From owner-software@net.bio.net Wed Jan 01 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news From: Jong Newsgroups: bionet.software Subject: perl subroutines for perl programs developers. Date: Thu, 02 Jan 1997 02:47:17 +0000 Organization: Biomatics Lines: 44 Message-ID: <32CB2187.7A65829E@cus.cam.ac.uk> NNTP-Posting-Host: sonja.acad.cai.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.1.13 i486) Hi, I have some subroutines which can be reused in your codes directly(if you can understand how to use them) or by modifications. At least you can see some simple ways to do things. It is meant to be used people who develop perl codes for sequence handling. Some can be also useful for general perl coding. I meant to convert them to Bioperl project standardization which is going to use object oriented features, but I realized not many people may understand how to use object modules so got lazy in doing so. Also, no release of Bioperl perl module has been made until now. To use, you are encouraged to search with keywords. If you want to get some hash handling stuff, search for 'hash' etc in the lib file, there might be some useful subs for you. It is in: http://sonja.acad.cai.cam.ac.uk/perl_sub_db.html Look at Big library part where you find B.pl It has automatic compilation of the documentation in the headboxes of the library. Jong -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Significantly, Spinoza titled his chief work The Ethics. He derived an ethic by deduction from fundamental principles, and so his ethics were closely linked to his view of "God or nature" as everything. The highest good, he asserted, was knowledge of God, which was capable of bringing freedom from tyranny by the passions, freedom from fear, resignation to destiny, and true blessedness. http://members.aol.com/Heraklit1/spinoza.htm From owner-software@net.bio.net Wed Jan 01 22:00:00 1997 Newsgroups: alt.fringeware,alt.os.linux.slackware,alt.support.warez.recovery,alt.tupperware,alt.warez.g0ff,alt.warez.ibm-pc,alt.warez.ibm-pc.apps,alt.warez.ibm-pc.games,alt.warez.ibm-pc.old,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet. Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!surfnet.nl!news.unisource.nl!news.tip.nl!news From: "Bitstream" Subject: REQ: reg code for in-cube for win95 (voice recognition) X-Nntp-Posting-Host: amsterdamis30.pop.tip.nl Message-ID: <01bbe833$12b5c8a0$1ed2b18f@t819096> Sender: news@tip.nl (The News User) Organization: The Internet Plaza X-Newsreader: Microsoft Internet News 4.70.1155 Date: Thu, 2 Jan 1997 13:58:55 GMT Lines: 1 Xref: biosci bionet.software:17532 bionet.software.acedb:1074 bionet.software.gcg:2167 From owner-software@net.bio.net Wed Jan 01 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!EU.net!Norway.EU.net!usenet From: eirikth@eunet.no (Eirik) Newsgroups: bionet.software Subject: Any program to create a spacefilling 3d-model from PDB-files? Date: Thu, 02 Jan 1997 17:11:46 GMT Organization: Trust Lines: 6 Message-ID: <32c80fbc.16745732@relay.eunet.no> NNTP-Posting-Host: pc11.aalesund-pm2-1.eunet.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99g/32.326 Want to create / convert a PDB (or similar) file to formats like .3ds .Pov. Just want a simple represantation, not an acurate. Thanks in advance Eirik From owner-software@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software,bionet.molbio.evolution Subject: Phylodendron, new software for phylogenetic tree drawing (java) Date: 3 Jan 1997 04:12:40 GMT Organization: Biology, Indiana University - Bloomington Lines: 41 Message-ID: <5ai0vo$loq@dismay.ucs.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu Xref: biosci bionet.software:17534 bionet.molbio.evolution:5477 Phylodendron an application for phylogenetic tree drawing version 0.2, beta Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology. It will read tree data in New Hampshire (Newick) format, then display graphical views of the phylogenetic tree. Various options allow you to modify, adorn and edit the tree. Standard application functions to save, print, edit and manage preferences are included. This program will not estimate nor produce the tree data. For that, software such as Phylip, Clustal W, and others may be used. Phylodendron is available at ftp://iubio.bio.indiana.edu/molbio/java/apps/trees/ http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/ Please read the help document and readme file for details on how to fetch and install the application on your computer. Phylodendron is written as a Java application. This means that it will run on most personal computers and workstations as a standard program. This application is an enhancement of the Mac Hypercard program "Tree Draw Deck" released by the author in 1990. One problem in using this program is that Java is still in preliminary stages. You currently must fetch and install a Java runtime system to use it. This can be obtained freely on the Internet. See for example Developers will find the source code in the iubio:/molbio/java/source folders. These files are not needed for running the program. Phylodendron is built on the beginnings of an application framework for Java, which may make it easier to develop new applications. Enjoy & let me know what you think of it - Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!BIOTOP.UMCS.LUBLIN.PL!TCHORZ From: TCHORZ@BIOTOP.UMCS.LUBLIN.PL ("Marek Tchorzewski") Newsgroups: bionet.software Subject: DNA software Date: 3 Jan 1997 04:00:31 -0800 Organization: Marie Curie-Sklodowska University Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <1ABF1C86569@biotop.umcs.lublin.pl> NNTP-Posting-Host: net.bio.net Dear Netters, First of all, Happy New Year 1997 to all of you !!! On the other hand, I need advice concerning programs for DNA and protein analysis. I am going to buy such program however I am not fully determined which program I should purchase. So far, I have seen DNAsis and DNAstar, however I am not sufficiently confident that these programs are reliable, and can provide me with the best options. So, could you advice me, which programs is actually the best on the market. Marek Tchorzewski PhD Univ. of Maria Curie-Sklodowska Dept. of Molecular Biology Lublin, Poland From owner-software@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.nacamar.de!news.icm.edu.pl!uw.edu.pl!news.nask.pl!lublin.pl!biopc07.umcs.lublin.pl!tchorz From: tchorz@biotop.umcs.lublin.pl (Marek Tchorzewski) Newsgroups: bionet.software Subject: DNA software Date: Fri, 3 Jan 1997 12:07:23 GMT Organization: Marie Curie-Sklodowska University Lines: 20 Message-ID: NNTP-Posting-Host: biopc07.umcs.lublin.pl Dear Netters, First of all, Happy New Year 1997 to all of you !!! On the other hand, I need advice concerning programs for DNA and protein analysis. I am going to buy such program however I am not fully determined which program I should purchase. So far, I have seen DNAsis and DNAstar, however I am not sufficiently confident that these programs are reliable, and can provide me with the best options. So, could you advice me, which programs is actually the best on the market. Marek Tchorzewski PhD Univ. of Maria Curie-Sklodowska Dept. of Molecular Biology Lublin, Poland From owner-software@net.bio.net Fri Jan 03 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: BIOSCI-REQUEST Newsgroups: bionet.software Subject: Info sheet for BIOSCI Date: 3 Jan 1997 16:40:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1069 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701040039.QAA00362@net.bio.net> NNTP-Posting-Host: net.bio.net Your request has been processed. Our instruction sheet follows. Thank you for your interest in the BIOSCI newsgroups. ---------------------------------------------------------------------- THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET (last revised 21-DEC-96) ---------------------------------------------------------------------- > IMPORTANT NOTE: As of 10-DEC-1995 one can participate in the BIOSCI > newsgroups through the World Wide Web in addition to using the USENET > and e-mail options described below. The URL is http://www.bio.net/. > After connecting to this site, click on the "Access the BIOSCI/bionet > Newsgroups" hyperlink. The old BIOSCI gopher site at net.bio.net > has been closed. This new WWW feature will also soon be available > at the U.K. BIOSCI site. This is the BIOSCI information sheet for the Americas and Pacific Rim countries. If you are located in Europe, Africa, or Central Asia, please retrieve that version of the information sheet by sending the command info ukinfo in the body of an e-mail message addressed to the Internet address biosci-server@net.bio.net Any text placed on the Subject: line of your message is ignored, so please be sure to put the "info ukinfo" command in the main body of your e-mail message. New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available by gopher to net.bio.net or anonymous FTP to net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ. It may also be requested by sending e-mail to biosci-server@net.bio.net as described above except that the command info faq should be used in the body of the mail message. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of both versions of the BIOSCI information sheet. ---------------------------------------------------------------------- Contents of this Document ------------------------- Introduction List of BIOSCI Mailing Lists and Newsgroups List of BIOSCI Newsgroup Topics BIOSCI Newsgroup Discussion Leaders Participating in BIOSCI Using USENET News Software Participating in BIOSCI by E-mail E-mail Subscription Requests and other Information Finding Your Current E-mail Subscription List E-mail Address Changes Interruption of E-mail Service Posting Messages to Newsgroups by E-mail Retrieval of old postings from the BIOSCI archives BIOSCI "prototype" newsgroups Retrieving Other BIOSCI Documentation Introduction ------------ The BIOSCI newsgroup network was developed to allow easy worldwide communications between biological scientists who work on a variety of computer networks. BIOSCI is supported by the Department of Energy and the National Science Foundation in the U.S.A. and by the CCL Daresbury Laboratory in the United Kingdom. BIOSCI services are available to users free of charge. ---------------------------------------------------------------------- The U.S. BIOSCI node also gratefully acknowledges the sponsorship of the organizations listed below. Molecular Dynamics, Inc., a leading producer of innovative instrumentation systems for the life sciences Knight-Ridder Information, Inc., a major provider of electronic information to business, research, and scientific professionals BIOSIS, publisher of Biological Abstracts and Zoological Record CLONTECH Laboratories, Inc., a leading manufacturer of innovative reagents and kits for the life sciences The UnCover Company, an internationally-known firm that offers article delivery and current issue alerting from 17,000 periodicals. LI-COR, Inc., manufacturer of automated infrared DNA sequencing and genetic analysis systems. The Nest Group, Inc. a value-added distributor of HPLC columns, DNA kits, and electrophoresis gels for biomolecule separation. Sun Microsystems, Inc., a leading provider of solutions for open network computing environments. Academic Press, a leading scientific publisher for more than 50 years. QIAGEN, a leading provider of innovative, user-friendly technologies for nucleic acid and protein purification. Trends in Biochemical Sciences, the leading monthly magazine in biochemisty and molecular biology. Research Diagnostics, Inc., distributor of fine immunochemical products Boehringer Mannheim Biochemicals, A Worldwide Healthcare Company Serving the Needs of the Life Science Community. Quantum Biotechnologies, Inc., quantum leap to the 21st century with innovative molecular biology tools We encourage our readers to visit our World Wide Web home page at URL http://www.bio.net/. Please thank our sponsors by visiting their Web pages via the logos/hypertext links displayed on our Web site. Use of these links by our readers will enable us to attract additional sponsors and continue to provide BIOSCI services to our readership after our government funding ends in mid-1996. If your organization is interested in sponsoring BIOSCI, please contact us at biosci-help@net.bio.net. ---------------------------------------------------------------------- BIOSCI messages are distributed by two means: USENET news software and electronic mail. WE STRONGLY ENCOURAGE ALL INTERESTED USERS TO EXPLORE GETTING "USENET NEWS" SOFTWARE AT YOUR SITE. The software is in the public domain, and you will find it much more convenient than subscribing to newsgroups by e-mail. Please consult your systems manager (the software may already be available on a machine at your institution) or contact biosci-help@net.bio.net for a list of software available free of charge on the Internet. NOTE, however, that the installation and maintenance of news software requires the assistance of a trained systems operator in most cases and is not a task to be undertaken by a computer novice. Why is news software preferable to e-mail? News software recovers messages automatically after network interruptions, whereas your e-mail address may have to be removed from the subscription list at times if your computer/network malfunctions and undelivered mail starts bouncing back to the BIOSCI administrative sites. You will have to manually retrieve lost messages from the archives if your e-mail subscription is suspended. News software organizes messages by topic and subtopic for easy browsing. In contrast if you subscribe by e-mail to more than one discussion list, messages from multiple lists arrive into your personal mail file in chronological order of posting only and are mixed in with your personal messages. You have to connect the discussion threads yourself if you use e-mail. In summary, e-mail participation should be seen as a LAST RESORT to be used only if news software can not be installed locally. Fortunately, BIOSCI offers advantages for e-mail users too. By having distribution sites or "nodes" on each major network, BIOSCI allows its e-mail users to contact people around the world without having to learn a variety of computer addressing tricks. Any user can simply post a message to his/her regional BIOSCI node and copies of that message will be distributed automatically to all other subscribers on all of the participating networks, including the Internet, USENET, BITNET, EARN, NETNORTH, HEANET, and JANET. List of BIOSCI Mailing Lists and Newsgroups ------------------------------------------- BIOSCI messages are distributed on the newsgroups in the "bionet" hierarchy of USENET and on the corresponding mailing lists indicated below. Contents of the USENET newsgroups and the e-mail distributions are *identical*, i.e., messages sent in by e-mail are also forwarded to USENET and messages posted to USENET newsgroups are also distributed to e-mail subscribers. An expanded description of the purpose of each newsgroup follows this list. MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AFCR ** bionet.prof-society.afcr AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry AIBS ** bionet.prof-society.aibs AMYLOID ** bionet.neuroscience.amyloid ARABIDOPSIS bionet.genome.arabidopsis ASCB ** bionet.prof-society.ascb AUDIOLOGY bionet.audiology AUTOMATED-SEQUENCING ** bionet.genome.autosequencing BIOCAN bionet.prof-society.cfbs BIOFORUM bionet.general BIO-INFORMATION-THEORY + bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS ** bionet.announce BIO-JOURNALS ** bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY ** bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIO-SRS bionet.software.srs BIOTECHNIQUES ** bionet.journals.letters.biotechniques BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW ** bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS ** bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY ** bionet.biology.computational CSM ** bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DEEPSEA ** bionet.biology.deepsea DIAGNOSTICS ** bionet.diagnostics DROSOPHILA bionet.drosophila ECOPHYSIOLOGY ** bionet.ecology.physiology EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO ** bionet.emf-bio EMPLOYMENT ** bionet.jobs.offered EMPLOYMENT-WANTED bionet.jobs.wanted FASEB ** bionet.prof-society.faseb FLUORESCENT-PROTEINS bionet.molbio.proteins.fluorescent FREE-RADICALS ** bionet.molecules.free-radicals G-PROTEIN-COUPLED-RECEPTOR bionet.molbio.proteins.7tms_r GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GLYCOSCI bionet.glycosci GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM ** bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg INSULIN-ACTION ** bionet.cellbiol.insulin JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLECULAR-REPERTOIRES bionet.molecules.repertoires MOLLUSC-MOLECULAR-NEWS ** bionet.molbio.molluscs MYCOLOGY bionet.mycology NAVBO ** bionet.prof-society.navbo NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PEPTIDES bionet.molecules.peptides PHOTOSYNTHESIS ** bionet.photosynthesis PLANT-BIOLOGY bionet.plants PLANT-EDUCATION bionet.plants.education PLANT-SIGNAL-TRANSDUCTION ** bionet.plants.signaltransduc POPULATION-BIOLOGY bionet.population-bio PRENATAL-DIAGNOSTICS bionet.diagnostics.prenatal PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista PSEUDOMONADS bionet.organisms.pseudomonas RAPD bionet.molbio.rapd RECOMBINATION bionet.molbio.recombination SCHISTOSOMA bionet.organisms.schistosoma SCIENCE-RESOURCES ** bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr SYMBIOSIS-RESEARCH ** bionet.biology.symbiosis TIBS ** bionet.journals.letters.tibs TOXICOLOGY bionet.toxicology TROPICAL-BIOLOGY bionet.biology.tropical URODELES ** bionet.organisms.urodeles VECTOR-BIOLOGY ** bionet.biology.vectors VIROLOGY ** bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio X-PLOR bionet.software.x-plor YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. List of BIOSCI Newsgroup Topics ------------------------------- MAILING LIST NAME TOPIC ----------------- ----- ACEDB-SOFT Discussions by users and developers of genome databases using the ACEDB software. AFCR ** American Federation for Clinical Research announcements AGEING Discussions about ageing research AGROFORESTRY Discussions about agroforestry research AIBS ** American Institute of Biological Sciences announcements AMYLOID ** Forum for researchers on Alzheimer's disease and related disorders including prion diseases ARABIDOPSIS Newsgroup for the Arabidopsis Genome Project ASCB ** Announcements from The American Society for Cell Biology AUDIOLOGY Topics in audiology and hearing science BIOFORUM Discussions about biological topics for which there is not yet a dedicated newsgroup AUTOMATED-SEQUENCING ** Research and support on automated DNA sequencing BIOCAN Newsgroup for the Canadian Federation of Biological Societies (CFBS) BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Applications of information theory to biology; this group is not for general information or for discussion of theories in general. BIONAUTS Question/answer forum for help using electronic networks, locating e-mail addresses, etc. BIONEWS ** General announcements of widespread interest to biologists BIO-JOURNALS ** Tables of Contents of biological journals BIO-MATRIX Applications of computers to biological databases BIOPHYSICAL-SOCIETY ** Official announcements/information from the Biophysical Society. BIOPHYSICS Discussion of issues related to the science and profession of biophysics BIO-SOFTWARE Information on software for the biological sciences BIO-SRS Discussions about the Sequence Retrieval System (SRS) software BIOTECHNIQUES ** Discussions of articles in the journal Biotechniques BIOTHERMOKINETICS Discussions about the kinetics, thermodynamics and control of biological processes at the cellular level BIO-WWW ** Announcements about new information resources in biology which can be accessed via electronic networked information retrieval software CARDIOVASCULAR-RESEARCH Research discussions in cardiovascular biology CELEGANS Research discussions on the model organism Caenorhabditis elegans and related nematodes CELL-BIOLOGY Discussions about cell biology including cancer research at the cellular level CHLAMYDOMONAS ** Discussions about the biology of the green alga Chlamydomonas and related genera CHROMOSOMES Discussions about mapping and sequencing of eucaryote chromosomes COMPUTATIONAL-BIOLOGY ** Mathematical and computer applications in biology CSM ** Announcements from the Canadian Society of Microbiologists. CYTONET Discussions about research on the cytoskeleton, plasma membrane, and cell wall DEEPSEA ** Research in deep-sea marine biology, oceanography, and geology DIAGNOSTICS ** Discussions of problems and techniques in all fields of diagnostics DROSOPHILA Discussions about biological research on Drosophila ECOPHYSIOLOGY ** Research and education in physiological ecology EMBL-DATABANK Messages to and from the EMBL database staff EMF-BIO ** Discussions about research on electromagnetic field interactions with biological systems EMPLOYMENT ** Job opportunities in biology EMPLOYMENT-WANTED Forum for posting resumes/CVs by individuals seeking employment in the biological sciences or in support of the biological sciences FASEB ** Announcements from the Federation of American Societies for Experimental Biology FLUORESCENT-PROTEINS Research on fluorescent proteins and bioluminescence FREE-RADICALS ** Research on free radicals in biology and medicine G-PROTEIN-COUPLED-RECEPTOR Discussions about signal transducing receptors which interact with G-proteins GDB Messages to and from the Genome Data Bank staff GENBANK-BB Messages to and from the GenBank database staff GENETIC-LINKAGE Newsgroup for genetic linkage analysis GLYCOSCI Discussions about carbohydrate and glycoconjugate molecules. GRASSES-SCIENCE Discussions regarding grasses, especially cereal, forage, and turf species HIV-MOLECULAR-BIOLOGY Discussions about the molecular biology of HIV HUMAN-GENOME-PROGRAM ** NIH-sponsored newsgroup on human genome issues IMMUNOLOGY Discussions about research in immunology INFO-GCG Discussions about the GCG sequence analysis software INSULIN-ACTION ** Discussions about the biology and chemistry of insulin and related receptors. JOURNAL-NOTES Practical advice on dealing with professional journals METHODS-AND-REAGENTS Requests for information and lab reagents MICROBIOLOGY Discussions about research in microbiology MOLECULAR-EVOLUTION Discussions about research in molecular evolution MOLECULAR-MODELLING Discussions about molecular modelling MOLECULAR-REPERTOIRES Generation and use of libraries of molecules MOLLUSC-MOLECULAR-NEWS ** Discussions about research on mollusc DNA MYCOLOGY Discussions about research on filamentous fungi NAVBO ** Forum for the North American Vascular Biology Organization NEUROSCIENCE Discussions about research in the neurosciences N2-FIXATION Discussion about biological nitrogen fixation PARASITOLOGY Discussions about research in parasitology PEPTIDES Chemical and biological aspects of peptides PHOTOSYNTHESIS ** Discussions about photosynthesis research PLANT-BIOLOGY Discussions about research in plant biology PLANT-EDUCATION Education issues in plant biology PLANT-SIGNAL-TRANSDUCTION ** Research on plant signal transduction POPULATION-BIOLOGY Discussions about research in population biology PRENATAL-DIAGNOSTICS Discussions about research in prenatal diagnostics PROTEIN-ANALYSIS Discussions about research on proteins and messages for the PIR and SWISS-PROT databank staffs PROTEIN-CRYSTALLOGRAPHY Discussion about crystallography of macromolecules and messages for the PDB staff PROTISTA Discussions about research on ciliates and other protists PSEUDOMONADS Research on the genus Pseudomonas RAPD Discussions about Randomly Amplified Polymorphic DNA RECOMBINATION Research on the recombination of DNA or RNA SCHISTOSOMA Discussions about Schistosoma research SCIENCE-RESOURCES ** Information from/about scientific funding agencies STADEN Discussions between scientists using the Staden molecular sequence analysis software STRUCTURAL-NMR Discussions about the use of NMR for macromolecular structure determination SYMBIOSIS-RESEARCH ** Discussions about symbiosis research TIBS ** "Letters to the Editor" of "Trends in Biochemical Sciences" TOXICOLOGY Discussions about research in toxicology TROPICAL-BIOLOGY Discussions about research in tropical biology URODELES ** Discussions about research in urodele amphibian biology VECTOR-BIOLOGY ** Research and control of arthropods which transmit disease VIROLOGY ** Discussions about research in virology WOMEN-IN-BIOLOGY Discussions about issues concerning women biologists X-PLOR Discussions about the X-PLOR software for 3D macromolecular structure determination YEAST Discussions about the molecular biology and genetics of yeast ZBRAFISH Discussions about research using the model organism Zebrafish (Danio rerio) ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. BIOSCI Newsgroup Discussion Leaders ----------------------------------- Most scientific specialty newsgroups (except for a few created several years ago) have individuals who are responsible for stimulating discussion on the newsgroup. General purpose forums such as METHODS-AND-REAGENTS do not have discussion leaders. If a group that you are interested in does not seem to have much activity recently, please contact the discussion leader and ask why. NEWSGROUP NAME Discussion Leader and their e-mail address -------------- ------------------------------------------ ACEDB-SOFT Mike Cherry (cherry@genome.stanford.edu) AFCR ** Jon T. Schafer (pp001101@interramp.com) AGEING Sydney Shall (bafa1@central.sussex.ac.uk) AGROFORESTRY Gerry Lawson (gjl@ite.ac.uk) AIBS ** Rebecca Chasan (moderator@aibs.org) AMYLOID ** David Small (david_small@muwayf.unimelb.edu.au) ARABIDOPSIS Chris Somerville (21847CRS@msu.edu) ASCB ** Vincent Shan (moderator@faseb.org) AUDIOLOGY Jeff Sirianni (sirianni@uts.cc.utexas.edu) and Susan Moreland (smorelan@magnus.acs.ohio-state.edu) AUTOMATED-SEQUENCING ** David Cain (dcain@hgmp.mrc.ac.uk) and Robert Feakes (rwf@mole.bio.cam.ac.uk) BIOCAN Leon Browder (browder@acs.ucalgary.ca) BIOFORUM None BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Tom Schneider (toms@ncifcrf.gov) BIONAUTS Rob Harper (harper@convex.csc.fi) BIONEWS ** David Kristofferson (biosci-help@net.bio.net) BIO-JOURNALS ** Julie Lawrence (biosci-help@net.bio.net) BIO-MATRIX Dan Davison (davison@uh.edu) BIOPHYSICAL-SOCIETY ** Carol Gross (cgross@biosci.cbs.umn.edu) BIOPHYSICS Carol Gross (cgross@biosci.cbs.umn.edu) BIO-SOFTWARE None BIO-SRS Thure Etzold (etzold@embl-heidelberg.de) and Reinhard Doelz (doelz@comp.bioz.unibas.ch) BIOTECHNIQUES ** Mary McCarthy (mmccarthy@biotechnet.com) BIOTHERMOKINETICS John Woods (eanv20@castle.edinburgh.ac.uk) BIO-WWW ** Reinhard Doelz (bio-www@comp.bioz.unibas.ch) CARDIOVASCULAR-RESEARCH Zhandong Zhou (zhandong@macc.wisc.edu) CELEGANS William Morgan (wmorgan@acs.wooster.edu) CELL-BIOLOGY Ola Myklebost (ola.myklebost@dnr.uio.no) CHLAMYDOMONAS ** Elizabeth H. Harris (chlamy@acpub.duke.edu) CHROMOSOMES Bruce Roe (broe@aardvark.ucs.uoknor.edu) and Greg Lennon (greg@mendel.llnl.gov) COMPUTATIONAL-BIOLOGY ** David Kristofferson (biosci-help@net.bio.net) CSM ** John Nash (csm@nrcbsa.bio.nrc.ca) CYTONET Nicholas C. Carpita (carpita@btny.purdue.edu) DEEPSEA ** Andrew Grant McArthur (mcarthur@onyx.si.edu) DIAGNOSTICS ** Kevin O'Donnell (odonnell@sasa.gov.uk) and Robert Burns (burns@sasa.gov.uk) DROSOPHILA Michael Ashburner (m.ashburner@gen.cam.ac.uk) ECOPHYSIOLOGY ** Martyn M. Caldwell (mmc@cc.usu.edu) EMBL-DATABANK None (datalib@embl-heidelberg.de) EMF-BIO ** Allan H. Frey (afrey@uunet.uu.net) EMPLOYMENT ** David Kristofferson (biosci-help@net.bio.net) EMPLOYMENT-WANTED None FASEB ** Vincent Shan (moderator@faseb.org) FLUORESCENT-PROTEINS Paul Kitts (paulki@clontech.com) Steve Kain (stevek@clontech.com) FREE-RADICALS ** Javier J. Zulueta (javier.zulueta@es.nemc.org) and Kevin Clancy PhD (clancy@eri.uchsc.edu) and Neil Hogg PhD (nhogg@post.its.mcw.edu) G-PROTEIN-COUPLED-RECEPTOR Lee F. Kolakowski, Jr. (lfk@receptor.mgh.harvard.edu) GDB Kerryn Brandt (kab@welchgate.welch.jhu.edu) GENBANK-BB Dennis Benson (benson@ncbi.nlm.nih.gov) GENETIC-LINKAGE Steve Bryant (s_bryant@icrf.ac.uk) GLYCOSCI Iain Wilson (iwilson@molbiol.ox.ac.uk) and Barry Hardy (bhardy@convex.ox.ac.uk) GRASSES-SCIENCE Allen Wright (adwright@iastate.edu) HIV-MOLECULAR-BIOLOGY Mika Salminen (msalminen@nphi.fi) HUMAN-GENOME-PROGRAM ** Betty Mansfield (k76@ornl.gov) IMMUNOLOGY Donald Forsdyke (forsdyke@qucdn.queensu.ca) INFO-GCG John Cargill (ontogen@nic.cerf.net) INSULIN-ACTION ** T. S. Pillay (tpillay@ucsd.edu) JOURNAL-NOTES Donald Forsdyke (forsdyke@qucdn.queensu.ca) METHODS-AND-REAGENTS None MICROBIOLOGY Martin Latterich (Martin_Latterich@qm.salk.edu) MOLECULAR-EVOLUTION Dan Davison (davison@uh.edu) MOLECULAR-MODELLING Philippe Stas (philstas@vub.ac.be) MOLECULAR-REPERTOIRES Andrew Wallace (a.wallace@queens-belfast.ac.uk) MOLLUSC-MOLECULAR-NEWS ** Elizabeth Grace Boulding (boulding@uoguelph.ca) MYCOLOGY Tom Adams (tom@bio.tamu.edu) Leland Ellis (leland@straylight.tamu.edu) Greg May (gsmay@bcm.tmc.edu) NAVBO ** Valeri Kolpakov (kolpakov@umich.edu) Steve Schwartz (steves@u.washington.edu) D. Gordon (David.Gordon@pobox.pds.med.umich.edu) NEUROSCIENCE Vincent A Mazzarella (vamg6792@uxa.cso.uiuc.edu) James L. Olds (olds@anatomy.org) N2-FIXATION Eng-Leong Foo (eng-leong_foo_mircen-ki%micforum@mica.mic.ki.se) PARASITOLOGY Daniel R. Brooks, Sherwin S. Desser and Henry Hong (parasite@zoo.toronto.edu) PEPTIDES George Barany (barany@maroon.tc.umn.edu) and Patricia Winter Cash (cash@bms.com) and S. Russ Lehrman (rlehrman@nexagen.com) PHOTOSYNTHESIS ** Larry Orr (larry.orr@asu.edu) PLANT-BIOLOGY Tony Travis (ajt@rri.sari.ac.uk) PLANT-EDUCATION Jonathan D. Monroe (monroejd@jmu.edu) and Susan R. Singer (ssinger@carleton.edu) PLANT-SIGNAL-TRANSDUCTION ** Bratislav Stankovic (stankovic.1@osu.edu) POPULATION-BIOLOGY None PRENATAL-DIAGNOSTICS Aneal Chandra (chandra@cardiff.ac.uk) and David Miller (davidm@pathology.leeds.ac.uk) and Tim Reynolds (timreyno@burton.demon.co.uk) PROTEIN-ANALYSIS Amos Bairoch (bairoch@cmu.unige.ch) and John Garavelli (garavelli@nbrf.georgetown.edu) PROTEIN-CRYSTALLOGRAPHY Morten Kjeldgaard (morten@oase.kemi.aau.dk) PROTISTA Marsha Altschule (marsha.i.altschuler@williams.edu) and Mark Farmer (farmer@emlab.zoo.uga.edu) PSEUDOMONADS Bruce W. Ritchings (bwr@icbr.ifas.ufl.edu) RAPD James Farmer (jlfarmer@bioag.byu.edu) RECOMBINATION Graham Dellaire (popa0206@po-box.mcgill.ca) and George Szatmari (szat@ere.umontreal.ca) and Terry Chow (MDTY@musica.mcgill.ca) and Dana Lasko (CZDL@musica.mcgill.ca) SCHISTOSOMA Werner Kunz (Werner.Kunz@uni-duesseldorf.de) and Christoph Grevelding (Christoph.Grevelding@uni-duesseldorf.de) and Lutz Gohr (Lutz.Gohr@uni-duesseldorf.de) SCIENCE-RESOURCES ** Julie Lawrence (biosci-help@net.bio.net) and David Kristofferson (biosci-help@net.bio.net) STADEN Tim Littlejohn (tim@bch.umontreal.ca) STRUCTURAL-NMR C. S. Raman (raman@bioc01.uthscsa.edu) SYMBIOSIS-RESEARCH ** James F. White, Jr. (jwhite@aesop.rutgers.edu) TIBS ** Jo McEntyre (TIBS@elsevier.co.uk) and David Kristofferson (biosci-help@net.bio.net) TOXICOLOGY Charles A. Miller (rellim@mailhost.tcs.tulane.edu) TROPICAL-BIOLOGY Matti Nummelin (mnummelin@cc.helsinki.fi) URODELES ** Susan Duhon (duhon@ucs.indiana.edu) and Anthony Mescher (mescher@ucs.indiana.edu) VECTOR-BIOLOGY ** Dennis Knudson (dknudson@lamar.colostate.edu) and Martin Ferguson (martinf@lamar.colostate.edu) VIROLOGY ** Marnix L. Bosch (marnix@saul.u.washington.edu) and Brett Lindenbach (bdl@borcim.wustl.edu) and Thomas Pfitzner (sttpfi@med-rz.uni-sb.de) WOMEN-IN-BIOLOGY Cassandra Smith (cls@buenga.bu.edu) X-PLOR Axel T. Brunger (brunger@laplace.csb.yale.edu) YEAST Francis Ouellette (francis@ncbi.nlm.nih.gov) ZBRAFISH Richard Vogt (vogt@biol.scarolina.edu) and Una Smith (smith-una@yale.edu) ** Note that newsgroups flagged with ** are moderated. Participating in BIOSCI Using USENET News Software -------------------------------------------------- Users who have access to USENET news software and the bionet USENET groups can participate immediately, i.e., they do not need to "subscribe" to anything. They can read and reply to messages using their local news software (e.g., "nn" or "rn") and post new messages of their own. Users will have to consult their local systems managers for help in using news software. There are many different programs available and the BIOSCI staff can not provide training in news software use. Fortunately, most news software is fairly simple to use and can be learned quickly. When posting new messages, USENET users should be sure to set the message "distribution" to "world" or else your message may not be distributed beyond your local computer. In most cases, messages are posted directly to the newsgroups without editorial intervention. Some groups (indicated in the lists above) are "moderated," however. This means that postings to these newsgroups will be sent to the newsgroup moderator who will decide whether or not the message is suitable for posting to the newsgroup in question. Participating in BIOSCI by E-mail --------------------------------- PLEASE NOTE THAT IF YOU HAVE ACCESS TO USENET NEWS YOU DO NOT NEED AN E-MAIL SUBSCRIPTION!! Simply read and post to the newsgroups in the "bionet" newsgroup hierarchy using your USENET news software. E-mail Subscription Requests and other Information -------------------------------------------------- For users in the Americas and Pacific Rim countries, e-mail subscription and cancellation requests are handled automatically by an e-mail server, although personal assistance is also available via the biosci-help@net.bio.net address. Once your e-mail address is added to a subscription list, mail will be sent to your address automatically each time someone posts a message. This will continue until you remove your address from the subscription list. You should first send the lists command to the address biosci-server@net.bio.net to obtain a listing of all current BIOSCI mailing lists. You may leave your message Subject: line blank in any message that is sent to the server (text on the Subject: line is *not* processed). Please place all commands only in the body of your mail message. Please be sure to substitute the appropriate mailing list name obtained from the "lists" command output for "listname" in the subscribe or unsubscribe commands illustrated below. The "listname" in subscription commands is always the <= 8 character mailing address for the mailing list (see also the table of mailing addresses further below). For example, the mailing address for the METHODS-AND-REAGENTS mailing list is methods@net.bio.net. To determine the "listname" to use with the "subscribe" or "unsubscribe" commands, take the portion of the address to the left of the @ sign, in this case "methods" is the listname derived from "methods@net.bio.net". After obtaining the names of the mailing lists using the "lists" command or by consulting the mailing address table further below, use the subscribe listname or unsubscribe listname commands to add or delete your address from the mailing lists. Please substitute "listname" above with the appropriate name of the list that you want to join/cancel. If you are trying to unsubscribe from a list but your address has changed, please see the instructions below in the section entitle "E-mail Address Changes." This section assumes that you are always operating from the same e-mail address. !!! PLEASE BE SURE to send all subscribe or unsubscribe commands only to !!! the biosci-server@net.bio.net address and not to the newsgroup posting !!! addresses where they will bother all of the readers! Your e-mail address is obtained automatically from the header of your mail message and should NOT be included on the subscribe/unsubscribe command line unless you need to sign up at a different address than the one you are currently using. Such requests must be handled manually by us and create extra work. (Also you would be surprised at how many people list their e-mail addresses incorrectly which then results in nondelivery of mail, so please let our server obtain this information automatically from your mail header.) Multiple commands may be placed on separate lines in the same mail message, i.e., you can include all of your subscribe and/or unsubscribe requests in one mail message as long as each is on a separate line. If you put multiple commands in your mail message, please put an end command as the last in your list of commands. This helps avoid sending to the server any signatures that might be automatically included in your mail messages. Here is a sample subscription message. The address public@state-u.edu would be automatically added to the BIONEWS and GRASSES-SCIENCE mailing lists as the result of this message. Note that the listname for GRASSES-SCIENCE is "grasses" as derived from the address portion to the left of the @ sign in the mailing address for GRASSES-SCIENCE (see address table further below). ---------------------------------------------------------------------- To: biosci-server@net.bio.net From: J.Q. Public Subject: subscribe bionews subscribe grasses end ---------------------------------------------------------------------- Other command details are included in the mail server help file from biosci-server@net.bio.net. To get the server help file (in computerese 8-), send in the help command to the server address. Finding Your Current E-mail Subscription List --------------------------------------------- If you are already a BIOSCI e-mail subscriber and need to determine which mailing lists you are on currently, send the command which to biosci-server@net.bio.net if you are signed up under the address that appears on the From: line of your mail message. If your address has changed, you can put a search string after the "which" command, e.g., if you are certain than your user name has always been jqpublic but do not remember the computer hostname, send the command which jqpublic This will find all instances of the text "jqpublic" on all mailing lists. E-mail Address Changes ---------------------- If you have subscribed to a newsgroup and are now leaving an institution or changing your e-mail address, it is imperative that you cancel your subscription! Non-existent addresses or overflowing mailboxes cause computer mail programs to send back "daemon" messages which might bother everybody on the newsgroup. In addition, mail systems continue for several days to try to contact bad addresses. This wastes CPU resources and slows mail delivery to others. We will eventually remove any address causing such a problem, but would prefer it if you would take care of changes in advance as a courtesy to the rest of the user community. To unsubscribe from the BIOSCI lists at net.bio.net, you will have to send mail from the e-mail account which has the same address as the one on our mailing lists. The server software only allows automatic cancellation of subscriptions if the e-mail address on your From: line of your "unsubscribe" message matches exactly the addresses on our lists (except for case differences). If the match is not exact, the server will send you an error message saying you are not on the lists. You can determine which mailing lists you are on by sending one of the two following commands to the server address biosci-server@net.bio.net. Please be sure to put all commands in the *body* of the mail message as any text put on the Subject: line is ignored by the server. which (the which command finds exact matches to your From: address) OR which xxx where xxx is any text, i.e., part or all of an e-mail address. The "which" command by itself will only find addresses on our list which match exactly (except for possible case differences) the address on the From: line of your mail message. If you are looking for an old address you will need to use the "which xxx" command. As an example of the "which" command output using the string "kristoff@bionet" ---------------------------------------------------------------------- which kristoff@bionet The string 'kristoff@bionet' appears in the following entries in lists served by biosci-server@net.bio.net: List Address ==== ======= faseb kristoff@bionet.ig.com tibs kristoff@bionet.ig.com ---------------------------------------------------------------------- The List names appear in the left hand column of the output. Please note your list names for use in the "unsubscribe" commands described below. If your address on our lists differs from your current address, you will not be able to unsubscribe automatically, so please forward the output of the "which xxx" command to biosci-help@net.bio.net and ask to have the old address removed manually. If your address is still the same as the one on our lists, you can cancel your subscriptions automatically by sending in a message to biosci-server@net.bio.net such as the following unsubscribe bionews unsubscribe molmodel unsubscribe bioforum end where you have used the listnames as determined from the "which" command output after the "unsubscribe" command. Once again, if "which" does not return any output to you unless you follow it by a text string, e.g., which xxx, you will *not* be able to unsubscribe automatically. Please follow the alternative instructions for manual address removal above. Interruption of E-mail Service ------------------------------ It is our policy to remove any address from our mailing lists which becomes inaccessible and causes mail to bounce back to the sender. This might happen to you if your local computer or network fails for a significant period of time. If you notice that you are no longer receiving BIOSCI postings, it may be because your address was removed for the above reason. It will be necessary for you to contact biosci-help@net.bio.net and resubscribe. Please see the BIOSCI FAQ, mentioned at the beginning of this document, for more details on how BIOSCI handles addresses which reject mail. Posting Messages to Newsgroups by E-mail ---------------------------------------- Those who use e-mail to post messages should send their mail to the following Internet addresses in the USA: ********************************************************************** DO NOT, REPEAT, DO NOT POST SUBSCRIPTION OR CANCELLATION REQUESTS DIRECTLY TO ANY OF THE NEWSGROUP E-MAIL POSTING ADDRESSES. PLEASE USE ONLY THE ADDRESS biosci-server@net.bio.net for subscription or cancellation requests as explained above. Your posting could go to several thousand people. Supposing that each person spends a couple of seconds to figure out that you did this, before they go on to the next message. You will have wasted the equivalent of several hours of one person's time, not to mention wasted computer time and disk storage. ********************************************************************** MAILING LIST NAME Mailing Address ----------------- ---------------- ACEDB-SOFT acedb@net.bio.net AFCR ** afcr@net.bio.net AGEING ageing@net.bio.net AGROFORESTRY ag-forst@net.bio.net AIBS ** aibslist@net.bio.net AMYLOID amyloid@net.bio.net ARABIDOPSIS arab-gen@net.bio.net ASCB ** ascb@net.bio.net AUDIOLOGY audiolog@net.bio.net AUTOMATED-SEQUENCING ** autoseq@net.bio.net BIOCAN biocan@net.bio.net BIOFORUM bioforum@net.bio.net BIO-INFORMATION-THEORY + bio-info@net.bio.net BIONAUTS bio-naut@net.bio.net BIONEWS ** bionews@net.bio.net BIO-JOURNALS ** bio-jrnl@net.bio.net BIO-MATRIX biomatrx@net.bio.net BIOPHYSICAL-SOCIETY ** bphyssoc@net.bio.net BIOPHYSICS biophys@net.bio.net BIO-SOFTWARE bio-soft@net.bio.net BIO-SRS bio-srs@net.bio.net BIOTECHNIQUES ** btechniq@net.bio.net BIOTHERMOKINETICS btk-mca@net.bio.net BIO-WWW ** bio-www@net.bio.net CARDIOVASCULAR-RESEARCH cardiors@net.bio.net CELEGANS celegans@net.bio.net CELL-BIOLOGY cellbiol@net.bio.net CHLAMYDOMONAS ** chlamy@net.bio.net CHROMOSOMES biochrom@net.bio.net COMPUTATIONAL-BIOLOGY ** comp-bio@net.bio.net CSM ** csm@net.bio.net CYTONET cytonet@net.bio.net DEEPSEA ** deepsea@net.bio.net DIAGNOSTICS ** diagnost@net.bio.net DROSOPHILA dros@net.bio.net ECOPHYSIOLOGY ** ecophys@net.bio.net EMBL-DATABANK embl-db@net.bio.net EMF-BIO ** emf-bio@net.bio.net EMPLOYMENT ** biojobs@net.bio.net EMPLOYMENT-WANTED wantjob@net.bio.net FASEB faseb@net.bio.net FLUORESCENT-PROTEINS fluorpro@net.bio.net FREE-RADICALS ** freerad@net.bio.net G-PROTEIN-COUPLED-RECEPTOR 7tms_r@net.bio.net GDB gdb@net.bio.net GENBANK-BB genbankb@net.bio.net GENETIC-LINKAGE gen-link@net.bio.net GLYCOSCI glycosci@net.bio.net GRASSES-SCIENCE grasses@net.bio.net HIV-MOLECULAR-BIOLOGY hiv-biol@net.bio.net HUMAN-GENOME-PROGRAM ** gnome-pr@net.bio.net IMMUNOLOGY immuno@net.bio.net INFO-GCG info-gcg@net.bio.net INSULIN-ACTION ** insulin@net.bio.net JOURNAL-NOTES jrnlnote@net.bio.net METHODS-AND-REAGENTS methods@net.bio.net MICROBIOLOGY microbio@net.bio.net MOLECULAR-EVOLUTION mol-evol@net.bio.net MOLECULAR-MODELLING molmodel@net.bio.net MOLECULAR-REPERTOIRES molreps@net.bio.net MOLLUSC-MOLECULAR-NEWS ** molluscs@net.bio.net MYCOLOGY mycology@net.bio.net NAVBO ** navbo@net.bio.net NEUROSCIENCE neur-sci@net.bio.net N2-FIXATION n2fix@net.bio.net PARASITOLOGY parasite@net.bio.net PEPTIDES peptides@net.bio.net PHOTOSYNTHESIS ** photosyn@net.bio.net PLANT-BIOLOGY plantbio@net.bio.net PLANT-EDUCATION plant-ed@net.bio.net PLANT-SIGNAL-TRANSDUCTION ** plsignal@net.bio.net POPULATION-BIOLOGY pop-bio@net.bio.net PRENATAL-DIAGNOSTICS prenatal@net.bio.net PROTEIN-ANALYSIS proteins@net.bio.net PROTEIN-CRYSTALLOGRAPHY xtal-log@net.bio.net PROTISTA protista@net.bio.net PSEUDOMONADS pseudomo@net.bio.net RAPD rapd@net.bio.net RECOMBINATION recom@net.bio.net SCHISTOSOMA schisto@net.bio.net SCIENCE-RESOURCES ** sci-res@net.bio.net STADEN staden@net.bio.net STRUCTURAL-NMR str-nmr@net.bio.net SYMBIOSIS-RESEARCH symbios@net.bio.net TIBS ** tibs@net.bio.net TOXICOLOGY toxicol@net.bio.net TROPICAL-BIOLOGY trop-bio@net.bio.net URODELES ** urodeles@net.bio.net VECTOR-BIOLOGY ** vect-bio@net.bio.net VIROLOGY ** virology@net.bio.net WOMEN-IN-BIOLOGY womenbio@net.bio.net X-PLOR x-plor@net.bio.net YEAST yeast@net.bio.net ZBRAFISH zbrafish@net.bio.net + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. Retrieval of old postings from the BIOSCI archives -------------------------------------------------- All BIOSCI newsgroups are archived on the World Wide Web at URL http://www.bio.net/. Users who have only e-mail access to the Internet can retrieve messages from our waismail e-mail server. For waismail instructions, send the word help in a message to waismail@net.bio.net. Please leave the Subject: line of your message blank. BIOSCI "prototype" newsgroups ----------------------------- To assist areas of research in developing their own electronic communication forums, BIOSCI at net.bio.net will set up, on request, a mailing list *without* an associated USENET newsgroup. The mailing list is created only at net.bio.net, the U.S. BIOSCI node, and all subscription requests must be sent to the e-mail server at biosci-server@net.bio.net regardless of one's geographical location. There is no charge for this or any other BIOSCI service, as usual. This procedure waives the rule that requires each new newsgroup proposal to be put to a vote of the readership first (see the BIOSCI FAQ, mentioned at the beginning of this document, for details on creating new full-fledged newsgroups and prototype newsgroups). Each mailing list ("prototype newsgroup") must have a scientist volunteer to serve as its discussion leader and an initial list of e-mail subscribers. The prototype newsgroup has six months to build up its readership after which time it is put out for a vote for full newsgroup status (i.e., to have both a mailing list *and* parallel USENET newsgroup created at both BIOSCI nodes in the U.S. and U.K.). If you are interested in establishing such a forum for your research specialty, please contact biosci-help@net.bio.net. The current prototype newsgroups are listed below. Please send subscription requests to biosci-server@net.bio.net and NOT to the newsgroup posting addresses. Prototype newsgroups may *not* be fully archived, so please be sure to save any messages that you may want to refer to again. Posting Address Purpose --------------- ------- annelida@net.bio.net Discussions of the scientific study of Phylum Annelida bigblue@net.bio.net Discussions between researchers who use transgenic animal systems for mutation assays. bioherv@net.bio.net Discussions about human endogenous retroviral elements. maize@net.bio.net Research on maize. mutation@net.bio.net Discussions about mutation research. phbiotec@net.bio.net Discussions about research in pharmaceutical biotechnology. radoncjc@net.bio.net Radiation Oncology journal club (moderated list) rna@net.bio.net Discussions about RNA editing, RNA splicing, and ribozyme activities of RNA. rust-mil@net.bio.net Research about the biotrophic foliar fungal diseases of cereals, including rusts, powdery mildews and downy mildews. yac@net.bio.net Discussions about yeast artificial chromosomes. Retrieving Other BIOSCI Documentation ------------------------------------- BIOSCI documents are kept in the anonymous FTP area on net.bio.net [134.172.2.69] in the directory pub/BIOSCI/doc and can be retrieved either via FTP or by gopher to net.bio.net or on the WWW to URL http://www.bio.net/. Documents can also be retrieved by addressing e-mail to the Internet address biosci-server@net.bio.net and including any of the commands below in the body of your mail message. Text placed on the Subject: line of your message is ignored, so please be sure that the commands are in the body of the mail message. Although multiple commands may be placed in one message, we recommend instead that one message be sent per command to avoid having to extract multiple documents from a single message. The server sends back all information requested from a multiple command query in a single response message. Document to Retrieve Command to send to biosci-server@net.bio.net -------------------- -------------------------------------------- BIOSCI FAQ info faq (Frequently Asked ?'s about using BIOSCI) BIOSCI info sheet for the Americas & Pacific Rim info usinfo BIOSCI info sheet for Europe, Africa, & Central Asia info ukinfo Information on Network Connections info internet How to set up USENET News at your site info usenet1 USENET Netiquette and other edifying reading info usenet2 FURTHER QUESTIONS??? Please address them to biosci-help@net.bio.net. PLEASE DO NOT DIRECT BIOSCI QUESTIONS TO THE PERSONAL E-MAIL ADDRESSES OF PEOPLE ON THE BIOSCI STAFF!! DUE TO OUR VOLUME OF MAIL, ANSWERS MAY BE DELAYED OR NOT SENT AT ALL!! From owner-software@net.bio.net Fri Jan 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!news.bconnex.net!news2.insinc.net!roger.interlynx.net!usenet From: "Lars Thomsen" Newsgroups: bionet.software Subject: Patch Reader betaversion 0.1 (free) Date: 4 Jan 1997 08:00:15 GMT Organization: 115 South Oval Lines: 20 Message-ID: <01bbfa14$8f1c3120$4cc032cc@boris.gate2.interlynx.net> NNTP-Posting-Host: ppp16-max2.interlynx.net X-Newsreader: Microsoft Internet News 4.70.1155 The first release of a preliminary version of my patch clamp analysis program is ready for download from my web site sunday 1200 noon. Take a preview at some of the programs current capabilities at : http://home.interlynx.net/~lthomsen/hotspot.htm The program has highly professional graphical routines. The program is not commercial or shareware, it is simply a help from me to you. The analysis is not so advanced yet, but Im working hard on fixing that. Right now the program is a really nice alternative to your PClamp6 graph struggling. If you want to become a betatester and thereby having some influence on the future shape of the program then you can download it at Sunday. However, you need a password to the zip file. You can get the password by sending me an email. lthomsen@interlynx.net -- Lars Thomsen, M.Sc. PhD. 115 South Oval, Hamilton, ON Canada L8S1R2 Email lthomsen@interlynx.net http://home.interlynx.net/~lthomsen/index.htm From owner-software@net.bio.net Fri Jan 03 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: BIOSCI-REQUEST Newsgroups: bionet.software Subject: Subscription to btechniq Date: 3 Jan 1997 16:41:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701040040.QAA00418@net.bio.net> NNTP-Posting-Host: net.bio.net Your subscription to btechniq has been deleted. Thank you for your interest BIOSCI/bionet Administration biosci@net.bio.net From owner-software@net.bio.net Fri Jan 03 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Pat Thoyts Newsgroups: bionet.software Subject: Re: Any Programm to create 3d animation by microscopic pic's Date: Sat, 04 Jan 1997 16:34:09 -0800 Organization: IACR Long Ashton Research Station Lines: 26 Message-ID: <32CEF701.11B3@bsa.bristol.ac.uk> References: NNTP-Posting-Host: pc0594.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win16; I) To: gbenro@amalia-atm.rz.uni-frankfurt.de gbenro@amalia-atm.rz.uni-frankfurt.de wrote: > > Hello, > Is there any Programm to create animations in 3d by multiple microscopic > frames in formates (like tif, gif, jpg, bmp, etc. but normaly tif) > > You may imagine that this slides of pic's will be stacked above each > other pic in certain order.... > > If you know any programm which fit to this problem (to solve), feel free > to conect me ... There is an extremely effective and simple program to create animated gif's as used on web pages if this is what you are after. It takes a list of gif files and merges them together to produce the animation. You can view the animation with any graphical web browser or xanim among others. I've been able to compile this under VAX/VMS (with minor modifications to put the output to a file and not to stdio), linux, irix, DOS and OS/2 so it's very portable! Its called: GIFMerge Rev 1.33 (C) 1991,1992 by Mark Podlipec Improvements by Rene K. Mueller 1996 and the help suggests you look at: http://www.iis.ee.ethz.ch/~kiwi/GIFMerge/ -- Pat Thoyts thoyts@bsa.bristol.ac.uk From owner-software@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-hub.sprintlink.net!news.sprintlink.net!news-dc-9.sprintlink.net!news1.infoave.net!dial-15 From: vessle@partake.net (Vessle) Newsgroups: bionet.software,bionet.software.acedb,bionet.software.gcg Subject: "100 Shateware Links Page" (Free Shareware Links) Date: Sat, 04 Jan 97 22:38:49 GMT Organization: Info Avenue INTERNET Access Lines: 3 Message-ID: <5ampo4$bt7@news1.infoave.net> NNTP-Posting-Host: dial-15.r02.tnsmvl.infoave.net X-Newsreader: News Xpress Version 1.0 Beta #4 Xref: biosci bionet.software:17543 bionet.software.acedb:1077 bionet.software.gcg:2170 "100 Shateware Links Page" (Free Shareware Links) 100 of the most current and active shareware links on the net! Go to: http://www.mamsofco.com/100sl From owner-software@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!uunet!in1.uu.net!152.163.170.17!newstf01.news.aol.com!audrey01.news.aol.com!not-for-mail From: hmeis92099@aol.com (HMeis92099) Newsgroups: bionet.software Subject: Expand your software market... Date: 5 Jan 1997 00:58:36 GMT Organization: AOL http://www.aol.com Lines: 19 Message-ID: <19970105005700.TAA05351@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com I represent an Irish software developer, marketing firm who is more that capable of launching your software in the European market. They can handle both Mac and Windows and can offer the following: disk duplication; user manual reprinting; translations; sales/marketing; sales tracking and reporting. This firm is in joint efforts with the Irish trade Board and Aerlingus. If you have a demo of your package, please forward 2 copies for a proposal back to you. Also include where and the pricing structure here in the states. Regards, Herbert Meister MEISTERDesign PO Box 171 Naugatuck, CT 06770 203.729.6094 203.729.4499 fax From owner-software@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!EU.net!sun4nl!surfnet.nl!news.unisource.nl!xs4all!xs4all!usenet From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: Re: DNA software --> SeqSearch v1.1 DNA analysis tools for Windows Date: 5 Jan 1997 16:12:33 GMT Organization: XS4ALL, networking for the masses Lines: 48 Message-ID: <5aojth$mrg@news.xs4all.nl> References: NNTP-Posting-Host: asd05-04.dial.xs4all.nl Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Sun, 05 Jan 1997 17:12:33 MET X-Newsreader: WinVN 0.99.7 In article , tchorz@biotop.umcs.lublin.pl says... > >Dear Netters, > >First of all, Happy New Year 1997 to all of you !!! > >On the other hand, I need advice concerning programs >for DNA and protein analysis. >I am going to buy such program however I am not >fully determined which program I should purchase. > >So far, I have seen DNAsis and DNAstar, however >I am not sufficiently confident that these programs >are reliable, and can provide me with the best options. > >So, could you advice me, which programs is actually >the best on the market. > SeqSearch v1.1 is a DNA analysis tool package developed for Windows 3.1` and Win95. It is especially developed for the general daily routines in a molecular lab. SeqSearch v1.1 offers the following features: - Multi user/project storage -Sequence storage in multiple databases: sequences/plasmids/constructs/oligo's and motifs - Restriction analysis with pre-defined and user-defined enzym sets - Mismatch primer design - Mutagenic primer design for codon substitution mutagenesis - Silent mutagenesis - Clone Bench for designing constructs - Fragment analysis with gel pattern simulation - Hydrophobic plot of proteins - Motif search on DNA sequences - Oligo Info - Reading frame analysis For more info and the latest release of SeqSearch v1.1 please check: http://www.xs4all.nl/~marker Niels Groot marker@xs4all.nl From owner-software@net.bio.net Sat Jan 04 22:00:00 1997 Newsgroups: bionet.software Subject: Program for randomization tests From: mikelevy@total.net (Michael Levy) X-Newsreader: WinVN 0.99.8 (beta 2) MIME-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII NNTP-Posting-Host: ppp-5200-1134.mtl.total.net Message-ID: <32cf155f.0@news.total.net> Date: 5 Jan 97 02:43:43 GMT Organization: TotalNet Inc. Lines: 6 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!news.msfc.nasa.gov!news.sgi.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.maxwell.syr.edu!news.emi.com!uunet!in1.uu.net!198.168.54.138!rcogate.rco.qc.ca!news.total.net!ppp-5200-1134.mtl.total.net I am attempting to find software that will allow me to carry out randomized MANOVA's. Any info would be greatly appreciated. Michael Levy michael@vax2.concordia.ca From owner-software@net.bio.net Sun Jan 05 22:00:00 1997 Newsgroups: bionet.software Path: biosci!rutgers!gatech!arclight.uoregon.edu!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!uchinews!dgorski From: dgorski@xsite.net (David H. Gorski) Subject: Re: DNA Software X-Nntp-Posting-Host: maxreader.bsd.uchicago.edu Content-Type: text/plain; charset=ISO-8859-1 Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Content-Transfer-Encoding: 8bit Organization: University of Chicago -- Academic Computing Services X-Newsreader: Yet Another NewsWatcher 2.4.0 References: Mime-Version: 1.0 Date: Mon, 6 Jan 1997 23:06:59 GMT Lines: 37 In article , tchorz@biotop.umcs.lublin.pl (Marek Tchorzewski) wrote: > On the other hand, I need advice concerning programs > for DNA and protein analysis. > I am going to buy such program however I am not > fully determined which program I should purchase. > > So far, I have seen DNAsis and DNAstar, however > I am not sufficiently confident that these programs > are reliable, and can provide me with the best options. > > So, could you advice me, which programs is actually > the best on the market. Personally, I used to use MacVector 4.0, but that was back in 1993 when I was finishing my Ph.D. Since I've taken time off from my clinical responsibilities to get back into the lab, I've been wondering if MacVector is still being supported. Apparently Kodak doesn't own it any more. Does anyone out there know? Is MacVector still available? Is it still good? How do I get a hold of a representative who could let me use a demo for a while, to see if I can convince my PI to buy a copy for the lab. I'm getting sick of suffering with an ancient version of DNA Strider. If MacVector isn't being supported anymore, what are the best DNA/protein analysis programs for the Mac? -- David H. Gorski, M.D., Ph.D. |"What is man, when you come to think Department of Surgery | upon him, but a minutely set, ingenious University of Chicago | machine for turning, with infinite 5841 S. Maryland Ave. | artfulness, the red wine of Shiraz Chicago, IL 60637 | into urine?" | E-Mail: | Primary: d-gorski@uchicago.edu| Isaak Dinesen Secondary: dgorski@xsite.net | From owner-software@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-paris.gsl.net!news.gsl.net!rain.fr!jussieu.fr!saphir.jouy.inra.fr!malbert.rennes.inra.fr!user From: malbert@st-gilles.rennes.inra.fr (Charles Henri Malbert) Newsgroups: bionet.software Subject: Current Contents V4 Date: Tue, 07 Jan 1997 12:59:52 +0200 Organization: INRA Lines: 26 Message-ID: NNTP-Posting-Host: saphir.jouy.inra.fr X-Newsreader: Value-Added NewsWatcher 2.12d0+ Dear all, Have anyone tried to use Current contents on disk for Mac (version 4, last one). They claimed to have a new version with this crap. However, thay have made the same as microsoft i.e. a bad adaptation of a windows software (just try to open it under Resedit to understand what I mean). The result is as expected tremendously SLOW (even on a powerMAC) I feel that it is important that the MAC user negate this kind of software programming If we want to support our platform. Therefore, I am asking anybody that is using this software on a mac to react directly to ISI by send as many Email as possible asking them to change their software. It is also important since the new version has so many bugs that it is very difficult to use it. -- Dr C.H Malbert Unite de controle de l'ingestion et des flux digestifs Station de Recherches Porcines, 35590 Saint gilles, France Tel: (33) 99 28 50 71 Fax: (33) 99 28 50 80. From owner-software@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!dmt From: David Tyler Newsgroups: bionet.software Subject: Re: DNA Software Date: Tue, 7 Jan 1997 15:50:29 +0000 Organization: University of Cambridge, England Lines: 32 Message-ID: References: NNTP-Posting-Host: mole.bio.cam.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: On Mon, 6 Jan 1997, David H. Gorski wrote: > Does anyone out there know? Is MacVector still available? Is it still good? > How do I get a hold of a representative who could let me use a demo for a > while, to see if I can convince my PI to buy a copy for the lab. I'm > getting sick of suffering with an ancient version of DNA Strider. If > MacVector isn't being supported anymore, what are the best DNA/protein > analysis programs for the Mac? MacVector is the best package I've seen for the Mac, although IMO Geneworks does some things more prettily. It's now owned by Oxford Molecular Group PLC, and version 5.5 is, I believe, imminent. N. America: (800) 486-7489 or (408) 879-6300 or support@oxmol.com Europe: +44 1865 784600 or support@oxmol.co.uk No affiliation etc. _______________________________________________________________________________ D a v i d T y l e r dmt@mole.bio.cam.ac.uk _______________________________________________________________________________ From owner-software@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!warwick!bham!usenet From: s.m.williams.bcm@bham.ac.uk (Stephen Williams) Newsgroups: bionet.software Subject: Re: Any program to create a spacefilling 3d-model from PDB-files? Date: Tue, 07 Jan 1997 15:48:07 GMT Organization: The School of Biochemistry, The University of Birmingham, UK Lines: 14 Message-ID: <32d26f72.30021271@news.bham.ac.uk> References: <32c80fbc.16745732@relay.eunet.no> NNTP-Posting-Host: bcs219.bham.ac.uk X-Newsreader: Forte Free Agent 1.1/32.230 On Thu, 02 Jan 1997 17:11:46 GMT, eirikth@eunet.no (Eirik) wrote: >Want to create / convert a PDB (or similar) file to formats like .3ds >.Pov. >Just want a simple represantation, not an acurate. There is an add on to PovRay to enable it to read PDB files. I only had a quick look a couple of months back but never got around to using it properly. E-mail me if you're interested and I'll try to find out where I downloaded it from. Steve From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!inca.biochem.wisc.edu!roca From: Alberto I Roca Newsgroups: bionet.software Subject: Re: Current Contents V4 Date: 8 Jan 1997 04:22:00 GMT Organization: Biochemistry, University of Wisconsin Lines: 23 Distribution: world Message-ID: <5av7d8$26g6@news.doit.wisc.edu> References: NNTP-Posting-Host: inca.biochem.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXMessage-ID: X-XXDate: Tue, 7 Jan 1997 04:27:10 GMT In article Charles Henri Malbert, malbert@st-gilles.rennes.inra.fr writes: >Therefore, I am asking anybody that is using this software on a mac to >react directly to ISI by send as many Email as possible asking them to >change their software. luckily you can request a "downgrade" of your weekly databases from v4.0 to v3.0. i have already changed our subscription back to the old style so that we can use the sleek 3.0 software. similar requests of this type will send a strong message to ISI. alberto :| p.s. i have no connection to ISI other than being an unhappy 4.0 customer. ================================================================= Alberto I. Roca Internet: roca@macc.wisc.edu Biochemistry Bitnet: roca@wiscmacc 420 Henry Mall University of Wisconsin-Madison Madison, Wisconsin 53706 USA From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!worldnet.att.net!arclight.uoregon.edu!netnews.nwnet.net!news-hub.interserv.net!news.sprynet.com!news From: naca@interserv.com Newsgroups: bionet.software Subject: aldus pagemaker for sale Date: 8 Jan 1997 00:25:02 GMT Organization: Sprynet News Service Lines: 8 Message-ID: <5aupgu$b21@juliana.sprynet.com> NNTP-Posting-Host: ad55-237.compuserve.com X-Newsreader: SPRY News 3.03 (SPRY, Inc.) Aldus Pagemaker 3.0 for Mac, $25.00 Aldus Pagemaker 4.0 for Mac, $40.00 Software is brand new! Prices include shipping. e-mail John at naca@interserv.com for ordering information This is no joke! From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!warwick!news.nott.ac.uk!granby!pazpmr From: peter murray rust Newsgroups: bionet.software Subject: ANNOUNCE: CML (Chemical Markup Language) V1.0 Date: Tue, 7 Jan 1997 23:38:46 +0000 Organization: Cripps Computing Centre, The University of Nottingham Lines: 84 Message-ID: NNTP-Posting-Host: granby.ccc.nottingham.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: pazpmr@granby Chemical Markup Language supports the management of molecular information across a wide spectrum (sequences and macromolecular structures being particularly relevant to this newsgroup). It is offered as a tool for those wishing to develop an object-oriented approach to interoperability of molecular information. This posting describes the first stable public release. CML V1.0 is finally ready and posted and available for anyone who wishes to develop applications. It's free, as are the supporting java classes, and we are already starting to build a community of developers. CML V1.0 has many new features, and has vastly expanded its potential applications. I have tackled many different disciplines and files and believe that CML is powerful enough to represent most of them, and certainly the chemical/* MIME types that I'm grafting through. The greatest enhancement is that CML is completely supported by Java classes. It's also compatible with the latest SGML developments on the Internet, so it represents a single universal mechanism for realising chemical/* MIME philosophy in being able to send and receive molecules regardless of the platform or software. It is also far easier to extend and develop and maintain software in Java than other languages. I would be interested in hearing from anyone interested in adding CML to their toolkit. It's particularly suitable for processing legacy information, database submission and retrieval, postprocessing and visualisation of program output, glossary development, scientific publication, searching of semi-structured information, etc. CML is being offered in close collaboration with the Open Molecule Foundation, a non-profit consortium of those interested in developing object-oriented approaches to molecules and their interoperability. PeterMR -------------------------------------------------------------------------------- CHEMICAL MARKUP LANGUAGE (CML) V1.0 CML is an SGML-based approach to managing molecular information, especially over the Inter- and Intra-networks. Version 1.0 is a major enhancement over previous releases and is available for anyone wishing to develop robust, Object-Oriented molecular applications. Among its features (many of which are new): Object-Oriented and implemented in JAVA with hundreds of classes Accepts many common file types, especially chemical/* MIME Can process arbitrarily large files with no information loss Human-readable and easy to learn Flexible and easily extensible to many disciplines Supported by a communal effort, including the Open Molecule Foundation Ideal for postprocessing output from calculations and instruments Supports complex documents, including scientific publications Applications in protein sequence, molecular and crystal structure, quantum chemistry, spectra, organic molecules, publication, education Closely linked to the new XML/SGML developments on the Internet Free, including Java classes and API. The home page http://www.venus.co.uk/omf/ includes many screenshots of the language at work, and Java applets are also served for those with compatible clients (For those primarily interested in general SGML applications, there is a complete package of java classes for SGML/XML parsing and rendering (including Shakespeare)). Peter Murray-Rust Peter Murray-Rust (PeterMR, ) Director, Virtual School of Molecular Sciences Pharmaceutical Sciences, Nottingham University, NG7 2RD, UK; Tel 44-115-9515100 Fax 5110 http://www.nottingham.ac.uk/vsms/; OMF: http://www.ch.ic.ac.uk/omf/ From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-xfer.netaxs.com!cs.utexas.edu!newshost.convex.com!newsgate.duke.edu!phanes94.mc.duke.edu!user From: nc1@acpub.duke.edu (Namjin Chung) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Software for quantitation of scanned images? Date: 8 Jan 1997 18:14:17 GMT Organization: Duke University Medical Center Lines: 12 Message-ID: NNTP-Posting-Host: phanes94.mc.duke.edu Xref: biosci bionet.molbio.methds-reagnts:53244 bionet.software:17557 Dear Netters, I'm looking for a software (except NIH Image) which can be used to quantitate images already scanned with a typical image scanner. My intention is to calculate the relative amount of proteins in each band in x-ray film. TIA. Namjin Chung Namjin Chung (Graduate Student) Program in Molecular Cancer Biology Duke University Medical Center, Box 3345 Durham, NC 27710 USA From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!news.Stanford.EDU!morrow.stanford.edu!usenet From: scoop@leland.stanford.edu (Todd McGee) Newsgroups: bionet.software Subject: New Journals online Date: 8 Jan 1997 06:35:07 GMT Organization: Stanford University Lines: 27 Sender: -Not-Authenticated-[9248] Message-ID: <5avf6r$610@morrow.stanford.edu> NNTP-Posting-Host: mcgee-isdn.stanford.edu X-Newsreader: InterNews 2.0.1@mcgee-isdn.stanford.edu[U] XDisclaimer: User not authenticated Hi folks, I wanted to take a minute to let everyone know that there have been a few additions to the number of journals that are online. Since the journals seem to be pretty terrible at publicizing their web sites, I thought they could use the help. Anyway, the latest additions are: PNAS at http://www.pnas.org Journal of Experimental Medicine at: http://www.jem.org/ Pediatrics at http://www.pediatrics.org/ All three of these journals have the full text and images of all their articles available online and are, for a limited time, freely available to anyone who wants to read them. I don't know about you but I'm getting pretty tired of the journals that only put their abstracts online. I can get that from Medline! Sorry for the cross-posting, hope I didn't annoy anyone too much. Todd McGee Dept. Biol. Sci. Stanford University From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsserver.jvnc.net!netnews.sbphrd.com!news From: William P Prichett Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: ?? Kinetics Software - Post Date: Wed, 08 Jan 1997 15:29:26 -0800 Organization: SmithKline Beecham Lines: 9 Message-ID: <32D42DD6.70A3@sbphrd.com> References: <32AEF4BF.5C7A@apl.washington.edu> <32BF3C94.4319@cam.org> NNTP-Posting-Host: ued656.um.us.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Xref: biosci bionet.software:17559 bionet.molbio.proteins:9675 bionet.molbio.methds-reagnts:53251 I would like to add to the list of Kaliedagraph users. I really like the easy of use, especially the non linear curve fit. Very simple. Synergy is at http://www.synergy.com/ Good Luck, Bill From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-xfer.netaxs.com!newsfeeds.sol.net!hammer.uoregon.edu!news.uoregon.edu!news.rediris.es!news.cica.es!news From: bb1rofra@uco.es (Antonio Rodriguez Franco) Newsgroups: bionet.software Subject: Looking for antigenicity software Date: Wed, 08 Jan 1997 20:29:58 GMT Organization: Universidad de Cordoba Lines: 7 Message-ID: <5b0sa7$k0t@erika.cica.es> Reply-To: bb1rofra@uco.es NNTP-Posting-Host: ciebbm11.uco.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8895-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Free Agent 1.0.82 I am trying to raise polyclonal antibodies using a short oligopeptide stick to albumin. Is there any reliable software in which to test the antigenicity and surface probability of my sequence? 1¾ From owner-software@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!agate!spool.mu.edu!newspump.sol.net!howland.erols.net!cam-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!hgsi.com!news From: "John M. Greene, Ph.D" Newsgroups: bionet.software Subject: Bioinformatics Associate Director Position Date: Wed, 08 Jan 1997 14:09:30 -0500 Organization: Human Genome Sciences, Inc./Bioinformatics Group Lines: 49 Message-ID: <32D3F0EA.D9F@hgsi.com> Reply-To: John_Greene@hgsi.com NNTP-Posting-Host: hgs/net2-78.hgsi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) CC: bionet.jobs.offered BIOINFORMATICS POSITION AVAILABLE As a result of expanded collaborations with Schering/Plough, Pharmacia and Upjohn, and others, Human Genome Sciences is expanding our Bioinformatics Group, under Mike Fannon, our Director. We have an immediate opening for an ASSOCIATE DIRECTOR - This person would essentially be "second in command" in our growing world-class Bioinformatics group. This position will be filled by someone with 3-5 years of experience in developing user interfaces and managing large quantities of biological data at a staff Bioinformatics Scientist level, preferably in the computer, biotechnology, or pharmaceutical industries. This person must be extremely comfortable in both the computer and biological spheres and has to have a substantial UNIX/Sybase background as well as extensive experience in sequence analysis and database design and manipulation. He or she would be involved in continuing to develop information management solutions to seek out novel genes of therapeutic value from our database of well over one million Expressed Sequence Tags. The ideal candidate must have top notch communication and managerial skills and would be capable of making presentations with and to senior management on short notice (to stock analysts, potential corporate partners, etc.). A Ph.D would be required in either biological or computer sciences. Please send a CV by FAX to 301-340-7159 or reply by E-mail as soon as possible. Human Genome Sciences, Inc. supports and is committed to the principle of equal employment opportunity. It is our policy to recruit, hire, train, and promote individuals, as well as to administer any and all personnel actions, without regard to race, color, national origin, sex, sexual orientation, religion, age, disability, or veteran status. In accord with the provisions of the Civil Rights Act of 1964, as amended. Executive Order No. 11246, as amended, and The Americans and Disabilities Act, this policy fully embraces equality of opportunity with respect to all employment matters, such as recruitment, hiring, compensation, benefits, transfer, promotion, demotion, discharge, layoff, training and development, educational assistance, and social and recreational programs. From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!worldnet.att.net!news.u.washington.edu!enviromicro.fish.washington.edu!user From: herwig@u.washington.edu (Russ Herwig) Newsgroups: bionet.software Subject: Cluster analysis software for RFLP results Date: Wed, 08 Jan 1997 20:03:51 -0800 Organization: University of Washington Lines: 8 Message-ID: NNTP-Posting-Host: enviromicro.fish.washington.edu Any recommendations for (non-commercial or free) cluster analysis software to use for presenting the results from restriction fragment length polymorphism (RFLP) studies. Thanks for your help! -- Russ Herwig University of Washington email: herwig@u.washington.edu From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!agate!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!visi.com!mr.net!newshub.tc.umn.edu!fu-berlin.de!news.th-darmstadt.de!tutor.oc.chemie.th-darmstadt.de!martin From: martin@tutor.oc.chemie.th-darmstadt.de (Martin Kroeker) Newsgroups: bionet.software Subject: Re: Any program to create a spacefilling 3d-model from PDB-files? Date: 9 Jan 1997 17:59:31 GMT Organization: Technische Hochschule Darmstadt Lines: 21 Message-ID: <5b3bm3$1dfr@rs18.hrz.th-darmstadt.de> References: <32c80fbc.16745732@relay.eunet.no> <32d26f72.30021271@news.bham.ac.uk> NNTP-Posting-Host: tutor.oc.chemie.th-darmstadt.de X-Newsreader: TIN [version 1.2 PL2] Stephen Williams (s.m.williams.bcm@bham.ac.uk) wrote: : There is an add on to PovRay to enable it to read PDB files. I only : had a quick look a couple of months back but never got around to using : it properly. E-mail me if you're interested and I'll try to find out : where I downloaded it from. One such program is pdb2pov by one Dr. Eric Suchanek. The latest version i found is 1.19 from 1994, and his email adress given in the readme is apparently no longer valid. I have corrected an off-by-one bug in a loop count in his code and placed it on out ftp server tutor.oc.chemie.th-darmstadt.de - the 'archie' servers should be able to lead you to original/official versions. Martin PS: If anybody knows the current address of Dr.Suchanek, i would appreciate this information. I have added ball-and-stick VRML output recently and would like to consult him before releasing my version. -- Dr.-Ing. Martin Kroeker Inst. f. Organ. Chemie martin@oc2.oc.chemie.th-darmstadt.de Univ. (TH) Darmstadt db7p@hrzpub.th-darmstadt.de Germany From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!uknet!usenet1.news.uk.psi.net!uknet!EU.net!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!leto!news.ou.edu!REX.RE.uokhsc.edu!not-for-mail From: ben@REX.RE.uokhsc.edu (Benjamin Z. Goldsteen) Newsgroups: bionet.software Subject: Re: Any program to create a spacefilling 3d-model from PDB-files? Date: 9 Jan 1997 11:21:03 -0600 Organization: University of Oklahoma Health Sciences Center Lines: 24 Message-ID: <5b39dv$lj1@REX.RE.uokhsc.edu> References: <32c80fbc.16745732@relay.eunet.no> <32d26f72.30021271@news.bham.ac.uk> Reply-To: benjamin-goldsteen@uokhsc.edu NNTP-Posting-Host: etowah.re.uokhsc.edu X-Newsreader: NN version 6.5.0 CURRENT s.m.williams.bcm@bham.ac.uk (Stephen Williams) writes: >On Thu, 02 Jan 1997 17:11:46 GMT, eirikth@eunet.no (Eirik) wrote: >>Want to create / convert a PDB (or similar) file to formats like .3ds >>.Pov. >>Just want a simple represantation, not an acurate. >There is an add on to PovRay to enable it to read PDB files. I only >had a quick look a couple of months back but never got around to using >it properly. E-mail me if you're interested and I'll try to find out >where I downloaded it from. I would be interested in this, too. Also, the program MOLMOL generates POVRAY input files. It might be a bit more than the original reader was looking for but the results are very nice. I can generate full resolution images for printers and slide makers. I have yet to find a method that generates better pictures. >Steve -- Benjamin Z. Goldsteen From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!spool.mu.edu!newspump.sol.net!mindspring!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!portc02.blue.aol.com!newsjunkie.ans.net!newsfeeds.ans.net!lantana.singnet.com.sg!usenet From: "Sutapa (Nupur) Ray" Newsgroups: bionet.software Subject: Help! Software to download data from Casio Digital Diary to PC required. Date: 9 Jan 1997 14:56:35 GMT Organization: OEM Preinstall Lines: 9 Message-ID: <01bbfe3e$0e398a20$81aa15a5@eozfaqvf> NNTP-Posting-Host: ts900-9313.singnet.com.sg X-Newsreader: Microsoft Internet News 4.70.1155 Can anybody give me a software to help me download data from a Casio Digital Diary SF7900 to the PC. I need this to take a backup of the diary which is malfunctioning. Thank you. Jayanta From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!rutgers!news.sgi.com!howland.erols.net!torn!newshub.ccs.yorku.ca!news From: philjs@yorku.ca (Phil Schappert) Newsgroups: bionet.software Subject: Re: aldus pagemaker for sale Date: Thu, 09 Jan 1997 11:36:26 GMT Organization: York University Lines: 19 Message-ID: <32d4d7b5.747732@newshub.ccs.yorku.ca> References: <5aupgu$b21@juliana.sprynet.com> NNTP-Posting-Host: fester03.slip.yorku.ca X-Newsreader: Forte Free Agent 1.1/32.230 naca@interserv.com wrote: >Aldus Pagemaker 3.0 for Mac, $25.00 >Aldus Pagemaker 4.0 for Mac, $40.00 >Software is brand new! Prices include shipping. >e-mail John at naca@interserv.com for ordering information >This is no joke! You might have a better chance of selling this older software in comp.emulators.mac.executor (Mac Executor is a system 6.0.8 emulator for DOS, LINUX and NeXT - check out http://www.ardi.com) Phil --- Phil Schappert Biology, York University Toronto, Ontario, Canada philjs@yorku.ca From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!news-feed.inet.tele.dk!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in1.uu.net!198.6.114.27!intac!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!dsinc!netnews.upenn.edu!news.cc.swarthmore.edu!yue From: yue@swarthmore.edu (Frank Yue) Newsgroups: bionet.software Subject: Re: DNA Software Date: Wed, 08 Jan 1997 11:05:05 -0400 Organization: Swarthmore College Computing Center Lines: 27 Message-ID: References: NNTP-Posting-Host: spidey.swarthmore.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 In article , David Tyler wrote: [snip] > MacVector is the best package I've seen for the Mac, although IMO > Geneworks does some things more prettily. Is MacVector the best Macintosh software for sequence analysis and primer creation? I remember another piece of software called oligo-something, but have not seen it around. I used to work in the molbio field and am now trying to help some collegues to find some quality software for the Mac. One of the primary aspects they are looking for is the creation of oligo primers for amplification. They want the software to be able to determine hairpins, melting points and stabilities in a simple format. Email me since I do not read these groups much anymore. Thanks! -- Frank Yue (Network Administrator) "I didn't do it." Swarthmore College Computing Center -Bart Simpson et. al. yue@swarthmore.edu finger yue@willow.swarthmore.edu for PGP key PGP Fingerprint: 7D 69 D7 5E 77 16 C4 E1 52 6B 87 A6 D3 A9 B3 1E From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!BIOTOP.UMCS.LUBLIN.PL!tchorz From: tchorz@BIOTOP.UMCS.LUBLIN.PL (Marek Tchorzewski) Newsgroups: bionet.software Subject: DNA software Date: 8 Jan 1997 23:07:58 -0800 Organization: Marie Curie-Sklodowska University Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, First of all, Happy New Year 1997 to all of you !!! On the other hand, I need advice concerning programs for DNA and protein analysis. I am going to buy such program however I am not fully determined which program I should purchase. So far, I have seen DNAsis and DNAstar, however I am not sufficiently confident that these programs are reliable, and can provide me with the best options. So, could you advice me, which programs is actually the best on the market. Marek Tchorzewski PhD Univ. of Maria Curie-Sklodowska Dept. of Molecular Biology Lublin, Poland From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!news-xfer.netaxs.com!feed1.news.erols.com!insync!eit.com!news From: Hemant Varma Newsgroups: bionet.software Subject: Fasta Documentation Online? Date: Thu, 09 Jan 1997 12:11:42 -0800 Organization: Pangea Systems Inc. Lines: 19 Message-ID: <32D550FE.794B@panbio.com> NNTP-Posting-Host: berkeley.panbio.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 6.2 IP22) Hello Folks, I have been looking for some comprehensive documentation of FASTA on line. Is there any available online or my best bet is to hit the library and get all the associated papers? Thanks, Hemant -- ------------------------------------------------------- integrating the world of drug discovery ------------------------------------------------------- Hemant Varma hvarma@panbio.com (510) 337-7910 ph Scientific Applications Specialist http://www.panbio.com (510) 522-9394 fx ------------------------------------------------------ P A N G E A S Y S T E M S I N C . From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in1.uu.net!198.80.1.4!interaccess!usenet From: Minh Luu Newsgroups: bionet.software Subject: Mac Program to find Loops??? Date: Thu, 09 Jan 1997 13:37:26 -0500 Organization: InterAccess, Chicago's best Internet Service Provider Lines: 7 Message-ID: <32D53ADE.6666@students.wisc.edu> NNTP-Posting-Host: d162.nwchi.interaccess.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Hello, Please help. I'm looking for a program that will find hair-pin loops/invert or direct repeats etc that also gives *Gs the loops as well. Thanks. Minh From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!worldnet.att.net!ix.netcom.com!news From: jeffhas@ix.netcom.com(Jeffrey Hastings) Newsgroups: bionet.software Subject: Looking for filtering routines for CAD/CAM digitized images Date: 9 Jan 1997 18:11:30 GMT Organization: Netcom Lines: 10 Message-ID: <5b3cci$5e@dfw-ixnews4.ix.netcom.com> NNTP-Posting-Host: spr-ma3-08.ix.netcom.com X-NETCOM-Date: Thu Jan 09 12:11:30 PM CST 1997 I am working on a developing a program for displaying and modifying digitized prosthetic limb sockets. I am interested in finding any software which uses 2D digital filtering and returns the coefficients for the filter. Jeffrey Hastings Shriners Hospital for Children Springfield, Mass. jeffhas@ix.netcom.com From owner-software@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Chana Gabay Newsgroups: bionet.immunology,bionet.molbio.proteins,bionet.molecules.peptides,bionet.software Subject: help: Replacement to Silent ratio calculation Date: 8 Jan 1997 23:07:38 -0800 Organization: The hebrew University of Jerusalem Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <5b25fq$c5@net.bio.net> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.immunology:10607 bionet.molbio.proteins:9678 bionet.molecules.peptides:589 bionet.software:17562 Dear Netters, We are interested in finding the R/S (R=replacement, S= silent) ratio of somatic point mutations in the immunoglobulin variable region genes. This is done by aligning the DNA sequence of the mutated gene to its germline counterpart defining its mutations, and determining their type (replacement or silent mutation). This is done by translating the sequence into a protein and comparing it to the translation of the germline sequence. (A silent mutation in the DNA will produce the same amino acid as is in the germline, while a replacement mutation will give rise to a different amino acid.) Since the random mutation frequency differs for each of the 4 DNA nucleotide bases, one has to introduce these frequencies into the calculation to obtain the expected R/S value for the studied gene. These calculations which lead to determination of the R/S values due to random mutations, could then be compared with the actual R/S ratio and large divergence from the expected random R/S value would suggest that a positive or negative selection process is taking place. I would like to know whether there is an available computer program to calculate the random R/S ratio, and from whom it can be obtained. I would appreciate if anyone could point me in the right direction and please, Cc: to me by e-mail chana_g@gene.md.huji.ac.il -------------------------- as well as to newsgroups. Thanks in advance, Chana Gabay From owner-software@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!rutgers!news.sgi.com!enews.sgi.com!arclight.uoregon.edu!gatech!nntp-xfer.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.software Subject: sequence alignment algorithms Date: Mon, 06 Jan 1997 13:20:56 -0500 Organization: North Carolina State University Lines: 21 Message-ID: <32D14288.5D34@unity.ncsu.edu> NNTP-Posting-Host: sparc5c-2203gardnr.ppath.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.4 sun4m) Hi, I'm new to programming so forgive me if I say something obviously stupid. I'm interested in writing a program to do some primer-design tasks, among other things. The first thing I want the program to do, however, is a multiple sequence alignment. I realise this is like reinventing the wheel, which I'd rather not do. Are there a few "standard" algorithms out there for this task? What about other "standard" molecualr biology algorithms? Also, maybe someone could suggest a few good beginning references for this sort of programing. Thanks! -- Susan http://www4.ncsu.edu/unity/users/s/sjhogart/public/home.html Check this! http://homepage.cistron.nl/~peterh/gsresources/ From owner-software@net.bio.net Thu Jan 09 22:00:00 1997 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!news-han1.dfn.de!news.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: Fasta Documentation Online? Message-ID: Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) Cc: fuellen Date: Fri, 10 Jan 1997 11:27:42 GMT To: Hemant Varma References: <32D550FE.794B@panbio.com> Nntp-Posting-Host: salbei.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Lines: 32 In article <32D550FE.794B@panbio.com>, Hemant Varma writes: |> Hello Folks, |> I have been looking for some comprehensive |> documentation of FASTA on line. Is there any available online |> or my best bet is to hit the library and get all the associated |> papers? Some transcripts of online Lectures by Dr. Pearson can be found at http://www.techfak.uni-bielefeld.de/bcd/Lectures/pearson3.html http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Lectures/pearson3.html http://www.biotech.ist.unige.it/bcd/Lectures/pearson3.html (Mirrors provided by David Steffen / MBCR, Baylor and Paolo Romano / CBA, Genoa) -- best wishes, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@mit.edu http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html |> Thanks, |> |> Hemant |> |> -- |> ------------------------------------------------------- |> integrating the world of drug discovery |> ------------------------------------------------------- |> Hemant Varma hvarma@panbio.com (510) 337-7910 ph |> Scientific Applications Specialist |> http://www.panbio.com (510) 522-9394 fx |> ------------------------------------------------------ |> P A N G E A S Y S T E M S I N C . From owner-software@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!news.uoregon.edu!news.hn.netlink.co.nz!clear.net.nz!news From: "The Gamers Share Net" Newsgroups: bionet.software Subject: Help, Games inofmration required at http://wsite.com/shareware Date: 10 Jan 1997 21:56:43 GMT Organization: LML Computing Lines: 1 Message-ID: <01bc0012$8f7d5be0$503261cb@xtr968878.xtra.co.nz> NNTP-Posting-Host: d1-u16.wgtn.clear.net.nz X-Newsreader: Microsoft Internet News 4.70.1155 Please visit me From owner-software@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!news-stkh.gsl.net!news.gsl.net!eru.mt.luth.se!news.algonet.se!hammer.uoregon.edu!arclight.uoregon.edu!worldnet.att.net!newsfeed.internetmci.com!iol!not-for-mail From: support@netsoft.ie (Albert Graham) Newsgroups: bionet.software Subject: NetSoft Announces Shareware Date: Fri, 10 Jan 1997 21:01:37 GMT Organization: NetSoft Computer Networks Lines: 165 Message-ID: <5b6ale$emb$109@nuacht.iol.ie> Reply-To: support@netsoft.ie NNTP-Posting-Host: dialup-021.galway.iol.ie X-Newsreader: Forte Free Agent 1.0.82 ------------- NEW SHAREWARE ANNOUNCEMENT --------------------- NetSoft LAN The complete peer-to-peer Network Operating System for DOS and Windows PC's and Laptops. Brief Description: ------------------ NetSoft LAN allows you to share any Hard Disk, Floppy Disk, CDROM Drive or even RAM Disk (compatible with any Disk Cache and any Compressed or Logical Drives. Any Dot Matrix or Laser Printer (Serial or Parallel) with other Network Users. Runs all Multi-user and single user software. NetSoft LAN includes Serial Port and Parallel Port Drivers that allow you to set-up a true network using a simple Null Modem cable or Laplink compatible parallel cable. In addition to the Serial and Parallel Zero-Slot networking you can add Ethernet Cards, Arcnet Cards and Modems or any combination. This allows you to create networks using old and new hardware and any existing cabling. the hardware is completely transparent to any software. NetSoft LAN is a true peer-to-peer Network Operating System. Company Name: NetSoft Computer Networks., 20 Sea Road, Galway, Ireland. Phone : (Ireland) +353 91-529607 Web Site : http://www.netsoft.ie/ : We also have a number of mirror sites. Contact Name: Albert Graham Email : agraham@netsoft.ie Software : NetSoft LAN - Complete Local Area Network Operating System for DOS and Windows PC's and Laptops. Version : Version 1.40a Platforms : DOS 3.1 or higher : Windows 3.0, Windows 3.x. Windows for Workgroups 3.x (Win95 will be available shortly) : Requires min. 18k Memory, Runs on any PC using 8086 : 80286, 80386, 80486, Pentiums and compatibles. File Name : NSLAN140.ZIP or NSLAN140.EXE Program Size: 292K zipped (about 500k unzipped) Supports : Up to 255 Users Price : $199.00 for Site License (Upto 255 Users). Status : Shareware version available, requires access codes : to unlock the 2 User Limitations and Nag messages Distribution: Primary sites: -------------- http://www.netsoft.ie/ http://www.netaccess.ie/~netsoft/ http://www.iol.ie/~agraham/ http://www.webdevelop.com/ Secondary sites: ---------------- Keith Petersen's Simtel.Net and mirror sites Coast to Coast Software Repository and mirror sites. Garbo archives and mirror sites. Documentation: The Netsoft LAN User's Guide is about 340 Pages. It's of the highest quality and is available on-line and in download-able formats (HP LaserJet and PostScript). Our "On-line Search Engine" allows you to search the entire User's Guide and On-line documentation from the WWW. For the most part, NetSoft LAN is self-documenting. History : Development of NetSoft LAN was started in 1989, as a true MS-NET and IBM PC LAN compatible network operating system for DOS, Windows and Desqview. The development has continued full-time for the past seven years and continues to do so. NetSoft LAN is 100% Winnet Compatible, which means Windows Based PC's can take directly to DOS based PC's etc. NetSoft LAN is Desqview and QEMM aware and compatible. The software has been tested extensively on all hardware from the original IBM PC with 256k RAM to the latest Pentium based machines. It's compatible with all known Ethernet Cards and Arcnet Cards. The Installation includes support directly for more than 125 Ethernet Cards and over 450 Modems (for Wide Area Networking) May also be installed as a secondary network OS, if you also require another network system. One of our primary goals was to make the installation as easy and simple as possible. 1. There are NO command line parameters. 2. There are NO CONFIG.SYS parameters or drivers. 3. There are NO AUTOEXEC.BAT parameters. All network configuration parameters are stored in a single ASCII test file. NetSoft LAN includes a complete "Network Set-up Program" that allows complete configuration without having to edit and files manually on your system. All the NetSoft LAN program files are self-aware and cannot be infected by any virus. Features : Includes everything and more than you'd expect from a product of this type. There are too many features to mention here. Tech Support: Technical Support is available free of charge via Phone, and email (support@netsoft.ie). --------------------- END of ANNOUNCEMENT ----------------------- Albert Graham (support@netsoft.ie) ------------------------------------------------------------- Download NetSoft LAN Version 1.40a Network Operating System for DOS and Windows PC's and Laptops. New Shareware Version. ------------------------------------------------------------- NetSoft LAN is a Complete Peer-to-Peer Local Area Network Includes easy netsetup program, server software, client software printer spooler,DOS Station Manager Remote Control, MS-NET and IBM PC LAN compatible. Includes Windows Network Drivers. for Windows 3.x and WFW 3.x Supports. Ethernet Cards, Arcnet Cards, Serial Ports, Parallel Portsand Modems. http://www.netsoft.ie/ ------------------------------------------------------------- From owner-software@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!EU.net!Belgium.EU.net!news From: Luyten Philippe Newsgroups: bionet.software Subject: Mega format Date: Sat, 11 Jan 1997 22:27:56 +0100 Organization: ping.be Lines: 3 Message-ID: <32D805DC.2AF1@ping.be> NNTP-Posting-Host: dialup15.namen.eunet.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) how to format HD disk in 2 mega density? many thanks Phil From owner-software@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!agate!spool.mu.edu!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.idt.net!cdc2.cdc.net!news.texas.net!uunet!not-for-mail From: henryl@connectnet.com (Henry Lee) Newsgroups: bionet.software Subject: Free Demo: Program Reversibly Translates Chemical Names to Structures Date: Sat, 11 Jan 97 10:59:31 PST Lines: 15 Message-ID: <5b8nlm$b1m@news1-alterdial.uu.net> NNTP-Posting-Host: henryl.connectnet.com Mime-Version: 1.0 X-Newsreader: WinVN 0.93.6 Chemistry 4-D Draw is an innovative program that combines three components in a package: easy-to-use drawing program, NamExpert, and Nomenclator. The program allows you to obtain high-quality structures quickly by entering molecular names. It also assigns systematic names to structures according to IUPAC rules. The program includes a full set of tools for drawing and text editing. Features include 3D-rotation, 256 colors, syntax checking, drag & drop to export pictures, import and export MDL MOL files. Chemistry 4-D Draw is the only commercially available program providing all these drawing and nomenclature capabilities. For more information and a FREE demo, see http://www.cheminnovation.com From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!agate!howland.erols.net!worldnet.att.net!arclight.uoregon.edu!news.bc.net!torn!nott!standby.nrc.ca!ratilal From: Pierre Juteau Newsgroups: bionet.software Subject: Looking for computer program for MPN calculation Date: Sat, 11 Jan 1997 16:58:34 +0000 Organization: Institut de Recherche en Biotechnologie Lines: 22 Message-ID: <32D7C6BA.66E@biotech.lan.nrc.ca> Reply-To: juteau@biotech.lan.nrc.ca NNTP-Posting-Host: 132.246.220.188 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) I am looking for a computer program (freeware or shareware) to make calculations for most probable number (MPN) assay. I would prefer this method instead of using tables. I found the code for a Basic program in Methods for General and Molecular Bacteriology (ASM, 1994), but it doesn't compute the error statistics. Is anybody know something better? Thank you for your help. Pierre -- ______________________________________________________________________ Pierre Juteau, M.Sc. Biotechnology Research Institute (NRC) Laval University 6100 Royalmount Avenue Chemical Engineering dept. Montreal, Quebec, Canada Sainte-Foy, Quebec, Canada H4P 2R2 G1K 7P4 (514) 496-2886 (418) 656-2634 pierre.juteau@nrc.ca ______________________________________________________________________ From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!harbinger.cc.monash.edu.au!news.latrobe.edu.au!lion.cs.latrobe.edu.au!not-for-mail From: bangg@compsoc.cs.latrobe.edu.au ( ** B A N G G **) Newsgroups: bionet.software Subject: Greek Multimedia ! Date: 11 Jan 1997 00:35:59 GMT Organization: Comp.Sci & Comp.Eng, La Trobe Uni, Australia Lines: 59 Message-ID: <5b6n9f$m2n@lion.cs.latrobe.edu.au> NNTP-Posting-Host: compsoc.cs.latrobe.edu.au X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] GREEK MULTIMEDIA!!!!!!!!!!!!!!!!!!! A fun way to learn Greek from an Australian Company called BP Software! The "Electronic Alphabet" is the brain child of two Greek Australian teachers Nick Bogiannidis and Jim Polites. Jim and Nick have had decades of experience at teaching Greek and Computer Studies to children born in both government and non government schools. The "Electronic Alphabet" encourages and helps children to: * Read * Write * Colour * Solve puzzles * Listen to Greek music and speech * Develop memory skills * Enrich there vocabulary * Enjoy learning Greek The "Eletronic Alphabet" is an excellent program for the learning of Greek, directed at children of a primary school age and at students with a limited knowledge of Greek. --- The program features animated presentations and enjoyable educational games and activities. It is a modern, interactive program full of attractive graphics, music, movement, sound effects and speech. It is simple and easy to use. For an enjoyable approach to the teaching of Greek lanuage, the "Electronic Alphabet" is a must in every classroom and every home! The CD sells for $120.00 AUSTRALIAN dollars. To order your copy or ask any further details send mail to: nickb@source.com.au OR Phone BP Software in Australia on 61 (03) 9850 2911 BP Software PO Box 411 Bulleen 3105 Melbourne, Victoria AUSTRALIA! PS: We are currently under the process of getting a www page running. Look out for it and spread the news about this exciting new product! . From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: Looking for antigenicity software Date: 12 Jan 1997 16:33:31 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 28 Message-ID: <5bb3or$irg@gap.cco.caltech.edu> References: <5b0sa7$k0t@erika.cica.es> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <5b0sa7$k0t@erika.cica.es>, bb1rofra@uco.es (Antonio Rodriguez Franco) writes: >I am trying to raise polyclonal antibodies using a short oligopeptide >stick to albumin. > >Is there any reliable software in which to test the antigenicity and >surface probability of my sequence? There is the program ANTIGENIC which is part of the EGCG package (which means you also have to have GCG). ANTIGENIC ANTIGENIC looks for potential antigenic regions using the method of Kolaskar. ANTIGENIC DESCRIPTION Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar (1990); FEBS Letters 276:172-174 "A semi-empirical method for prediction of antigenic determinants on protein antigens." Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!math.ohio-state.edu!jussieu.fr!fdn.fr!r2d2.fdn.org!med.univ-tours.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!pasteur.fr!oleane!calvacom!dd11 From: dd11@calvanet.calvacom.fr (Dominique Delefortrie) Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: ?? Kinetics Software - Post Date: Sun, 12 Jan 1997 20:09:52 +0100 Organization: CalvaCom Data Networks International Communications Lines: 14 Message-ID: <19970112200952561895@mar17.calvacom.fr> References: <32AEF4BF.5C7A@apl.washington.edu> <32BF3C94.4319@cam.org> <32D42DD6.70A3@sbphrd.com> NNTP-Posting-Host: mar22.calvacom.fr X-Newsreader: MacSOUP F2.2b5 Xref: biosci bionet.software:17586 bionet.molbio.proteins:9711 bionet.molbio.methds-reagnts:53398 William P Prichett wrote: > I would like to add to the list of Kaliedagraph users. I really like the > easy of use, especially the non linear curve fit. Very simple. Synergy I do agree ! It is very simple to enter the equation of the studied phenomenon, e.g. the Michaelis-Menten equation, and plot against it ! There exists also a not-so-bad shareware : EnzymeKinetics 1.3 Demo along with numerous models -- <> (-8 DD From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!EU.net!Norway.EU.net!sn.no!hermod.uio.no!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!news-han1.dfn.de!news.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: sequence alignment algorithms Message-ID: Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) Date: Sun, 12 Jan 1997 19:38:35 GMT To: Susan Jane Hogarth References: <32D14288.5D34@unity.ncsu.edu> Nntp-Posting-Host: salbei.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Lines: 33 In article <32D14288.5D34@unity.ncsu.edu>, Susan Jane Hogarth writes: |> [..] multiple sequence alignment. [..] Are there a few "standard" algorithms |> out there for this task? What about other "standard" molecualr biology |> algorithms? |> |> Also, maybe someone could suggest a few good beginning references for |> this sort of programing. A couple of resources, including a tutorial I wrote for an online course, are listed at http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html (the Multiple Alignment Internet Resource Summary). I'd like to take the chance to ask everyone to please MAIL ME ADDITIONS, CORRECTIONS, etc. I'll update the list, and the newest version will be kept available at the URL above, and its mirrors at http://www.biotech.ist.unige.it/bcd/Curric/MulAli/welcome.html http://merlin.mbcr.bcm.tmc.edu:8001/bcd/MulAli/Curric/welcome.html Also, if you're interested to test beta Perl code for handling multiple alignments, please drop me a note ! (Despite some delays, it's very likely that we can post an announcement to prospective testers in 2-3 weeks.) --- best wishes, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@MIT.EDU http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html |> Thanks! |> -- |> Susan |> |> http://www4.ncsu.edu/unity/users/s/sjhogart/public/home.html |> Check this! http://homepage.cistron.nl/~peterh/gsresources/ From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!portc02.blue.aol.com!newsfeed.pitt.edu!bb3.andrew.cmu.edu!nntp.sei.cmu.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!infoserver.bgsu.edu!woody.wcnet.org!usenet From: "George Baty" Newsgroups: bionet.software Subject: Looking for Software for Conventions Date: 12 Jan 1997 17:07:18 GMT Organization: Cresset Chemical Company Lines: 16 Message-ID: <01bc00ab$804f0080$4bab85cd@default> Reply-To: "George Baty" NNTP-Posting-Host: ts75.wcnet.org X-Newsreader: Microsoft Internet News 4.70.1155 I would like to get some software to assist in help running a non-profit 300 person convention. (This group thinks I'm a computer junkie, I'm not, ...when all I did was miss a meeting.) If possible, I would like the software to help keep track of the attendees, their fees, where they are staying, payments, as well as other convention related items. If you have experience using any of these packages I would also appreciate that knowledge. Thanking you in advance, George Baty gbaty@wcnet.org From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!news.idt.net!cdc2.cdc.net!newsfeed.concentric.net!news-master!news From: "Ed Williams" Newsgroups: bionet.software Subject: Time Expired Software! Date: 12 Jan 1997 23:50:44 GMT Organization: Concentric Internet Services Lines: 15 Message-ID: <01bcd759$9692de40$b355adce@CRC3.concentric.net> NNTP-Posting-Host: 61037d0023at.concentric.net X-Newsreader: Microsoft Internet News 4.70.1155 How do you get around "Timed expired software."? I would like to post a page on my web site (http://www.cris.com/~elwm/Win95_hpage.htm) about this subject. If you know techniques on how to get around "time expiring software," please forward your idea to me. I will post it and give credit if you would like. If you want your name posted with your submission, please state so in your e-mail message. Thank you! Eddie From owner-software@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!newsxfer.itd.umich.edu!news.mtu.edu!not-for-mail From: huang@mtu.edu (Xiaoqiu Huang) Newsgroups: bionet.software Subject: Analysis and Annotation Email Server Date: 12 Jan 1997 17:56:22 -0500 Organization: Michigan Technological University Lines: 32 Message-ID: <5bbq6m$gk4@string.cs.mtu.edu> NNTP-Posting-Host: string.cs.mtu.edu X-Newsreader: TIN [version 1.2 PL2] We like to announce an email server for comparing a genomic DNA sequence against SwissProt and d