From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!newsfeed.nacamar.de!univ-lyon1.fr!macg3jt.univ-lyon1.fr!user From: Jean.ThioulouseNOSPAM@biomserv.univ-lyon1.fr (Jean Thioulouse) Newsgroups: bionet.software Subject: ADE-4 multivariate analysis software Date: Mon, 02 Mar 1998 11:16:28 +0100 Organization: Universite Lyon 1 - Laboratoire de Biometrie Lines: 11 Message-ID: NNTP-Posting-Host: macg3jt.univ-lyon1.fr Please note that the address of Web page of the free ADE-4 multivariate analysis and graphical display software has changed. It is now : http://pbil.univ-lyon1.fr/ADE-4/ Jean -- Jean Thioulouse - Laboratoire de Biometrie - Universite Lyon 1 69622 Villeurbanne CEDEX - France Fax: (33) 78 89 27 19 http://pbil.univ-lyon1.fr/ADE-4/JTHome.html From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!news.ucsc.edu!usenet From: hroddy@chemistry.ucsc.edu (Hector M. Rodriguez) Newsgroups: bionet.software Subject: Molscript and Windows 95 Date: 2 Mar 1998 01:58:59 GMT Organization: UCSC Lines: 7 Message-ID: <6dd3p3$12i@darkstar.ucsc.edu> NNTP-Posting-Host: m196.issp.ucsc.edu Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Has an one compiled Molscript under windows 95? I think it might be possible with the new version since it is all written in C and Windows 95 implements openGL. If anyone has please drop me a note on how you did it. Hector M. Rodriguez hroddy@chemistry.ucsc.edu From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!singer.cent.gla.ac.uk!usenet From: "Roderic D. M. Page" Newsgroups: bionet.software Subject: TreeView 1.5 Date: Mon, 02 Mar 1998 09:53:19 +0000 Organization: University of Glasgow Lines: 37 Message-ID: <34FA818F.477C@bio.gla.ac.uk> NNTP-Posting-Host: r-page.zoology.gla.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.02 (Win95; I) TreeView 1.5 is now available for Macintosh (68K and PowerPC) and Windows 95/NT systems from http://taxonomy.zoology.gla.ac.uk/rod/treeview.html. TreeView can read and display most phylogenetic tree formats. New features in 1.5 include: - a MacClade/COMPONENT-style interactive tree editor - ability to copy tree descriptions to the Clipboard - ability paste tree descriptions (e.g., "(a,(b,(c,d)));" directly into TreeView - improved drawing of unrooted trees - support for MEGA file format For more details see the online manual (http://taxonomy.zoology.gla.ac.uk/rod/treeview/treeview_manual.html). To be kept informated about bug fixes and new releases, you can join the TreeView mailing list by emailing the message subscribe treeview to majordomo@gla.ac.uk. The message should not contain anything else. You will automatically be added to the TreeView mailing list. -- =================================================== Dr Roderic D M Page Lecturer in Taxonomy Division of Environmental & Evolutionary Biology, IBLS University of Glasgow Glasgow G12 8QQ Scotland, U.K. Tel: (0141) 330 4778 Fax: (0141) 330 5971 email:r.page@bio.gla.ac.uk home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html =================================================== From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!ix.netcom.com!news From: "Joseph James" Newsgroups: bionet.software Subject: Re: Help: How do I Transfer files between two computers? Date: Mon, 2 Mar 1998 11:36:16 -0500 Organization: Netcom Lines: 53 Message-ID: <6den49$dg3@sjx-ixn8.ix.netcom.com> References: <01bd45d8$94bb5780$473073cf@default> NNTP-Posting-Host: nwk-nj17-19.ix.netcom.com X-NETCOM-Date: Mon Mar 02 8:35:21 AM PST 1998 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hello, Tape backups, hard drive swapping, writable CD and DVD, and LapLink parallel port data transfers are all options. Assuming that both the old and new compters will be available in close proximity for the duration of the data transfer, the easiest, least expensive way to copy the complete contents of the old hard drives to the new ones would be to install LapLink on both the source and target machines, and then copy the data from the source machine to the target machine through the parallel port one logical drive at a time. Of course, the disadvantage to this method is the length of time it will take, which depends upon how much data has to be transferred. I would try to configure the target machines for use with a secondary "slave" hard drive, then simply remove the hard drives from the old machines, plug them into the slave slot on the new machines, reboot, and use XCOPY with the appropriate parameters to copy one logical drive at a time. You could also use tape backups, although I would not recommend this method, as I have a lot of experience with backing up and restoring between hard drives and tapes, and even the most recent Travan tape cartridges and the latest backup software are not without some major bugs! (However, if you do decide to use tape, make sure to back up one logical drive at a time, and DO NOT use the backup software's "Full Backup" option ...) I have some experience using writable CD media, but I would not recommend it due to its current imperfections. As a consulting software engineer, I try to avoid hardware issues whenever possible, but I will admit that data transfers between hard drives, tape, and other media is one of my special interests, and, unfortunately, something I am forced to do quite frequently, as I am constantly running out of hard disk space, and now have three 6 GB hard drives on my main machine, and looking for another ... I hope this helps! Cordially, Joseph James qtechsof@ix.netcom.com Rocky Frazier wrote in message <01bd45d8$94bb5780$473073cf@default>... >Hi, I am replacing a Novell 3.11 network with an NT 4.0 SBS and all new >computers...I'd like to find an easy way to transfer all hardrive files >from the old machines to the new ones...any ideas on the best route to >follow? >-- >James "Rocky" Frazier >Rockwell_F@Prodigy.net > From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 From: "Prof. Dr. Dietmar Schomburg" Newsgroups: bionet.software Subject: Job offer: Postdoctoral position Date: Mon, 02 Mar 1998 15:32:00 +0100 Organization: Universitaet zu Koeln Lines: 24 Message-ID: <34FAC2E0.E82BED28@uni-koeln.de> NNTP-Posting-Host: 134.95.151.4 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [de] (Win95; I) Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!wuff.mayn.de!news.CS.Uni-Magdeburg.De!RRZ.Uni-Koeln.DE!usenet University of Cologne Institute for Biochemistry Post-doctoral Position in Enzyme Data Base Development Applications are invited for a three-year postdoctoral position for the development of an enzyme data base in the context of a metabolic network project. Applicants are expected to have a ph.d. in biochemistry, chemistry or biology, a strong background in enzymology, and an interest in the computer-aided storage and retrieval of scientific data. The project includes literature search and evaluation, control of the scientific quality of the data and conversion of the data for construction of a metabolic data base in cooperation with the European Bioinformatics Institute in Cambridge, UK. Applications including a CV and a list of publications, as well as the names and e-mail addresses of two references should be sent to Prof. Dr. Dietmar Schomburg, University at Cologne, Institute for Biochemistry, Zuelpicher Strasse 47, 50674 Koeln, Germany. Further information can be obtained from Prof. Dietmar Schomburg, phone: +49- 221-470-6441, E-mail: D.Schomburg@uni-koeln.de From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: michael.baron@bbsrc.ac.uk Newsgroups: bionet.software Subject: ANNOUNCE: MacBoxShade v2.0 Date: Mon, 02 Mar 1998 14:03:49 +0000 Organization: institute for animal health Lines: 49 Message-ID: <34FABC45.2B64@bbsrc.ac.uk> NNTP-Posting-Host: pc0258.avri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) ***ANNOUNCEMENT***** March 2nd 1998 MACBOXSHADE version 2.0 is now available from the BOXSHADE ftp server: ftp://ulrec3.unil.ch/pub/boxshade/MacBoxshade/ MACBOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for MACBOXSHADE. MacBoxShade is a version of the VMS/Unix program BOXSHADE which has been given a full Mac user interface, and a few different options. It requires at least system 7 to run. NEW in version 2: - Faster (3-4x) in calculating consensus and preparing RTF, PS or ASCII output; - Colour PostScript output option; - RTF and PS/EPSF colour selection now allow any colour for foreground or background, as PICT did in version 1; - Identity/Similarity matrix calculation; - Marker line (ruler line) option; - Sequence numbering at either end of the line (or both); - Shading by residue type (as an alternative to shading by consensus); - Allows any number of spaces or other characters after the sequence name and after/before the sequence numbering; - Fixes a number of outstanding bugs, including the printability of PICT files. Gave up on the compact (new) PICT option because it always printed badly. PICT files now have each residue placed individually as the only way of getting around some inconsistancies of printers and drawing programs. As always, please send any reports of bugs or other problems with MacBoxshade to: Michael D. Baron Ph.D. E-mail: michael.baron@bbsrc.ac.uk Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U.K. From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!novo.dk!PBO From: PBO@novo.dk (PBO) Newsgroups: bionet.software Subject: Re[2]: Bug in TIGR assembler? Date: 2 Mar 1998 06:01:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 112 Sender: daemon@net.bio.net Distribution: world Message-ID: <000D311B.1556@novo.dk> NNTP-Posting-Host: net.bio.net Thank you very much for the infomation! Everything works fine now. Best regards Peter Bjarke Olsen _______________________ Reply Separator _______________________ Subject: Re: Bug in TIGR assembler? Author: Granger Sutton at Internet Date: 27/2/98 10:48 Dear Dr. Olsen, If Irix is on an SGI box you might try the following: ----- Begin Included Message ----- From mdf12736@ggr.co.uk Wed Feb 5 10:22 EST 1997 From: "De Francesco, Massimo" To: "'Granger Sutton'" Subject: TIGR_assembler Date: Wed, 5 Feb 1997 14:54:16 -0000 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Lines: 39 Dear Granger, I've looked into the problem of the TIGR assembler crashing on the Silicon Graphics unix boxes, and found that the problem comes from the SGI cc compiler, which treats the char type as unsigned by default (while Sun's compiler defines them signed by default). That causes problems in several parts of the program, like for instance when reading sequences at the beginning (the trans_char codes for end of lines are positives in an unsigned char environment, so \n chars contaminate the sequence. The unsigned char value for -2 is 254, so the quad_val that will be computed will be out of range of hash_array, which makes SGI crash). Once compiled with the special -signed flag on the cc command line, the program runs fine. You will be glad to know as well that we could compile and run it without problems on a Pentium Pro Windows NT machine, as well as on a Power PC mac (although the mac version needs some polishing work since there is no true console on macs). Thanks again for giving us access to the sources; we will of course give you feedback on our usage, eventual problems encountered as well as any changes or development based on your code. Regards, Massimo ---------------------------------------- Massimo de Francesco, PhD Geneva Biomedical Research Institute Bioinformatics Group 14, rue des Aulx CH-1228 Plan les Ouates Switzerland ----- End Included Message ----- > From arkerlav@tigr.org Tue Feb 10 08:45 EST 1998 > X-Sender: arkerlav@mail.tigr.org > Mime-Version: 1.0 > Date: Tue, 10 Feb 1998 08:49:01 -0500 > To: grange > From: Peter Bjarke Olsen (by way of Anthony R. Kerlavage) > Subject: Bug in TIGR assembler? > X-Lines: 19 > > Dear Sir, > > I have tried using TIGR assembler to assemble various EST libraries (In > the range from 500 to 2000 sequences) and in most cases the run results > in segmentation violation. The run always results in segment violation > when the program is compiled under Irix 6.3 and most of the times when > compiled under linux 2.0. I would be very happy if you could help me > with the problem. Is there an updated version of the source code? > > Best regards, > > Peter Bjarke Olsen > Building 1as31 > 2880 Bagsvaerd > Novo Nordisk A/S > Denmark > Phone +4544423326 > > > Yes there is a new version of TIGR Assembler which we plan to release in the near future but we have been optimizing it for genomic projects and still use the old version for our EST assemblies. We might do a new EST version as well. Granger Sutton From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: Marc Saric Newsgroups: bionet.software Subject: Re: Molscript and Windows 95 Date: Mon, 02 Mar 1998 13:56:01 +0100 Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 52 Message-ID: <34FAAC61.2AAF57C7@bph.ruhr-uni-bochum.de> References: <6dd3p3$12i@darkstar.ucsc.edu> NNTP-Posting-Host: bessel.bph.ruhr-uni-bochum.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) To: "Hector M. Rodriguez" Hector M. Rodriguez wrote: > > Has an one compiled Molscript under windows 95? I think it might be > possible with the new version since it is all written in C and Windows > 95 implements openGL. If anyone has please drop me a note on how you > did it. I have compiled Molscript 2 under Win95 with Cygwin (32bit gcc-port for Win32). I have only tried the basic version (no OpenGL or other extensions), and have run into some problems concerning a statement in some source-files. After fiddling around with the source, it was possible to compile the basic version, but it seems that it is unstable with some input (the examples render perfectly well though) which could be run under SGI Irix. I asked Per Kraulis for assistance, but he told me, that his source should be ok, and the error should be due to an error in the cygwin-package or an error caused by the changes. I can send you the precompiled executable (together with cygwin.dll) in case that you want to have it (you can also have the changes sources in case that you are interested in that -I might also be able to send you a diff-file or a simple description of the changes). Just tell me. If I have the time, I might try to compile molscript with djgpp (also basic command-line-version only). I have also tried it on a MS C++ 5.0 environment, but failed -most likely due to my VERY limited experience with C and the MS C++ environment. BTW. You can always replace the functionality of the OpenGL-output with Rasmol -it is able to write basic Molscript output (helix/beta-sheet/turn), which can be edited afterwards. -- Bye, Marc Saric Lehrstuhl fuer Biophysik Projektgruppe Theoretische Biophysik http://www.bph.ruhr-uni-bochum.de/ Ruhr-Universitaet Bochum Germany From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!feed2.news.erols.com!erols!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!portc02.blue.aol.com!prodigy.com!prodigy.com!not-for-mail From: "Rocky Frazier" Newsgroups: bionet.software Subject: Help: How do I Transfer files between two computers? Date: 2 Mar 1998 12:41:50 GMT Organization: Prodigy Services Corp Lines: 8 Message-ID: <01bd45d8$94bb5780$473073cf@default> NNTP-Posting-Host: ppp-207.115.48.71.prodigy.net X-Post-Time: 2 Mar 1998 12:41:50 GMT X-Auth-User: 000011236/c9ae6846189dde21 X-Problems-To: abuse@prodigy.net X-Newsreader: Microsoft Internet News 4.70.1155 Hi, I am replacing a Novell 3.11 network with an NT 4.0 SBS and all new computers...I'd like to find an easy way to transfer all hardrive files from the old machines to the new ones...any ideas on the best route to follow? -- James "Rocky" Frazier Rockwell_F@Prodigy.net From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!sdd.hp.com!usc!news1.chicago.iagnet.net!qual.net!iagnet.net!newsfeed.direct.ca!Supernews60!supernews.com!Supernews69!not-for-mail From: Ray Smith Newsgroups: bionet.software Subject: Re: Cluster analysis software Date: Mon, 02 Mar 1998 15:34:39 -0500 Organization: Media Cybernetics, L.P. Lines: 36 Message-ID: <34FB17DF.1650@mediacy.com> References: <34fa6896.220617@151.99.250.3> Reply-To: ray@mediacy.com NNTP-Posting-Host: 2672@208.209.115.196 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) To: Mauro CC: iec-info@immaginiecomputer.it Mauro wrote: > > I need to find a cluster analysis software, possibly freeware, for > ecological study. > Thanks in advance. > > @@@@@@@@@@@@@@@@@@@@ > Dr. Mauro D'Ambroso > Freelance in Foresty > damm@tvol.it > @@@@@@@@@@@@@@@@@@@@ Mauro, For imformation on Image-Pro Plus image anlysis software, and imaging systems in general, contact: Immagini & Computer Snc. Laura Soffientini Via Don Carlo Riva 4 20010 Bareggio (MI) Italy Tel: (02) 90.36.40.90 Fax: (02) 90.36.40.57 Email: iec-info@immaginiecomputer.it Web: http://www.immaginiecomputer.it Best regards, -Ray ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Raymond Smith, Sales Information Systems Mgr. "Image-Pro Plus - The Proven Solution" Tel: +301-495-3305 x249 Media Cybernetics, L.P. Fax: +301-495-5964 8484 Georgia Avenue ray@mediacy.com Silver Spring, MD 20910 U.S.A. http://www.mediacy.com From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!mserv1.dl.ac.uk!uninett.no!news.algonet.se!news.maxwell.syr.edu!news.idt.net!howland.erols.net!newsxfer.itd.umich.edu!uunet!in3.uu.net!server-b.cs.interbusiness.it!usenet From: damm@tvol.it (Mauro) Newsgroups: bionet.software Subject: Cluster analysis software Date: Mon, 02 Mar 1998 19:13:26 GMT Organization: Freelance Lines: 10 Message-ID: <34fa6896.220617@151.99.250.3> NNTP-Posting-Host: slipc9.tvol.it X-Newsreader: Forte Free Agent 1.11/32.235 I need to find a cluster analysis software, possibly freeware, for ecological study. Thanks in advance. @@@@@@@@@@@@@@@@@@@@ Dr. Mauro D'Ambroso Freelance in Foresty damm@tvol.it @@@@@@@@@@@@@@@@@@@@ From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed1.telenordia.se!newsfeed1.funet.fi!news.kolumbus.fi!news.uninet.ee!kadri.ut.ee!not-for-mail From: "Üllar Esinurm" Newsgroups: bionet.software Subject: WINDOWS98 and QUAKE2 Date: Mon, 2 Mar 1998 20:46:40 +0200 Lines: 38 Message-ID: <6deuoq$4ar$1@kadri.ut.ee> NNTP-Posting-Host: hi1-124.dyn.online.ee Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_006F_01BD461C.4F52D8A0" X-Trace: kadri.ut.ee 888864346 4443 (None) 194.106.108.124 X-Complaints-To: usenet@kadri.ut.ee X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_006F_01BD461C.4F52D8A0 Content-Type: text/plain; charset="iso-8859-4" Content-Transfer-Encoding: quoted-printable Download WIN98 and Quake2 @ http://www.eol.ee/~yllar ------=_NextPart_000_006F_01BD461C.4F52D8A0 Content-Type: text/html; charset="iso-8859-4" Content-Transfer-Encoding: quoted-printable
 
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------=_NextPart_000_006F_01BD461C.4F52D8A0-- From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.algonet.se!newsfeed1.telenordia.se!newsfeed1.funet.fi!news.kolumbus.fi!news.uninet.ee!kadri.ut.ee!not-for-mail From: "Üllar Esinurm" Newsgroups: bionet.software Subject: WINDOWS98 and QUAKE2 Date: Mon, 2 Mar 1998 10:11:55 +0200 Lines: 35 Message-ID: <6det4r$rak$1@kadri.ut.ee> NNTP-Posting-Host: hi1-124.dyn.online.ee Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01BD45C3.A1523320" X-Trace: kadri.ut.ee 888862683 27988 (None) 194.106.108.124 X-Complaints-To: usenet@kadri.ut.ee X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01BD45C3.A1523320 Content-Type: text/plain; charset="iso-8859-4" Content-Transfer-Encoding: quoted-printable You can download them from: Http://www.eol.ee/~yllar ------=_NextPart_000_0006_01BD45C3.A1523320 Content-Type: text/html; charset="iso-8859-4" Content-Transfer-Encoding: quoted-printable
 
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------=_NextPart_000_0006_01BD45C3.A1523320-- From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!sanger.ac.uk!solovyev From: solovyev@sanger.ac.uk ("Victor Solovyev") Newsgroups: bionet.software Subject: The First International conference on Bioinformatics of Genome Regulation and Structure Date: 2 Mar 1998 09:03:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 203 Sender: daemon@net.bio.net Distribution: world Message-ID: <9803021653.ZM29340@octane> NNTP-Posting-Host: net.bio.net --PART-BOUNDARY=.19803021653.ZM29340.octane Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u The First International conference on Bioinformatics of Genome Regulation and Structure (BGRS'98) Novosibirsk - Altai mountains, Russia August 31th - September 8th,1998 BGRS'98 web sites:http://bgrs.bionet.nsc.ru/(Russia) and http://genomic.sanger.ac.uk/bgrs.html (UK) Program/organizing committee Nikolay Kolchanov, Institute of Cytology and Genetics, Novosibirsk, Russia (Chairman of the confer= ence) Victor Solovyev, The Sanger Centre, Cambridge, UK (Co-chairman of BGRS'98= ) Martin Bishop, Human Genome Mapping Project Resource Centre (UK) Philip Bourne, SDSC, San-Diego, USA. S=F8ren Brunak, Center for Biological Sequence Analysis,Denmark Jean-Michel Claverie, Centre of Structural & Genetic Informatiom,France George Michaels, George Mason University, USA (USA - co-organizer) Luciano Milanesi, ITBA, Milan, Italy Masaru Tomita, Bioinformatics laboratory of Keio University, Japan Vladimir Tumanian, Engelgardt Institute of Molecular Biology,Moscow, Russ= ia Edgar Wingender, GBF, Braunschweig, Germany Michael Zhang Cold Spring Harbor Laboratory, Cold Spring Harbor,USA.= We expect a shift of experimental activity from strait sequencing to investigation of genome functioning and regulation in near future and therefore accumulation, analysis and recognition of genome regulatory sequences should become soon one of the major Bioinformatics' problems. The First International conference on Bioinformatics of Genome regulation= and Structure (BGRS'98) provides a forum to discuss the basic approaches, problems with data description and analysis as well as the future trends in this f= ield. TOPICS OF PARTICULAR INTEREST: 1) Databases on regulatory genomic sequences and regulatory proteins; 2) Integration of data on regulation of gene expression; 3) Genenets: databases, computer analysis and modeling of metabolic pathway/response 4) Computer methods of analysis and recognition of regulatory genomic sequences; 5) Methods of analysis and prediction of functional site activity; 6) Computer technologies for automatic knowledge discovery on gene regulation; 7) Gene structure prediction; 8) Models of transcriptional and translational control 9) Large-scale genome analysis and functional annotation of nucleotide sequences; the search for objective methods in annotating and finding signals in= genomic sequences 10) Evolution of regulatory genomic sequences 11) Aspects of protein structure connected with regulation GENERAL INFORMATION: This conference will be the first in the series, runs from August 31 t= o September 8, 1998. Our goal is to bring together about 60 researchers that are intereste= d in these problems to discuss the basic approaches, problems with data description and analysis as well as the future trends in this field. We look forward to an exciting, productive conference and encourage you t= o take part. LOCAL ORGANIZING/ARRANGEMENT COMMITTEE: SCIENTIFIC SESSIONS: Plenary lectures, symposia, posters and computer demos, round table sessions PROCEEDINGS: Short communications of all accepted presentations (up to 4 pages) including posters and computerdemos will be published in the conference Proceedings= which will be distributed to all participants. It is planned that a full length papers will be invited by the Organizing Committee for publication= in a special issue of the journal "BIOINFORMATICS" (CABIOS) after the reviewing process. SUBMISSION PROCEDURES: The closing date for receiving extended abstracts of presentations is APRIL 31, 1998. The decision on acceptance for presentation will be communicated by May 31, 1996. Authors are urged to specify the categor= y to which they are submitting their paper (oral presentation, poster, or demo). Submissions must be written in English and should include title, author's name, mailing address, telephone number, fax number, email addre= ss and a list of keywords. They should be sent to: Prof. Nickolay Kolchanov Institute of Cytology and Genetics, Novosibirsk, 630090, Russia: TEL, +7(3832)353335 Fax, +7(3832)356558 mail: kol@bionet.nsc.ru LOCATION The Conference will will take place in 2 locations: starting in the Instutute of Cytology and Genetics (Novosibirsk, Akademgorodok) and later in Altai mountains. Akademgorodok is the one of largest scientific centres in Russia. University and more than 30 research institutes are situated in there. The Institute of Cytology and Genetics is conducting the active reasearch in Bioinformatics, developing databases of regulatory sequences (TRRD) and computational approaches for sequence analysis. The first part of the conference will take place in the conference hall of this institute. The second part will be in the place located about 600 km from Novosibirsk near one of the Sibirian archeological monuments so called Denisova Cave. There are a lot of drawings of ancient people living 10-20 thousand years ago on the walls of this cave. The Institute of Archeology has Altai International center at this place, created as research and tourist center. This place is suitable for conference location and prolongation of sessions. The Altai is one of the place associated with the most important events of world history, from the settlement of man of modern type in Asia and genesis of the most ancient cultures of the Stone Age. Also it is one of the centres of biological diversity and origin of unique plants and animals. TRAVEL, INFORMATION (will be on the WEB later) SPONSORING information will be released on the WEB, additional sponsors a= re welcome. /////////////////////////////////////////////////////////////////////////= /// Please, send to Victor Solovyev: solovyev@sanger.ac.uk the application form as soon as possible, it will help to arrange possibl= e travel/accomodation support and reserve the mountain hotel facility. Application form (to send preferably by email): Prof/Dr/Mr/Ms Surname First name: Organization: Address: Town/City Post/Zip Code Country Email: Tel. /Fax: I would like to present ( ) no ORAL ( ) POSTER ( ) COMPUTERDEMO ( ) Title Contact adresses: Prof. Nickolay Kolchanov Institute of Cytology and Genetics, Novosibirsk, 630090, Russia: TEL, +7(3832)353335 Fax, +7(3832)356558 mail: kol@bionet.nsc.ru WWW: Dr. Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 -- = Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 --PART-BOUNDARY=.19803021653.ZM29340.octane-- From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news1.best.com!nntp1.ba.best.com!shell7.ba.best.com!jquinn From: Greg Newsgroups: bionet.software Subject: Re: Molscript and Windows 95 Date: 2 Mar 1998 04:05:24 GMT Organization: BEST Internet Communications, Inc. Lines: 12 Message-ID: <6ddb64$hv9$1@nntp1.ba.best.com> References: <6dd3p3$12i@darkstar.ucsc.edu> NNTP-Posting-Host: shell7.ba.best.com X-Trace: 888811524 18409 jquinn 206.184.139.132 X-Newsreader: TIN [UNIX 1.3 unoff BETA 970731; i386 FreeBSD 2.2.5-STABLE] Hector M. Rodriguez wrote: > Has an one compiled Molscript under windows 95? I think it might be possible > with the new version since it is all written in C and Windows 95 implements > openGL. If anyone has please drop me a note on how you did it. Hector, it should be fairly easy to do with most any of the major compilers; I compiled the old version of Molscript (1.4 was it?) for windows by using f2c and believe it or not that worked fine. It would be particularly interesting to get the GL and JPEG going on it; I currently don't even have the time to think about doing it, so if you make a binary could you post a notice here saying that you've done so. Greg From owner-software@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!sunqbc.risq.qc.ca!carnaval.risq.qc.ca!not-for-mail From: no.junk.casgrain@ere.umontreal.ca (Philippe Casgrain) Newsgroups: bionet.software Subject: Re: Cluster analysis software Message-ID: References: <34fa6896.220617@151.99.250.3> Organization: Université de Montréal X-Newsreader: MT-NewsWatcher 2.4.1 Lines: 9 Date: Mon, 02 Mar 1998 22:05:30 GMT NNTP-Posting-Host: biol02.biol.umontreal.ca NNTP-Posting-Date: Mon, 02 Mar 1998 17:05:30 EST In article <34fa6896.220617@151.99.250.3>, damm@tvol.it (Mauro) wrote: > I need to find a cluster analysis software, possibly freeware, for > ecological study. > Thanks in advance. > The "R" Package for multivariate and spatial analysis has a "Cluster" module. And it's free! From owner-software@net.bio.net Mon Mar 02 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!mr.net!newshub.tc.umn.edu!lynx.unm.edu!bubba.NMSU.Edu!NMSU.Edu!dkim From: D. KIM Newsgroups: bionet.software Subject: Re: Reading Mac disks in PC Date: 2 Mar 1998 20:23:30 GMT Organization: New Mexico State University Lines: 9 Message-ID: <6df4g2$nh5@bubba.NMSU.Edu> References: <6c1o3l$9ca@mserv1.dl.ac.uk> <34e7598a.12396608@194.126.82.8> NNTP-Posting-Host: hector.nmsu.edu X-Newsreader: TIN [UNIX 1.3 unoff BETA 970324; AIX 4.2] There is a shareware program called "Mac-ette", which can read, write and format MAC high-density 3.5" diskettes. I have found it to be very convenient, and well worth the rather low price. It will work without registration, if you want to try it out. Check www.download.com or some such service to locate it. Daniel Kim dkim@nmsu.edu From owner-software@net.bio.net Mon Mar 02 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!woodstock.news.demon.net!demon!news.demon.co.uk!demon!cmtech.demon.co.uk!not-for-mail From: "Richard P. Grant" Newsgroups: bionet.software Subject: Re: Languages for bioinformatics Date: Tue, 03 Mar 1998 08:26:04 +0000 Organization: In a box by the door Message-ID: <34FBBE9A.E14463D2@delete.this.cmtech.co.uk> References: <34E891F3.D22B3433@musc.edu> <6d3pei$r2a@web3.tcd.ie> <34F61DA7.32AE@anti-spam.bbsrc.ac.uk> <6d4kbq$t8f@web3.tcd.ie> <6d67fj$ige$1@vixen.cso.uiuc.edu> Reply-To: "postmaster"@[127.0.0.1] NNTP-Posting-Host: cmtech.demon.co.uk X-NNTP-Posting-Host: cmtech.demon.co.uk [158.152.187.63] X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 21 Andrew Dalke wrote: > > > > > OK, that's pretty convincing. Now tell us, be honest, the downsides of Python vs Perl. (This is a genuine request, not flame bait) -- Richard P. Grant MA DPhil | Cambridge Molecular Technologies Senior R&D Scientist | rgrant at cmtech co uk Tel: +44 1223 508345 | http://www.cmtech.co.uk/ -- Standard corporate disclaimers apply -- From owner-software@net.bio.net Mon Mar 02 22:00:00 1998 Path: biosci!agate!arclight.uoregon.edu!logbridge.uoregon.edu!ais.net!vixen.cso.uiuc.edu!ks.uiuc.edu!dalke From: dalke@ks.uiuc.edu (Andrew Dalke) Newsgroups: bionet.software Subject: Re: Languages for bioinformatics Date: 3 Mar 1998 10:07:16 GMT Organization: TB BI Lines: 67 Distribution: world Message-ID: <6dgkok$1ds$1@vixen.cso.uiuc.edu> References: <34E891F3.D22B3433@musc.edu> <6d3pei$r2a@web3.tcd.ie> <34F61DA7.32AE@anti-spam.bbsrc.ac.uk> <6d4kbq$t8f@web3.tcd.ie> <6d67fj$ige$1@vixen.cso.uiuc.edu> <34FBBE9A.E14463D2@delete.this.cmtech.co.uk> NNTP-Posting-Host: ophelia.ks.uiuc.edu Richard P. Grant asked: > OK, that's pretty convincing. Now tell us, be honest, the downsides > of Python vs Perl. > (This is a genuine request, not flame bait) (I'll see when the wires start burning :) I wasn't able to come up with many; most are related to perl's existing prevalance. Perhaps someone else has a better list? Downsides of Python v. Perl: 1) regular expressions are not as fast as perl4 or 5. As I aluded to at the end of my earlier email, I did some tests of the (new) re module in python (uses the "perl 5 compatible regular expression library"). In the domain of Prosite regular expressions, it had about 1/2 the performance of perl5, which itself had about 1/2 the performance of perl4. (The re module is new, so its performance is likely to get better.) 2) Regular expressions aren't as easy to use in python as perl. 3) beginners to python don't like whitespaces, which turns some people off. It takes a bit of getting used to, but then people like it (I don't know if this is a downside or not) 4) one-liners in Perl are highly useful in Makefiles, system() calls, etc. For example: perl -pei.bak 's/this/that/g' *.txt does an amazing number of thing 5) I've used perl a lot longer than python so it is still easier to get a lot of small things done in perl. 6) It is more likely that perl is available on a customer/remote machine. Only linux systems ship with python (that I know of) while SGI has shipped perl for several years and perl is usually available as a "freeware" disk for other OSes. 7) There isn't a Python equivalent to CPAN; ie, a common place for people to go and find extensions and modules. 8) There are many contributions to CPAN. (On the other hand, I'm looking at the CPAN list and there are a lot of modules that aren't needed for Python, like Class::Template, Data::Dumper and Ref, and it is quite easy to integrate Python with existing C code.) 9) Python namespaces are a bit strange in that there are three scopes (local, class and global) and no more. But then Perl's are strange. 10) Perl has closures while you can emulate them in Python with a Schwartzian transform (don't ask me, I'm quoting from what I read elsewhere!). 11) Python doesn't have "real" private members (though it can be emulated). But then, neither does Perl. And it is easy to fake C++ out about that. You might want to read http://www.python.org/python/Comparisons.html (bear in mind some of the evaulations are 2+ years old and some things have improved since then. BTW, for a fun observation, look at http://www.tpj.com/tpj/rules Andrew Dalke From owner-software@net.bio.net Mon Mar 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!univ-lyon1.fr!macg3jt.univ-lyon1.fr!user From: Jean.ThioulouseNOSPAM@biomserv.univ-lyon1.fr (Jean Thioulouse) Newsgroups: bionet.software Subject: Re: Cluster analysis software Date: Tue, 03 Mar 1998 08:59:26 +0100 Organization: Universite Lyon 1 - Laboratoire de Biometrie Lines: 22 Message-ID: References: <34fa6896.220617@151.99.250.3> NNTP-Posting-Host: macg3jt.univ-lyon1.fr In article (Dans l'article) , no.junk.casgrain@ere.umontreal.ca (Philippe Casgrain) wrote (écrivait) : >In article <34fa6896.220617@151.99.250.3>, damm@tvol.it (Mauro) wrote: > >> I need to find a cluster analysis software, possibly freeware, for >> ecological study. >> Thanks in advance. >> > >The "R" Package for multivariate and spatial analysis has a "Cluster" >module. And it's free! And ADE-4 too ! ;-) http://pbil.univ-lyon1.fr/ADE-4/ -- Jean Thioulouse - Laboratoire de Biometrie - Universite Lyon 1 69622 Villeurbanne CEDEX - France Fax: (33) 78 89 27 19 http://pbil.univ-lyon1.fr/ADE-4/JTHome.html From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!HERCULES.SDSC.EDU!bourne From: bourne@HERCULES.SDSC.EDU (Philip Bourne) Newsgroups: bionet.software Subject: Database Developer Date: 4 Mar 1998 13:36:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Biological Database Developer (Ref # 98-002) The National Partnership for Advanced Computational Infrastructure (NPACI) as administered by the University of California, San Diego (UCSD) has an immediate opening in the Computational Biology Group to work in the area of biological database development. We have previously developed a Property Object Model (POM) approach for representing biological data (CABIOS, 1997, 13:487-496). The objective is to extend the model and provide tools for users to maintain their own databases covering a variety of biological data either on their own client or as a personal virtual database on an NPACI server. The ideal candidate will have at least an MS in Computer Science or a PhD in molecular biology and preferably be comfortable in both disciplines. A knowledge of C++, Java and Perl programming is essential. The successful candidate will be located at the San Diego Supercomputer Center (SDSC) on the UCSD campus in beautiful La Jolla. The initial appointment will be for one year starting immediately. Salary will be commensurate with experience. For further information or to apply contact (preferably by email) Prof. Philip E. Bourne, San Diego Supercomputer Center, University of California 9500 Gilman Drive 0505, La Jolla, San Diego CA 92093-0505 (bourne@sdsc.edu; Fax: (619) 534-5113), providing a CV and the names of three references. Relevant URLs are: http://www.npaci.edu, http://www.sdsc.edu, and http://www.sdsc.edu/pb. Please indicate reference number 98-002 on your application. From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!uninett.no!online.no!not-for-mail From: "Bjorn P." Newsgroups: bionet.software Subject: Laboratory Database Software Date: 4 Mar 1998 22:14:31 GMT Organization: Telenor Online Public Access Lines: 15 Message-ID: <01bd47ba$7f195e20$f1004382@LTD> NNTP-Posting-Host: ti01a03-0049.dialup.online.no X-Newsreader: Microsoft Internet News 4.70.1155 We are interested in using a database system for handling of laboratory research data. The system should include these features: - be flexible on making templates suting our needs - be able to handle relatively large amounts of data for each separate analysis, - it must be easy to register large amounts of data - be easy to do searches on separate data in within an analysis (The program we are currently using is not bad, but seems a little unadequate for handling the amount of data we are working with. For some applications, especially concerning large amounts of data and searches, we could want some functions this program do not have.) From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software,bionet.software.gcg Subject: Re: Codon Usage Tables Date: Wed, 04 Mar 1998 16:14:08 +0000 Organization: SEQNET Lines: 31 Distribution: bionet Message-ID: <34FD7DD0.A5224D99@dl.ac.uk> References: NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP12) Xref: biosci bionet.software:20640 bionet.software.gcg:3023 Mike Mitchell wrote: > > I am looking for upto date codon usage tables for use with various GCG progs, > however I have only been able to find either old tables in GCG format or new > tables not in GCG format. > > Does anybody know of a source of "fresh" tables, or a reformatting tool that > can convert the CUTG (http://www.dna.affrc.go.jp/~nakamura/CUTG.html) format > into GCG? > cutg transformed into gcg format is available via the SEQNET srs server (http://www.seqnet.dl.ac.uk/srs5). A (clumsy - but it works) perl script for the transformation can be picked from http://www.seqnet.dl.ac.uk/srsdoc/getcutg note that this script will put all tables into one file, for indexing/retrieving via srs. Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!206.48.177.12!news.glo.be!not-for-mail From: "Roose" Newsgroups: bionet.software Subject: need dll Date: Wed, 4 Mar 1998 17:56:25 +0100 Organization: Customer of Globe Internet NV Lines: 4 Message-ID: <6dk16v$sb9$1@rhea.glo.be> NNTP-Posting-Host: p1-06.z016.glo.be X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 I need Ctsframe.dll SamX@cyberdude.com From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!news.icnet!m.mitchell From: m.mitchell@icrf.icnet.uk (Mike Mitchell) Newsgroups: bionet.software,bionet.software.gcg Subject: Codon Usage Tables Date: Wed, 04 Mar 1998 15:46:56 +0000 Organization: Imperial Cancer Research Fund Lines: 15 Message-ID: NNTP-Posting-Host: morpheus.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: biosci bionet.software:20638 bionet.software.gcg:3022 I am looking for upto date codon usage tables for use with various GCG progs, however I have only been able to find either old tables in GCG format or new tables not in GCG format. Does anybody know of a source of "fresh" tables, or a reformatting tool that can convert the CUTG (http://www.dna.affrc.go.jp/~nakamura/CUTG.html) format into GCG? Thanx. -- Michael Mitchell "Smoke me a kipper, User Support I'll be back for breakfast." Molecular Biology Software Ace Rimmer, Test Pilot +44 (0)171 269 3115 BBC-TV Red Dwarf ENFJ From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsxfer3.itd.umich.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software,bionet.software.gcg Subject: [ANN] MacBOB 1.3 available for ftp Date: Wed, 04 Mar 1998 13:55:32 +0000 Organization: Roslin Institute Lines: 23 Message-ID: NNTP-Posting-Host: pc0810.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 Xref: biosci bionet.software:20637 bionet.software.gcg:3021 The laest version of my Macintosh Blast (and FASTA) output browser (MacBOB) is available for download from . Changes since the last version are:- New file format now handled. BLAST2 as supplied by Michael Mitchell of ICRF. You can now copy from the hit list in the top pane of a MacBOB window (requested by David Morrice) MacBOB now remembers the scroll bar settings for each alignment in each window. No-one specifically asked for that, but I figured it was a neater way of functioning. Enjoy. Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!howland.erols.net!usc!usc!not-for-mail From: william@neuro.usc.edu (William Sun) Newsgroups: bionet.software Subject: sequence analysis software Date: 3 Mar 1998 20:29:46 -0800 Organization: University of Southern California, Los Angeles, CA Lines: 15 Sender: william@neuro.usc.edu Message-ID: <6dilbq$rh6@neuro.usc.edu> NNTP-Posting-Host: neuro.usc.edu Hello all, I'm looking into purchasing a comprehensive DNA/protein sequence analysis software package. Two I came across are Hitachi's DNAsis and Oxford Molecular's MacVector. I would appreciate any feedback from users of these two software packages or any other that might be good for the Mac or PC. BTW, my budget is limited to about $3000. Thanks. William -- William Sun, Ph.D Phone: (619) 622-3930 Metabasis Therapeutics, Inc. FAX: (619) 622-5545 9390 Towne Centre Drive Pager: (310) 243-9878 San Diego, CA 92121 http://rana.usc.edu:8376/~wisun/ From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: haroldb786@aol.com (HaroldB786) Newsgroups: bionet.software Subject: Re: sequence analysis software Date: 4 Mar 1998 20:39:29 GMT Lines: 12 Message-ID: <19980304203900.PAA10917@ladder03.news.aol.com> NNTP-Posting-Host: ladder03.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com References: <6dilbq$rh6@neuro.usc.edu> Any reason you need to purchase software..... This must mean that you have already used all the 'freeware' that is offered at the EBI web site.... If not, I would suggest you look at it: http://www.embl-ebi.ac.uk/biocat/biocat.html, And that is not the only site.... but is a good start.... It just depends on what your needs are.... I hope this helps (besides saving a whole lot of money!!!!) harold berninghausen From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!news-relay.ncren.net!ussun2n!news@ussun2n.glaxo.com From: "Gary H. Merrill" Newsgroups: bionet.software,comp.ai,comp.ai.nat-lang,sci.med.informatics Subject: Final CFP: AAAI-98 Workshop on Knowledge Sharing Across Biological and Medical KBS Date: Wed, 04 Mar 1998 14:34:32 -0500 Organization: GlaxoWellcome Inc Lines: 78 Message-ID: <34FDACC7.12412DCD@glaxowellcome.com> Reply-To: ghm48805@glaxowellcome.com NNTP-Posting-Host: 152.51.45.146 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) TITLE AAAI-98 Workshop on KNOWLEDGE SHARING ACROSS BIOLOGICAL AND MEDICAL KNOWLEDGE BASED SYSTEMS DATE AND LOCATION National Conference on Artificial Intelligence (AAAI-98) in Madison, Wisconsin, July 26 - July 27, 1998. See the AAAI web site at http://www.aaai.org for additional details. DESCRIPTION The amount of biological and medical information is growing at an exponential rate and overwhelming researchers and clinicians. Various groups have applied the technology of knowledge based systems to help in the effective utilization of available information. These systems have been used for applications in information retrieval, natural language processing, database integration, machine learning, data mining, and decision-making. While there is a substantial overlap of knowledge represented in these knowledge based systems there has been very limited dialog among the various groups creating such systems. This one-day workshop explores ways in which the knowledge contained in the various systems can be shared. Specifically, the workshop goals include: 1. Understanding the scope of knowledge contained in various knowledge based systems in biology and medicine. 2. Understanding strengths and limitations of different knowledge representation formalisms, inference engines, and knowledge acquisition methods for biological and medical systems. 3. Identifying strategies for knowledge sharing across different development groups as we move toward more comprehensive knowledge bases for researchers and clinicians in biology and medicine. SUBMISSIONS Potential presenters should submit a short paper (5-8 pages) addressing any of the issues relevant to the workshop goals. Others interested in participating should submit a 1-2 page statement of background and interest. E-mail in PostScript or MS Word format to Dhiraj K. Pathak at dp33010@glaxowellcome.com or Gary H. Merrill at ghm48805@glaxowellcome.com Submission Deadline: March 11, 1998 Notification Date: April 1, 1998 ORGANIZING COMMITTEE Dhiraj K. Pathak, Glaxo Wellcome (Co-chair) (dp33010@glaxowellcome.com) Gary H. Merrill, Glaxo Wellcome (Co-chair) (ghm48805@glaxowellcome.com) Carol Bean, National Library of Medicine (bean@nlm.nih.gov) Andy Brass, University of Manchester (abrass@manchester.ac.uk) Ed Hammond, Duke University (hammo001@mc.duke.edu) Rober Jenders, Columbia University (jenders@cucis.cis.columbia.edu) -- Gary H. Merrill / Principal Consultant, International Advanced Technologies [Views and opinions expressed here are my own and not necessarily those of GlaxoWellcome Inc.] From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!news.ysu.edu!Cabal.CESspool!bofh.vszbr.cz!fu-berlin.de!masternews.telia.net!News.Amsterdam.UnisourceCS!news.wxs.nl!not-for-mail From: "Danny Stollé" Newsgroups: bionet.software Subject: kernel32.dll Date: Wed, 4 Mar 1998 20:26:59 +0100 Organization: World Access Lines: 7 Message-ID: <6dk9qu$lbb8@reader2.wxs.nl> NNTP-Posting-Host: ah0173.wxs.nl X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Somebody heard of "Kernel32.dll" It seems to be a dll-file in Windows 95, which you can download??? Somebody tell me what this file means or is!!! Danny From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 From: "Arnulf Hartl" Newsgroups: bionet.software References: <6dilbq$rh6@neuro.usc.edu> <34FD6961.7DC22877@usa.net> Subject: Re: sequence analysis software Date: Wed, 4 Mar 1998 17:49:17 +0100 Lines: 45 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 NNTP-Posting-Host: dche43.che.sbg.ac.at Message-ID: <34fd8566.0@news.sbg.ac.at> Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!wnfeed!worldnet.att.net!128.230.129.106!news.maxwell.syr.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!newsfeed.ecrc.net!newscore.univie.ac.at!193.171.255.24.MISMATCH!newsfeed03.univie.ac.at!03-newsfeed.univie.ac.at!news.sbg.ac.at!dche43.che.sbg.ac.at Hi William Just look at http://www.informaxinc.com/ Their Vector NTI Software works on MAC and PCs - and does a really good job ! The Mac version (a colleague of mine has owned) seems to work a little bit slower than the PC version .. Especially the Internet connectivity features (sequence from programm is automatically pasted e.g. in a localy installed blast html page, submitted - the search results can be imported back into the programm and will be graphically interpreted using all the genbank qualifiers) are very useful for my special purposes. I´ve heard that their new version will include protein sequence analysis features (v.4 was mainly focused on DNA-sequences) - but then Vector NTI is hard to beat. Arnulf J. Hartl University of Salzburg, Institute of Biochemistry arnulf.hartl@sbg.ac.at >William Sun wrote: > >> Hello all, >> >> I'm looking into purchasing a comprehensive DNA/protein sequence analysis >> software package. Two I came across are Hitachi's DNAsis and Oxford >> Molecular's MacVector. I would appreciate any feedback from users of these >> two software packages or any other that might be good for the Mac or PC. >> BTW, my budget is limited to about $3000. Thanks. >> >> William >> >> -- >> William Sun, Ph.D Phone: (619) 622-3930 >> Metabasis Therapeutics, Inc. FAX: (619) 622-5545 >> 9390 Towne Centre Drive Pager: (310) 243-9878 >> San Diego, CA 92121 http://rana.usc.edu:8376/~wisun/ > > > > From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!lhc.nlm.nih.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!news.idt.net!psinntp!pubxfer.news.psi.net!ss From: ss@posoe.com Newsgroups: biz.comp.telebit,torfree.fccs.news.business,pa.smallbusiness,bionet.software,us.sc.charleston.business,uw.business-club,ukr.business.vestlan,uk.business.telework,us.sc.gsp.business,us.sc.chester.business,scot.business.internet,us.sc.lancaster.business,spb.fido.business,pdaxs.calendar.business,us.sc.rockhill.business,us.sc.columbia.business,ntu.dep.business_adm,seattle.business,biz.comp.telebit.netblazer,ntu.adm.business-affs,nb.forsale,us.sc.florence.business Subject: Business Software Solutions -- http://www.eesco.com/ Date: Wed, 04 Mar 1998 11:55:11 -0500 Organization: PSINet Lines: 17 Message-ID: NNTP-Posting-Host: 38.244.114.101 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Business Software Solutions -- http://www.eesco.com/ Point of Sale, Retail, Mail Order, Distribution, Wholesale, Inventory Control, Customer Tracking, Purchase Orders, Accounting, Credit Card Processing, Invoices, Orders, Service Orders, Custom Reports, Import-Export, EDI, Back Orders, Auto-PO Generator, Single User/Multi User, Macintosh, Windows, Internet web order processing, and more!! ALSO, check out our shopping cart where we sell our POS/OE demo software, hardware and supplies, other software products we produce, and more! (check out the pricing on the WINBOOK memory 64MB module) http://www.eesco.com/ees/products.html http://www.eesco.com/ From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!uninett.no!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.237.162.48.MISMATCH!news.datakom.su.se!not-for-mail From: rebecca Newsgroups: bionet.software Subject: Re: sequence analysis software Date: Wed, 04 Mar 1998 16:47:11 +0200 Organization: Stockholm University Lines: 38 Message-ID: <34FD6961.7DC22877@usa.net> References: <6dilbq$rh6@neuro.usc.edu> Reply-To: rebsilver@usa.net NNTP-Posting-Host: ppp2.poolman.physto.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) To: William Sun Hi, I have used MacVector on a Mac. It is really nice. It makes pretty plots and pictures out of its protein analysis tools (publishable even). It has alot of analysis options from the obvious aa translation to hydrophobicity and acidity plots. In general, it is intuitive to use and the results are presented in an easy to understand way (I am a pure user, I have never authored any software). I learned alot just using it to explore my clones. Draw back. It is expensive. The site liscence is prohibitive. Otherwise, they give you decoder keys for as many copies as you buy, and you can't get around it by using a network. Hope this helps, Reb William Sun wrote: > Hello all, > > I'm looking into purchasing a comprehensive DNA/protein sequence analysis > software package. Two I came across are Hitachi's DNAsis and Oxford > Molecular's MacVector. I would appreciate any feedback from users of these > two software packages or any other that might be good for the Mac or PC. > BTW, my budget is limited to about $3000. Thanks. > > William > > -- > William Sun, Ph.D Phone: (619) 622-3930 > Metabasis Therapeutics, Inc. FAX: (619) 622-5545 > 9390 Towne Centre Drive Pager: (310) 243-9878 > San Diego, CA 92121 http://rana.usc.edu:8376/~wisun/ From owner-software@net.bio.net Tue Mar 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!140.186.1.17!newsie2.cent.net!not-for-mail From: Gil Kedem Newsgroups: bionet.software Subject: I need a parser for BLAST Date: Wed, 04 Mar 1998 17:14:14 -0500 Organization: Kedem Associates (http://www.yoga.com/kedem) Lines: 12 Message-ID: <34FDD236.1D0CBFDE@yoga.com> NNTP-Posting-Host: ahimsa.yoga.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (WinNT; I) Hello, I'm searching for a parser (commercial or freeware) for the Blast program. Are there any out there? Thanks, Gil From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: sprinkle@np2.mcg.edu Newsgroups: bionet.software Subject: DNA,RNA, protein sequence LINUX 5.0 software Date: Thu, 05 Mar 1998 09:53:06 -0600 Organization: Deja News - The Leader in Internet Discussion Lines: 17 Message-ID: <6dmhns$sj0$1@nnrp1.dejanews.com> NNTP-Posting-Host: 158.93.202.179 X-Article-Creation-Date: Thu Mar 05 15:53:06 1998 GMT X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) I am trying to locate freeware, shareware and commercial software for molecular biology that runs under LINUX 5.0. I am particularly interested in software that does local, multiple Clustal W alignments, DNA/RNA/protein editing, database format conversions, searches, graphical presentation of nucleic acids and small proteins for teaching and publication, local motif analysis and ability to add new motifs, sequence retrieval software and general utilities that might be useful in this area. I do have access to GCG programs, but the link to the main university computers is some 90 miles distant and not always reliable. I do have the OMIGA program, PC Gene and some other programs, but many of these must have been taken to LINUX. I would appreciate any help pointing me in the right direction to locate these type programs. Thank you for your help and suggestions. sprinkle@np2.mcg.edu -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/ Now offering spam-free web-based newsreading From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!agate!howland.erols.net!ais.net!newsfeed.concentric.net!global-news-master From: Ketchup**NOSPAM**@cris.com (Ketchup) Newsgroups: bionet.software Subject: GeneDoc release 2.3: Alignment Editor for Windows: Freeware Date: Thu, 05 Mar 1998 07:13:10 GMT Organization: Concentric Internet Services Lines: 56 Message-ID: <34fe4fdb.12927012@news.cris.com> NNTP-Posting-Host: ts018d19.cup-ca.concentric.net X-Newsreader: Forte Free Agent 1.11/32.235 Greetings All, Please be informed that GeneDoc version 2.3 has been released to the GeneDoc web site: http://www.cris.com/~ketchup/genedoc.shtml This version has plenty of bug fixes and plenty of new features. Highlights center around DNA support, with Enzyme Fragment reports for the whole alignment and includes usage of GeneDoc superfamily group features. Also added is support for ambiguous DNA codes and a very nifty DNA Set Analysis display. Other features include an Identity Display, Start Sequence Numbering option, some RasMol script generation options and in general lots of cleanup. Thanks again for your continued support, feedback and kind words about GeneDoc. Eventually we'll get all your requests in there! Karl Nicholas. 2.3 * Fixed Configuration Variables not being initialized properly. * Added DNA Ambiguity code. * Fixed input sequences detecting gap chars. * Possible fix of input sequences duplicating data. * Added DNA group set analysis display. * Fixed Contrast mode to not include zero level scores. * Fixed GeneDoc .msf header reader to be forward compatible. * Fixed rebase file read for larger patterns. * Added Rebase Search Filters. * Added user configurable rebase shading overlap color. * Added export of search list to rebase readable file. * Added reporting of duplicate sequence names. * Added Display/No Display of individual Physiochemical properties. * Fixed bug ReBase patterns found twice if following a gap char. * Added Rebase cut sites/fragment length/unique fragment/unique frags per group report. * Added Plot of unique fragment lengths. * Added Display of reports that can handle any size files. * Added print function to reports. * Added ability to print shading only. * Added Identity Display Mode. * Fixed Changing project type setting properties and score tables. * Fixed change gap char for alignment code. * Fixed RasMol script to not blank display when no sidechains selected. * Added Shade backbone only and sidechain only to rasmol script. * Added Sequence Start Position attribute. * Added Ident All or Ident conserved styles to Ident Display Mode. * Fixed Structure Shading changing when have both Non-Group and Groups structure info loaded. * Added PDB Read routines for structure shading. From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!199.0.154.56!ais.net!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!not-for-mail From: "Charlie Mantel" Newsgroups: bionet.software Subject: Re: Looking for SIGMAPLOT----HAVE Peakfit Date: Wed, 4 Mar 1998 22:05:52 -0500 Organization: Indiana University - Purdue Univeristy At Indianapols,IN Lines: 3 Message-ID: <6dl52p$k7l$1@hercules.iupui.edu> References: <34F14BCF.3B108A8F@Blow.Goats> NNTP-Posting-Host: c3p5.dialin.iupui.edu X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Why dont you try "BUYING" it? From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!newsfeed.dacom.co.kr!europa.clark.net!207.106.0.20!news-xfer.netaxs.com!colon.ba.net!not-for-mail From: waltertd Newsgroups: bionet.software Subject: Corel DRAW 8.0 Date: Wed, 04 Mar 1998 23:48:27 -0300 Organization: Argentina On-Line Lines: 4 Message-ID: <34FE127B.877A9431@ba.net> Reply-To: waltertd@ba.net NNTP-Posting-Host: tsrcu01-ppp3.starnet.net.ar Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Quien tenga conocimiento sobre este maravilloso software favor de escribir a: waltertd@yahoo.com Tks!! From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!news.icnet!m.mitchell From: m.mitchell@icrf.icnet.uk (Mike Mitchell) Newsgroups: bionet.software Subject: Re: I need a parser for BLAST Date: Thu, 05 Mar 1998 15:34:08 +0000 Organization: Imperial Cancer Research Fund Lines: 52 Message-ID: References: <34FDD236.1D0CBFDE@yoga.com> NNTP-Posting-Host: morpheus.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article <34FDD236.1D0CBFDE@yoga.com>, Gil Kedem wrote: > Hello, > > I'm searching for a parser (commercial or freeware) for the Blast > program. > Are there any out there? What sort of parsing? There was UNIX x windows application called BOB (Blast Output Browser) that displayed Blast output in a multi-pane window to allow easy looking at the alignments by clicking on the ranked list. Currently there is a text version of BOB available, and Andy Law (BBSRC,UK) has written a very nice Mac version: >> Begin << The laest version of my Macintosh Blast (and FASTA) output browser (MacBOB) is available for download from . Changes since the last version are:- New file format now handled. BLAST2 as supplied by Michael Mitchell of ICRF. You can now copy from the hit list in the top pane of a MacBOB window (requested by David Morrice) MacBOB now remembers the scroll bar settings for each alignment in each window. No-one specifically asked for that, but I figured it was a neater way of functioning. Enjoy. Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) >> End << Hope that this helps. -- Michael Mitchell "Smoke me a kipper, User Support I'll be back for breakfast." Molecular Biology Software Ace Rimmer, Test Pilot +44 (0)171 269 3115 BBC-TV Red Dwarf ENFJ From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!206.48.177.12!news.glo.be!not-for-mail From: "Roose" Newsgroups: bionet.software Subject: dll & vxd needed Date: Thu, 5 Mar 1998 18:58:34 +0100 Organization: Customer of Globe Internet NV Lines: 13 Message-ID: <6dmp7i$pj$1@rhea.glo.be> NNTP-Posting-Host: p1-24.z016.glo.be X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hi, I need a dll and a vxd file: CTSFRAME.DLL and MTRR.VXD. It is probarly on your computer! Just search it a second. The dll do you sure have if you are using Creative Labs Soundblaster. Please send it me: SamX@cyberdude.com ! My homepage: http://titan.glo.be/f-toys From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Supernews60!supernews.com!Supernews69!not-for-mail From: "JMonahan" Newsgroups: bionet.software Subject: Source code for UNIX .shar and .tar file formats Date: Thu, 5 Mar 1998 14:16:01 -0800 Organization: All USENET -- http://www.Supernews.com Lines: 9 Message-ID: <6dn8di$4k3$1@usenet11.supernews.com> NNTP-Posting-Host: 4739@206.14.241.180 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Could somebody point me to source code to unpack UNIX files that are written in xxxx.shar.z and xxxx.tar.z file formats. I have code for the .z part. How do I do the other components. i.e. expand out a xxxx.shar or xxxx.tar file. I wish to incorporate this capability in an application in for windows NT (C++/MFC). From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.algonet.se!newspeer.monmouth.com!woodstock.news.demon.net!demon!bullseye.news.demon.net!demon!newsfeed.xs4all.nl!xs4all!gate.news.unisource.nl!amsterdam.news.unisource.nl!News.Amsterdam.UnisourceCS!news.wxs.nl!not-for-mail From: Leo's Software Service's Newsgroups: fido7.sex,aus.forsale,atl.forsale,alt.drugs,alt.drugs.chemistry,alt.drugs.culture,alt.drugs.hard,alt.drugs.pot,alt.drugs.pot.cultivation,alt.drugs.psychedelics,alt.drugs.usenet,comp.cannabis.policy,news.cannabis.admin,news.cannabis.announce,news.cannabis.misc,news.cannabis.policy,rec.cannabis.policy,rec.drugs.cannabis,sci.med.cannabis,talk.cannabis.policy,alt.binaries.pictures.sex,alt.binaries.stories.sex,alt.christnet.sex,sci.med.diseases.hepatitis,bionet.immunology,bionet.neuroscience,bionet.software,fido7.drugs,misc.foresale,de.soc.drogen,alt.hemp,alt.hemp.octa,alt.hemp.politics,alt.hemp.recreational,de.markt.misc Subject: Medical Cannabis for sale Date: Thu, 05 Mar 1998 10:28:00 +0100 Organization: Software Service's Message-ID: <34FE701F.D21614D@4u.net> Reply-To: cannabiss@4u.net NNTP-Posting-Host: asd0147.wxs.nl Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------2793BC1CE4E766588CAD3159" X-Mailer: Mozilla 4.03 [en] (Win95; I) Lines: 710 Xref: biosci bionet.immunology:13513 bionet.neuroscience:21535 bionet.software:20653 This is a multi-part message in MIME format. --------------2793BC1CE4E766588CAD3159 Content-Type: multipart/related; boundary="------------677309CDB99AD48456E5CD47" --------------677309CDB99AD48456E5CD47 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit
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Pafort Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: L. Pafort n: Pafort;L. org: Software Service's adr: V. da Gamastraat 16a;;;Amsterdam;;1057 VL;Netherlands email;internet: cannabiss@4u.net title: Managing Director tel;work: +31 066 535 8220 tel;fax: +31 20 4121847 tel;home: +31 066 535 8220 note: First Legal Medical Hemp Shop on the Web.. x-mozilla-cpt: ;2 x-mozilla-html: TRUE version: 2.1 end: vcard --------------2793BC1CE4E766588CAD3159-- From owner-software@net.bio.net Wed Mar 04 22:00:00 1998 Path: biosci!agate!spool.mu.edu!uwm.edu!chicago-news-feed2.bbnplanet.com!news.bbnplanet.com!news-feed.fnsi.net!news.idt.net!news-peer.gip.net!news.gsl.net!gip.net!europa.clark.net!152.158.16.55!newsfeed2.uk.ibm.net!ibm.net!sackheads.org!news-ge.switch.ch!news.rediris.es!news.cesca.es!lilith.uab.es!newsmgr From: Alfons Newsgroups: bionet.software Subject: DNA strider or similar Date: Thu, 05 Mar 1998 16:48:35 +0100 Organization: IMIM Lines: 9 Distribution: inet Message-ID: <34FEC952.5C70497A@imim.es> NNTP-Posting-Host: 193.144.6.30 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [es] (Win95; I) Hello, I'm looking for something like DNA-strider but for a PC running win95 instead of a Macintosh...Does anybody know where can I find something like that? (It would be nice if it's freeware....) Thanks Alfons From owner-software@net.bio.net Thu Mar 05 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!131.103.1.114!news1.chicago.iagnet.net!qual.net!iagnet.net!129.79.6.160!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: DNA,RNA, protein sequence LINUX 5.0 software Date: 6 Mar 1998 00:37:40 GMT Organization: Biology, Indiana University - Bloomington Lines: 10 Message-ID: <6dnggk$tpa$1@jetsam.uits.indiana.edu> References: <6dmhns$sj0$1@nnrp1.dejanews.com> NNTP-Posting-Host: chipmunk.bio.indiana.edu SeqPup, the new java version, will run on linux (as well as any platform with a Java 1.1 system). It is free, and does a good bit of what you ask for. See http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/ or ftp://iubio.bio.indiana.edu/molbio/seqpup/java/ - don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Mar 05 22:00:00 1998 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!wnfeed!worldnet.att.net!128.230.129.106!news.maxwell.syr.edu!rill.news.pipex.net!pipex!btnet-peer!btnet-feed1!btnet!peer.news.zetnet.net!zetnet.co.uk!user-10002114.zetnet.co.uk!not-for-mail From: Garth Williams Newsgroups: bionet.software Subject: Laboratory test comparison software Date: Fri, 6 Mar 1998 11:38:02 GMT Lines: 24 Message-ID: <1998030611380271355@zetnet.co.uk> NNTP-Posting-Host: user-10002114.zetnet.co.uk X-Mailer: ZIMACS Version 1.20c 10002114 Hi all, We are searching for statistical software which will enable us to easily compare results from two (or more) analyses. Spreadsheets such as Excel or Quattro are very good, but don't have the range of analysis tools we want, such as Deming regression, ROC etc. We've used an old DOS program called Statgraphics for some time, but find it complex and user-unfriendly. Many packages are very expensive in the UK, sometimes over 1,000 pounds sterling. What do others use and recommend? We use Excel for Windows 3.1 so an Excel add-on program would be suitable. It would be an advantage if there was a shareware or limited use version available so that we could try it out first. Regards, -- Garth Williams, Worcester. email: garth.williams@zetnet.co.uk www: http://www.users.zetnet.co.uk/jgw.computing/ From owner-software@net.bio.net Thu Mar 05 22:00:00 1998 Path: biosci!agate!spool.mu.edu!uwm.edu!news.he.net!news-feed.inet.tele.dk!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!tome From: tome@ebi.ac.uk (Patricia Rodriguez-Tome) Newsgroups: bionet.software,bionet.general Subject: [ANNOUNCE] BioCatalog release 5.7 Date: 6 Mar 1998 16:23:23 GMT Organization: European Bioinformatics Institute (EMBL) - UK Lines: 34 Distribution: world Message-ID: <6dp7tr$17b$1@niobium.hgmp.mrc.ac.uk> Reply-To: tome@ebi.ac.uk NNTP-Posting-Host: sol6.ebi.ac.uk Xref: biosci bionet.software:20666 bionet.general:29504 Release 5.7 of the BioCatalog is now available at http://www.ebi.ac.uk/biocat/biocat.html The BioCatalog is a software directory of general interest in molecular biology and genetics. Another project the DBcat at Infobiogen (the French EMBnet node) lists the databases in this domain. The Text files are available from EBI anonymous FTP server at ftp://ftp.ebi.ac.uk/pub/databases/biocat This database cannot be maintained up-to-date without the help of the biocomputing community, that is to say the programs authors, archive adminsitrators and end-users. You can submit new entries describing software not already listed in the BioCatalog by filling the form at : http://www.ebi.ac.uk/biocat/biocat_form.html enjoy Patricia -- ======================================================================= Dr. Patricia Rodriguez-Tome | URL: http://www.ebi.ac.uk The EMBL Outstation, Hinxton - The European Bioinformatics Institute Wellcome Trust genome Campus, Hinxton | Tel: +44 (0)1223 494 409 Cambridge CB10 1SD, UK | Fax: +44 (0)1223 494 468 ======================================================================== From owner-software@net.bio.net Thu Mar 05 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!metro.atlanta.com!news.pcslink.com!news.millennianet.com!franklin!not-for-mail From: greg@columbia.digiweb.com () Newsgroups: bionet.software Subject: Re: Molscript and Windows 95 Date: 6 Mar 1998 09:00:39 GMT Organization: Millennia Communications, LLC Lines: 6 Message-ID: <6dodvn$e8v@news.millennianet.com> References: <6dd3p3$12i@darkstar.ucsc.edu> <34FAAC61.2AAF57C7@bph.ruhr-uni-bochum.de> NNTP-Posting-Host: burnham.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Marc Saric (saric@bph.ruhr-uni-bochum.de) wrote: : BTW. You can always replace the functionality of the OpenGL-output with : Rasmol -it is able to write basic Molscript output : (helix/beta-sheet/turn), which can be edited afterwards. True enough, but that's one of the neater aspects of the new version. From owner-software@net.bio.net Thu Mar 05 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Supernews60!supernews.com!Supernews69!not-for-mail From: iget@nospam.at.all Newsgroups: bionet.software Subject: Re: DNA,RNA, protein sequence LINUX 5.0 software Date: Fri, 06 Mar 1998 08:33:34 GMT Organization: All USENET -- http://www.Supernews.com Lines: 35 Message-ID: <6docct$ajs$1@usenet48.supernews.com> References: <6dmhns$sj0$1@nnrp1.dejanews.com> NNTP-Posting-Host: 10876@207.194.207.3 X-Newsreader: Forte Free Agent 1.0.82 Hi Here's some links to molbio software for Linux: Molecular Linux http://evolution.bmc.uu.se/~thomas/mol_linux Linux Software Encyclopedia - science app oriented http://stommel.tamu.edu/~baum/linuxlist/linuxlist.html or http://www.llp.fu-berlin.de/baum/ Linux Lab Project http://www.llp.fu-berlin.de Scientific Applications on Linux (SAL) http://SAL.KachinaTech.COM Rasmol 2.6 Beta Linux Patch http://dasher.wustle.edu/~reece/src/ sprinkle@np2.mcg.edu wrote: >I am trying to locate freeware, shareware and commercial software for >molecular biology that runs under LINUX 5.0. I am particularly interested in >software that does local, multiple Clustal W alignments, DNA/RNA/protein >editing, database format conversions, searches, graphical presentation of >nucleic acids and small proteins for teaching and publication, local motif >analysis and ability to add new motifs, sequence retrieval software and >general utilities that might be useful in this area. I do have access to GCG <> Murphy OOOOOOOmurphyOOOOOOOOOOOOOOradiantOOOOOnetOOOOO From owner-software@net.bio.net Thu Mar 05 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news.mu-luebeck.de!not-for-mail From: "Lars Komorowski" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.software Subject: Proposal for a new bionet newsgroup Date: Fri, 6 Mar 1998 09:13:33 +0100 Organization: Med. Universitaet zu Luebeck Lines: 7 Message-ID: <6dobf1$4cj$1@gwsun.medinf.mu-luebeck.de> NNTP-Posting-Host: 141.83.167.168 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Xref: biosci bionet.molbio.methds-reagnts:65549 bionet.molbio.proteins:12408 bionet.software:20661 I propose to set up a new newsgroup for used l