From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 03:11:35 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8D75D17A62; Mon, 1 Nov 1999 03:11:34 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA12128 for ; Mon, 1 Nov 1999 03:11:32 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA18926 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 03:11:31 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: amplicom@my-deja.com X-Newsgroups: bionet.software Subject: GeneLinkDB online database Date: Mon, 01 Nov 1999 02:56:05 GMT Organization: Deja.com - Before you buy. Lines: 13 Message-ID: <7vivg4$6d3$1@nnrp1.deja.com> X-Article-Creation-Date: Mon Nov 01 02:56:05 1999 GMT X-Http-User-Agent: Mozilla/4.61 [en] (WinNT; I) X-Http-Proxy: 1.0 x41.deja.com:80 (Squid/1.1.22) for client 24.30.142.24 X-MyDeja-Info: XMYDJUIDamplicom To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk GeneLinkDB, a knowledge database system, is now up and running at a bioinformatics portal http://www.amplicom.com GeneLinkDB provides a comprehensive and searchable informations of genes, proteins, associate diseases, publications and reagents. We are constantly adding new informations and improving our web contents. If you have any suggestions, please feel free to contact me at webmaster@amplicom.com Sent via Deja.com http://www.deja.com/ Before you buy. From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 07:35:20 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 209A917A62; Mon, 1 Nov 1999 07:35:20 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA25086; Mon, 1 Nov 1999 07:35:15 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA22235; Mon, 1 Nov 1999 07:35:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: J G X-Newsgroups: alt.angst,alt.aol-sucks,alt.auqria,bionet.neuroscience,bionet.plants,bionet.software Subject: Get rich while doing nothing Date: Mon, 01 Nov 1999 02:37:08 +0800 Organization: Ohio State University Lines: 9 Message-ID: <381C8C54.D74F78E6@yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 941441678 27723 140.254.113.192 (1 Nov 1999 07:34:38 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk, neur-sci@hgmp.mrc.ac.uk, plantbio@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Are you getting paid while surfing yet? Are you only getting paid from one company? If your answer to these is NO, please check the web site http://www.geocities.com/gj254b/getpaid.html From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 13:10:30 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7BE6217A43; Mon, 1 Nov 1999 13:10:29 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA16368 for ; Mon, 1 Nov 1999 13:10:26 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA02044 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 13:10:25 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@nospam.net X-Newsgroups: bionet.software Subject: Sanger Centre Image? Message-ID: <381d919f.34154251@news-server> X-Newsreader: Forte Agent .99d/32.168 Lines: 18 Date: Mon, 01 Nov 1999 13:13:23 GMT X-Complaints-To: abuse@rr.com X-Trace: viper 941461496 24.26.156.133 (Mon, 01 Nov 1999 08:04:56 EST) Organization: Road Runner Columbus To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Is there anyone out there who has gotten the Image program from the Sanger Centre, the one for analysis of Bac digest fingerprints, to work on a Linux, or a Digital, system? I've tried 3.9a and 3.6 for Linux so far, and I'm getting nothing but frustration. Documentation is for 3.5. I can't tell what the settings mean because the new fields in 3.9 are undocumented. The program just gives error messages which seem to refer to these mystery settings when tried. I've just tried 3.6, and I get a "permission denied" error when I try running bstt, or im3. Root, user, no difference. The environment is set up as instructed. The files are found on the path just fine. The standards file is a complete mystery. The values and columns are undefined. Messages to image@sanger.ac.uk have not been answered for a week. Is there other software for this task? We'd like to arrange Bac clones by their restriction digest fingerprints. Thanks, Mike Holloway holloway.53@osu.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 15:30:27 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E69C617A43; Mon, 1 Nov 1999 15:30:26 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA27296 for ; Mon, 1 Nov 1999 15:30:25 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA03772 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 15:30:23 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Dyre Tjeldvoll X-Newsgroups: bionet.software Subject: Re: Sanger Centre Image? Date: 01 Nov 1999 16:25:46 +0100 Organization: Norwegian university of science and technology Message-ID: References: <381d919f.34154251@news-server> X-Trace: kopp.stud.ntnu.no 941469946 23164 129.241.103.4 (1 Nov 1999 15:25:46 GMT) X-Complaints-To: usenet@itea.ntnu.no X-Newsreader: Gnus v5.6.45/XEmacs 20.2 Lines: 19 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk nospam@nospam.net writes: > Is there anyone out there who has gotten the Image program from the Sanger > Centre, the one for analysis of Bac digest fingerprints, to work on a Linux, > or a Digital, system? I've tried 3.9a and 3.6 for Linux so far, and I'm > getting nothing but frustration. Documentation is for 3.5. I can't tell > what the settings mean because the new fields in 3.9 are undocumented. The > program just gives error messages which seem to refer to these mystery > settings when tried. I've just tried 3.6, and I get a "permission denied" > error when I try running bstt, or im3. Root, user, no difference. The > environment is set up as instructed. The files are found on the path just > fine. The standards file is a complete mystery. The values and columns are > undefined. Messages to image@sanger.ac.uk have not been answered for a week. If you get "permission denied" as root, the problem clould be that you need set execute permission for the file. -- dt From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 18:45:22 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5319517B11; Mon, 1 Nov 1999 18:45:22 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA12463 for ; Mon, 1 Nov 1999 18:45:20 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA06259 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 18:45:15 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.lang.pascal.delphi.misc Subject: Free software, chat, wallpaper and more on a coolwebsite - www.freespeech.org/gunsoft Date: Mon, 1 Nov 1999 18:34:28 -0000 Organization: Gunsoft Lines: 16 Message-ID: <7vkmh8$9v$1@nclient11-gui.server.virgin.net> X-Trace: nclient11-gui.server.virgin.net 941481320 319 62.252.8.246 (1 Nov 1999 18:35:20 GMT) X-Complaints-To: abuse@virgin.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Our website which offers FREE PROGRAMS 4 all! has a new discussion page where you can discuss absolutely anything you like!! So pay us a visit www.freespeech.org/gunsoft ! U WILL NOT BE DISAPPOINTED! -- >From Steve <><><><><> visit www.freespeech.org/gunsoft icq #48322092 This isn't Spam as it was only posted on newsgroups talk about stuff related to us! From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 19:22:00 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2C62B17A93; Mon, 1 Nov 1999 19:21:59 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA14152 for ; Mon, 1 Nov 1999 19:21:58 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA06730 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 19:21:57 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.lang.pascal.delphi.misc,alt.comp.software.tools Subject: Download ASBSOLUTELY free software! Date: Mon, 1 Nov 1999 19:14:56 -0000 Organization: Gunsoft Lines: 14 Message-ID: <7vkote$t3g$1@nclient13-gui.server.virgin.net> X-Trace: nclient13-gui.server.virgin.net 941483758 29808 62.252.7.208 (1 Nov 1999 19:15:58 GMT) X-Complaints-To: abuse@virgin.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Our website which offers FREE PROGRAMS 4 all! has a new discussion page where you can discuss absolutely anything you like!! So pay us a visit www.freespeech.org/gunsoft ! U WILL NOT BE DISAPPOINTED! -- >From Steve <><><><><> visit www.freespeech.org/gunsoft icq #48322092 This isn't Spam as it was only posted on newsgroups talk about stuff related to us! From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 21:37:34 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E331917A64; Mon, 1 Nov 1999 21:37:33 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA19399 for ; Mon, 1 Nov 1999 21:37:32 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA16636 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 21:37:31 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Nadeem Sheikh" X-Newsgroups: bionet.software Subject: Plotting Packages Date: Mon, 1 Nov 1999 13:37:03 -0800 Organization: University of Washington Lines: 30 Message-ID: <7vl0v2$puk$1@nntp4.u.washington.edu> X-Trace: nntp4.u.washington.edu 941492002 26580 (None) 140.142.17.40 X-Complaints-To: help@cac.washington.edu 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Does anyone have any advice for basic scientific plottng packages ? I am currently a happy user of Origin (versin 3.5). However I have been charged with purchasing a cross platform package (for windows and mac users), though origin is extremely user friendly and gives good output, there is no mac version available (yet). Hence any advice/poinetrs to which would be a good package to opt for. Many thanks in advance. regards, nadeem Nadeem Sheikh, **************************************************************************** ************ RPRC Department of Pharmaceutics University of Washington University of Washington Box 357331 Box 357610 Seattle, WA 98195 Seattle, WA 98195 voice : +1 206 221 2356 fax : +1 206 956 0573 e-mail : nadeem@bart.rprc.washington.edu http://www.rprc.washington.edu/ From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 1 22:35:19 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4DA6417A64; Mon, 1 Nov 1999 22:35:19 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA26031 for ; Mon, 1 Nov 1999 22:35:16 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA17346 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 Nov 1999 22:35:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: g.dragicevic@medicine.unimelb.edu.au (George Dragicevic) X-Newsgroups: bionet.software Subject: Chemresearch150 Date: Mon, 01 Nov 1999 23:28:38 GMT Organization: The University of Melbourne Lines: 7 Message-ID: <381e20a1.854508@news> X-Trace: ariel.ucs.unimelb.edu.au 941495295 19668 128.250.216.129 (1 Nov 1999 22:28:15 GMT) X-Complaints-To: news@news.unimelb.edu.au X-Newsreader: Forte Free Agent 1.11/32.235 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I am searching for software (and a computer interface) which controls the pouring of gradient gels. Isco used to produce a package and interface called Chemresearch150 which did this job, however it is no longer in production. Any leads as to where I could source this software, or suggestions as to alternatives appreciated. Please respond via email. Thanks From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 01:15:48 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 56A1117B37; Tue, 2 Nov 1999 01:15:45 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA01170; Tue, 2 Nov 1999 01:15:31 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA19476; Tue, 2 Nov 1999 01:15:29 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Herbert M Sauro" X-Newsgroups: bionet.metabolic-reg,bionet.software Subject: ANNOUNCE: New Experimental Metabolic Systems Lanaguage Date: 1 Nov 1999 17:12:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Distribution: world Message-ID: <941284658.6133.0.nnrp-02.c2de3927@news.demon.co.uk> References: <7veg4g$dnk$1@nclient13-gui.server.virgin.net> To: bio-software@hgmp.mrc.ac.uk, btk-mca@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I have uploaded a new and experimental metabolic systems language at http://members.tripod.co.uk/sauro/biotech.htm under the Jarnac menu. The software runs under Windows 95/98/NT4 and is currently supplied with only limited documentation but numerous sample scripts. Because Jarnac is very new, still undergoing changes and not fully tested, it is being released into the public domain free of charge, however the author still retains full copyright and exclusive commerical rights. Some features Jarnac can be used as a general purpose language for performing arithmetic operations, including matrix and vector arithmetic, numerical differentiation and integration and from within the Jarnac Windows front-end a function or data grapher. Jarnac is an easy to learn control language, similar to the Basic language and supports many of the constructs one would expect, for loops, conditionals, while/do and repeat/until. It supports at least 7 different data types, including integers, floats, booleans, strings, vectors, matrices and lists. Jarnac also supports user defined functions and external modules. There is built-in computational support for: Describing and manipulating metabolic and cellular systems. Dynamic Simulation (using LSODA integrator) Steady State Analysis (using a modified Newton solver) Simple Stability Analysis (eigenvalues) Matrix Arithmetic (All the main operators including things like transpose, det etc) Metabolic Control Analysis (All steady state control coefficients and elasticities) Metabolic Structural Analysis. Herbert Sauro From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 03:43:05 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B2FC517A64; Tue, 2 Nov 1999 03:43:04 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA05565; Tue, 2 Nov 1999 03:43:00 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA21256; Tue, 2 Nov 1999 03:42:59 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: pepper99@NOSPAM.home.com (Mark Morissette) X-Newsgroups: alt.angst,alt.aol-sucks,alt.auqria,bionet.neuroscience,bionet.plants,bionet.software Subject: Re: Get rich while doing nothing Message-ID: <381e5d92.98850031@news2.rdc1.on.wave.home.com> References: <381C8C54.D74F78E6@yahoo.com> X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 16 Date: Tue, 02 Nov 1999 03:41:23 GMT X-Complaints-To: abuse@home.net X-Trace: news2.rdc1.on.home.com 941514083 24.112.228.16 (Mon, 01 Nov 1999 19:41:23 PST) Organization: @Home Network Canada To: bio-software@hgmp.mrc.ac.uk, neur-sci@hgmp.mrc.ac.uk, plantbio@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk >Are you getting paid while surfing yet? >Are you only getting paid from one company? > >If your answer to these is NO, please check the web site >http://www.geocities.com/gj254b/getpaid.html Geocities account cancelled, 'net access from Ohio State University soon to follow! Spam be gone! :-) --- Mark, Oshawa, Ontario, Canada pepper99@NOSPAM.home.com - Remove NOSPAM to respond via Email! Send all spam to "send.spam.here@home.com" - Promptly forwarded to www.spamcop.net! :-) From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 11:45:37 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 301E417B28; Tue, 2 Nov 1999 11:45:35 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA02668; Tue, 2 Nov 1999 11:45:28 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA27037; Tue, 2 Nov 1999 11:45:26 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Bernhard Roth" X-Newsgroups: bionet.cellbiol,bionet.molbio.methds-reagnts,bionet.software Subject: Re: MS Access for cell lines Date: Tue, 2 Nov 1999 12:31:27 +0100 Organization: CC University of Hohenheim (not responsible for contents) Lines: 40 Message-ID: <7vmh9o$87g$1@newspc4.rz.uni-hohenheim.de> References: <7vc4qa$19r6$1@www.univie.ac.at> <2anS3.6117$6y2.141474@carnaval.risq.qc.ca> X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 To: bio-software@hgmp.mrc.ac.uk, cellbiol@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Is it possible to get a copy too ??? Thank´s a lot! Bernhard Roth University of Hohenheim General Virology Germany Paula Lavery schrieb in Nachricht <2anS3.6117$6y2.141474@carnaval.risq.qc.ca>... >Hi Martin > >If you give me your email address I will send you a copy of a database I use >as an inventory for all my cell lines in LN2. I tried to email you directly >but the message was refused. > >Paula Lavery >Transplant Immunology Lab. >Royal Victoria Hospital >McGill University >Montreal (QC) Canada > >"If we knew what we were doing it wouldn't be called research, would it?" >-- Albert Einstein > >Martin Offterdinger wrote in message <7vc4qa$19r6$1@www.univie.ac.at>... >>Hi! >>I just wonder if anyone used MS Access to handle cell lines in a database. >>If yes I would be interested in receiving information how to design the >>database. >>Thank you very much! >>Martin >> >> > > From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 13:07:21 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 86B1B17A64; Tue, 2 Nov 1999 13:07:20 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08359 for ; Tue, 2 Nov 1999 13:07:18 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA28103 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 13:07:16 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: jan.diblik@lfmotol.cuni.cz ("Jan Diblik") X-Newsgroups: bionet.software Subject: Re: Software for viewing (and editing) ABI files on Windows Date: 2 Nov 1999 13:07:15 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 20 Message-ID: <199911021306.OAA16040@mail.lf2.cuni.cz> References: <7v8cdo$5g2$1@nntp1.atl.mindspring.net> Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT X-Trace: niobium.hgmp.mrc.ac.uk 941548036 28100 193.62.192.80 (2 Nov 1999 13:07:16 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from mail.lf2.cuni.cz (mail.lf2.cuni.cz [195.113.40.16]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08341 for ; Tue, 2 Nov 1999 13:06:54 GMT X-Received: from pc-1-1-3-4 ([192.168.4.128]) by mail.lf2.cuni.cz (8.9.3/8.9.3) with ESMTP id OAA16040 for ; Tue, 2 Nov 1999 14:06:40 +0100 X-To: bio-software@hgmp.mrc.ac.uk X-Priority: normal X-In-reply-to: <7v8cdo$5g2$1@nntp1.atl.mindspring.net> X-Mailer: Pegasus Mail for Win32 (v3.12a) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk That is all nice, but is there a windows program for viewing and getting data from files made by ABI Genescan (for microsatellite analysis)? Or does anyone know more about the format the data are stored in? Jan Diblik On 28 Oct 99, at 2:29, John Barlow wrote: > A number of people asked about software that allows viewing of ABI trace files > (chromatograms) on the Windows platform. There are quite many choices - some > programs allow viewing and printing only, others provide sophisticated tools > for contig assembly and proofreading. Some programs are free (and very good - > see BioEdit), other cost several thousands of dollars and are difficult to use, > or have a confusing interface resulting from porting from the Mac. > --- From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 14:05:27 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 65FBB17A64; Tue, 2 Nov 1999 14:05:26 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA13251 for ; Tue, 2 Nov 1999 14:05:24 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA28848 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 14:05:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) X-Newsgroups: bionet.software Subject: Software for identifying new members of gene families Date: 02 Nov 1999 08:54:30 -0500 Organization: University of Virginia Lines: 39 Message-ID: X-Newsreader: Gnus v5.7/Emacs 20.4 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk We have developed a simple computational/graphical strategy for screening nightly updates of Genbank (actually we do the screens weekly on the 7 nightly updates) for new members of large protein families. Retief, J. D., Lynch, K. R., and Pearson, W. R. (1999) Panning for genes - a visual strategy for identifying novel gene orthologs and paralogs. Genome Res. 9:373-382. The software is available free for academic users from http://www.uvasoftware.org. The strategy searches DNA databases using 20 - 60 protein query sequences, which represent the different known branches of the protein family, with tfastx3. The 20 - 60 tfastx3 search results are then scanned and rearranged and summarized graphically in a way that greatly simplifies identification of new family members. For an example, see: http://fasta.bioch.virginia.edu/fasta/pan_demo/gt_demo.pdf http://fasta.bioch.virginia.edu/fasta/pan_demo/gtm_demo.pdf http://fasta.bioch.virginia.edu/fasta/pan_demo/gstn_old.pdf http://fasta.bioch.virginia.edu/fasta/pan_demo/gstn_new.pdf If you view these pages using the acrobat plug-in to Netscape or IE, you can click on each panel to see the underlying alignments. I mention this because several investigators in this field were unaware of the approach and were scanning for new gene family members in a more cumbersome fashion. The program is relatively easy to set up if you are getting your data from the NCBI (e.g. est_human or genbank nightly updates) and you have the fasta3 package of programs from the University of Virginia. People have had more difficulties when using other databases, and it will not work with the GCG version of FASTA. Bill Pearson From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 15:10:19 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id DB59617A64; Tue, 2 Nov 1999 15:10:18 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA19834 for ; Tue, 2 Nov 1999 15:10:17 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA29716 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 15:10:16 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: james.o.mcinerney@may.ie (James McInerney) X-Newsgroups: bionet.software Subject: Molecular Systematics Website Date: 2 Nov 1999 07:03:42 -0800 Organization: National University of Ireland Lines: 63 Distribution: world Message-ID: <381EFB78.20DDDC2A@may.ie> Reply-To: james.o.mcinerney@may.ie To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk (Apologies for cross-posting) Dear all, Martin Embley, Mark Wilkinson, Robert Hirt and myself have conspired to create a website that can be used as a teaching resource for Molecular Systematics. This has come about principally as a result of our teaching efforts in conjunction with the Instituto Oswaldo Cruz, Rio de Janeiro, Brazil and The Natural History Museum, London. This website contains lecture material, both as internet presentations and as a downloadable (?) Microsoft Powerpoint file with 344 slides. There is also a rudimentary glossary of terms that are used in the area of molecular systematics, a list of internet resources and some information about the participants, organisers and teachers on these courses. There is no restriction on the use of this material. Please feel free to download the slides and use the site as you wish. We would appreciate an email, though, just to say you have visited and taken something away. We can then keep you abreast of developments and additions. The site is currently mounted on two servers, but will soon be available as part of The Natural History Museum, London main website. It is being re-branded so that it is recognisable as a product of the work of the museum. The sites are: Brazil: http://www.dbbm.fiocruz.br/james/index.html Ireland: http://www.may.ie/academic/biology/jmbioinformatics.shtml and choose the link for the molecular systematics course. A portion of his course was also taught as part of this summers' EMBO-funded Bioinformatics Course (Bioinformatics: From genome sequences to protein structures) at Uppsala, Sweden: http://xray.bmc.uu.se/EMBO The site will soon be available on The Natural History Museum server. http://www.nhm.ac.uk/ Please pass this email on to anybody that might conceivably be interested. If there are any problems, errors or ommissions please do not hesitate to inform us. Kindest regards, James -- Dr. James O. McInerney, Dept. Biology, Dept. Zoology, Natl. Univ. Ireland, The Natural History Museum, Maynooth, and Cromwell road, Co. Kildare, Ireland London SW7 5BD, UK. Phone +353 1 708 3860 +44 171 938 9163 Fax +353 1 708 3845 +44 171 938 9158 email james.o.mcinerney@may.ie j.mcinerney@nhm.ac.uk http://www.may.ie/academic/biology/jmbioinformatics.shtml From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 16:15:37 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A8FA917A64; Tue, 2 Nov 1999 16:15:36 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA26342 for ; Tue, 2 Nov 1999 16:15:27 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA00698 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 16:15:25 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Bill_A_Nussbaumer@ms.bd.com X-Newsgroups: bionet.software Subject: Re: Software for viewing (and editing) ABI files on Windows Date: 2 Nov 1999 08:07:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Distribution: world Message-ID: <8525681D.0057D8C5.00@7crmta_md.ms.bd.com> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Bill A Nussbaumer@BDX 11/02/99 10:59 AM I'm not familiar with ABI genescan so I don't know if this is quite what you need or not. But it should only take you a couple of minutes to figure it out. Check out Chromas at : http://www.technelysium.com.au/chromas.html Hope it helps you, Bill That is all nice, but is there a windows program for viewing and getting data from files made by ABI Genescan (for microsatellite analysis)? Or does anyone know more about the format the data are stored in? Jan Diblik From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 17:45:39 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E440B17AB2; Tue, 2 Nov 1999 17:45:38 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA03275 for ; Tue, 2 Nov 1999 17:45:36 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA01786 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 17:45:35 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Bill_A_Nussbaumer@ms.bd.com X-Newsgroups: bionet.software Subject: Re: Software for viewing (and editing) ABI files on Windows Date: 2 Nov 1999 09:25:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Distribution: world Message-ID: <8525681D.005EFE82.00@7crmta_md.ms.bd.com> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Bill A Nussbaumer@BDX 11/02/99 12:17 PM Looked at the whole thread and this had already been mentioned. Whoops. :-) Bill I'm not familiar with ABI genescan so I don't know if this is quite what you need or not. But it should only take you a couple of minutes to figure it out. Check out Chromas at : http://www.technelysium.com.au/chromas.html Hope it helps you, Bill From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 19:19:16 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8729317A58; Tue, 2 Nov 1999 19:19:15 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA07205 for ; Tue, 2 Nov 1999 19:19:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA02873 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 19:19:12 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.land.pascal.delphi.misc Subject: Free BRILLIANT software - www.freespeech.org/gunsoft Date: Tue, 2 Nov 1999 19:15:09 -0000 Organization: Gunsoft Message-ID: <7vndbo$rsp$1@nclient13-gui.server.virgin.net> X-Trace: nclient13-gui.server.virgin.net 941570232 28569 62.252.8.12 (2 Nov 1999 19:17:12 GMT) X-Complaints-To: abuse@virgin.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Lines: 17 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Check it out now, FREE SOFTWARE!! (About 20 downloads) and TONNES more on the site! www.freespeech.org/gunsoft -- >From Steve <><><><><> visit www.freespeech.org/gunsoft From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 2 20:05:23 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E2C0117A58; Tue, 2 Nov 1999 20:05:22 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA08962 for ; Tue, 2 Nov 1999 20:05:20 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA03453 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 Nov 1999 20:05:19 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "John" X-Newsgroups: bionet.software Subject: Re: Plotting Packages Date: Tue, 2 Nov 1999 19:27:02 -0000 Organization: Scotland-On-Line Message-ID: <7vndu7$ob5$1@phys-ma.sol.co.uk> References: <7vl0v2$puk$1@nntp4.u.washington.edu> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Lines: 49 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi You may want to check out a product called Prism from GraphPad software (http://www.graphpad.com/). We use this and it is a good graphing package. >From your point of view it is available on both Mac and Windows platforms although there are version differences. You can also mount the Windows version on a Network (Mac?) Hope this helps John Nadeem Sheikh wrote in message news:7vl0v2$puk$1@nntp4.u.washington.edu... > Does anyone have any advice for basic scientific plottng packages ? > > I am currently a happy user of Origin (versin 3.5). However I have been > charged with purchasing a cross platform package (for windows and mac > users), though origin is extremely user friendly and gives good output, > there is no mac version available (yet). Hence any advice/poinetrs to which > would be a good package to opt for. > > Many thanks in advance. > > regards, > > nadeem > > > Nadeem Sheikh, > **************************************************************************** > ************ > RPRC Department of > Pharmaceutics > University of Washington University of Washington > Box 357331 Box 357610 > Seattle, WA 98195 Seattle, WA 98195 > > voice : +1 206 221 2356 > fax : +1 206 956 0573 > e-mail : nadeem@bart.rprc.washington.edu > http://www.rprc.washington.edu/ > > From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 04:10:14 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9AF1E17A61; Wed, 3 Nov 1999 04:10:13 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id EAA29069 for ; Wed, 3 Nov 1999 04:10:10 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id EAA17473 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 04:10:09 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: a.walden@wave.co.nz (Adrian Walden) X-Newsgroups: bionet.software Subject: LINUX/standalone blast question Date: Wed, 03 Nov 1999 17:09:56 +1300 Organization: Walden Lines: 28 Message-ID: X-Trace: news.wave.co.nz 941602092 32581 203.96.196.36 (3 Nov 1999 04:08:12 GMT) X-Complaints-To: abuse@wave.co.nz To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I am installing standalone BLAST on a Pentium running redhat linux 6.1. This is somewhoat of a challange for me as my previous experience installing software etc is on a Macintosh. My most recent success's on linux have included some minor improvments to my .bash_profile and .bashrc files and the installation of the Staden Package (a great victory). You should conclude from this that I am a beginner ! My question concerns a few problems I have had with blast and the requirement to setup a file called .ncbirc in my root directory or the directory from which I call the BLAST application. The contents of the .ncbirc file are supposed to be [ ncbi] Data=/path/blast/data I would like to know what this file does and why it is there. Is it supposed to export the variable "Data" to the environment. If so, why is it that when I query th environment with echo $Data that I get a blank line instead of a path to the directory "data" ? Thanks for your help Adrian walden a.walden@(delete)wave.co.nc From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 05:35:27 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0667217A61; Wed, 3 Nov 1999 05:35:25 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA07048 for ; Wed, 3 Nov 1999 05:35:23 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA18387 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 05:35:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Lawrence Ryan" X-Newsgroups: bionet.software Subject: BIOLOGICAL NEURAL NETWORK SIMULATION Lines: 3 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: <1JPT3.95$qA.275904@news.bctel.net> Date: Tue, 2 Nov 1999 21:27:17 -0800 X-Complaints-To: news@bctel.net X-Trace: news.bctel.net 941606845 209.53.102.57 (Tue, 02 Nov 1999 21:27:25 PDT) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk www.sfu.ca/~loryan/neural.html From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 08:55:30 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 28C3017A61; Wed, 3 Nov 1999 08:55:28 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA13023 for ; Wed, 3 Nov 1999 08:55:26 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA20767 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 08:55:25 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux) X-Newsgroups: bionet.software Subject: ANNOUNCE: MIRA 1.3.17 shotgun assembler Date: 3 Nov 1999 08:47:03 GMT Organization: Speaking for myself (really) Lines: 40 Message-ID: Reply-To: b.chevreux@dkfz-heidelberg.de X-Newsreader: slrn (0.9.5.2 UNIX) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Deutsches Krebsforschungszentrum Heidelberg MIRA V1.3.17 a DNA shotgun fragment assembler with integrated trace file analysis MIRA is a DNA shotgun sequence data assembly program which takes reads/sequences gained by (gel or capillary) electrophoresis experiments and defined in the Staden experiment (EXP), Sanger CAF or even FASTA file format as input and assembles them into contigs. SCF signal electrophoresis trace files are used, if present, to adjudicate between contradicting stretches of bases in reads. The resulting assembly is being written as standard CAF file which can easily be imported into numerous finishing tools like GAP4. We provide two versions of MIRA. One uses the automatic contig editor EdIt that has been trained on standard ABI traces (mira_j), the other version has been trained on LICOR traces (mira_l). Currently supported platforms are SGI IRIX64, SUN Solaris and Linux (i386). The canonical homepage of MIRA and EdIt, including download possibilities, is: http://www.dkfz-heidelberg.de/mbp-ased/ A complete documentation can be found in the 'doc' directory of the tarballs as HTML, texinfo and man page. Please mail suggestions, critics, bug reports etc. to b.chevreux@dkfz-heidelberg.de t.pfisterer@dkfz-heidelberg.de Have fun. ------------------------------------------------------------------------------- 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-bio-software@hgmp.mrc.ac.uk Wed Nov 3 10:55:33 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4B02C17ABE; Wed, 3 Nov 1999 10:55:32 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA21740; Wed, 3 Nov 1999 10:55:22 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA22404; Wed, 3 Nov 1999 10:55:21 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Nanci E Donacki" X-Newsgroups: bionet.cellbiol,bionet.molbio.methds-reagnts,bionet.software Subject: Re: MS Access for cell lines Date: Wed, 3 Nov 1999 05:46:06 -0500 Lines: 51 Message-ID: <7vp3vc$qo$1@autumn.news.rcn.net> References: <7vc4qa$19r6$1@www.univie.ac.at> <2anS3.6117$6y2.141474@carnaval.risq.qc.ca> <7vmh9o$87g$1@newspc4.rz.uni-hohenheim.de> X-Trace: zqZPFIrq7OgMRK8VZ3dA2ZIN/6Fg1OnlJx8rNl1f2jQ= X-Complaints-To: abuse@rcn.com X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MSMail-Priority: Normal X-Priority: 3 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 To: bio-software@hgmp.mrc.ac.uk, cellbiol@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk There is also a cell line database that is available for download at http://www.protocol-online.net in the cell culture section. -ned Bernhard Roth wrote in message news:7vmh9o$87g$1@newspc4.rz.uni-hohenheim.de... | Is it possible to get a copy too ??? | Thank´s a lot! | | Bernhard Roth | University of Hohenheim | General Virology | Germany | | | Paula Lavery schrieb in Nachricht | <2anS3.6117$6y2.141474@carnaval.risq.qc.ca>... | >Hi Martin | > | >If you give me your email address I will send you a copy of a database I | use | >as an inventory for all my cell lines in LN2. I tried to email you directly | >but the message was refused. | > | >Paula Lavery | >Transplant Immunology Lab. | >Royal Victoria Hospital | >McGill University | >Montreal (QC) Canada | > | >"If we knew what we were doing it wouldn't be called research, would it?" | >-- Albert Einstein | > | >Martin Offterdinger wrote in message <7vc4qa$19r6$1@www.univie.ac.at>... | >>Hi! | >>I just wonder if anyone used MS Access to handle cell lines in a database. | >>If yes I would be interested in receiving information how to design the | >>database. | >>Thank you very much! | >>Martin | >> | >> | > | > | | From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 11:58:55 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CBF0317A5A; Wed, 3 Nov 1999 11:58:54 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA26293 for ; Wed, 3 Nov 1999 11:58:49 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA23268 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 11:58:48 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Dyre Tjeldvoll X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: 03 Nov 1999 12:56:17 +0100 Organization: Norwegian university of science and technology Message-ID: References: X-Trace: kopp.stud.ntnu.no 941630178 5638 129.241.103.4 (3 Nov 1999 11:56:18 GMT) X-Complaints-To: usenet@itea.ntnu.no X-Newsreader: Gnus v5.6.45/XEmacs 20.2 Lines: 71 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk a.walden@wave.co.nz (Adrian Walden) writes: [snip] > > My question concerns a few problems I have had with blast and the > requirement to setup a file called .ncbirc in my root directory or the > directory from which I call the BLAST application. The contents of the > .ncbirc file are supposed to be > > [ ncbi] > Data=/path/blast/data > > I would like to know what this file does and why it is there. Many programs have a .programrc file, and I think (!) the rc stands for resource, and these files are typically for saving settings. > Is it supposed to export the variable "Data" to the environment. If > so, why is it that when I query th environment with > > echo $Data > > that I get a blank line instead of a path to the directory "data" ? The line in your file sets the local shell-variable Data, not an environment variable, if the file is treated as a shell-script. The difference is that a local variable is only known to shell in which you set it, whereas an environment variable is inherited to the processes started by the shell. You can test this by doing the following: dyret@vier~$ DUMMY=value dyret@vier~$ bash dyret@vier~$ echo $DUMMY dyret@vier~$ exit dyret@vier~$ echo $DUMMY value dyret@vier~$ export DUMMY=newvalue dyret@vier~$ echo $DUMMY newvalue dyret@vier~$ bash dyret@vier~$ echo $DUMMY newvalue It could of course be that the program itself exports the variable after having read the file. The conventional way to make an environment variable is to: 1) Export the variable using the export command, i.e. export Data=/path/blast/data or 2) Declare the variable to be an environment variable: declare -x Data=/path/blast/data Either is typically done in your .bashrc, .bash_profile (or .profile) The bash man page, or alternatively the emacs info page, has more info. My advice is that you export Data on the command line (export Data=/path/blast/data) and then run your program. If it works you put the export command to your startup file, if not... well, then you have a different problem. HTH. -- dt From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 15:14:03 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D29B117AFC; Wed, 3 Nov 1999 15:14:02 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA10748 for ; Wed, 3 Nov 1999 15:14:00 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA25715 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 15:13:59 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Andrew Rambaut X-Newsgroups: bionet.software Subject: Program to Estimate Rates of evolution for sequences... Date: Wed, 03 Nov 1999 15:13:29 +0000 Organization: Oxford University, England Lines: 16 Message-ID: <031119991513290722%andrew.rambaut@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 941642009 76 163.1.210.37 (3 Nov 1999 15:13:29 GMT) X-Complaints-To: newsmaster@ox.ac.uk User-Agent: YA-NewsWatcher/4.2.6 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I have just released a new software package that some people may find useful (mainly people analysing viral sequences) when sequences have been isolated at different points in time: TipDate is an application for estimating the rate molecular evolution (and hence a time-scale) for a phylogeny consisting of dated tips. These will most frequently be from viruses or other fast-evolving pathogens that have been isolated over a range of dates. The program can also return the likelihood for the simple molecular clock model (i.e., assuming that all sequences are contemporary) or the non-clock model. These are useful for likelihood ratio tests of the fit of the model to the data. It is available at: http://evolve.zoo.ox.ac.uk/TipDate/TipDate.html From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 15:35:45 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9D6EE17AFC; Wed, 3 Nov 1999 15:35:44 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA12356 for ; Wed, 3 Nov 1999 15:35:32 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA25975 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 15:35:30 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: friard@molinette.unito.it (Olivier) X-Newsgroups: bionet.software Subject: Re: Primers design program from sequence alignment? Message-ID: <38204587.22987794@news.free.fr> References: <381BF420.C91C2B6B@bionet.nsc.ru> X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 21 Date: Wed, 03 Nov 1999 15:31:08 GMT X-Complaints-To: abuse@proxad.net X-Trace: nnrp1.proxad.net 941643068 130.192.126.7 (Wed, 03 Nov 1999 16:31:08 MET) Organization: Guest of ProXad - France To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, I wrote a DOS program to help to design primers on multi-alignment (CLUSTALW format). This program is called PRIMERS and you can find it at http://annhyb.free.fr I hope that this program will help you! Bye Olivier >If there is any program or web resource which could make conservative >PCR primers from DNA sequence alignments? Please let me know. >Denis M.Larkin >Institute of Cytology and Genetics >Novosibirsk >Russia > From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 15:45:28 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C0F8E17B54; Wed, 3 Nov 1999 15:45:27 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA13195 for ; Wed, 3 Nov 1999 15:45:24 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA26114 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 15:45:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: jfryan@NHGRI.NIH.GOV (Joe Ryan) X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: 3 Nov 1999 07:38:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Distribution: world Message-ID: <19991103103140.X14861@nhgri.nih.gov> References: To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk You may want to have a look at http://www.ncbi.nlm.nih.gov/BLAST/newblast.html http://genome.nhgri.nih.gov/blastall/blast_install/ ftp://ncbi.nlm.nih.gov/blast/db/README --Joe On Wed, Nov 03, 1999 at 05:09:56PM +1300, Adrian Walden wrote: > I am installing standalone BLAST on a Pentium running redhat linux 6.1. > This is somewhoat of a challange for me as my previous experience > installing software etc is on a Macintosh. My most recent success's on > linux have included some minor improvments to my .bash_profile and .bashrc > files and the installation of the Staden Package (a great victory). You > should conclude from this that I am a beginner ! > > My question concerns a few problems I have had with blast and the > requirement to setup a file called .ncbirc in my root directory or the > directory from which I call the BLAST application. The contents of the > .ncbirc file are supposed to be > > [ ncbi] > Data=/path/blast/data > > I would like to know what this file does and why it is there. Is it > supposed to export the variable "Data" to the environment. If so, why is > it that when I query th environment with > > echo $Data > > that I get a blank line instead of a path to the directory "data" ? > > Thanks for your help > > Adrian walden > > a.walden@(delete)wave.co.nc > From owner-bio-software@hgmp.mrc.ac.uk Wed Nov 3 19:15:28 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 06C7417B58; Wed, 3 Nov 1999 19:15:26 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA28081 for ; Wed, 3 Nov 1999 19:15:24 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA28767 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 Nov 1999 19:15:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: see@sig.for.address (Harry) X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: Wed, 03 Nov 1999 11:11:55 -0800 Organization: University of California, Los Angeles Lines: 25 Message-ID: References: X-Newsreader: MT-NewsWatcher 2.4.4 X-Archive: no X-No-Archive: yes X-Face: "+f;Y+f#~]y.r9$qF||y9km?$=Ro%c*KEe=|m}${Wyg18&t3J/gWv(3"jSNeo @WB9I-b(CBv"%kS,E+;>qsCH=TMLwv7^r$K4M4QEK)[Xl3Gn285Cr7?${";ACAZ)?(dV W&(V:8cnu8'HY To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article , a.walden@wave.co.nz (Adrian Walden) wrote: > [ ncbi] > Data=/path/blast/data .ncbirc is a "settings" file used internally by NCBI's programs, ala windows.ini or Mac/Preferences files. As far as I can tell, the settings in this file don't alter your shell environment. I'm guessing they went this route because not all operating systems that NCBI supports have an "environment" in the Unix sense (MacOS comes to mind), so for cross-platform issues, the rc file. Nevertheless, I believe you can use environment variables on Unix-like systems to substitute for .ncbirc. For example, with standalone blast, export $BLASTMAT=/path/blast/data would accomplish the same as the .ncbirc lines above, I believe. -Harry -- Harry

From owner-bio-software@hgmp.mrc.ac.uk Thu Nov 4 10:25:21 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4682017A59; Thu, 4 Nov 1999 10:25:20 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA11982 for ; Thu, 4 Nov 1999 10:25:17 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA18286 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 10:25:16 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Sales" X-Newsgroups: alt.hk,alt.marketing,alt.marketing.online,alt.med.software,alt.pcdos,alt.publish,alt.publish.books,alt.sex.cd-rom,alt.www.marketing,alt.www.marketing.adverts,aus.computers.cdrom,autodesk.mcad.marketing,bionet.software,bnr.software-eng Subject: CDs replication Date: Thu, 4 Nov 1999 17:59:44 +0800 Organization: IMS Netvigator Lines: 21 Message-ID: <7vrm9p$r6o14@imsp212.netvigator.com> 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk We are the CDs manufacturer in Hong Kong and we can provide the replication of Audio CD, CD-ROM, CD-R, Super-VCD, Video CD, Wallet CD (Business name card), Wonder CD (Irregular shaped CD) discs and the multimedia CD-ROM production. Besides, we are also the exporter/distributor of CD jewel box and DVD box. We commit to provide our best quality services for processing from you provided your master media to having up to 5 colors silk screen or offset printing of your products. Special design and packaging service are provided upon request. Should you have any queries, please feel free to contact with us by phone (852) 2898-1082 or fax (852) 2898-1262 or email sales@chinaeast.com.hk We are looking forward to co-operate with you in the future. Yours Sincerely Sales Department From owner-bio-software@hgmp.mrc.ac.uk Thu Nov 4 11:15:17 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 045C817A92; Thu, 4 Nov 1999 11:15:14 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA16016 for ; Thu, 4 Nov 1999 11:15:11 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA18917 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 11:15:10 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: spam@127.0.0.1 (Bernard Murray, PhD) X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: Wed, 03 Nov 1999 16:05:18 -0700 Organization: UCSF Lines: 19 Message-ID: References: To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article , Dyre Tjeldvoll wrote: > Many programs have a .programrc file, and I think (!) the rc stands > for resource, and these files are typically for saving settings. Actually I believe that the "rc" stands/used to stand for "run control". I am showing my age here. I remember when the "ESC" key used to stand for "Extended System Command" but there's no way you'll be able to convince newcomers that it isn't "ESCape". Bernard -- Bernard P. Murray, PhD bpmurray at cgl . ucsf . edu Department of Cellular & Molecular Pharmacology, UCSF From owner-bio-software@hgmp.mrc.ac.uk Thu Nov 4 13:35:18 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A1A6817A99; Thu, 4 Nov 1999 13:35:17 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA27112 for ; Thu, 4 Nov 1999 13:35:15 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA20635 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 13:35:13 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Mike Sternberg X-Newsgroups: bionet.software Subject: Postdoc Bioinformatics Data Mining London UK Date: Thu, 04 Nov 1999 13:22:00 +0000 Organization: Imperial Cancer Research Fund Message-ID: <38218878.84C81EBE@icrf.icnet.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en Lines: 33 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Bioinformatics + Data Mining + London Postdoctoral Fellow £21,730 - £23,447 Initially 2 years Contract London WC2A A postdoctoral research position is available at the Imperial Cancer Research Funds Biomolecular Modelling Laboratory in central London to work on the application of machine learning to discover rules governing protein structure. The object is to use inductive logic programming and other data mining algorithms to find rules to assist in the prediction of protein structure from sequence The project is supported by the United Kingdom BBSRC/EPSRC Bioinformatics Initiative and the contract will initially be for two years with possibility of subsequent extension for a third year. The applicant must be skilled in computational approaches in bioinformatics and familiarity of protein structure will be advantageous. For enquiries please contact Dr Mike Sternberg at m.sternberg@icrf.icnet.uk. For more information about the project see http://www.bmm.icnet.uk/ilp. Salary UK pounds 21,730 - 23,477 p.a. according to age and experience. From owner-bio-software@hgmp.mrc.ac.uk Thu Nov 4 14:45:16 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F26BE17A5C; Thu, 4 Nov 1999 14:45:15 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA02588 for ; Thu, 4 Nov 1999 14:45:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA21595 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 14:45:12 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Dyre Tjeldvoll X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: 04 Nov 1999 15:43:11 +0100 Organization: Norwegian university of science and technology Lines: 30 Message-ID: References: X-Trace: kopp.stud.ntnu.no 941726596 5742 129.241.103.4 (4 Nov 1999 14:43:16 GMT) X-Complaints-To: usenet@itea.ntnu.no X-Newsreader: Gnus v5.6.45/XEmacs 20.2 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk spam@127.0.0.1 (Bernard Murray, PhD) writes: [snip] > > Many programs have a .programrc file, and I think (!) the rc stands > > for resource, and these files are typically for saving settings. > > Actually I believe that the "rc" stands/used to stand for > "run control". Ah..., well admittedly, rc is a poor abbreviation for resource. But now I know... > I am showing my age here. I think I got that resource-idea from the fact that many program settings can be modified by changing x-resources. I guess this shows my lack of age, since I have X as my point of reference... :) > I remember when the "ESC" key used > to stand for "Extended System Command" but there's no way you'll > be able to convince newcomers that it isn't "ESCape". I must admit I thought it was "Escape" too, but as a dedicated (X)emacs user I like "Extended System Command" much better! I think the widespread use of PC's and DOS/Windows programs has contributed to the "Escape" view, since those systems frequently use "Esc" to exit from menus and programs. -- dt From owner-bio-software@hgmp.mrc.ac.uk Thu Nov 4 21:45:31 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A1BE017A79; Thu, 4 Nov 1999 21:45:30 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA28161 for ; Thu, 4 Nov 1999 21:45:22 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA05091 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 21:45:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: see@sig.for.address (Harry) X-Newsgroups: bionet.software Subject: fasta against BLAST2.0 format library Date: Thu, 04 Nov 1999 13:43:11 -0800 Organization: University of California, Los Angeles Lines: 28 Message-ID: X-Newsreader: MT-NewsWatcher 2.4.4 X-Archive: no X-No-Archive: yes X-Face: "+f;Y+f#~]y.r9$qF||y9km?$=Ro%c*KEe=|m}${Wyg18&t3J/gWv(3"jSNeo @WB9I-b(CBv"%kS,E+;>qsCH=TMLwv7^r$K4M4QEK)[Xl3Gn285Cr7?${";ACAZ)?(dV W&(V:8cnu8'HY To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I've been trying to get fasta33t00 to recognize a library/db in BLAST2.0 format (created by NCBI's formatdb, part of the standalone BLAST package). If I create a fastlib file and point FASTLIB to it, the fasta programs find and recognize the library fine. However, for my uses, I'd like to run the fasta programs in a manner that doesn't depend on such a pointer file. Instead, I'd like to point it at the library file on the command line. For example: fasta33 query.fasta /path/to/blastdb where the actual library files are blastdb.nsq, .nin, and .nhr. This generates a "cannot open" error when it gets to the library. This works fine if the library specified on the command line is in fasta format so I tried setting LIBTYPE to 12, as described in the docs, to indicate it is in BLAST2.0 format, but I still get the error. Is there something I'm missing or is this just not possible and I am misunderstanding the purpose of LIBTYPE? Thanks, Harry -- Harry

From owner-bio-software@hgmp.mrc.ac.uk Thu Nov 4 22:45:35 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BAED217B82; Thu, 4 Nov 1999 22:45:29 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA05073 for ; Thu, 4 Nov 1999 22:45:23 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA05851 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 22:45:21 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux) X-Newsgroups: bionet.software Subject: Announcement: MIRA 1.3.17 shotgun assembler Date: 4 Nov 1999 14:32:19 -0800 Organization: DKFZ Heidelberg Lines: 38 Distribution: world Message-ID: Reply-To: b.chevreux@dkfz-heidelberg.de To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk MIRA V1.3.17 A DNA shotgung fragment assembler with integrated automatic editor MIRA is a DNA shotgun sequence data assembly program which takes reads/sequences gained by (gel or capillary) electrophoresis experiments and defined in the Staden experiment (EXP), Sanger CAF or even FASTA file format as input and assembles them into contigs. SCF signal electrophoresis trace files are used, if present, to adjudicate between contradicting stretches of bases in reads. The resulting assembly is being written as standard CAF file which can easily be imported into numerous finishing tools like GAP4. We provide two versions of MIRA. One uses the automatic contig editor EdIt that has been trained on standard ABI traces (mira_j), the other version has been trained on LICOR traces (mira_l). The canonical homepage of MIRA and EdIt, including download possibilities, is: http://www.dkfz-heidelberg.de/mbp-ased/ A complete documentation can be found in the 'doc' directory of the tarballs as HTML, texinfo and man page. Please mail suggestions, critics, bug reports etc. to b.chevreux@dkfz-heidelberg.de and t.pfisterer@dkfz-heidelberg.de Have fun. 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-bio-software@hgmp.mrc.ac.uk Fri Nov 5 09:25:28 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9154417A9B; Fri, 5 Nov 1999 09:25:27 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA05383 for ; Fri, 5 Nov 1999 09:25:25 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA13630 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 09:25:24 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: crepinau@sb-roscoff.fr (Crepineau florent) X-Newsgroups: bionet.software Subject: from phrap to ReAligner Date: 5 Nov 1999 09:24:31 GMT Organization: Station biologique de Roscoff Lines: 20 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Dear Neter, I am looking for a software which could take an .ace file from phrap as an input and transform it to a multiple alignment suitable for ReAligner and which could use the multiple alignment resulting from ReAligner to transforme it to a .ace file from phrap. Does anybody has an idea? Thanks in advance, Yours sincerely Florent -- Florent Crépineau Station Biologique de Roscoff BP 74 29682 Roscoff cedex From owner-bio-software@hgmp.mrc.ac.uk Fri Nov 5 16:05:26 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 79AEB17A6E; Fri, 5 Nov 1999 16:05:24 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA11385 for ; Fri, 5 Nov 1999 16:05:22 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA18653 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 16:05:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) X-Newsgroups: bionet.software Subject: Re: fasta against BLAST2.0 format library Date: 05 Nov 1999 10:49:40 -0500 Organization: University of Virginia Lines: 19 Message-ID: References: X-Newsreader: Gnus v5.7/Emacs 20.4 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I've been trying to get fasta33t00 to recognize a library/db in BLAST2.0 format (created by NCBI's formatdb, part of the standalone BLAST package). ... I'd like to point it at the library file on the command line. For example: fasta33 query.fasta /path/to/blastdb where the actual library files are blastdb.nsq, .nin, and .nhr. ================ The solution is to put the library type in the library file name argument like this: fasta33 query.fasta "/path/to/blastdb 12" Bill Pearson From owner-bio-software@hgmp.mrc.ac.uk Fri Nov 5 16:35:28 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CE60017A58; Fri, 5 Nov 1999 16:35:26 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA13892 for ; Fri, 5 Nov 1999 16:35:24 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA19063 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 16:35:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: =?iso-8859-1?Q?T=F5nu?= margus X-Newsgroups: bionet.software Subject: predicting termination signal in procaryotes? Date: Fri, 05 Nov 1999 18:33:00 +0200 Lines: 7 Message-ID: <382306BC.21B97857@ebc.ee> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: kadri.ut.ee 941819524 29036 193.40.23.30 (5 Nov 1999 16:32:04 GMT) X-Complaints-To: usenet@news.ut.ee X-Mailer: Mozilla 4.6 [en] (WinNT; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Is there some software for predicting transcriptional termination signals in procaryotes? Many Thanks in Advance Tonu Margus From owner-bio-software@hgmp.mrc.ac.uk Fri Nov 5 18:05:26 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D242917A58; Fri, 5 Nov 1999 18:05:25 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA19718 for ; Fri, 5 Nov 1999 18:05:23 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA20147 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 18:05:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: see@sig.for.address (Harry) X-Newsgroups: bionet.software Subject: Re: fasta against BLAST2.0 format library Date: Fri, 05 Nov 1999 10:01:23 -0800 Organization: University of California, Los Angeles Lines: 15 Message-ID: References: X-Newsreader: MT-NewsWatcher 2.4.4 X-Archive: no X-No-Archive: yes X-Face: "+f;Y+f#~]y.r9$qF||y9km?$=Ro%c*KEe=|m}${Wyg18&t3J/gWv(3"jSNeo @WB9I-b(CBv"%kS,E+;>qsCH=TMLwv7^r$K4M4QEK)[Xl3Gn285Cr7?${";ACAZ)?(dV W&(V:8cnu8'HY To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article , wrp@alpha0.bioch.virginia.edu (William R. Pearson) wrote: > The solution is to put the library type in the library file name argument > like this: > > fasta33 query.fasta "/path/to/blastdb 12" Thanks Bill - of course that did the trick. I tried that w/o the quotes and am now kicking myself. -Harry -- Harry

From owner-bio-software@hgmp.mrc.ac.uk Fri Nov 5 18:15:16 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B98D217A58; Fri, 5 Nov 1999 18:15:15 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA20395 for ; Fri, 5 Nov 1999 18:15:14 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA20285 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 18:15:13 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.lang.pascal.delphi.misc Subject: Absolutely no-cost, free software! Date: Fri, 5 Nov 1999 18:08:16 -0000 Organization: Gunsoft Lines: 8 Message-ID: <7vv6gq$t1r$1@nclient15-gui.server.virgin.net> X-Trace: nclient15-gui.server.virgin.net 941825370 29755 62.252.4.205 (5 Nov 1999 18:09:30 GMT) X-Complaints-To: abuse@virgin.net 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk www.freespeech.org/gunsoft Visit the above site 4 brilliant software! which is free to you! and u can download it! talk to other people! get wallpaper! chat! and check out cool links! From owner-bio-software@hgmp.mrc.ac.uk Fri Nov 5 20:45:28 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9E01517A4E; Fri, 5 Nov 1999 20:45:27 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA26378 for ; Fri, 5 Nov 1999 20:45:25 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA22268 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 20:45:24 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Roland Mainz X-Newsgroups: bionet.software Subject: Re: Software for viewing (and editing) ABI files on Windows Date: Fri, 05 Nov 1999 21:31:48 +0100 Organization: University of Giessen, Germany Lines: 29 Message-ID: <38233EB4.C04D6B07@informatik.med.uni-giessen.de> References: <7v8cdo$5g2$1@nntp1.atl.mindspring.net> <199911021306.OAA16040@mail.lf2.cuni.cz> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi ! ---- Jan Diblik wrote: > That is all nice, but is there a windows program for viewing and > getting data from files made by ABI Genescan (for microsatellite > analysis)? > Or does anyone know more about the format the data are stored in? Yup, me. I'm working on an import library for ABI, SCF, XSD etc. written in JAVA. Drop me a mail if there's any interest... ---- Bye, Roland -- __ . . __ (o.\ \/ /.o) Roland.Mainz@informatik.med.uni-giessen.de \__\/\/__/ gisburn@informatik.med.uni-giessen.de /O /==\ O\ MPEG specialist, C&&JAVA&&Sun&&Unix programmer (;O/ \/ \O;) TEL +49 (0) 641/99-13193 FAX +49 (0) 641/99-41359 From owner-bio-software@hgmp.mrc.ac.uk Sat Nov 6 10:14:30 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BB30717A4E; Sat, 6 Nov 1999 10:14:29 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA05661 for ; Sat, 6 Nov 1999 10:14:27 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA10332 for bio-software-list@hgmp.mrc.ac.uk; Sat, 6 Nov 1999 10:14:27 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.lang.pascal.delphi.misc Subject: Everything 4 FREE! www.freespeech.org/gunsoft Date: Sat, 6 Nov 1999 10:13:13 -0000 Organization: Gunsoft Lines: 4 Message-ID: <800v1m$9u6$1@nclient13-gui.server.virgin.net> X-Trace: nclient13-gui.server.virgin.net 941883254 10182 62.252.8.161 (6 Nov 1999 10:14:14 GMT) X-Complaints-To: abuse@virgin.net 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk We let YOU download tonnes of stuff FOR FREE! Including software, quake2 maps, fonts, wall-paper and More!!!!!!!!!! From owner-bio-software@hgmp.mrc.ac.uk Sat Nov 6 11:39:19 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6A75217A4E; Sat, 6 Nov 1999 11:39:18 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA07658 for ; Sat, 6 Nov 1999 11:39:16 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA11251 for bio-software-list@hgmp.mrc.ac.uk; Sat, 6 Nov 1999 11:39:15 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.lang.pascal.delphi.misc Subject: The NUMBER 1 place for FREE SOFTWARE Date: Sat, 6 Nov 1999 11:34:33 -0000 Organization: Gunsoft Lines: 4 Message-ID: <8013ra$95j$1@nclient11-gui.server.virgin.net> X-Trace: nclient11-gui.server.virgin.net 941888170 9395 62.252.4.149 (6 Nov 1999 11:36:10 GMT) X-Complaints-To: abuse@virgin.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk www.freespeech.org/gunsoft The NUMBER 1 place for FREE SOFTWARE From owner-bio-software@hgmp.mrc.ac.uk Sat Nov 6 17:18:21 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E351917A4E; Sat, 6 Nov 1999 17:18:20 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA16605 for ; Sat, 6 Nov 1999 17:18:19 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA15294 for bio-software-list@hgmp.mrc.ac.uk; Sat, 6 Nov 1999 17:18:17 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: gyy@tc.umn.edu (Guo-Yun Yu) X-Newsgroups: bionet.software Subject: MS Access for small # of EST, any suggestion? Date: 6 Nov 1999 17:15:55 GMT Organization: University of Minnesota Lines: 11 Message-ID: <801nob$kto$1@news1.tc.umn.edu> Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (x86 32bit) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, Any body have build a Access database to handle small EST project (about 1000)? If possible, could you let us share with you. We'd appreciate your help very much. We welcome any suggestion. Guo-Yun Yu Department of Agronomy and Plant Genetics University of Minnesota email: gyy@tc.umn.edu From owner-bio-software@hgmp.mrc.ac.uk Sun Nov 7 02:45:16 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2154317A43; Sun, 7 Nov 1999 02:45:16 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id CAA05062 for ; Sun, 7 Nov 1999 02:45:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id CAA00196 for bio-software-list@hgmp.mrc.ac.uk; Sun, 7 Nov 1999 02:45:11 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: hcwang@WH.MATH.UWATERLOO.CA (Huai-chun Wang) X-Newsgroups: bionet.software Subject: multiple alignment of text files Date: 6 Nov 1999 18:33:22 -0800 Organization: Dept. of Computer Science, University of Waterloo Lines: 14 Distribution: world Message-ID: <3824F286.16121ACC@wh.math.uwaterloo.ca> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello, I wonder whether there are softwares that do multiple alignment of any plain text files in addition to DNA or protein sequence file. I tested ClustalW but it can only align legal DNA base or amino acid residues, and igonore all other English characters and symbols that typically occured in an English text. Does any one suggest such a program for this new need? Thank you. Huaichun Wang University of Waterloo From owner-bio-software@hgmp.mrc.ac.uk Sun Nov 7 08:17:51 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A716117A43; Sun, 7 Nov 1999 08:17:50 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA18726 for ; Sun, 7 Nov 1999 08:17:48 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA04039 for bio-software-list@hgmp.mrc.ac.uk; Sun, 7 Nov 1999 08:17:47 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Greg Subject: XML interfaces; BioML/BSML X-Newsgroups: bionet.software Summary: User-Agent: tin/pre-1.4-980818 ("Laura") (UNIX) (FreeBSD/2.2.8-STABLE (i386)) Date: 07 Nov 1999 08:05:19 GMT Lines: 7 Message-ID: <382532bf$0$208@nntp1.ba.best.com> X-Trace: nntp1.ba.best.com 941961919 208 jquinn@206.184.139.138 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I'm currently designing an XML interface to a protein database system, and I'm finding it difficult to find any real-life examples, aside from software produced by either ProteoMetrics and/or Vidual Genomics, of who/what is using BioML or BSML. Any suggestions? Cheers Greg From owner-bio-software@hgmp.mrc.ac.uk Sun Nov 7 17:55:17 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8A5F217A43; Sun, 7 Nov 1999 17:55:15 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA02561 for ; Sun, 7 Nov 1999 17:55:11 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA10873 for bio-software-list@hgmp.mrc.ac.uk; Sun, 7 Nov 1999 17:55:10 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Piotr Kozbial X-Newsgroups: bionet.software Subject: Re: XML interfaces; BioML/BSML Date: Sun, 07 Nov 1999 18:44:53 +0100 Organization: http://news.icm.edu.pl/ Lines: 12 Message-ID: <3825BA94.B797D421@ibb.waw.pl> References: <382532bf$0$208@nntp1.ba.best.com> Reply-To: piotrk-NO@SPAMM-ibb.waw.pl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: sunsite.icm.edu.pl 941996649 12399 212.87.28.79 (7 Nov 1999 17:44:09 GMT) X-Complaints-To: abuse@news.icm.edu.pl X-Accept-Language: en X-Mailer: Mozilla 4.7 [en] (X11; U; Linux 2.2.10 i686) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Greg wrote: > > I'm currently designing an XML interface to a protein database > system, and I'm finding it difficult to find any real-life > examples, aside from software produced by either ProteoMetrics > and/or Vidual Genomics, of who/what is using BioML or BSML. > Any suggestions? > Cheers > Greg http://ala.vsms.nottingham.ac.uk/biodom/software/ http://204.112.55.140/BIOML/index.html From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 8 04:17:51 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C820717A81; Mon, 8 Nov 1999 04:17:50 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id EAA23197 for ; Mon, 8 Nov 1999 04:17:48 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id EAA26574 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 04:17:47 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: amartin@stagleys.demon.co.uk (Andrew Martin) X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: Sun, 7 Nov 1999 21:38:58 GMT Organization: Private Address Message-ID: References: X-Trace: mail2news.demon.co.uk 942034549 mail2news:10828 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!tele-post-20.mail.demon.net!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 24 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Dyre Tjeldvoll (dyret@idi.ntnu.no) wrote: : a.walden@wave.co.nz (Adrian Walden) writes: : > Is it supposed to export the variable "Data" to the environment. If : > so, why is it that when I query th environment with : > : > echo $Data : > : > that I get a blank line instead of a path to the directory "data" ? : The line in your file sets the local shell-variable Data, not an : environment variable, if the file is treated as a shell-script. : The difference is that a local variable is only known to shell in : which you set it, whereas an environment variable is inherited to the : processes started by the shell. You can test this by doing the : following: NO! It doesn't even set a local (shell) variable. The file is read by the BLAST program not the shell, so it is used to set a parameter internal to the program. Andrew From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 8 09:45:01 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C3DF217A64; Mon, 8 Nov 1999 09:45:00 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA10369 for ; Mon, 8 Nov 1999 09:44:59 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA00591 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 09:44:58 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Soeren W. Rasmussen" X-Newsgroups: bionet.software Subject: Re: MS Access for small # of EST, any suggestion? Date: Mon, 08 Nov 1999 08:45:38 +0100 Organization: UNI-C Lines: 41 Message-ID: <38267FA2.2CDC6C10@crc.dk> References: <801nob$kto$1@news1.tc.umn.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 942047123 37252 130.226.182.97 (8 Nov 1999 07:45:23 GMT) X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi Guo-Yun Yu, DNATools is a small software package (not an access database) which is designed for this purpose. The program includes facilities for automated local and global blast searching and information retrieval as well as clustal multi-sequence alignment, restriction mapping, translation, comparing and merging, re-naming files plus a number of other functions useful for handling small (6-10,000) EST projects. Sequence annotation (e.g. blast search result) is accessable for free text searching. You can download it from http://www.crc.dk/phys/dnatools.htm and try it out. It can be used free of charge. Regards Soeren Guo-Yun Yu wrote: > Hi, > > Any body have build a Access database to handle small EST project (about > 1000)? If possible, could you let us share with you. We'd appreciate your > help very much. We welcome any suggestion. > > Guo-Yun Yu > Department of Agronomy and Plant Genetics > University of Minnesota > email: gyy@tc.umn.edu -- 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-bio-software@hgmp.mrc.ac.uk Mon Nov 8 10:33:42 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 441CC17A61; Mon, 8 Nov 1999 10:33:42 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA14893 for ; Mon, 8 Nov 1999 10:33:40 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA01247 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 10:33:39 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "A.C. Bakker" X-Newsgroups: bionet.software Subject: http://members.tripod.lycos.nl/svenb/index.html Date: Sun, 7 Nov 1999 15:54:21 +0100 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Lines: 3 Message-ID: <382592ab$0$16287@news2.zeelandnet.nl> X-Trace: dreaderd.zeelandnet 941986475 16287 212.92.70.55 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk http://members.tripod.lycos.nl/svenb/index.html From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 8 10:52:58 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1613317A61; Mon, 8 Nov 1999 10:52:57 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA16559 for ; Mon, 8 Nov 1999 10:52:56 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA01501 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 10:52:51 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Dyre Tjeldvoll X-Newsgroups: bionet.software Subject: Re: LINUX/standalone blast question Date: 08 Nov 1999 11:51:34 +0100 Organization: Norwegian university of science and technology Lines: 21 Message-ID: References: X-Trace: kopp.stud.ntnu.no 942058295 13166 129.241.103.4 (8 Nov 1999 10:51:35 GMT) X-Complaints-To: usenet@itea.ntnu.no X-Newsreader: Gnus v5.6.45/XEmacs 20.2 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk amartin@stagleys.demon.co.uk (Andrew Martin) writes: [snip] > : The line in your file sets the local shell-variable Data, not an > : environment variable, if the file is treated as a shell-script. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ I added this condition because I have never used the program in question. > NO! It doesn't even set a local (shell) variable. The file is read > by the BLAST program not the shell, so it is used to set a parameter > internal to the program. I will take your word for it. I just guessed (wrongly, it appears), that the file in question was a shell script that was sourced by the program since the syntax of the snippet resembled that of a(n) (ba)sh script. -- dt From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 8 15:25:24 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3429A17A8A; Mon, 8 Nov 1999 15:25:24 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA06744 for ; Mon, 8 Nov 1999 15:25:22 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA04901 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 15:25:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Donald D. Bustamante" X-Newsgroups: bionet.software Subject: NBIF Clip Art Server Date: Mon, 08 Nov 1999 08:05:35 -0700 Organization: National Biotechnology Information Facility Lines: 12 Message-ID: <3826E6BF.380B@nbif.org> Reply-To: dbustama@nbif.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: bubba.NMSU.Edu 942073135 8555 128.123.36.225 (8 Nov 1999 14:58:55 GMT) X-Complaints-To: usenet@bubba.NMSU.Edu X-Mailer: Mozilla 3.01Gold (WinNT; I) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk The National Biotechnology Information Facility is pleased to announce its biotechnology clip art server. Clip art on this server includes black & white line art, graphical images, and stock photos. All may be used royalty free for personal and instructional use. Commercial uses require a license from NBIF. -- 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-bio-software@hgmp.mrc.ac.uk Mon Nov 8 20:14:03 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8498817A60; Mon, 8 Nov 1999 20:14:02 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA24078 for ; Mon, 8 Nov 1999 20:14:00 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA08619 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 20:13:59 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: jfryan@NHGRI.NIH.GOV (Joe Ryan) X-Newsgroups: bionet.software Subject: Re: Alu Sequences Date: 8 Nov 1999 11:56:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Distribution: world Message-ID: <19991108144907.G2618@nhgri.nih.gov> References: <9467.991108@uchsc.edu> Lines: 18 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Check RepBASE www.girinst.org Joe On Mon, Nov 08, 1999 at 10:22:07AM -0800, Yong Li wrote: > Hi, > > I need mouse Alu family sequences. Does anybody know where can I > easily get them? > > Thanks in advance. > > Yong Li > > > From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 8 20:47:24 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4BE9417A60; Mon, 8 Nov 1999 20:47:24 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA25397 for ; Mon, 8 Nov 1999 20:47:21 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA08967 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 20:47:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: acad@ACCEFYN.ORG.CO (AGC) X-Newsgroups: bionet.software Subject: bioinformatica Date: 8 Nov 1999 09:49:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Distribution: world Message-ID: <3827093A.E2E7073D@accefyn.org.co> Reply-To: acad@ACCEFYN.ORG.CO To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk para hispanoparlantes, agradecere sus comentarios, aun no esta completamente montados los files, pero algo esta, todos sus comentarios son bienvenidos, gracias. http://www.accefyn.org.co/bioinfo/indice.html From owner-bio-software@hgmp.mrc.ac.uk Mon Nov 8 22:09:54 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 462C217A60; Mon, 8 Nov 1999 22:09:53 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA01648 for ; Mon, 8 Nov 1999 22:09:51 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA18171 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 22:09:50 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: yong.li@UCHSC.EDU (Yong Li) X-Newsgroups: bionet.software Subject: Alu Sequences Date: 8 Nov 1999 10:22:07 -0800 Organization: UCHSC Lines: 10 Distribution: world Message-ID: <9467.991108@uchsc.edu> Reply-To: Yong Li To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, I need mouse Alu family sequences. Does anybody know where can I easily get them? Thanks in advance. Yong Li From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 05:02:42 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7BC7917AA3; Tue, 9 Nov 1999 05:02:42 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA14809 for ; Tue, 9 Nov 1999 05:02:41 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA23094 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 05:02:40 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paul Adams X-Newsgroups: bionet.software Subject: Job Posting: Computer Systems Engineer I/II Date: Mon, 08 Nov 1999 20:56:54 -0800 Organization: Lawrence Berkeley National Laboratory Lines: 59 Message-ID: <3827A996.C0FF2D2F@nospam.lbl.gov> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 [en]C-CCK-MCD LBNL V4.51 Build 1 (Win98; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Computer Systems Engineer I/II Job PB/011299/CJO CSE I $3605-$5717/Mo. CSE II $4326-$7210/Mo. Computational Crystallography Initiative, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California. NOTE: One vacancy exists. Classification will depend upon the applicant's level of skills, knowledge, and abilities. This is a one-year term appointment with the possibility of renewal contingent upon continued funding. DUTIES: Essential -- Under the general direction of the principal investigator of the Computational Crystallography Initiative, assist with the development and implementation of a high-level crystallographic computing language and numerical algorithms for a scientific application. The overall objectives of the Computational Crystallography Initiative include the design of a high-level crystallographic computing language, implemented as an "interpreter" using common computer language creation tools. The resulting computational architecture will create a highly flexible and open environment in which to execute new algorithms for the automation of the multi-wavelength anomalous diffraction method, model building, structure refinement, and eventually all major aspects of X-ray crystallography. Essential for the CSE II -- In addition to the CSE I duties, the CSE II will be expected to provide technical guidance to other group members and to engage in independent research. QUALIFICATIONS: Essential -- Candidates will be considered from across all levels of computer systems engineering experience. Most important is extensive experience with C/C++ and Javascript, PERL or a similar scripting language. Familiarity with one or more of the following is desirable: current language translation tools (e.g., PCCTS/ANTLR), source code revision systems, API design, web-based interfaces. Marginal -- Experience in development and implementation of numerical algorithms for scientific applications. Familiarity with UNIX or Windows system management. Essential for the CSE II -- In addition to the qualifications for the CSE I, the CSE II will have a proven ability to assume lead roles in activities and to grasp complex problems and independently develop solutions and will possess an in-depth background in software development. POSTING DATE: October 21, 1999. CLOSING DATE: Open until filled. Further details about the position can be obtained from Paul Adams (principal investigator) by email to PDAdams@lbl.gov Please submit one copy of your resume via email (our preferred method) to: employment@lbl.gov (no attachments, please). Reference job number PB/011299 in your cover letter. Or mail to: Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 937-0600, Berkeley, CA 94720. Or FAX: 510-486-5870. Visit the Berkeley Lab Web site at: http://www.lbl.gov/CJO. Berkeley Lab is an AA/EEO employer. From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 06:15:06 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5977417A43; Tue, 9 Nov 1999 06:15:06 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id GAA23013 for ; Tue, 9 Nov 1999 06:15:04 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id GAA24035 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 06:15:03 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: spam@127.0.0.1 (Bernard Murray, PhD) X-Newsgroups: bionet.software Subject: Re: multiple alignment of text files Date: Mon, 08 Nov 1999 18:07:04 -0700 Organization: UCSF Lines: 40 Distribution: world Message-ID: References: <3824F286.16121ACC@wh.math.uwaterloo.ca> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <3824F286.16121ACC@wh.math.uwaterloo.ca>, hcwang@WH.MATH.UWATERLOO.CA (Huai-chun Wang) wrote: > Hello, > I wonder whether there are softwares that do multiple alignment of any > plain text files in addition to DNA or protein sequence file. I tested > ClustalW but it can only align legal DNA base or amino acid residues, > and igonore all other English characters and symbols that typically > occured in an English text. Does any one suggest such a program for this > new need? Thank you. Clustal can take external alignment matrices. You could create one of your own (perhaps a simple "identity" style matrix) which includes any characters you would like to consider valid. I can't remember how Clustal handles invalid characters during input (I believe they are simply ignored) so you would probably have to change the source for that section. The standard UNIX text utility "diff" might prove useful in this situation but this is line-based so you would have to place each "sequence" in a separate file with one character per line. (I have never tried this approach). If the degree of "homology" is low you could try programs which look for statistically significant groups of characters. Such programs can operate without pre-determined matrices. I have used MEME from SDSC to identify motifs in groups of sequences. My personal preference would be to strip the sequences of invalid characters (sed script) and then run Clustal with an identity matrix. This would give an indication of similarity but would not tell you how good the punctuation is in the individual files. Bernard -- Bernard P. Murray, PhD bpmurray at cgl . ucsf . edu Department of Cellular & Molecular Pharmacology, UCSF From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 07:16:56 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 29BFA17A43; Tue, 9 Nov 1999 07:16:56 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA24604 for ; Tue, 9 Nov 1999 07:16:54 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA24791 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 07:16:53 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paul Adams X-Newsgroups: bionet.software Subject: Job Posting: Computational Crystallography Scientist Date: Mon, 08 Nov 1999 20:46:59 -0800 Organization: Lawrence Berkeley National Laboratory Lines: 56 Message-ID: <3827A743.6588588@nospam.lbl.gov> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 [en]C-CCK-MCD LBNL V4.51 Build 1 (Win98; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Computational Crystallography Scientist Job PB/011300/CJO $3515-$7029/Mo. Computational Crystallography Initiative, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California. NOTE: This is a one-year term appointment with the possibility of renewal contingent upon continued funding. DUTIES: Essential -- Under the general direction of the principal investigator of the Computational Crystallography Initiative, assist with the development and implementation of algorithms for automatic protein structure determination based on multi-wavelength X-ray diffraction data. The overall objectives of the Computational Crystallography Initiative include the design of a high-level crystallographic computing language, implemented as an "interpreter" using common computer language creation tools. The resulting computational architecture will create a highly flexible and open environment in which to execute new algorithms for the automation of the multi-wavelength anomalous diffraction (MAD) method, model building, structure refinement, and eventually all major aspects of X-ray crystallography. The successful candidate will assist with research on all aspects of computational methods for protein structure determination: heavy atom location, MAD phasing, density modification, automatic electron density interpretation and structure refinement. Will collaborate in preparation of manuscripts for scientific publication and other reports and documentation as needed. It is expected that research results are presented at group meetings, seminars and scientific conferences. QUALIFICATIONS: Essential -- Ph.D. or equivalent experience in computational crystallography, biology, chemistry, physics, computer science, mathematics or engineering. Experience in development and implementation of scientific algorithms. Experience with at least two programming languages from the following list: C/C++, Java, Javascript, PERL, Python. Strong publication record in the area of computational methods development or a related field. Marginal -- Familiarity with or experience developing research proposals in the area of computational crystallography. POSTING DATE: October 21, 1999. CLOSING DATE: Open until filled. Further details about the position can be obtained from Paul Adams (princical investigator) by email to PDAdams@lbl.gov Please submit one copy of your resume via email (our preferred method) to: employment@lbl.gov (no attachments, please). Reference job number PB/011300 in your cover letter. Or mail to: Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 937-0600, Berkeley, CA 94720. Or FAX: 510-486-5870. Visit the Berkeley Lab Web site at: http://www.lbl.gov/CJO. Berkeley Lab is an AA/EEO employer. From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 13:17:25 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D434917A59; Tue, 9 Nov 1999 13:17:24 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA19883 for ; Tue, 9 Nov 1999 13:17:21 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA29372 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 13:17:21 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Emmett Power" X-Newsgroups: bionet.software Subject: CEO WANTED FOR AI-BASED PHARMACEUTICAL START-UP Date: Tue, 9 Nov 1999 12:46:22 -0000 Organization: BT Internet Lines: 41 Message-ID: <8096l5$nv9$6@plutonium.btinternet.com> 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk CEO WANTED FOR AI-BASED PHARMACEUTICAL START-UP Our client is a start-up in the field of the application of artificial intelligence-based knowledge management solutions for pharmaceutical and biotechnology research and development. The company has an alliance with one of the leading academic centres of excellence for computer-driven artificial research in the world. The company also has highly-experienced sales and technology directors in place and an impressive list of non-executive directors. The company is now negotiating with venture funders for funding and with a major pharmaceutical company to develop and trial the product. We are now looking for a CEO to complete the management team and to lead the company through the venture funding, launch and flotation stages. It is essential that the successful candidate carries credibility within client organisations in the pharmaceutical and biotechnology sectors. As a minimum requirement, he or she will have occupied a senior managerial position, ideally within the pharmaceutical sector. By the nature of both the industry and the product, the role will call for an individual of the very highest intellectual calibre. The CEO will receive an equity stake in the business and a performance-related option package. The post will be based in the South East of England. This is a chance to share in the wealth creation process and to steer an exciting, intellectually-challenging business to flotation. Please reply in the first instance by email or post with a resume to Emmett Power, CEO, The MIB Group, 126 Aldersgate Street, London EC1A 4JQ, United Kingdom, telephone: 0171 687 0352, fax: 0171 687 0358, email: Emmett@MIB-Group.com. All applications will be treated in the strictest confidence and will be used for no other purpose than consideration for the post described above. **Please excuse any inappropriate or cross-postings** From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 14:57:03 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0941217A92; Tue, 9 Nov 1999 14:57:01 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA27756 for ; Tue, 9 Nov 1999 14:56:59 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA01460 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 14:56:58 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: zw2@duke.edu (Zhong Wang) X-Newsgroups: bionet.software Subject: Need help for Software that can do codon usage analysis Date: Tue, 09 Nov 1999 14:59:30 GMT Organization: Duke University, Durham, NC, USA Lines: 6 Message-ID: <1103_942159570@oboe> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, Anybody knows about software that can do codon usage analysis? I remember MacVector can do it, this way it is much easier to pick up a frameshift mutation in your DNA sequence. But I am working on IBM PC, there should be a software like that. Thanks. From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 16:26:12 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BFBD817A43; Tue, 9 Nov 1999 16:26:11 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA04715 for ; Tue, 9 Nov 1999 16:26:09 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA02575 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 16:26:07 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Rich Dudley X-Newsgroups: bionet.software Subject: Re: Need help for Software that can do codon usage analysis Date: Tue, 09 Nov 1999 10:40:41 -0500 Organization: University of Pittsburgh, Dept. of Cell Biology and Physiology Lines: 24 Message-ID: <38284078.9BD62DD4@pitt.edu> References: <1103_942159570@oboe> Reply-To: rdudley+@pitt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk How about a web site? Try: http://www.kazusa.or.jp/codon/ Zhong Wang wrote: > Hi, > > Anybody knows about software that can do codon usage analysis? I remember MacVector can do it, this way it is much easier to pick up a frameshift mutation in your > DNA sequence. But I am working on IBM PC, there should be a software like that. > Thanks. -- Richard J. Dudley (rdudley+@pitt.edu) Research Specialist V Cystic Fibrosis Research Center Dept. of Cell Biology and Physiology University of Pittsburgh http://www.cbp.pitt.edu ---> search BIONET archives at http://www.bio.net <--- From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 16:35:21 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E3F4C17A43; Tue, 9 Nov 1999 16:35:20 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA05535 for ; Tue, 9 Nov 1999 16:35:15 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA02695 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 16:35:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Antonio Castelluzzo" X-Newsgroups: alt.2600.hackerz,alt.binaries.games,bionet.software,biz.comp.software,it.annunci.commerciali,it.annunci.varie,it.comp.giochi,it.comp.giochi.annunci,it.news.software,it.scuola,alt.bbs.school Subject: ---------- FIFA 2000 OFFERTA SPECIALE ---------- Date: Tue, 9 Nov 1999 16:50:20 +0100 Organization: Italia Com - Il Primo Consorzio di Internet Providers italiani Lines: 9 Message-ID: <809huq$4k8@dante.italia.com> X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk E' in vendita FIFA 2000 ad un prezzo bassissimo e conveniente per tutti quelli che non vogliono spendere molto. Per contattarci scrivete a sdavide@libero.it o backy@freemail.it Sito internet http://backy.webjump.com From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 18:15:15 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 93A7C17A78; Tue, 9 Nov 1999 18:15:14 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA13422 for ; Tue, 9 Nov 1999 18:15:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA03939 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 18:15:11 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Steve G" X-Newsgroups: alt.comp.freeware.gdp,alt.comp.shareware,alt.comp.software.tools,bionet.software,de.comp.shareware.misc,comp.lang.pascal.delphi.misc Subject: Free-software, discussion, MP3 music, chat, links, wallpaper, quake2 maps, fonts, awards offered AND EVEN MORE!! Date: Tue, 9 Nov 1999 18:12:35 -0000 Organization: Gunsoft Lines: 15 Message-ID: <809o9a$37d$1@nclient15-gui.server.virgin.net> X-Trace: nclient15-gui.server.virgin.net 942171242 3309 62.252.9.114 (9 Nov 1999 18:14:02 GMT) X-Complaints-To: abuse@virgin.net 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Free-software, discussion, MP3 music, chat, links, wallpaper, quake2 maps, fonts, awards offered AND EVEN MORE!! AT www.freespeech.org/gunsoft -- >From Steve <><><><><> visit www.freespeech.org/gunsoft icq #48322092 From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 19:21:55 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6066517A78; Tue, 9 Nov 1999 19:21:53 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA15868 for ; Tue, 9 Nov 1999 19:21:50 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA04788 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 19:21:50 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Marcel Dinger" X-Newsgroups: bionet.software Subject: Re: Need help for Software that can do codon usage analysis Date: Wed, 10 Nov 1999 08:14:52 +1300 Organization: The Internet Group (Hamilton) Lines: 24 Message-ID: <942175244.892832@ham.ihug.co.nz> References: <1103_942159570@oboe> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Cache-Post-Path: ham.ihug.co.nz!unknown@p57-max7.ham.ihug.co.nz X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Zhong Wang wrote in message news:1103_942159570@oboe... > Hi, > > Anybody knows about software that can do codon usage analysis? I remember MacVector can do it, this way it is much easier to pick up a frameshift mutation in your > DNA sequence. But I am working on IBM PC, there should be a software like that. > Thanks. Try Genamics SoftwareSeek, http://genamics.com/software Just enter the keywords "codon usage" and links to several programs will come up. Hope this helps. Marcel Dinger, Genamics. From owner-bio-software@hgmp.mrc.ac.uk Tue Nov 9 21:25:22 1999 Return-Path: Delivered-To: bio-software-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 252D917A61; Tue, 9 Nov 1999 21:25:22 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA20945 for ; Tue, 9 Nov 1999 21:25:20 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA14506 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 21:25:19 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "quaderno.com" X-Newsgroups: bionet.software Subject: QUADERNO The Musical Expression. Date: Tue, 9 Nov 1999 22:21:41 +0100 Lines: 147 Message-ID: <80a3a6$t93$4@news5.isdnet.net> Reply-To: "quaderno.com" X-Trace: news5.isdnet.net 942182534 29987 213.36.2.134 (9 Nov 1999 21:22:14 GMT) X-Complaints-To: abuse@isdnet.net 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 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk 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