From owner-software@net.bio.net Wed Sep 01 14:26:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: penny@krtraining.com Newsgroups: bionet.software Subject: mouse colony software Date: Wed, 01 Sep 1999 15:05:33 GMT Organization: M.D. Anderson Cancer Center - Science Park Research Division Lines: 18 Message-ID: <7qjfbj$lr2$1@nnrp1.deja.com> Reply-To: riggs@sprd1.mdacc.tmc.edu NNTP-Posting-Host: 143.111.133.113 X-Article-Creation-Date: Wed Sep 01 15:05:33 1999 GMT X-Http-User-Agent: Mozilla/4.06 (Macintosh; I; PPC) X-Http-Proxy: 1.0 x41.deja.com:80 (Squid/1.1.22) for client 143.111.133.113 X-MyDeja-Info: XMYDJUIDpennyriggs Our lab is looking for software options for keeping track of mice, cages, breeders, etc. for our transgenic mouse colonies. Any info, recommendations would be appreciated. please copy your reply to me at riggs@sprd1.mdacc.tmc.edu as my news reader access is limited. Tbanks, Penny Riggs MD Anderson Cancer Center Science Park Research Division Smithville TX riggs@sprd1.mdacc.tmc.edu Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Thu Sep 02 00:28:00 1999 Path: biosci!GENEMARK.BIOLOGY.GATECH.EDU!john From: john@GENEMARK.BIOLOGY.GATECH.EDU ("John D. Besemer") Newsgroups: bionet.software Subject: UPDATE_Bioinformatics_Conference_in_Atlanta Date: 1 Sep 1999 18:28:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 142 Sender: daemon@net.bio.net Distribution: world Message-ID: <199909020117.VAA12991@genemark.biology.gatech.edu> NNTP-Posting-Host: net.bio.net Early registration is now in progress for the Second International Georgia Tech Conference on Bioinformatics. The organizers would like to inform you that the following deadlines are approaching: * September 10 - Deadline for poster abstract submission * October 1 - Deadline for early registration We encourage you to register as soon as possible, as participation will be limited to about 250 people. For more information, please see the conference website at: http://exon.biology.gatech.edu/conference We look forward to seeing you in Atlanta, The Conference Organizers ********************************************************************** SECOND GEORGIA TECH INTERNATIONAL CONFERENCE ON BIOINFORMATICS In silico BIOLOGY: SEQUENCE & STRUCTURE & FUNCION ATLANTA NOVEMBER 11 - 14, 1999 SPONSORS: National Institutes of Health US Department of Energy Alfred P. Sloan Foundation Georgia Tech College of Science Parker H. Petit Institute for Bioengineering & Bioscience SouthEastern Center for Applied Analysis SmithKline Beecham AGENDA: The conference agenda includes keynote lectures, plenary lectures, as well as poster sessions. The list of confirmed speakers is as follows: KEYNOTE SPEAKERS: Russell Doolittle University of California, San Diego, CA Walter Fitch University of California, Irvine, CA PLENARY SPEAKERS: David Baker University of Washington, Seattle, WA Pierre Baldi University of California, Irvine, CA Steven Brenner Stanford University, Stanford, CA Chris Burge MIT, Cambridge, MA Antoine Danchin Institute Pasteur, Paris, France Sean Eddy Washington University School of Medicine, St. Louis, MO Patrick Forterre University Paris-Sud, Paris, France David Haussler University of California, Santa Cruz, CA Samuel Karlin Stanford University, Stanford, CA Jeffrey Lawrence University of Pittsburgh, Pittsburgh, PA Steven Henikoff Fred Hutchinson Cancer Research Center, Seattle, WA Christine Orengo University College, London, UK Burkhard Rost Columbia University, New York, NY Andrej Sali Rockefeller University, New-York, NY William Taylor National Institute for Medical Research, London, UK STEERING/PROGRAM COMMITTEE: Pierre Baldi Net-ID Mark Borodovsky, Co-chair Georgia Tech Soren Brunak Technical University of Denmark Chris Burge MIT Jim Fickett SmithKline Beecham Steven Henikoff Fred Hutchinson Cancer Research Center Eugene Koonin, Co-chair NCBI/NIH Andrej Sali Rockefeller University Chris Sander Millennium Pharmaceuticals Gary Stormo University of Colorado DEADLINES: POSTER SUBMISSION: Deadline for poster abstract submission: September 10, 1999 REGISTRATION: Early registration ends: October 1, 1999 CONFERENCE SCHEDULE: Registration opens at 6:00pm on Thursday, November 11 The program starts 8:00am Friday, November 12 and ends at noon Sunday, November 14. LOCATION: The conference will be held at the Renaissance Atlanta Hotel Downtown located near the center of 1996 Olympic development, close to the Fox Theatre & Georgia Tech. ORGANIZING COMMITTEE: General co-ordination Mark Borodovsky, Georgia Tech mark@amber.gatech.edu "Bioinformatics" magazine publication Chris Burge MIT cburge@mit.edu Poster sessions Scott Sammons Emory University sammons@bimcore.emory.edu Administrative & Public Relations Assistant Amanda Besemer Emory University Amanda_Besemer@bus.emory.edu Publicity John Besemer Georgia Tech john@amber.gatech.edu Registration and general events Michael Moryc Georgia Tech michael.moryc@conted.gatech.edu MORE INFORMATION To obtain more information on poster submission & registration visit the WWW page: http://exon.biology.gatech.edu/conference or contact us by e-mail: register@conted.swann.gatech.edu Phone: (404) 894-2400 Fax: (404) 894-8925 From owner-software@net.bio.net Thu Sep 02 00:29:00 1999 Path: biosci!GENEMARK.BIOLOGY.GATECH.EDU!john From: john@GENEMARK.BIOLOGY.GATECH.EDU ("John D. Besemer") Newsgroups: bionet.software Subject: UPDATE_Bioinformatics_Conference_in_Atlanta Date: 1 Sep 1999 18:29:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 142 Sender: daemon@net.bio.net Distribution: world Message-ID: <199909020117.VAA12995@genemark.biology.gatech.edu> NNTP-Posting-Host: net.bio.net Early registration is now in progress for the Second International Georgia Tech Conference on Bioinformatics. The organizers would like to inform you that the following deadlines are approaching: * September 10 - Deadline for poster abstract submission * October 1 - Deadline for early registration We encourage you to register as soon as possible, as participation will be limited to about 250 people. For more information, please see the conference website at: http://exon.biology.gatech.edu/conference We look forward to seeing you in Atlanta, The Conference Organizers ********************************************************************** SECOND GEORGIA TECH INTERNATIONAL CONFERENCE ON BIOINFORMATICS In silico BIOLOGY: SEQUENCE & STRUCTURE & FUNCION ATLANTA NOVEMBER 11 - 14, 1999 SPONSORS: National Institutes of Health US Department of Energy Alfred P. Sloan Foundation Georgia Tech College of Science Parker H. Petit Institute for Bioengineering & Bioscience SouthEastern Center for Applied Analysis SmithKline Beecham AGENDA: The conference agenda includes keynote lectures, plenary lectures, as well as poster sessions. The list of confirmed speakers is as follows: KEYNOTE SPEAKERS: Russell Doolittle University of California, San Diego, CA Walter Fitch University of California, Irvine, CA PLENARY SPEAKERS: David Baker University of Washington, Seattle, WA Pierre Baldi University of California, Irvine, CA Steven Brenner Stanford University, Stanford, CA Chris Burge MIT, Cambridge, MA Antoine Danchin Institute Pasteur, Paris, France Sean Eddy Washington University School of Medicine, St. Louis, MO Patrick Forterre University Paris-Sud, Paris, France David Haussler University of California, Santa Cruz, CA Samuel Karlin Stanford University, Stanford, CA Jeffrey Lawrence University of Pittsburgh, Pittsburgh, PA Steven Henikoff Fred Hutchinson Cancer Research Center, Seattle, WA Christine Orengo University College, London, UK Burkhard Rost Columbia University, New York, NY Andrej Sali Rockefeller University, New-York, NY William Taylor National Institute for Medical Research, London, UK STEERING/PROGRAM COMMITTEE: Pierre Baldi Net-ID Mark Borodovsky, Co-chair Georgia Tech Soren Brunak Technical University of Denmark Chris Burge MIT Jim Fickett SmithKline Beecham Steven Henikoff Fred Hutchinson Cancer Research Center Eugene Koonin, Co-chair NCBI/NIH Andrej Sali Rockefeller University Chris Sander Millennium Pharmaceuticals Gary Stormo University of Colorado DEADLINES: POSTER SUBMISSION: Deadline for poster abstract submission: September 10, 1999 REGISTRATION: Early registration ends: October 1, 1999 CONFERENCE SCHEDULE: Registration opens at 6:00pm on Thursday, November 11 The program starts 8:00am Friday, November 12 and ends at noon Sunday, November 14. LOCATION: The conference will be held at the Renaissance Atlanta Hotel Downtown located near the center of 1996 Olympic development, close to the Fox Theatre & Georgia Tech. ORGANIZING COMMITTEE: General co-ordination Mark Borodovsky, Georgia Tech mark@amber.gatech.edu "Bioinformatics" magazine publication Chris Burge MIT cburge@mit.edu Poster sessions Scott Sammons Emory University sammons@bimcore.emory.edu Administrative & Public Relations Assistant Amanda Besemer Emory University Amanda_Besemer@bus.emory.edu Publicity John Besemer Georgia Tech john@amber.gatech.edu Registration and general events Michael Moryc Georgia Tech michael.moryc@conted.gatech.edu MORE INFORMATION To obtain more information on poster submission & registration visit the WWW page: http://exon.biology.gatech.edu/conference or contact us by e-mail: register@conted.swann.gatech.edu Phone: (404) 894-2400 Fax: (404) 894-8925 From owner-software@net.bio.net Thu Sep 02 08:52:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!blackbush.xlink.net!news-kar1.dfn.de!news-han1.dfn.de!newsserver.rrzn.uni-hannover.de!not-for-mail From: Bernhard Mayr Newsgroups: bionet.software Subject: Tool for signal transduction pathways Date: Thu, 02 Sep 1999 11:36:43 +0200 Organization: RRZN - Newsserver Message-ID: <37CE452B.890A9295@rrzn-serv.de> NNTP-Posting-Host: h76.ts1.rrzn-serv.de Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------2E97954E93B8168CA91ABF4F" X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.7 i586) X-Accept-Language: en Lines: 53 This is a multi-part message in MIME format. --------------2E97954E93B8168CA91ABF4F Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear colleagues As someone interested in signal transduction I=B4m looking for a software= tool / database that can store and graphically display signalling pathways like =B4MyNewKinase inhibits YourWellKnownFactor by phosphorylation=B4. I would also like to store new data from the literature with this tool. Has anyone heard about such software ? Any suggestions are wellcome. -- Bernhard Mayr Dept. Clinical Endocrinology MHH Hannover 30161 Hannover, Germany Fon +49 511 3940075 Fax +49 511 532 3825 --------------2E97954E93B8168CA91ABF4F Content-Type: text/x-vcard; charset=us-ascii; name="ndxdbmay.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Bernhard Mayr Content-Disposition: attachment; filename="ndxdbmay.vcf" begin:vcard n:Mayr;Bernhard tel;cell:+49 177 4363136 tel;fax:+49 511 532 3825 tel;home:+49 511 3940075 tel;work:+49 511 532 2211 x-mozilla-html:FALSE org:MHH Hannover;Dept. Clinical Endocrinology adr:;;In der Steinriede 5;Hannover;;30161;Germany version:2.1 email;internet:ndxdbmay@rrzn-serv.de title:Dr. x-mozilla-cpt:;0 fn:Bernhard Mayr end:vcard --------------2E97954E93B8168CA91ABF4F-- From owner-software@net.bio.net Thu Sep 02 13:19:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newspeer.monmouth.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Jean-Jack M. Riethoven" Newsgroups: bionet.software Subject: [ANNOUNCE] Conference: Datamining in Bioinformatics - towards in Silico Biology Date: Thu, 2 Sep 1999 15:12:47 +0100 Organization: EMBL - European Bioinformatics Institute Lines: 64 Message-ID: <7qm0kv$oqf$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: ntserv-03.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 936281567 25423 193.62.196.83 (2 Sep 1999 14:12:47 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 2 Sep 1999 14:12:47 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 DATAMINING IN BIOINFORMATICS - TOWARDS IN SILICO BIOLOGY 10 to 12 November 1999 EBI - Wellcome Trust Genome Campus - Hinxton - Cambridge INTRODUCTION During the last few years bioinformatics has been overwhelmed with increasing floods of data, both in terms of volume and in terms of new databases and new types of data. We are now entering the post-genomic age, where, in addition to complete genome sequences, we are learning about gene expression patterns and protein interactions on genomic scales. This poses new challenges. Old ways of dealing with data item by item are no longer sustainable and it is necessary to create new opportunities for discovering biological knowledge "in silico" by data mining. SCOPE Data mining is defined as "exploration and analysis by automatic and semi-automatic means, of large quantities of data in order to discover meaningful patterns and rules". Our conference on 'Data mining for Bioinformatics' will bring together researchers interested in both fields, with the aim of generating new ideas and insights into how to tackle the challenge of floods of data in molecular biology. We will cover data mining applications in: molecular sequence and structure data, gene expression and other high thru-put data, and in existing knowledge buried in large biological texts. A list of speakers include: o Rolf Apweiler (EMBL-EBI) o Phil Bourne (UC San Diego Supercomputer Center) o Inge Jonassen (University of Bergen) o Heikki Mannila (Helsinki University, Microsoft) o Christos Ouzounis (EMBL-EBI) o Paul Spellman (Stanford University) o Isidore Rigoutsos (IBM Research) o Ron Taylor (National Cancer Institute, NIH) o Martin Vingron (DKFZ, Germany) o David Westhead (University of Leeds) VENUE The conference will be held at Hinxton Hall Conference Centre on the Wellcome Trust Genome Campus, near Cambridge, UK, and will consist of invited talks and poster sessions. The conference will commence late afternoon on November 10 with a key-note address followed by a conference dinner. The conference will end at noon November 12. REGISTRATION The number of participants will be restricted to 200. The early registration and abstract (1 page) submission deadline is September 19. The early registration fee, excluding the conference dinner, is GBP 100; late registration has been set at GBP 175. Registration and submission of abstracts can be done online. MORE INFORMATION Our website has the latest information on the conference; we cordially invite you to visit it at http://industry.ebi.ac.uk/datamining99/ With kind regards, Jean-Jack Riethoven on behalf of the organising committee (datamining99@ebi.ac.uk) From owner-software@net.bio.net Thu Sep 02 15:10:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!fu-berlin.de!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software Subject: Re: Tool for signal transduction pathways Date: 2 Sep 1999 16:03:48 GMT Organization: Station biologique de Roscoff Lines: 28 Message-ID: References: <37CE452B.890A9295@rrzn-serv.de> NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <37CE452B.890A9295@rrzn-serv.de>, Bernhard Mayr wrote: > Dear colleagues > > As someone interested in signal transduction I=B4m looking for a software= > > tool / database that can store and graphically display signalling > pathways like =B4MyNewKinase inhibits YourWellKnownFactor by > phosphorylation=B4. I would also like to store new data from the > literature with this tool. > > Has anyone heard about such software ? > Any suggestions are wellcome. Try ACEDB, there is a special database which has been developed by Takako Takai-Igarashi and Tsuguchika Kaminuma just for that purpose (well, it seems...:-) http://geo.nihs.go.jp:80/csndb.html Florent -- Florent Crépineau Station Biologique de Roscoff BP 74 29682 Roscoff cedex From owner-software@net.bio.net Thu Sep 02 17:12:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.berkeley.edu!ihnp4.ucsd.edu!news.service.uci.edu!usenet From: Harry Mangalam Newsgroups: bionet.software Subject: new sites for web version of tacg Date: Thu, 02 Sep 1999 10:52:47 -0700 Organization: University of California, Irvine Lines: 73 Message-ID: <37CEB96F.56912AB1@home.com> NNTP-Posting-Host: cx408397-a.irvn1.occa.home.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.6 [en] (X11; U; Linux 2.2.9 i686) X-Accept-Language: en Hi All, tacg is a command-line restriction mapping and pattern-matching tool that runs on unixy systems (and has been ported in command-line mode to DOS, Windows95/98/NT and even the Mac). Version 3 will be forthcoming Real Soon Now. However, this note is about public WWWtacg server availability. The server that hosted the publicly available version of tacg at UC Irvine crashed some time ago and was not restored. A number of people have asked about replacement servers so here are some that I know about: http://24.1.175.29/tacg (this is the primary site - all new versions will be available here 1st) http://darwin.bio.uci.edu/tacg Catherine Letondal has also set up her own tacg interface at: http://bioweb.pasteur.fr/seqanal/interfaces/tacg.html which is a bit different than mine, but actually adds some more functionality to it. I'm compiling a list of alternative public servers to place on my web page for when I release the beta of version 3 - I'm just finishing off the docs and tacking on the last few functions which include: - integration with Jim Knight's seqio (and therefore multiple sequence analysis as well as automatic reformatting), - matrix matching (using TRANSFAC-formatted matrices), - reverse translation (as part of 'Silent Sites', also new), - more protein info (est. pI, absolute and % composition of peptides) - some elementary stats, - regular expression matching, - sliding window analysis - 'surrounding sequence' extraction, with auto rev. compl or not - per-pattern min/Max filtering and logic (in a sliding window or not) - allows alternative pattern files for patterns, matrices, regular expressions, etc. - lots of bug fixes, code cleanup, memory leak plugs, better formatting - introduction of more bugs, but hopefully fewer than I fixed :) - an example function to show how to explicitly add your own functions to it - autoconf configuration and - RPM packaging (mostly for Linux) on top of the previous: - Proximity matching, - searching with errors - 1|3|6 frame translations in 1|3 letter codes, using any Codon Translation table, ouput in FASTA format - some primitive ORF finding (but not real gene finding yet), - degenerate (IUPAC) sequence handling in input sequence and patterns, - gel simulations (w/ hi/lo cutoffs), - ladder maps, - Linear maps, - tabular Sites, - multiply sorted tabular Fragments, written in ANSI C, w/ dynamic mem for most ops, developed on Lintel, tested so far on SGI and Solaris; final targets are those and PPC Linux, Alpha Linux, Compaq Tru64 (aka DEC Unix aka OSF), the BSDs, and maybe NT and MacOS X. The new WWW interface is also under development. It will hopefully include graphic plasmid map functionality. -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 -- mangalam@home.com From owner-software@net.bio.net Thu Sep 02 22:06:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!wn4feed!worldnet.att.net!128.230.129.106!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: lxl7392@usl.edu Newsgroups: bionet.software Subject: Measuring area of images Date: Thu, 02 Sep 1999 22:50:36 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 13 Message-ID: <7qmuvo$988$1@nnrp1.deja.com> NNTP-Posting-Host: 129.118.76.22 X-Article-Creation-Date: Thu Sep 02 22:50:36 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows NT) X-Http-Proxy: 1.1 x30.deja.com:80 (Squid/1.1.22) for client 129.118.76.22 X-MyDeja-Info: XMYDJUIDrashidas I am trying to count and measure the area of duckweed leaves. I already have a free shareware program called ImageTool. I can use it to count leaves but have not as yet been able to measure areas successfully. Can anyone in internet land answer one of these questions: 1. How do you measure image areas in ImageTool? 2. What other free software programs exist that could measure duckweed area? Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Fri Sep 03 03:15:00 1999 Path: biosci!ucalgary.ca!hausner From: hausner@ucalgary.ca (hausner) Newsgroups: bionet.software Subject: mostlikelihood methods Date: 2 Sep 1999 21:15:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <37CF48EA.440AC605@ucalgary.ca> NNTP-Posting-Host: net.bio.net Hello I would appreciate some pointers with regards to phylogenetic soft ware packages/programs that are user-friendly, work in windows 95 etc., and can perform or infer phylogenetic relationships based on amino acid sequence alignments. Thanks for the help. George. From owner-software@net.bio.net Fri Sep 03 09:37:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!infeed.is.co.za!feeder.is.co.za!news.is.co.za!not-for-mail From: "winhide" Newsgroups: bionet.software Subject: SANBI EST clustering benchmark dataset Date: Fri, 3 Sep 1999 12:12:06 +0200 Organization: An Internet Solution Customer Lines: 29 Message-ID: <7qo7oa$vuf$2@news.is.co.za> NNTP-Posting-Host: yebo.sanbi.ac.za X-Trace: news.is.co.za 936354378 32719 196.38.142.74 (3 Sep 1999 10:26:18 GMT) X-Complaints-To: abuse@is.co.za NNTP-Posting-Date: 3 Sep 1999 10:26:18 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 SANBI is making available a dataset of masked ESTs suitable for benchmarking. We are keen to evaluate the *hardware* performance of clustering applications, and also the *clustering* performance and accuracy. The dataset represents a randomly chosen set of Human eye-expressed ESTs that have been masked for repeats and vector sequences. It has not as yet been assigned to 'true' gene classes, as these have not all been assigned against available genome data. The dataset can be found at ftp.sanbi.ac.za/STACK/benchmarks/ The dataset is made available with the proviso that results of benchmarking should be made broadly available. Our own results and a suggested format are found in ftp.sanbi.ac.za/STACK/benchmarks/README Algorithmic benchmarks can be found at ftp.sanbi.ac.za/STACK/benchmarks/ALGO_BENCH Unfortunately, due to spamming, uploads to the FTP site are not possible. Please email results including clusters if possible to info@sanbi.ac.za and they will be posted. Win Hide, Alan Christoffels, Andrey Ptitsyn and Antoine van Gelder From owner-software@net.bio.net Fri Sep 03 11:37:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.icl.net!dispose.news.demon.net!demon!news.demon.co.uk!demon!genesys.demon.co.uk!Duncan From: "Dr. Duncan Clark" Newsgroups: bionet.software Subject: Re: Measuring area of images Date: Fri, 3 Sep 1999 09:40:48 +0100 Organization: DNAmp Ltd. Message-ID: References: <7qmuvo$988$1@nnrp1.deja.com> Reply-To: "Dr. Duncan Clark" NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk:158.152.17.110 X-Trace: news.demon.co.uk 936361814 nnrp-01:11964 NO-IDENT genesys.demon.co.uk:158.152.17.110 X-Complaints-To: abuse@demon.net MIME-Version: 1.0 X-Newsreader: Turnpike Integrated Version 4.02 U Lines: 31 In article <7qmuvo$988$1@nnrp1.deja.com>, lxl7392@usl.edu writes >I am trying to count and measure the area of duckweed leaves. I already >have a free shareware program called ImageTool. I can use it to count >leaves but have not as yet been able to measure areas successfully. >Can anyone in internet land answer one of these questions: > >1. How do you measure image areas in ImageTool? > >2. What other free software programs exist that could measure >duckweed area? > > >Sent via Deja.com http://www.deja.com/ >Share what you know. Learn what you don't. Low Tech solution. Photocopy a leaf (assuming it is big enough) and cut it out. Weigh. Compare to weight of known area of identical photocopy paper. Duncan -- The problem with being on the cutting edge is that you occasionally get sliced from time to time.... Duncan Clark DNAmp Ltd. Tel: +44(0)1252376288 FAX: +44(0)8701640382 http://www.dnamp.com http://www.genesys.demon.co.uk From owner-software@net.bio.net Fri Sep 03 14:32:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!skynet.be!fu-berlin.de!watson.bio.nat.tu-bs.DE!not-for-mail From: Andrea Hansen Newsgroups: bionet.software Subject: Re: mostlikelihood methods Date: 03 Sep 1999 17:25:06 +0200 Lines: 30 Sender: andi@watson.bio.nat.tu-bs.de Message-ID: References: <37CF48EA.440AC605@ucalgary.ca> NNTP-Posting-Host: watson.bio.nat.tu-bs.de (134.169.70.93) Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Access: 16 [4974] X-Trace: fu-berlin.de 936372330 15946 (none) 134.169.70.93 X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald" hausner@ucalgary.ca (hausner) writes: Hi George, look at this this: http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/Windows/ You will find a lot of useful links for phylogentic programs for windows. You can also try this site: http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/Online_Tools/ to find some online tools for making trees. But first, you should look at this site to make online some aligments with your sequences: http://www.bioinformatik.de/cgi-bin/browse/Catalog/Databases/Online_Multiple_Alignment/ > Hello I would appreciate some pointers with > regards to phylogenetic soft ware > packages/programs that are user-friendly, work in > windows 95 etc., and can perform or infer > phylogenetic relationships based on amino acid > sequence alignments. Andrea -- Andrea Hansen Institut fuer Genetik Tel : ++49-531-391-5783 TU Braunschweig Fax : ++49-531-391-5765 Spielmannstr. 7 email : webmaster@bioinformatik.de 38106 Braunschweig http://www.bioinformatik.de From owner-software@net.bio.net Fri Sep 03 15:10:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!grolier!news-raspail.gip.net!news.gsl.net!gip.net!oleane!pasteur.fr!nefertiti.pasteur.fr!letondal From: letondal@pasteur.fr (Catherine Letondal) Newsgroups: bionet.software Subject: Re: mostlikelihood methods Date: 3 Sep 1999 16:04:28 GMT Organization: Institut Pasteur, Paris Sender: letondal@nefertiti.pasteur.fr (Catherine Letondal) Distribution: world Message-ID: <7qoric$urt$1@desdemone.pasteur.fr> References: <37CF48EA.440AC605@ucalgary.ca> Reply-To: letondal@pasteur.fr (Catherine Letondal) NNTP-Posting-Host: nefertiti.pasteur.fr X-Trace: desdemone.pasteur.fr 936374668 31613 157.99.64.20 (3 Sep 1999 16:04:28 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 3 Sep 1999 16:04:28 GMT X-Newsreader: mxrn 6.18-31 Lines: 20 In article <37CF48EA.440AC605@ucalgary.ca>, hausner@ucalgary.ca (hausner) writes: > > >Hello I would appreciate some pointers with >regards to phylogenetic soft ware >packages/programs that are user-friendly, work in >windows 95 etc., and can perform or infer >phylogenetic relationships based on amino acid >sequence alignments. > >Thanks for the help. George.  Hi, You may have a look at : http://www.pasteur.fr/recherche/BNB/bnb-en.html (and select software+evolution criteria) -- Catherine Letondal -- letondal@pasteur.fr -- +33 (1) 40 61 31 91 From owner-software@net.bio.net Sat Sep 04 01:06:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.axxsys.net!newspump.monmouth.com!newspeer.monmouth.com!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: "Stan Hicks" Newsgroups: bionet.software Subject: Data Graphics Software Date: Fri, 3 Sep 1999 20:53:44 -0500 X-Posted-Path-Was: not-for-mail X-Priority: 3 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-ELN-Date: 4 Sep 1999 01:54:18 GMT X-ELN-Insert-Date: Fri Sep 3 18:55:05 1999 Organization: EarthLink Network, Inc. X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MSMail-Priority: Normal Lines: 8 Reply-To: "Stan Hicks" NNTP-Posting-Host: ip126.lubbock4.tx.pub-ip.psi.net Message-ID: <7qpu4a$483$1@holly.prod.itd.earthlink.net> ClickIt Graph is state of the art data graphics for Windows. Over 23 different graph types are supported for business, science and engineering reports and presentations. www.clickitgraph.com From owner-software@net.bio.net Sat Sep 04 12:18:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!feeder.qis.net!news-peer1.sprintlink.net!news-in-central.sprintlink.net!news.sprintlink.net!news.monad.net!not-for-mail From: Calvin Winey Newsgroups: bionet.software Subject: FACSMate comand set?? Date: Sat, 04 Sep 1999 09:08:02 -0400 Organization: MonadNet Lines: 12 Message-ID: NNTP-Posting-Host: tcr4-7.keene.monad.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.6/32.525 I have recently purchased a Becton Dickenson FACSMate without the HP9800 controller. I have an industrial application and would like to be able to control the cytology unit directly from a PC without the HP9800. I am an experienced C/C++ programmer. it should be an easy task if I could find the correct information. I am looking for anyone who might have documentation of the communication protocall and command set used by the unit. thanks, Calvin Winey CalvinW@sanders-prototype.com From owner-software@net.bio.net Sat Sep 04 15:26:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.direct.ca!newsfeed.enteract.com!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: straker@istar.ca Newsgroups: bionet.software Subject: Re: mouse colony software Date: Sat, 04 Sep 1999 16:13:00 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 62 Message-ID: <7qrge6$dfm$1@nnrp1.deja.com> References: <7qjfbj$lr2$1@nnrp1.deja.com> NNTP-Posting-Host: 137.186.176.145 X-Article-Creation-Date: Sat Sep 04 16:13:00 1999 GMT X-Http-User-Agent: Mozilla/2.01KIT (Win95; I) X-Http-Proxy: 1.0 x39.deja.com:80 (Squid/1.1.22) for client 137.186.176.145 X-MyDeja-Info: XMYDJUIDmichael6334 In article <7qjfbj$lr2$1@nnrp1.deja.com>, riggs@sprd1.mdacc.tmc.edu wrote: > Our lab is looking for software options for keeping > track of mice, cages, breeders, etc. for our transgenic > mouse colonies. Any info, recommendations would be appreciated. > > please copy your reply to me at riggs@sprd1.mdacc.tmc.edu > as my news reader access is limited. > > Tbanks, > > Penny Riggs > MD Anderson Cancer Center > Science Park Research Division > Smithville TX > riggs@sprd1.mdacc.tmc.edu Hi Penny, I think we have the software you're looking for. I formed Aisle3 Software after leaving my postdoc at HHMI, UCSD with the intention of creating an application that would facilitate easy entry of new litter, tail, and phenotype data and then provide sophisticated analysis of this data across the colony as a whole. Colony Manager is a Mac (soon to be Windows) database that allows you to track an unlimited number of genotypes and phenotypes in your colony using very straightforward menu based entry. Once you've entered the data you can not only keep and print records but analyze your colony data as a whole, e.g. by graphically displaying pedigrees tracking phenotype vs. genotype inheritance, or by performing searches identifying which mice in the colony bear any desired combination of genotypes. If you're interested, please let me know and I'll tell you more about Colony Manager. Best Regards, Rob =========================== Rob Campbell, M.D., Ph.D. Creator and Developer Aisle3 Software web: www.aisle3.com email: rob@aisle3.com =========================== > > Sent via Deja.com http://www.deja.com/ > Share what you know. Learn what you don't. > Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. 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CALL NOW FOR INFO.....209-669-3628 From owner-software@net.bio.net Tue Sep 07 05:42:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!europa.netcrusader.net!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!netnews.hinet.net!news From: Brandon Leung Newsgroups: bionet.software,alt.radio.networks.cbc,bionet.software.acedb,at.network.eunet,alt.tv.twin-peaks Subject: hello again Date: Tue, 07 Sep 1999 14:36:48 +0800 Organization: DCI HiNet Message-ID: <37D4B27F.68510250@hongkong.com> Reply-To: oopsbrandon@hongkong.com NNTP-Posting-Host: h73.s4.ts30.hinet.net Mime-Version: 1.0 Content-Type: text/plain; charset=big5; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 (Macintosh; I; PPC) X-Accept-Language: en Lines: 2 Xref: biosci bionet.software:24114 bionet.software.acedb:2596 q From owner-software@net.bio.net Tue Sep 07 08:33:00 1999 Path: biosci!CMMT.UBC.CA!francis From: francis@CMMT.UBC.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: electronic (e) PCR Date: 7 Sep 1999 02:32:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net > From: CSC > To: bio-soft@net.bio.net > I need info on ePCR. Thanks in advance ! the URL: http://www.ncbi.nlm.nih.gov/STS/ the ciatation: > Schuler GD, Trends Biotechnol 1998 Nov;16(11):456-9 > Electronic PCR: bridging the gap between genome mapping > and genome sequencing. the PubMed abstract: http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9830153&form=6&db=m&Dopt=b cheers, f. -- | B.F. Francis Ouellette tel: (604) 875-3815 | | Director, Bioinformatics Core Facility fax: (604) 875-3840 | | CMMT, UBC, Canada eFax: (425) 740-6978 | | francis@cmmt.ubc.ca http://www.cmmt.ubc.ca | From owner-software@net.bio.net Tue Sep 07 08:36:00 1999 Path: biosci!CMMT.UBC.CA!francis From: francis@CMMT.UBC.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: electronic (e) PCR Date: 7 Sep 1999 02:36:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net oops, sorry, the 'original' paper is: http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9149949&form=6&db=m&Dopt=b > Schuler GD, Genome Res 1997 May;7(5):541-50 > > Sequence mapping by electronic PCR. cheers, f. -- | B.F. Francis Ouellette tel: (604) 875-3815 | | Director, Bioinformatics Core Facility fax: (604) 875-3840 | | CMMT, UBC, Canada eFax: (425) 740-6978 | | francis@cmmt.ubc.ca http://www.cmmt.ubc.ca | On Tue, 7 Sep 1999, Francis Ouellette wrote: > Date: Tue, 7 Sep 1999 02:27:38 -0700 (PDT) > From: Francis Ouellette > To: bio-soft@net.bio.net > Subject: Re: electronic (e) PCR > > > From: CSC > > To: bio-soft@net.bio.net > > > I need info on ePCR. Thanks in advance ! > > the URL: http://www.ncbi.nlm.nih.gov/STS/ > > the ciatation: > > > Schuler GD, Trends Biotechnol 1998 Nov;16(11):456-9 > > > Electronic PCR: bridging the gap between genome mapping > > and genome sequencing. > > the PubMed abstract: > > http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9830153&form=6&db=m&Dopt=b > > cheers, > > f. From owner-software@net.bio.net Tue Sep 07 08:47:00 1999 Path: biosci!sb-roscoff.fr!crepinau From: crepinau@sb-roscoff.fr (Crepineau Florent) Newsgroups: bionet.software Subject: Re : Measuring area of images Date: 7 Sep 1999 02:47:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <37D4F9F9.346E@sb-roscoff.fr> Reply-To: crepinau@sb-roscoff.fr NNTP-Posting-Host: net.bio.net Hello In article <7qmuvo$988$1@nnrp1.deja.com>, lxl7392@usl.edu writes >I am trying to count and measure the area of duckweed leaves. I already >have a free shareware program called ImageTool. I can use it to count >leaves but have not as yet been able to measure areas successfully. >Can anyone in internet land answer one of these questions: > >1. How do you measure image areas in ImageTool? I don't know. >2. What other free software programs exist that could measure >duckweed area? I know of NIH image that could do that but I don't know if it is straightforward. What you could do is what I did a few years ago a) outline the leaf edge b) layer an electronic sheet covered with dots onto your leaves c) count first the dots fully inside a leaf and then all the dots even slightly touching the leaf, average the total. d) use the formula that translate a number of dots to an area (I do not have my course notes here but I am sure that formula can be easily found, look in geology book I know this is used to measure the size of cristals) I think this process can be automated in NIHimage. Hope this help. Florent From owner-software@net.bio.net Tue Sep 07 09:02:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!dispose.news.demon.net!demon!newsfeed.icl.net!newsfeed.icl.net!easynet-tele!easynet.net!news.vas-net.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: pujadas@argo.urv.es (Gerard Pujadas) Newsgroups: bionet.software Subject: Enzymology software Date: 7 Sep 1999 10:55:57 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Trace: niobium.hgmp.mrc.ac.uk 936698158 29519 193.62.192.80 (7 Sep 1999 09:55:58 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 7 Sep 1999 09:55:58 GMT X-Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA19848 for ; Tue, 7 Sep 1999 10:55:55 +0100 (BST) X-Received: from argo.urv.es (argo.urv.es [130.206.36.12]) by mserv1.dl.ac.uk with ESMTP id KAA16233 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from pujadas@argo.urv.es); Tue, 7 Sep 1999 10:55:57 +0100 (BST) X-Precedence: first-class X-Received: from [130.206.36.86] (macbi77.urv.es [130.206.36.86]) by argo.urv.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id LAA05005 for ; Tue, 7 Sep 1999 11:49:35 +0200 (MDT) X-To: bio-software@dl.ac.uk X-MIME-Autoconverted: from quoted-printable to 8bit by hgmp.mrc.ac.uk id KAA19849 Lines: 24 Dear all, I would like to find a shareware/freeware or cheap soft that allow to make an enzyme purification simulation. This is for teaching. Thanks in advances for your help. Yours sincerely. Gerard. =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== --- From owner-software@net.bio.net Tue Sep 07 11:21:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.algonet.se!newsfeed1.telenordia.se!algonet!newsfeed1.funet.fi!newsfeed.uninet.ee!news.ut.ee!not-for-mail From: Peeter Toomik Newsgroups: bionet.software Subject: Re: Enzymology software Date: Tue, 07 Sep 1999 15:16:42 +0300 Organization: Tartu University Lines: 28 Message-ID: <37D50229.84141A92@ut.ee> References: NNTP-Posting-Host: biochem3.bio.ut.ee Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: kadri.ut.ee 936706349 6819 193.40.8.203 (7 Sep 1999 12:12:29 GMT) X-Complaints-To: usenet@news.ut.ee NNTP-Posting-Date: 7 Sep 1999 12:12:29 GMT X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en Try protlab.exe from http://www.leeds.ac.uk/bionet/compend/bn11cftp.htm It is really very good. Gerard Pujadas wrote: > Dear all, > > I would like to find a shareware/freeware or cheap soft that allow > to make an enzyme purification simulation. This is for teaching. > > Thanks in advances for your help. > > Yours sincerely. > > Gerard. > > =========================================================================== > DR. GERARD PUJADAS > BIOTECNOLOGIA COMPUTACIONAL > DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es > UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 > PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 > 43005 TARRAGONA (CATALONIA) > STATE: SPAIN (EUROPEAN UNION) > =========================================================================== > > --- From owner-software@net.bio.net Tue Sep 07 12:49:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.icl.net!colt.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: michael.baron@bbsrc.ac.uk Newsgroups: bionet.software Subject: Re: Measuring area of images Date: Tue, 07 Sep 1999 14:33:46 +0100 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 25 Message-ID: <37D5143A.16B2@deletethis.bbsrc.ac.uk> References: <7qmuvo$988$1@nnrp1.deja.com> NNTP-Posting-Host: pc0294.avri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) lxl7392@usl.edu wrote: > > I am trying to count and measure the area of duckweed leaves. I already > have a free shareware program called ImageTool. I can use it to count > leaves but have not as yet been able to measure areas successfully. > Can anyone in internet land answer one of these questions: > > 1. How do you measure image areas in ImageTool? > > 2. What other free software programs exist that could measure > duckweed area? ImageTool is a Windows program, so I presume that is your platform of preference. I would recommend getting the Windows port of NIHImage, which is available from Scion Corp http://www.scioncorp.com You will need to have DirectX installed in Windows95/NT. In Image, outline the leaf, click in it with the wand tool and the area will come up in one of the windows. Image has an extensive macro facility, so a lot of this could be automated if you want to/can be bothered. Michael From owner-software@net.bio.net Tue Sep 07 14:26:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!skynet.be!newspeer.ebone.net!news.net.uni-c.dk!not-for-mail From: =?iso-8859-1?Q?S=F8ren?= W. Rasmussen Newsgroups: bionet.software Subject: DNATools revision 617 Date: Tue, 07 Sep 1999 16:56:09 +0200 Organization: UNI-C Lines: 23 Message-ID: <37D52789.19258595@crc.dk> NNTP-Posting-Host: 117-02.crc.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 936717113 31786 130.226.182.97 (7 Sep 1999 15:11:53 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 7 Sep 1999 15:11:53 GMT X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en Revision 617 of DNATools includes an interface to the newly released clustalx program for multi-sequence alignment. It is now possible to take full advantage of the powerful clustal program while still managing your sequences in DNATools. You can read more about DNATools - and download the upgrade and the clustal programs at http://www.crc.dk/phys/dnatools.htm. Regards Soeren -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. 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Gpg@ From owner-software@net.bio.net Tue Sep 07 22:16:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!brown.telepac.pt!news.telepac.pt!duke.telepac.pt!news.telepac.pt!not-for-mail From: jotajustino@mail.telepac.pt Newsgroups: bionet.software Subject: ARE YOU MEN OR ARE YOU AMEBAS? Date: Wed, 08 Sep 1999 00:05:07 +0100 Lines: 90 Message-ID: <37D59A23.159D7CFC@mail.telepac.pt> NNTP-Posting-Host: 194.65.220.206 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------1AFC0E0C24C0906C30D1EB07" X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en --------------1AFC0E0C24C0906C30D1EB07 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please Help If you are men, please send a email to the powerful of this world, demanding the stop of the genocide that is taken place in East Timor. Don't be indifferent and let murder a all nation. Please send the petition above. PETITION Widespread death and destruction are happening in East Timor. Unless world leaders exert maximum pressure on the Indonesian Government the results of last Monday's referendum will be followed by a growing massacre and destruction of thousands of citizens who braved everything to vote, expressing overwhelmingly their wish to become independent. Regrettably, the Indonesian Government is not fullfiling the New York agreements and has allowed the violence to spread. An international force is essential to prevent the total slaughter of the people by the anti-independence militias. Therefore, I call upon you to URGENTLY exert all of the available means at your disposal to make the killings stop and prevent the deportation and massacre of the people of East Timor. If you agree send emails to: President Bill Clinton President B. J. Habibie: Mr. Kofi Annan --------------1AFC0E0C24C0906C30D1EB07 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Please Help
If you are men,  please send a email to the powerful of this world, demanding the stop of the genocide that is taken place in East Timor.
Don't be indifferent and let murder a all nation.

Please send the petition above.

                                         PETITION

Widespread death and destruction are happening  in East Timor.
Unless world leaders exert  maximum pressure on the Indonesian
Government the  results of last Monday's referendum
will be followed by a growing massacre and destruction of thousands of
citizens who braved everything to vote,  expressing
overwhelmingly their wish to become independent.
Regrettably, the Indonesian Government is not fullfiling the New York
agreements and has allowed the violence to spread.

An   international force is essential to prevent the  total  slaughter
of the people by the    anti-independence militias.

                                         Therefore,

  I call upon you to  URGENTLY exert all of the available means at your
disposal to make the killings stop and prevent the
                         deportation and massacre of the people of East
Timor.

 

If you agree send emails to:

                   President Bill Clinton

                      President B. J. Habibie:

                                               Mr. Kofi Annan

--------------1AFC0E0C24C0906C30D1EB07-- From owner-software@net.bio.net Tue Sep 07 22:38:00 1999 Path: biosci!bloom-beacon.mit.edu!panix!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!not-for-mail From: Mohyeddin Kassar Newsgroups: bionet.software Subject: Jobs: Statistics/Bio Date: Tue, 07 Sep 1999 17:44:25 -0500 Organization: Energy Resources Center Lines: 35 Message-ID: <37D59548.37A6CB88@uic.edu> NNTP-Posting-Host: mcgrath.erc.uic.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------6A8A14A46A3E00A3521D3231" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en This is a multi-part message in MIME format. --------------6A8A14A46A3E00A3521D3231 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Several positions for PH.D. Statistics or Biostatistics available, If Interested send resume to: jobs@penet-careers.com http://www.penet-careers.com/ --------------6A8A14A46A3E00A3521D3231 Content-Type: text/x-vcard; charset=us-ascii; name="mkassar.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Mohyeddin Kassar Content-Disposition: attachment; filename="mkassar.vcf" begin:vcard n:Kassar;Mohyeddin tel;fax:312-996-5620 tel;home:312-829-1485 tel;work:312-413-3615 x-mozilla-html:FALSE org:University Of Illinois at Chicago;Energy Resources Center version:2.1 email;internet:mkassar@uic.edu title:Research Economist adr;quoted-printable:;;(MC156)=0D=0A851 S. Morgan Street, 12th Floor SEO;Chicago;IL;60607-7054;USA fn:Mohyeddin Kassar end:vcard --------------6A8A14A46A3E00A3521D3231-- From owner-software@net.bio.net Wed Sep 08 02:08:00 1999 Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Drawseq, a biosequence drawing tool, preliminary release Date: 8 Sep 1999 03:02:14 GMT Organization: Biology, Indiana University - Bloomington Lines: 25 Message-ID: <7r4jjm$6im$1@jetsam.uits.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu A preliminary release of Drawseq, a biosequence drawing tool, is available for comments and testing. This program draws pretty views of single or aligned sequences to various graphic formats. Various styles can be set. Features are drawn when available. You can use it as an application (still in a preliminary form), web form (still more primitive, few style choices), or from a command-line for the hardy computist. Graphic output formats include PDF, PICT, GIF and Postscript. Drawseq is an updated module from the SeqPup sequence analysis package; it now can be used as a separate application or component in other packages. Home of this package is http://iubio.bio.indiana.edu/soft/molbio/java/apps/drawseq/ A Web form for this is http://iubio.bio.indiana.edu/cgi-bin/drawseq.cgi -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Sep 08 10:00:00 1999 Path: biosci!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!unlisys!news.snafu.de!isdnet!news-ge.switch.ch!diablo.dera.gov.uk!server1.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: Help wanted on alignments Date: Wed, 08 Sep 1999 11:49:07 +0100 Organization: Nottingham University Lines: 16 Message-ID: NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: oyez.ccc.nottingham.ac.uk 936787779 25380 128.243.183.228 (8 Sep 1999 10:49:39 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 8 Sep 1999 10:49:39 GMT X-Newsreader: Yet Another NewsWatcher 2.4.0 Problem: I want to align a domain present in a superfamily of proteins against a specific example of that domain. Er..that is to generate a large number of pairwise alignments of the different examples of this domain against my target sequence (at leat I think that is what I want to do?), and then order them in respect to similarity/identity. Is there a program that will do this in a single pass? Thanks for any advice -- Fergus Doherty, Dept Biochemistry, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-software@net.bio.net Wed Sep 08 10:00:00 1999 Path: biosci!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!unlisys!news.snafu.de!isdnet!news-ge.switch.ch!diablo.dera.gov.uk!server1.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: Ig superfamily database? Date: Wed, 08 Sep 1999 11:49:50 +0100 Organization: Nottingham University Lines: 11 Message-ID: NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: oyez.ccc.nottingham.ac.uk 936787822 25380 128.243.183.228 (8 Sep 1999 10:50:22 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 8 Sep 1999 10:50:22 GMT X-Newsreader: Yet Another NewsWatcher 2.4.0 Is there a dedicated Ig superfamily database/resource anywhere? Thanks -- Fergus Doherty, Dept Biochemistry, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-software@net.bio.net Wed Sep 08 12:32:00 1999 Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.esat.net!news.heanet.ie!web3.tcd.ie!acer.gen.tcd.ie!tpwalsh From: tpwalsh@acer.gen.tcd.ie () Newsgroups: bionet.software Subject: Re: Ig superfamily database? Date: 8 Sep 1999 13:06:47 GMT Organization: N.O.T. Lines: 19 Message-ID: <7r5n17$45l@web3.tcd.ie> References: NNTP-Posting-Host: acer.gen.tcd.ie Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) wrote: >Is there a dedicated Ig superfamily database/resource anywhere? Is you're interested in structures look at: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.1.002.001.html ( the SCOP database) or http://www.biochem.ucl.ac.uk/bsm/cath/CATH.0002.0060.0040.html ( the CATH database ) The Pfam database has a huge set of aligned Ig sequences with links to the SwissProt entry for each sequence: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00047 Tom From owner-software@net.bio.net Wed Sep 08 13:06:00 1999 Path: biosci!CADUS.COM!brian.osborne From: brian.osborne@CADUS.COM ("Osborne, Brian") Newsgroups: bionet.software Subject: RE: sequence assembler Date: 8 Sep 1999 07:05:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D3428FD6CDFD111A72800104B2351B76319A1@weebo.cadus.com> NNTP-Posting-Host: net.bio.net Brent, I would get a hold of the free bash shell for NT/Windows from Cygnus Solutions (http://sourceware.cygnus.com/cygwin/). The "full" installation includes gcc. Now you can compile phrap. In the shell you view the NT dir structure. Brian O. OSI 777 Old Saw Mill River Rd. Tarrytown NY 10591 brian.osborne@cadus.com TEL 914 467 6291 FAX 914 345 3565 -----Original Message----- From: Brent Nichols [mailto:pbnichol@chuma.cas.usf.edu] Sent: Tuesday, September 07, 1999 3:15 PM To: nobody@net.bio.net Subject: sequence assembler Hi everyone, Does anyone know of a PC compatible assembly program that can use ABI electropherogram files to reassemble the sequences. Thanks in advance!! Brent From owner-software@net.bio.net Wed Sep 08 13:40:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newspeer1.nac.net!newspeer.monmouth.com!nf1.mgmt.sympatico.ca!news1.bellglobal.com!qcarh002.nortelnetworks.com!bcarh189.ca.nortel.com!bmerhc5e.ca.nortel.com!bcarh8ab.ca.nortel.com!not-for-mail From: "Young, George [CAR:9F12:EXCH]" Newsgroups: a.bsu.programming,alt.music.fleetwood-mac,alt.radio.networks.npr,alt.tv.twin-peaks,bionet.software,bionet.software.acedb,bionet.software.gcg Subject: Re: =?iso-8859-1?Q?=B3o=A6=5E=B1z=A5i=ADn=AC=DD=B2M=B7=A1?= Date: Wed, 08 Sep 1999 10:22:25 -0400 Organization: Nortel Networks Lines: 16 Message-ID: <37D67121.9EEA3898@americasm01.nt.com> References: <7q5apt$mu5@netnews.hinet.net> Reply-To: georgey@bnr.ca NNTP-Posting-Host: wcars0w1.ca.nortel.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 4.6 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en Xref: biosci bionet.software:24133 bionet.software.acedb:2601 bionet.software.gcg:3709 Peter wrote: > =A7=DA=A6=B3=A4@=C0=C9=B0=AA=B0=AA=B0=AA=B0=AA=AC=EC=A7=DE=AA=D1=ADn=BD= =E6,=A8=C6=C3=F6=BE=F7=B1K,=A4=A3=AF=E0=A6b=B9q=B8=A3=A4W=BB=A1=A5X,=BD=D0= =A8=A3=BD=CC.=A4=A3=B9L=A5=A6=A8C=A6~=C1=C8=BF=FA, > =B8=EA=B5=A6=B7|=A4@=BC=CB=B8=C9=A7U=A5=A6.=B3o=A5=AB=ACO=A8=BA=A4@=AEa= =A4=BD=A5q?=A6]=AC=B0=B6q=A4=D6,=A8C=A4H=B3=CC=A6h=A4Q=B1i.=B7Q=A4F=B8=D1= =BD=D0=B9q > :0939872586 (O.)89215405 (H.)32334286 =AE}=BF=B3=BD=E5 Seems Peter is from Taepei and writes Chineese Unicode set. Unfortunately= his Outlook client doesn't tell us this. Just ignore unless you are really interested= =2E From owner-software@net.bio.net Wed Sep 08 13:47:00 1999 Path: biosci!CADUS.COM!brian.osborne From: brian.osborne@CADUS.COM ("Osborne, Brian") Newsgroups: bionet.software Subject: RE: sequence assembler Date: 8 Sep 1999 07:47:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D3428FD6CDFD111A72800104B2351B76319A4@weebo.cadus.com> NNTP-Posting-Host: net.bio.net Brent, I apologize for replying to my own post and for being somewhat lacking in detail ! I just did the experiment of compiling phrap on NT with these Cygwin utilities. It seems to create the phrap executable (first change "cc" to "gcc" in the makefile, then do "make"), which runs and gives the proper error message. I am guessing it will work well, and I am also guessing that phred will compile as easily. Here's a link for obtaining phred and phrap : http://bozeman.mbt.washington.edu/consed/consed.html#howToGet Brian O. -----Original Message----- From: brian.osborne@cadus.com [mailto:brian.osborne@cadus.com] Sent: Wednesday, September 08, 1999 10:06 AM To: bio-soft@net.bio.net Subject: RE: sequence assembler Brent, I would get a hold of the free bash shell for NT/Windows from Cygnus Solutions (http://sourceware.cygnus.com/cygwin/). The "full" installation includes gcc. Now you can compile phrap. In the shell you view the NT dir structure. Brian O. OSI 777 Old Saw Mill River Rd. Tarrytown NY 10591 brian.osborne@cadus.com TEL 914 467 6291 FAX 914 345 3565 -----Original Message----- From: Brent Nichols [mailto:pbnichol@chuma.cas.usf.edu] Sent: Tuesday, September 07, 1999 3:15 PM To: nobody@net.bio.net Subject: sequence assembler Hi everyone, Does anyone know of a PC compatible assembly program that can use ABI electropherogram files to reassemble the sequences. Thanks in advance!! Brent From owner-software@net.bio.net Wed Sep 08 14:51:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!newsfeed.berkeley.edu!newsfeed.direct.ca!logbridge.uoregon.edu!newsgate.cuhk.edu.hk!netnews.hinet.net!spring.edu.tw!feeder.seed.net.tw!news.seed.net.tw!not-for-mail From: "christian" Newsgroups: at.network.ping,bionet.software,bionet.software.acedb,microsoft.public.tw.ie30,microsoft.public.tw.ie40,microsoft.public.tw.inetexplorer.ie5beta,microsoft.public.win95.networking,microsoft.public.win98.networking,tw.announce Subject: Ãø±oªº¾÷·|~~§A¤£®e¿ù¹L³á~~!! Date: 8 Sep 1999 15:44:01 GMT Organization: SEEDNet News Service Lines: 28 Message-ID: <7r6081$9vj$3@news.seed.net.tw> NNTP-Posting-Host: cl89-137.dialup.seed.net.tw X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2014.211 Xref: biosci bionet.software:24136 bionet.software.acedb:2603 ¥H¤U§¹¥þ§K¶O¡A¤S¦³¿úÁÈ cf168¹q¤l³ø,¤@¥÷ÄÝ©ó±zªº±M·~ºô¸ô¹q¤l³ø cf168¹q¤l³ø¨C¤ë´£¼·¼s§i§Q¼íª¾80%»P­q¤á¦@¨É,Åý±z ¦b®a¬Ý§K¶O¹q¤l³ø,¨C¤ëÁÙ¦³Á~¤ô¥i®³ §Y¤é°_¥u­n±z¤Wºô­q¾\cf168±M·~ºô¸ô¹q¤l³ø,(¤£¦ý §¹¥þ§K¶O,µL¥ô¦ó±ø¥ó),¨C¤ëÁÙ¦³©T©wÁ~¤ô¥i®³(¬ù¥x¹ô 5¸U¥H¤W),¤£¥Î©â¼ú,¤H¤H³q³q¦³¼ú ~~~~~~~~~~ ºô§}: http://www.cf168.com.tw ~~~~~~~~~~~~~~~~~~~~~~~~~~ ¦]cf168¹q¤l³ø¤§§Q¼í¥u­­·|­û¦@¨É,¥B¬°«O»Ù·|­ûÅv¯q ,±Ä·|­û±ÀÂ˨î,±ý¤J·|ªÌ»Ý¥Ñ·|­û±ÀÂˤè¥i¤J·| ¦b¦¹´£¨Ñ¤U¦C¸ê®Æ,¨Ñ¦³¿³½ìªÌ­q¾\¥Î ±ÀÂˤH¡G±i¯qÄÁ ±ÀÂ˽s¸¹¡G934879047 ps:½s¸¹»Ý¥HÁä½L¿é¤J¤£¥i¥H¥Î½Æ»sªº ¦]¦¹¯¸ªñ¨Ó·¥¬°¼öªù,­Y¤@®É¶¡µLªkµn¿ý,½Ð¦h¸Õ´X¦¸ From owner-software@net.bio.net Thu Sep 09 00:56:00 1999 Path: biosci!USA.COM!invrep From: invrep@USA.COM Newsgroups: bionet.software Subject: ADV: Date: 8 Sep 1999 18:56:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <989.283923.675944.invrep@usa.com> NNTP-Posting-Host: net.bio.net ''''''''''''''''''''''''''''''''''''''''''' ' To be removed, simply reply with the ' ' subject "remove". 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Click here to learn more about this exclusive offer and to receive your free video! http://www.234235438797.net@3522794473/~invrep/src.html From owner-software@net.bio.net Thu Sep 09 01:10:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news.mel.connect.com.au!news.syd.connect.com.au!nsw.nntp.telstra.net!203.2.75.4.MISMATCH!news.mpx.com.au!news1.optus.net.au!optus!news.usyd.edu.au!news.nsw.CSIRO.AU!csiro!lanimg-mi From: Vidana.Epa@bioresi.com.au (Vidana Epa) Newsgroups: bionet.software Subject: Multiple Seq. Alignment program Date: 8 Sep 1999 21:42:31 GMT Organization: C.S.I.R.O Australia Lines: 21 Message-ID: <7r6l87$dj5@gutter.its.csiro.au> NNTP-Posting-Host: tpysz-pp.pp.molsci.csiro.au Keywords: PRRP X-Newsreader: News Xpress Version 1.0 Beta #4 Dear Bionetters, Does anybody know how one may obtain the multiple sequence alignment program PRRP by Osamu Gotoh (J.Mol.Biol., vol. 264, 823-838(1996)) or Dr. Gotoh's contact email address? Over the past month I've sent email to gotoh@saitama-cc.go.jp, but they've always been returned undeliverable. Thanks very much. Cheers, Vidana. Vidana C. Epa Biomolecular Research Institute, 343 Royal Parade, Parkville, Vic. 3052, AUSTRALIA. email:Vidana.Epa@molsci.csiro.au From owner-software@net.bio.net Thu Sep 09 02:13:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!newsfeed.berkeley.edu!nntp.kreonet.re.kr!usenet.seri.re.kr!not-for-mail From: =?iso-8859-1?Q?=B1=E8=C1=BE=C7=F6?= Newsgroups: bionet.software Subject: =?iso-8859-1?Q?=C0=CC=B7=B1=20=C1=A6=B1=E6?= Date: Thu, 09 Sep 1999 12:07:34 +0900 Organization: =?iso-8859-1?Q?=BC=BA=B1=D5=B0=FC=B4=EB=C7=D0=B1=B3=20=B9=FD=C7=D0=B0=FA?= Lines: 3 Message-ID: <37D72476.44D67F9B@hanmail.net> NNTP-Posting-Host: 203.252.52.51 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: en ÀÌ·± Á¦±æ Á×°Ú´Ù.. From owner-software@net.bio.net Thu Sep 09 07:12:00 1999 Path: biosci!newsfeed.stanford.edu!arclight.uoregon.edu!logbridge.uoregon.edu!news.net.uni-c.dk!not-for-mail From: =?iso-8859-1?Q?S=F8ren?= W. Rasmussen Newsgroups: bionet.software Subject: DNATools - setup problem Date: Thu, 09 Sep 1999 09:34:33 +0200 Organization: UNI-C Lines: 35 Message-ID: <37D76309.27CC39F6@crc.dk> NNTP-Posting-Host: 117-02.crc.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 936863425 38402 130.226.182.97 (9 Sep 1999 07:50:25 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 9 Sep 1999 07:50:25 GMT X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en Dear DNATools users, I recently (from revision 610 onwards) removed clustalw.exe from the installation files and instead included the two clustal programs (clustalw.exe, clustalx.exe and clustal.hlp) in a separate zip file: clustal.zip. Unfortunately I forgot to remove the entry for clustalw in the setup.lst telling the setup program which files to install. This has the consequence that during installation setup.exe tries to install clustalw.ex_ - which is not there any more. The simplest solution is to edit the setup.lst in your temporary installation directory (i.e. the directory where you unzipped the downloaded installation file dt_51617.zip). Simply open setup.lst in a text editor and delete the line: File32=1,,CLUSTALW.ex_,clustalw.exe,$(AppPath),,,1/16/1998 13:19:58,344378,,"","","" save setup.lst and run setup.exe again. The problem is now corrected. Sorry! Soeren -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 33275230/45 36162259, Fax 45 33274766 swr@crc.dk, http://www.crc.dk/phys/ DNATools sequencing software: http://www.crc.dk/phys/dnatools.htm From owner-software@net.bio.net Thu Sep 09 08:43:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: Paul@pdchem.demon.co.uk (Paul Davis) Newsgroups: bionet.software Subject: Re: Multiple Seq. Alignment program Date: Thu, 09 Sep 1999 09:34:41 GMT Organization: Myorganisation Message-ID: <936869681snz@pdchem.demon.co.uk> References: <7r6l87$dj5@gutter.its.csiro.au> Reply-To: Paul@pdchem.demon.co.uk X-Trace: mail2news.demon.co.uk 936869774 mail2news:8454 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!pdchem.demon.co.uk X-Newsreader: SNews 1.30+mods(jlw981005) Lines: 35 Try ftp://ftp.genome.ad.jp/pub/genome/saitama-cc/scc_soft.2.5.2.tar.gz On 8 Sep, in article <7r6l87$dj5@gutter.its.csiro.au> Vidana.Epa@bioresi.com.au "Vidana Epa" wrote: > > Dear Bionetters, > > Does anybody know how one may obtain the multiple sequence > alignment program PRRP by Osamu Gotoh (J.Mol.Biol., vol. 264, 823-838(1996)) > or Dr. Gotoh's contact email address? Over the past month I've sent email > to gotoh@saitama-cc.go.jp, but they've always been returned undeliverable. > Thanks very much. > > Cheers, > > Vidana. > > > > Vidana C. Epa > Biomolecular Research Institute, > 343 Royal Parade, > Parkville, Vic. 3052, > AUSTRALIA. > email:Vidana.Epa@molsci.csiro.au > -Paul -- -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk From owner-software@net.bio.net Thu Sep 09 09:58:00 1999 Path: biosci!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.tli.de!grolier!ciril.fr!news.u-strasbg.fr!frenzy.u-strasbg.fr!francis.durst From: francis.durst@bota-ulp.u-strasbg.fr (Francis Durst) Newsgroups: bionet.software Subject: Re: Multiple Seq. Alignment program Date: Thu, 9 Sep 1999 12:52:36 LOCAL Organization: CNRS Lines: 26 Message-ID: References: <7r6l87$dj5@gutter.its.csiro.au> NNTP-Posting-Host: frenzy.u-strasbg.fr X-Trace: news.u-strasbg.fr 936878068 1543 130.79.129.1 (9 Sep 1999 11:54:28 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 9 Sep 1999 11:54:28 GMT Keywords: PRRP X-Newsreader: Trumpet for Windows [Version 1.0 Rev B.7] In article <7r6l87$dj5@gutter.its.csiro.au> Vidana.Epa@bioresi.com.au (Vidana Epa) writes: >From: Vidana.Epa@bioresi.com.au (Vidana Epa) >Subject: Multiple Seq. Alignment program >Date: 8 Sep 1999 21:42:31 GMT >Keywords: PRRP >Dear Bionetters, > Does anybody know how one may obtain the multiple sequence >alignment program PRRP by Osamu Gotoh (J.Mol.Biol., vol. 264, 823-838(1996)) >or Dr. Gotoh's contact email address? Over the past month I've sent email >to gotoh@saitama-cc.go.jp, but they've always been returned undeliverable. >Thanks very much. >Cheers, >Vidana. Osamu Gotoh's e-mail is gotoh@cancer-c.pref.saitama.jp All the best Francis From owner-software@net.bio.net Thu Sep 09 12:18:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software Subject: EMBOSS First Beta Release Date: 09 Sep 1999 14:12:06 +0100 Organization: The Sanger Centre Lines: 51 Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 936882729 25059 193.60.84.160 (9 Sep 1999 13:12:09 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 9 Sep 1999 13:12:09 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 After many months of work in Hinxton (at the Sanger Centre and HGMP), we are able to announce that EMBOSS is ready for beta testing by users. To date there are around 80 applications in the package. We would like your comments on the current package and on any improvements you would like to suggest. We will use your comments to set priorities for further development. EMBOSS is still in a beta state so you can expect bugs, but we will fix them as quickly as possible. A new distribution is built each night from our CVS master copy, and is available from ftp://ftp.sanger.ac.uk/pub/EMBOSS/ There is a script in the distribution that should be able to build everything automatically for the core distribution. Just follow these simple steps: pick up file EMBOSS-0.0.4.tar.gz gunzip EMBOSS-0.0.4.tar.gz tar xvf EMBOSS-0.0.4.tar cd EMBOSS-0.0.4/ csh ./make-all-static If you have any problems with the build please contact the new EMBOSS support list emboss-bug@sanger.ac.uk We will continue to add library functions, applications and documentation. There is a weekly project meeting in Hinxton to discuss progress, with the minutes available on the EMBOSS Web pages. Useful URLs are: Home page http://www.sanger.ac.uk/Software/EMBOSS/ Weekly meetings http://www.sanger.ac.uk/Software/EMBOSS/Meetings/ Applications http://www.sanger.ac.uk/Software/EMBOSS/Apps/ Documentation http://www.sanger.ac.uk/Software/EMBOSS/Doc/ ACD files http://www.sanger.ac.uk/Software/EMBOSS/Acd/ The source code documentation is also indexed on the Sanger Centre SRS server as databases "EFUNC" for functions and "EDATA" for data types. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-software@net.bio.net Thu Sep 09 14:37:00 1999 Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!infeed.is.co.za!feeder.is.co.za!news.is.co.za!not-for-mail From: "winhide" Newsgroups: bionet.software Subject: STACK 2.3 is now available for search and download Date: Thu, 9 Sep 1999 16:55:30 +0200 Organization: An Internet Solution Customer Lines: 22 Message-ID: <7r8jn3$jpn$2@news.is.co.za> NNTP-Posting-Host: yebo.sanbi.ac.za X-Trace: news.is.co.za 936890915 20279 196.38.142.74 (9 Sep 1999 15:28:35 GMT) X-Complaints-To: abuse@is.co.za NNTP-Posting-Date: 9 Sep 1999 15:28:35 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3110.3 STACK 2.3 is now available for download. It has been processed from GenBank (110). STACK is a processed database of human EST assemblies and consensus sequences. It is organised according to organ level expression classes. A full body index is in development for late September release. STACK is freely available to academic and not for profit organisations. STACK can be searched at: http://ziggy.sanbi.ac.za/stack/stacksearch.htm For download access and information on STACK please visit: www.sanbi.ac.za/STACK_REQUEST Win Hide SANBI. From owner-software@net.bio.net Thu Sep 09 16:46:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!enews.sgi.com!news.corp.sgi.com!not-for-mail From: Haruna Cofer Newsgroups: bionet.software Subject: Parallel CLUSTALW 1.8 for IRIX available Date: Thu, 09 Sep 1999 13:39:22 -0400 Organization: Silicon Graphics, Inc. Lines: 70 Message-ID: <37D7F0CA.50DBEF60@columbus.sgi.com> NNTP-Posting-Host: 169.238.139.137 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en Hello! SGI has parallelized the latest version of CLUSTALW, Version 1.8, and it is now available at the following site (for free, of course!): http://www.sgi.com/chembio/resources/clustalw/parallel_clustalw.html Additional information about CLUSTALW on SGI/IRIX is available here: http://www.sgi.com/chembio/resources/clustalw/ Please note that our Parallel CLUSTALW 1.8 contains a fix for a memory access bug in the original code, so your results may be slightly different with our Parallel CLUSTALW 1.8 versus the original CLUSTALW 1.8 distribution. More information about this fix is available in the README file (attached below). Thank you again, and please do let me know if you have any questions or comments! With regards, Haruna Cofer :) ===== 30 August 1999 This distribution contains a parallelized version of CLUSTAL W 1.8 for SGI systems running IRIX 6.5. Specifically, the Pairwise Alignments and Guide Tree computations are parallelized. It should be noted that this release uses a modification of the original pairalign.c file, which was modified to fix a memory access bug in the original code. Specifically, the original CLUSTAL W code read beyond the bounds of an allocated array, resulting in either a numerical error or a core dump of the program. The change made in pairalign.c is as follows: Replace line 214 of pairalign.c: maxscore = diff(sb1, sb2, se1-sb1+1, se2-sb2+1, (sint)0, (sint)0); with the following line: maxscore = diff(sb1-1, sb2-1, se1-sb1+1, se2-sb2+1, (sint)0, (sint)0); To use this parallelized version of CLUSTAL W, simply set the MP_SET_NUMTHREADS environment variable to the number of processors you want to use. For example, to use 4 processors: setenv MP_SET_NUMTHREADS 4 If this environment variable is not set, then the default is to use the maximum number of processors on your machine. Then use the "clustalw_mp" executable to run the parallelized version of CLUSTAL W in the same way you would use the original "clustalw" program. Please send questions or problems to Haruna Cofer (haruna@sgi.com). -- -------------------------------------------------------------------- Haruna N. Cofer 614-855-5245 (tel) Applications - Chem/Bio 248-848-5653 (fax) SGI 800-859-1020 x4553 (v-mail) 715 Affirmed Court x6-265-4553 (internal) Columbus, OH 43230 haruna@sgi.com (e-mail) -------------------------------------------------------------------- From owner-software@net.bio.net Thu Sep 09 22:37:00 1999 Path: biosci!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.direct.ca!gw12.nn.bcandid.com!gw22.nn.bcandid.com!gate.bCandid.com!typ11.nn.bcandid.com.POSTED!not-for-mail From: "John Monahan" Newsgroups: bionet.software References: <37D76309.27CC39F6@crc.dk> Subject: Re: DNATools - setup problem Lines: 51 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Message-ID: NNTP-Posting-Host: 206.14.241.131 X-Trace: typ11.nn.bcandid.com 936919818 206.14.241.131 (Thu, 09 Sep 1999 19:30:18 EDT) NNTP-Posting-Date: Thu, 09 Sep 1999 19:30:18 EDT Date: Thu, 9 Sep 1999 16:18:02 -0700 Am I the only one getting fed up reading about trivial items on DNATools. This is a pseudo commercial program/operation. Other real commercial applications do not clog the airways with this kind of stuff ! Søren W. Rasmussen wrote in message news:37D76309.27CC39F6@crc.dk... > Dear DNATools users, > > I recently (from revision 610 onwards) removed clustalw.exe from the installation files and instead > included > the two clustal programs (clustalw.exe, clustalx.exe and clustal.hlp) in a separate zip file: > clustal.zip. > > Unfortunately I forgot to remove the entry for clustalw in the setup.lst telling the setup program > which files > to install. This has the consequence that during installation setup.exe tries to install > clustalw.ex_ - which > is not there any more. > > The simplest solution is to edit the setup.lst in your temporary installation directory (i.e. the > directory > where you unzipped the downloaded installation file dt_51617.zip). Simply open setup.lst in a text > editor and delete the line: > > File32=1,,CLUSTALW.ex_,clustalw.exe,$(AppPath),,,1/16/1998 13:19:58,344378,,"","","" > > save setup.lst and run setup.exe again. The problem is now corrected. Sorry! > > Soeren > > -- > Dr. scient. Søren W. Rasmussen > Carlsberg Laboratory, Department of Physiology > 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark > Phone 45 33275230/45 36162259, Fax 45 33274766 > swr@crc.dk, http://www.crc.dk/phys/ > > DNATools sequencing software: > http://www.crc.dk/phys/dnatools.htm > > From owner-software@net.bio.net Thu Sep 09 23:26:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!newsfeed.berkeley.edu!hermes.visi.com!news-out.visi.com!gw12.nn.bcandid.com!gate.bCandid.com!cyclone1.gnilink.net!typhoon2.gnilink.net.POSTED!not-for-mail From: dary.nospam@bellatlantic.net (DAY) Newsgroups: bionet.software Subject: FrameMaker 5 software CD for UNIX is being offered at Ebay, no reserve! Message-ID: <37d8793e.4048835@news5.bellatlantic.net> X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 8 Date: Fri, 10 Sep 1999 00:22:20 GMT NNTP-Posting-Host: 141.150.127.85 X-Trace: typhoon2.gnilink.net 936922940 141.150.127.85 (Thu, 09 Sep 1999 20:22:20 EDT) NNTP-Posting-Date: Thu, 09 Sep 1999 20:22:20 EDT FrameMaker 5 software CD for UNIX is being offered at Ebay, no reserve! Check it out at http://cgi.ebay.com/aw-cgi/eBayISAPI.dll?ViewItem&item=161666517 --------------------------------------------------- To reply, please remove the .nospam from my e-mail address. From owner-software@net.bio.net Fri Sep 10 02:32:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.uchicago.edu!newsswitch.lcs.mit.edu!netnews.com!chnws02.mediaone.net!24.92.226.137!cyclone.nyroc.rr.com!news.nyroc.rr.com!typhoon.nyroc.rr.com.POSTED!not-for-mail From: "James Yegerlehner" Newsgroups: bionet.software Subject: Molecular biology: online studies? Lines: 11 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Message-ID: Date: Thu, 9 Sep 1999 23:22:25 -0400 NNTP-Posting-Host: 24.95.177.196 X-Complaints-To: abuse@twcny.rr.com X-Trace: typhoon.nyroc.rr.com 936933928 24.95.177.196 (Thu, 09 Sep 1999 23:25:28 EDT) NNTP-Posting-Date: Thu, 09 Sep 1999 23:25:28 EDT Organization: Time Warner Road Runner - Syracuse NY Hello everyone: I plan to pursue the Stanford bioinformatics certificate online, but need to fulfill the molecular biology prerequisite. Would anyone care to suggest either a self-study course or an online course? Thanks in advance, Jim From owner-software@net.bio.net Fri Sep 10 06:12:00 1999 Path: biosci!newsfeed.stanford.edu!skynet.be!newspeer.ebone.net!news.net.uni-c.dk!not-for-mail From: "Søren W. Rasmussen" Newsgroups: bionet.software Subject: Re: DNATools - setup problem Date: Fri, 10 Sep 1999 08:39:04 +0200 Organization: UNI-C Lines: 35 Message-ID: <37D8A788.79A05C2F@crc.dk> References: <37D76309.27CC39F6@crc.dk> NNTP-Posting-Host: 117-02.crc.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 936946497 16650 130.226.182.97 (10 Sep 1999 06:54:57 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 10 Sep 1999 06:54:57 GMT To: John Monahan X-Mailer: Mozilla 4.03 [en] (Win95; I) Dear John, I'm sorry if I have offended you and perhaps wasted a few seconds of your precious time. I just have a simple question to you: why do you keep reading my notices about DNATools if you are fed up with reading them?? The message you refer to is addressed to DNATools users and the subject of the message is clearly stated in the subject line. It would have been a lot more relevant for the readers of the news group if you had been a bit more specific in your criticism of the program. Whether or not the software is pseudo or real commercial is a rather unscientific argument - of little help for other people in evaluating it. I might add that many commercial software packages would greatly improve their reputation if they reported bugs publicly - and supplied the corrected version the next day for free downloading!! Regards Soeren John Monahan wrote: > Am I the only one getting fed up reading about trivial items on DNATools. > This is a pseudo commercial program/operation. Other real commercial > applications do not clog the airways with this kind of stuff ! -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 33275230/45 36162259, Fax 45 33274766 swr@crc.dk, http://www.crc.dk/phys/ DNATools sequencing software: http://www.crc.dk/phys/dnatools.htm From owner-software@net.bio.net Fri Sep 10 10:51:00 1999 Path: biosci!biosci!not-for-mail From: Hans Sluiman Newsgroups: bionet.software, Subject: The G4 revolution Date: 10 Sep 1999 04:51:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <7rarb6$e5a@net.bio.net> NNTP-Posting-Host: net.bio.net Now that the new generation of G4 Powermacs is about to arrive, can we expect a substantial increase in speed and performance compared to G3 based systems when running phylogenetic applications such as PAUP 4, Puzzle, Phylip and fastDNAml? This is particularly relevant for those of us doing timeconsuming bootstrap analyses of relatively large data sets on Mac platforms. Obviously, existing softeware needs to be rewritten to make use of the new Multiprocessing and AltiVec technologies that are built into the G4. However, the extent to which applications will benefit from the enhanced FPU speed of the G4 will depend on whether they use floating point instructions or integers. How do PAUP et al. work? My obvious dilemma is this: would it be more sensible at this point in time to invest in a high speed G3 Mac (tried and tested technology available at reasonable prices), or to pay a premium price for a top of the range superfast G4 whose improved performance may well be disappointing? Hans From owner-software@net.bio.net Fri Sep 10 12:26:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!news.sgi.com!nntp.primenet.com!nntp.gctr.net!feeder.qis.net!dca1-hub1.news.digex.net!intermedia!lynx.unm.edu!news.NMSU.Edu!not-for-mail From: "Donald D. Bustamante" Newsgroups: bionet.software Subject: Outbreak! is available Date: Fri, 10 Sep 1999 07:05:35 -0600 Organization: National Biotechnology Information Facility Lines: 15 Message-ID: <37D9021F.3EC6@nbif.org> Reply-To: dbustama@nbif.org NNTP-Posting-Host: nbif01.nmsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: bubba.NMSU.Edu 936968613 13900 128.123.36.225 (10 Sep 1999 13:03:33 GMT) X-Complaints-To: usenet@bubba.NMSU.Edu NNTP-Posting-Date: 10 Sep 1999 13:03:33 GMT X-Mailer: Mozilla 3.01Gold (WinNT; I) The National Biotechnology Information Facility is to pleased to announce the availability of Outbreak!©. Outbreak!© is an interactive teaching tool for use by students and science educators. Players must use microbial identification techniques to identify the causative agent of an illness outbreak. The game supports multiple scenarios, and is highly graphical. Outbreak!© may be accessed via: http://www.nbif.org/outbreak -- -- Donald D. Bustamante, Project Manager/Co-PI National Biotechnology Information Facility Box 30002, Dept. 3548 Las Cruces, New Mexico USA 88003 (505)-646-5031 FAX: (505)-522-9373 URL: http://www.nbif.org From owner-software@net.bio.net Fri Sep 10 13:11:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!newspeer.clara.net!news.clara.net!btnet-peer!btnet!news5-gui.server.ntli.net!ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: Message to moderator of this group Date: Fri, 10 Sep 1999 14:51:58 +0100 Organization: Nottingham University Message-ID: NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: oyez.ccc.nottingham.ac.uk 936971549 16220 128.243.183.228 (10 Sep 1999 13:52:29 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 10 Sep 1999 13:52:29 GMT X-Newsreader: Yet Another NewsWatcher 2.4.0 Lines: 20 hello, A company contacted me as they are unable to post to this group, and don't understand why. Could the moderator contact David Adcock at: haybrook@cix.co.uk They want to advertise a vacancy in bioinformatics programming - which seems a reasonable use of this group to me, but they would appreciate contact with the moderator. Thanks -- Fergus Doherty, Dept Biochemistry, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-software@net.bio.net Fri Sep 10 14:24:00 1999 Path: biosci!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.direct.ca!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software Subject: Re: Message to moderator of this group Date: 10 Sep 1999 16:12:32 +0100 (BST) Organization: Linux Unlimited Lines: 20 Message-ID: <8KE*4FK9n@news.chiark.greenend.org.uk> References: NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) In article , Fergus Doherty wrote: >hello, > >A company contacted me as they are unable to post to this group, and don't >understand why. Could the moderator contact David Adcock at: > >haybrook@cix.co.uk > >They want to advertise a vacancy in bioinformatics programming - which >seems a reasonable use of this group to me, but they would appreciate >contact with the moderator. 1) I'm not sure there is a moderator on the group 2) The correct group for job offers is not this one, but bionet.jobs.offered 3) Posting problems could be a configuration error in the local news server. Tim. From owner-software@net.bio.net Fri Sep 10 14:52:00 1999 Path: biosci!newsfeed.stanford.edu!skynet.be!dispose.news.demon.net!demon!news.demon.co.uk!demon!genesys.demon.co.uk!Duncan From: "Dr. Duncan Clark" Newsgroups: bionet.software Subject: Re: Message to moderator of this group Date: Fri, 10 Sep 1999 16:39:39 +0100 Organization: DNAmp Ltd. Message-ID: References: Reply-To: "Dr. Duncan Clark" NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk:158.152.17.110 X-Trace: news.demon.co.uk 936978252 nnrp-06:28550 NO-IDENT genesys.demon.co.uk:158.152.17.110 X-Complaints-To: abuse@demon.net MIME-Version: 1.0 X-Newsreader: Turnpike Integrated Version 4.02 M Lines: 26 In article , Fergus Doherty writes >hello, > >A company contacted me as they are unable to post to this group, and don't >understand why. Could the moderator contact David Adcock at: > >haybrook@cix.co.uk > >They want to advertise a vacancy in bioinformatics programming - which >seems a reasonable use of this group to me, but they would appreciate >contact with the moderator. This is not a moderated group. Duncan -- The problem with being on the cutting edge is that you occasionally get sliced from time to time.... Duncan Clark DNAmp Ltd. Tel: +44(0)1252376288 FAX: +44(0)8701640382 http://www.dnamp.com http://www.genesys.demon.co.uk From owner-software@net.bio.net Fri Sep 10 15:19:00 1999 Path: biosci!FCIEN.EDU.UY!eletor From: eletor@FCIEN.EDU.UY (Hector Romero) Newsgroups: bionet.software Subject: Bibliography software Date: 10 Sep 1999 09:19:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Hello, I am trying to get a software (free if possible) capable of producing the bibliography or referneces of papers in different formats. Thank you, Q.L. Hector Romero Facultad de Ciencias Uruguay From owner-software@net.bio.net Fri Sep 10 16:37:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.algonet.se!algonet!newsfeed.tli.de!do.de.uu.net!fu-berlin.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!news.urz.uni-heidelberg.de!chevreux From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux) Newsgroups: bionet.software Subject: Re: Bibliography software Date: 10 Sep 1999 17:03:38 GMT Organization: Speaking for myself (really) Lines: 23 Message-ID: References: Reply-To: b.chevreux@dkfz-heidelberg.de NNTP-Posting-Host: mbp-lserv1.inet.dkfz-heidelberg.de X-Trace: news.urz.uni-heidelberg.de 936983018 4444 193.174.59.113 (10 Sep 1999 17:03:38 GMT) X-Complaints-To: usenet@news.urz.uni-heidelberg.de NNTP-Posting-Date: 10 Sep 1999 17:03:38 GMT X-Newsreader: slrn (0.9.5.2 UNIX) On 10 Sep 1999 09:19:38 -0700, Hector Romero wrote: >Hello, > I am trying to get a software (free if possible) capable of >producing the bibliography or referneces of papers in different formats. > Thank you, > >Q.L. Hector Romero >Facultad de Ciencias >Uruguay Use bibtex in conjunction with makebst and you'll be happy. Of course, only when working with LaTeX. On the other hand, LaTeX is the only viable alternative to everything else :) Salut, Bastien ------------------------------------------------------------------------------- Dipl.-Inform. Med. Bastien Chevreux -- b.chevreux@dkfz-heidelberg.de Deutsches Krebsforschungszentrum Heidelberg -- Abteilung Molekulare Biophysik Im Neuenheimer Feld 280 -- 69120 Heidelberg -- Phone: +49 6221 42 2336 ------------------------------------------------------------------------------- -It's mine. =Nope, it's my one. *CRASH* =Alright. It WAS yours. From owner-software@net.bio.net Fri Sep 10 18:23:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software, Subject: Re: The G4 revolution Followup-To: bionet.software, Date: 10 Sep 1999 19:20:32 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 35 Distribution: world Message-ID: <7rblm0$807$1@franklin.ljcrf.edu> References: <7rarb6$e5a@net.bio.net> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Good questions Hans; As far as I'm aware, the prices I've been quoted on G4's are no more than those previously given me for G3's. Can anyone with a G4 supply some details to about what its multitasking abilities are like? This would also be interesting in respect to using programs such as Clustal on a Mac too. (Indidentally, Has anyone performed a cost-effectiveness comparison in respect to performing computationally intensive processes on a Mac versus a PC (running either Windows or Linux/FreeBSD/Solaris)? Platform wars aside, I'm not at all convinced that the Mac comes even close to PC's in terms of speed for a variety of often performed mb programs without blowing a hole in your wallet.) Hans Sluiman (h.sluiman@rbge.org.uk) wrote: : Now that the new generation of G4 Powermacs is about to arrive, can we : expect a substantial increase in speed and performance compared to G3 : based systems when running phylogenetic applications such as PAUP 4, : Puzzle, Phylip and fastDNAml? This is particularly relevant for those of : us doing timeconsuming bootstrap analyses of relatively large data sets : on Mac platforms. : : Obviously, existing softeware needs to be rewritten to make use of the : new Multiprocessing and AltiVec technologies that are built into the G4. : However, the extent to which applications will benefit from the enhanced : FPU speed of the G4 will depend on whether they use floating point : instructions or integers. How do PAUP et al. work? : : My obvious dilemma is this: would it be more sensible at this point in : time to invest in a high speed G3 Mac (tried and tested technology : available at reasonable prices), or to pay a premium price for a top of : the range superfast G4 whose improved performance may well be disappointing? : : Hans : : From owner-software@net.bio.net Fri Sep 10 20:05:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.uchicago.edu!newsswitch.lcs.mit.edu!newsfeed.enteract.com!news.maxwell.syr.edu!howland.erols.net!news.idt.net!news.globix.net!uunet!nyc.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: NMR Shifts Date: Fri, 10 Sep 1999 15:28:49 -0400 Organization: The Internet Connection Lines: 10 Message-ID: <7rblqn$rj3$1@bashir.ici.net> NNTP-Posting-Host: d-gnaps-194.ici.net Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NMRPen -- C-13 NMR Shifts -- http://home.ici.net/~hfevans/nmrpen.htm -- Hilton Evans Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm ChemPen3D Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm Chempen Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm From owner-software@net.bio.net Sat Sep 11 13:47:00 1999 Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!fu-berlin.de!news.uni-stuttgart.de!news.belwue.de!News.Uni-Marburg.DE!not-for-mail From: "Mandarin" Newsgroups: bionet.software Subject: free software Date: 11 Sep 1999 14:38:56 GMT Organization: HRZ Uni Marburg Lines: 5 Message-ID: <7rdpi0$7pe$1@surz18.HRZ.Uni-Marburg.DE> NNTP-Posting-Host: pool134.mabi.de X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 free software www.creasoftcorp.de From owner-software@net.bio.net Sun Sep 12 09:36:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newspeer.monmouth.com!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: mhabio@my-deja.com Newsgroups: bionet.software Subject: Freeware DAQ software for fermentors Date: Sun, 12 Sep 1999 10:18:10 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 27 Message-ID: <7rful1$l2c$1@nnrp1.deja.com> NNTP-Posting-Host: 130.225.8.202 X-Article-Creation-Date: Sun Sep 12 10:18:10 1999 GMT X-Http-User-Agent: Mozilla/4.61 [en] (Win95; I) X-Http-Proxy: 1.0 x21.deja.com:80 (Squid/1.1.22) for client 130.225.8.202 X-MyDeja-Info: XMYDJUIDmhabio Freeware control and data collection software for the BioStat fermentors B, C, D and Micro-DCU has been released, version 1.1. The host control software runs on NT/95/98 PC's and is a user-friendly control and data acquisition program. All parameters (setpoints) can be adjusted from the computer and with the software you can collect all process data which are displayed in a graphical window. Fermentation time and dates are logged as are user and remote connections. To reduce ‘on-site' time, a TCP/IP client program enables you to control and review collected data from any online computer in the world. The remote control program is essentially the same as the host but gets data via the TCP/IP connection from the host control program. Process parameters can be send to the fermentor. For safety, on the host the remote IP number can be specified or set to allow any connection via the client program. For program downloads, more information, and screen shots goto: imsb.au.dk/~mha/biohome.htm Regards, Mikkel Holmen Andersen Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Sun Sep 12 21:22:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!skynet.be!News.Amsterdam.UnisourceCS!news.otenet.gr!not-for-mail From: "Pliktro Software" Newsgroups: bionet.software Subject: OfficePro. Keep all your Appointments, Tasks, Business Associates, Images etc. Date: Mon, 13 Sep 1999 01:14:08 +0300 Organization: Pliktro Software Message-ID: <7rh8ml$gpm$1@newssrv.otenet.gr> NNTP-Posting-Host: athe530-i077.otenet.gr X-Trace: newssrv.otenet.gr 937174549 17206 195.167.111.77 (12 Sep 1999 22:15:49 GMT) X-Complaints-To: abuse@otenet.gr NNTP-Posting-Date: 12 Sep 1999 22:15:49 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Lines: 16 OfficePro is far from a desktop PIM. Õou can keep all your appointments, write down any task, have an extended database of all your business associates, make email list, print in labels your clients addresses, make direct phone calls from within the program and even group your images either in thumbnailed or in photo album format. Download 20 days trial version of OfficePro from Pliktro Software. Look at http://www.pliktro.gr/English/eofficepro.htm From owner-software@net.bio.net Mon Sep 13 00:36:00 1999 Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!brown.telepac.pt!news.telepac.pt!duke.telepac.pt!news.telepac.pt!not-for-mail From: zacu@mail.telepac.pt (zack) Newsgroups: bionet.software Subject: Top Software Date: 13 Sep 1999 00:04:30 GMT Lines: 3 Message-ID: <7rhf2e$i4g$1@duke.telepac.pt> Reply-To: zack@mail.telepac.pt NNTP-Posting-Host: 212.55.178.41 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) Top Software http://www.beyond.com/AF55162/bestsellers.htm From owner-software@net.bio.net Mon Sep 13 08:08:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.wirehub.nl!news.belnet.be!news.rediris.es!News.cica.es!""!no From: Gonzalo Newsgroups: bionet.software Subject: Re: Bibliography software Date: Mon, 13 Sep 1999 10:42:25 +0200 Organization: C.I.C.A. Lines: 10 Distribution: world Message-ID: <130919991042258393%no@spam.me> References: NNTP-Posting-Host: bioq13.cie.uma.es Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: mercurio.cica.es 937212090 2299 150.214.50.45 (13 Sep 1999 08:41:30 GMT) X-Complaints-To: news@cica.es NNTP-Posting-Date: 13 Sep 1999 08:41:30 GMT Mail-Copies-To: nobody User-Agent: YA-NewsWatcher/4.2.3 In article , Hector Romero wrote: > I am trying to get a software (free if possible) capable of > producing the bibliography or referneces of papers in different formats. I do not know any free soft about this, but I really like (and use) EndNote (for mac and PC) and others like Reference Manager. Gonzalo From owner-software@net.bio.net Mon Sep 13 08:08:00 1999 Path: biosci!YAWMAIL.COM!82a3wyxo2 From: 82a3wyxo2@YAWMAIL.COM Newsgroups: bionet.software Subject: Increase Sales Up To 1500% W/4 Very Powerful Words!!! 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From owner-software@net.bio.net Mon Sep 13 09:53:00 1999 Path: biosci!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!dispose.news.demon.net!demon!ayres.ftech.net!news.ftech.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.ox.ac.uk!andrew.rambaut From: Andrew Rambaut Newsgroups: bionet.software, Subject: Re: The G4 revolution Date: Mon, 13 Sep 1999 11:46:50 +0100 Organization: Oxford University, England Distribution: world Message-ID: <130919991146504912%andrew.rambaut@zoo.ox.ac.uk> References: <7rarb6$e5a@net.bio.net> NNTP-Posting-Host: andyrmac.zoo.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.ox.ac.uk 937219610 2211 163.1.210.37 (13 Sep 1999 10:46:50 GMT) X-Complaints-To: newsmaster@ox.ac.uk NNTP-Posting-Date: 13 Sep 1999 10:46:50 GMT User-Agent: YA-NewsWatcher/4.2.4 Lines: 27 In article <7rarb6$e5a@net.bio.net>, Hans Sluiman wrote: > My obvious dilemma is this: would it be more sensible at this point in > time to invest in a high speed G3 Mac (tried and tested technology > available at reasonable prices), or to pay a premium price for a top of > the range superfast G4 whose improved performance may well be disappointing? Actually the Macintosh compiler that everyone uses already has AltiVec support in it so significant improvements can be expected with just a recompile. For optimum speed, some rewriting (of a few core bits) would be required. To answer your last question, PAUP and such programs use floating point when doing analyses like maximum likelihood but not with most parsimony analyses. The floating point processor (that is seperate from the AltiVec) is much faster on the G4 than the G3. With the exception of PAUP all the other programs you mentioned are free and have source code so you can expect G4 versions as soon as someone with an interest in them buys a new machine. I expect PAUP will have G4 support in a reasonable time frame. But remember these applications will run faster on a G4 of the same clock speed even without recompiling (faster processor, faster floating point unit). Expect a 25% improvement (i.e. with a 500MHz G4 that would be about 38% faster than a 450MHz G3). Hope this helps, Andrew From owner-software@net.bio.net Mon Sep 13 10:11:00 1999 Path: biosci!rutgers!uwm.edu!logbridge.uoregon.edu!sunqbc.risq.qc.ca!mtu.ru!news.rssi.ru!not-for-mail From: Anatoly Mikhalsky Newsgroups: bionet.software Subject: Re: Bibliography software Date: Fri, 10 Sep 1999 03:23:59 -0700 Organization: Institute of Control Sciences Lines: 16 Message-ID: <37D8DC3F.3282@ipu.rssi.ru> References: Reply-To: mikhalsk@ipu.rssi.ru NNTP-Posting-Host: markovic.ipu.rssi.ru Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: zware.space.ru 937220661 24830 193.232.196.99 (13 Sep 1999 11:04:21 GMT) X-Complaints-To: usenet@news.rssi.ru NNTP-Posting-Date: 13 Sep 1999 11:04:21 GMT X-Mailer: Mozilla 3.01Gold (Win16; I) Hector Romero wrote: > > Hello, > I am trying to get a software (free if possible) capable of > producing the bibliography or referneces of papers in different formats. > Thank you, > > Q.L. Hector Romero > Facultad de Ciencias > Uruguay Hector, try Ref141, look for it http://www.shareware.com/ Anatoli From owner-software@net.bio.net Mon Sep 13 19:13:00 1999 Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!sunqbc.risq.qc.ca!newsfeed.tli.de!grolier!club-internet!not-for-mail From: "quaderno.com" Newsgroups: bionet.software Subject: QUADERNO The Musical Expression. Date: Mon, 13 Sep 1999 22:06:01 +0200 Organization: Club-Internet (France) Lines: 147 Message-ID: <7rjlgs$b0r$4@front2.grolier.fr> Reply-To: "quaderno.com" NNTP-Posting-Host: ppp-170-178.villette.club-internet.fr X-Trace: front2.grolier.fr 937253212 11291 195.36.170.178 (13 Sep 1999 20:06:52 GMT) NNTP-Posting-Date: 13 Sep 1999 20:06:52 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Greetings, The following is a text-only description of a new program for music composition. Please don't hesitate to download the demo version on the Web at http://www.quaderno.com QUADERNO > THE MUSICAL EXPRESSION QUADERNO is a program for MIDI sequencing and an aid to musical composition and research. It runs on PC (or on Power Mac using Virtual PC) QUADERNO was created by two musicians who envisioned a program that would serve their needs as composers. This software is the result of 5 years of intense work and musical research. It was first developed on the Atari and since one year for the PC . It's a program based entirely on MIDI; you can perform many types of data transformations very quickly allowing immediate feedback based upon your musical idea. The interface is attractively colored; it allows you to link music and color in a very intuitive way. A virtual Remote-Control panel allows you to: 1- determine your Recording choices 2- use special Functions to transform your music 3- access the different "Spaces" (various views of your musical data) 1 - RECORDING can be done in different ways: - Normal MIDI recording with a keyboard or any MIDI instrument - Simple Recording with the mouse (1 Pattern) - Multitrack MIDI recording with the mouse (up to 56 Patterns all together) - Multitrack MIDI recording (16 tracks or 16 MIDI instrumentalists) in real-time. 2 - FUNCTIONS: The functions are very powerful mathematical algorithms that allows you to transform your music with a single click of the mouse. Quaderno's Functions include: Accents- Agitation - Random - Rhythm Analysis - Arpeggiator - Cadences - Calculation - Canons - Chords - Conversions - Untie - Echoes - Melodic Evolution - Expression - Harmonization - Legato - Morphing - Suppress Controllers - Reduce Controllers - Progressions - Quantize-Random - Quantize-Fill - Quantize-Logic - Quantization Reduction - Re-Injection - Harmonic Resolution - Rhythm Tracker - Staccato - Suppress Doubles - Suppress Recovey - Send Sysex - Tessitura - Melodic Transposition - Formula - Sorting - Wave Creation . 3 - SPACES: > SESSION: The basic space of the program . It is made up of a large checkerboard filled up with 196 small squares, each square is called: an Area. Each Area is characterized by a name, a number, a MIDI channel, a synthesizer, a sound, a Scale and a Quaderno. On the left of this large checkerboard you can find a column with numbers from 1 to 56. Each number represents a Pattern. Around this axis revolve 14 "satellite" spaces. > LIBRARY: For saving all the files you create in the different spaces with a very convenient feature, the ability to audition items from the Library before importing them. > SONG: For structuring and organizing all the Patterns (musical figures) you have developed in the SESSION space, in the same manner as with a classic sequencer but with functions specific to Quaderno. It's also the place for export/import of MIDI files. > MICRO-EDITION: A graphic representation of all the MIDI events of the selected Pattern. Each curve is a linear event representation of the various parameters of your music. You can modify each of these curves independently and use functions specific to this space: expansion, compression, horizontal and vertical inversion. > NOTE-EDIT: Note events on a grid that represent the pitch on the vertical axis and time on the horizontal axis. You can make modifications and transformations on the selected notes instantaneously, and choose to visualize the color of notes according to their velocity or pitch, > CHORDS: This space allows creation and auditioning of all sorts of chords according to the set of available scales in use in QUADERNO. You can use your chord grids in different ways (send them to a free Area, or use them to reharmonize one or several Patterns). > HARMONIC MODULATIONS : To create principles of harmonic modulation that you will be able to apply in several ways. These harmonic modulations can be used in real time. > MIDI SETUP: To manage and program all Midi peripherals. > MONITORS: To "see" the music that you have created in a very original way. The different Monitors translate into images (color, speed, movement..) the MIDI events of your music. > MUSICAL ANALYSIS : To analyze the harmonic contents of any Pattern and see immediately which scales the harmony involves and also to extract a chord grid from this harmonic analysis and use these results in different ways. > ORCHESTRATION: To select and extract the different musical elements of a Pattern according to 7 criteria and 2 Modes. Once you have selected the desired elements, you can sort them out and send them into different Plans (up to 6 Plans). > DYNAMIC PADS: To re-write in real time your sequence by playing with the mouse on the 4 fundamental elements of a Pattern: Velocities, Durations, Notes and Rhythms. > COMPOSER: To algorithmically generate MIDI sequences without user input (without keyboard or mouse). You'll select several musical parameters (rhythms, notes, durations, MIDI controller ) and QUADERNO will generate music based upon your program (up to 70 tracks). > REAL-TIME: Today, we are no longer work in a linear fashion but rather from a multidimensional perspective. It is in the Real-Time space that you will understand this new approach. Here, multiple MIDI instrumentalists can play and record together. Thank you for taking the time to familiarize yourself with QUADERNO .We hope that QUADERNO will enable you to compose in a completely different way and that you will discover a new and pleasurable approach to making music. For contact information or demos please email or phone: (33) 1 43 73 25 96 or (33) 1 48 74 59 19 (Paris/FRANCE) From owner-software@net.bio.net Mon Sep 13 22:27:00 1999 Path: biosci!newsfeed.stanford.edu!nntp.stanford.edu!saga3.Stanford.EDU!jefftc From: Jeffrey Chang Newsgroups: bionet.software Subject: ANN: Biopython.org (Call for Participation) Date: Mon, 13 Sep 1999 16:18:35 -0700 Lines: 19 Sender: jefftc@saga3.Stanford.EDU Message-ID: NNTP-Posting-Host: saga3.stanford.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Biopython Project (http://www.biopython.org/) is a new open collaborative effort to develop freely available Python libraries and applications that address the needs of current and future work in bioinformatics, including sequence analysis, structural biology, pathways, expression data, etc. When available, the source code will be released as open source (http://www.biopython.org/License.shtml) under terms similar to Python. This is a Call for Participation for interested people to join the project. We are hoping to attract people from a diverse set of backgrounds to help with code development, site maintenance, scientific discussion, etc. This project is open to everyone. If you're interested, please visit the web page, join the biopython mailing list, and let us know what you think! Jeffrey Chang Andrew Dalke From owner-software@net.bio.net Tue Sep 14 01:28:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.us.ibm.net!ibm.net!pln-e!spln!extra.newsguy.com!newsp.newsguy.com!enews2 From: "Chen, Lin" Newsgroups: bionet.software Subject: look for a site for gene family categorization? Date: Mon, 13 Sep 1999 21:34:39 -0400 Organization: http://extra.newsguy.com Lines: 9 Message-ID: <37DDA62F.23057D7@thomcomp.com> NNTP-Posting-Host: p-449.newsdawg.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en I am looking for a site of gene classification database for superfamily, subfamily etc. I hope if I have a gene or sequence and I can find what family it belongs to. Is there such a database available? Many thanks for any suggestions. Jin From owner-software@net.bio.net Tue Sep 14 13:50:00 1999 Path: biosci!newsfeed.stanford.edu!skynet.be!diablo.theplanet.net!newsfeed.icl.net!oleane!pasteur.fr!nefertiti.pasteur.fr!letondal From: letondal@pasteur.fr (Catherine Letondal) Newsgroups: bionet.software Subject: Re: look for a site for gene family categorization? Date: 14 Sep 1999 14:43:19 GMT Organization: Institut Pasteur, Paris Lines: 20 Sender: letondal@nefertiti.pasteur.fr (Catherine Letondal) Message-ID: <7rlmu7$voi$1@desdemone.pasteur.fr> References: <37DDA62F.23057D7@thomcomp.com> Reply-To: letondal@pasteur.fr (Catherine Letondal) NNTP-Posting-Host: nefertiti.pasteur.fr X-Trace: desdemone.pasteur.fr 937320199 32530 157.99.64.20 (14 Sep 1999 14:43:19 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 14 Sep 1999 14:43:19 GMT X-Newsreader: mxrn 6.18-31 In article <37DDA62F.23057D7@thomcomp.com>, "Chen, Lin" writes: >I am looking for a site of gene classification database for superfamily, >subfamily etc. >I hope if I have a gene or sequence and I can find what family it >belongs to. Is there such a database available? Many thanks for any >suggestions. > > >Jin > > This may be useful: http://www.pasteur.fr/recherche/BNB/bnb-en.html query : super -- Catherine Letondal -- letondal@pasteur.fr -- +33 (1) 40 61 31 91 From owner-software@net.bio.net Tue Sep 14 14:51:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newspump.monmouth.com!newspeer.monmouth.com!dispose.news.demon.net!demon!btnet-peer!btnet!news3-gui.server.ntli.net!news5-gui.server.ntli.net!ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: pujadas@argo.urv.es (Gerard Pujadas) Newsgroups: bionet.software Subject: Making massive "structural querys" to PDB Date: 14 Sep 1999 16:39:21 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Trace: niobium.hgmp.mrc.ac.uk 937323562 5990 193.62.192.80 (14 Sep 1999 15:39:22 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 14 Sep 1999 15:39:22 GMT X-Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA29550 for ; Tue, 14 Sep 1999 16:39:19 +0100 (BST) X-Received: from argo.urv.es (argo.urv.es [130.206.36.12]) by mserv1.dl.ac.uk with ESMTP id QAA10100 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from pujadas@argo.urv.es); Tue, 14 Sep 1999 16:39:22 +0100 (BST) X-Precedence: first-class X-Received: from [130.206.36.86] (macbi77.urv.es [130.206.36.86]) by argo.urv.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id RAA02245; Tue, 14 Sep 1999 17:32:21 +0200 (MDT) X-To: pdb-l@rcsb.org, bio-software@dl.ac.uk X-MIME-Autoconverted: from quoted-printable to 8bit by hgmp.mrc.ac.uk id QAA29551 Lines: 37 Dear all, I would like to know if there is any software that can do "structural querys" to the full PDB (or in