorithms with Perl_ book, which > > discuss the implementation of some of the classic data structures > > (heaps, B trees, stack/queues/deques, etc.) in Perl. You will learn a > > staggering amount. > > Thanks for this great piece of information. I am a bioprogrammer of the > variety you described (which couldn't have been put better ;-) Sounds like good advice... And how about "functional programming languages"? A friend of mine (a mathematician) told me to check out a language called Haskell . It was __very__ different from __anything__ I'd seen before. Has anyone here ever used it? They have this a qicksort algorithm written in haskell, and I was amazed to see how beautiful (conceptually) it looked in haskell. For sure, it isn't for text processing, but hey, who cares? And what about Tannenbaum's "Data structures in C". He's supposed to be a pundit... Regards, Henry From rmp at sanger.ac.uk Thu Sep 27 06:30:26 2001 From: rmp at sanger.ac.uk (Roger Pettett) Date: Thu, 27 Sep 2001 11:30:26 +0100 (BST) Subject: [BiO BB] review on bioinformatic developments in pharmacogenomics In-Reply-To: Message-ID: On Thu, 27 Sep 2001, Hayli Chwang wrote: > If anyone > could suggest any sites, references or resources in the area, it would be > greatly appreciated... Or if anyone involved in the field who wouldn't > mind giving me some insight, that would be fantastic too. Please email: > hchw9194 at mail.usyd.edu.au http://www.ensembl.org/ is a good place to start. R. -- +---------------------------------------------------------------+ Roger Michael Pettett Email: rmp at sanger.ac.uk Senior Web Developer, Web: http://www.sanger.ac.uk/ The Sanger Centre Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA +---------------------------------------------------------------+ From rmp at sanger.ac.uk Thu Sep 27 06:39:10 2001 From: rmp at sanger.ac.uk (Roger Pettett) Date: Thu, 27 Sep 2001 11:39:10 +0100 (BST) Subject: [BiO BB] How to write Algorithm In-Reply-To: <20010927001550.A2732@siddhi.samsara.org> Message-ID: On Thu, 27 Sep 2001 hzi at uol.com.br wrote: > And how about "functional programming languages"? A friend of mine (a > mathematician) told me to check out a language called Haskell > . > It was __very__ different from __anything__ I'd seen before. Has > anyone here ever used it? > They have this a qicksort algorithm written in haskell, and I was > amazed to see how beautiful (conceptually) it looked in haskell. > For sure, it isn't for text processing, but hey, who cares? Haskell is a great language for doing most things mathematical. It's really good for evaluating infinite values & expressions. It's fast, compact and extremely neat. In my opinion it's way underused for bioinformatics applications. Whilst I worked with it I used a system called HUGS, the Haskell Users' Gofer System. My ex-tutor was heavily involved in its development and has some good links on his homepage: http://www.cs.nott.ac.uk/~gmh/ > And what about Tannenbaum's "Data structures in C". He's supposed to > be a pundit... Tannenbaum's Algorithms & Data Structures books are excellent resources for hardcore programmers, but probably of slightly limited use to bioinformaticians. R. -- +---------------------------------------------------------------+ Roger Michael Pettett Email: rmp at sanger.ac.uk Senior Web Developer, Web: http://www.sanger.ac.uk/ The Sanger Centre Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA +---------------------------------------------------------------+ From trey at veggie.stu.wesleyan.edu Thu Sep 27 07:14:50 2001 From: trey at veggie.stu.wesleyan.edu (Ashton Trey Belew) Date: Thu, 27 Sep 2001 11:14:50 +0000 Subject: [BiO BB] How to write Algorithm In-Reply-To: References: <20010927001550.A2732@siddhi.samsara.org> Message-ID: <20010927111450.A16756@veggie.wesleyan.edu> Greetings, > > It was __very__ different from __anything__ I'd seen before. Has > > anyone here ever used it? Haskell is really fun to write in. If you enjoyed it, you should definitely check out Bell Labs' ML. It is more strict than, well, pretty much everything and has some fun X libraries as well as a host of other utilities. http://cm.bell-labs.com/cm/cs/what/smlnj/ Have a nice day, -Trey -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ashton Trey Belew e-mail: trey at veggie.wesleyan.edu http://veggie.wesleyan.edu/trey/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The Chinese discovered gunpowder by accident while trying to invent a potion that would alchemically lengthen life. --Tom Robbins, Jitterbug Perfume (page 288) -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 232 bytes Desc: not available URL: From indraneel at indialine.org Fri Sep 28 05:55:23 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Fri, 28 Sep 2001 04:55:23 -0500 Subject: [BiO BB] How to write Algorithms In-Reply-To: References: Message-ID: <20010928045523.A26143@indialine.org> Hi, On Wed, Sep 26, 2001 at 04:21:49PM +0200, Jan Torleif Pedersen wrote: > them extensively, so please do not misunderstand my point, which is - Find a > problem first and then start thinking about how you want to solve it. Thanks for pointing out this basic idea. I tried pointing this out to my colleague yesterday (who insists that I solve my yet undefined problems using matrix algebra, which is well greek to me). But the more I look around, it seems that is a question no one wants to ask, and far less answer. Most professionals get thrust onto a project, never being asked to implement their own ideas from scratch (that's how programmers spend 80% of their time debugging other people's code ;-) \Indraneel -- http://www.indialine.org/indraneel/ From jeff at bioinformatics.org Sun Sep 30 16:14:59 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 30 Sep 2001 16:14:59 -0400 Subject: [BiO BB] connectivity problems Message-ID: <200109302014.QAA02788@www.bioinformatics.org> Greetings. This message is for people using our primary server. We noticed some access problems over the weekend, particularly disconnections and access denials. Some administrators worked from late Saturday night until Sunday afternoon trying to hunt down the problem, which seemed to evade us. The problem did not appear to be internal, as no programs were being executed during outage times, and there were no signs of a break-in. It turns out that someone else on the local network decided to "borrow" our static IP address, and this is causing some "confusion" on the network. We're going to work with the IT department on Monday to find the offenders, and when we do, we will kill and eat them with ketchup and a side order of fries. Anyway, we apologize for the inconvenience. -- The Lab Rats