From owner-software@net.bio.net Sat Jul 01 23:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!EMBL-EBI.ac.uk!apweiler From: apweiler@EMBL-EBI.ac.uk (Rolf Apweiler) Subject: Re: Alignment Soft. on Internet Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Sat, 1 Jul 1995 10:46:16 GMT Lines: 22 Reply-To: apweiler@EMBL-EBI.ac.uk (Rolf Apweiler) References: Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-32 In article , Osman El-maarri writes: > >Hi there, > >I am looking for a common-share program on the internet that can do >on-line sequence alignment by E.mail ( using Lynx, Mosaic,... ), It does >not have to be free of charge ! > >Osman El-maarri >Bogazici University >Department of Molecular Biology and Genetics >Bebek 80815, Istanbul, Turkey > Try the following URL: http://www.ebi.ac.uk/searches/searches.html Hope that helps. Rolf Apweiler (SWISS-PROT Protein Sequence Data Bank Coordinator) From owner-software@net.bio.net Sat Jul 01 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!ari.net!news-admin From: Soon Paik Newsgroups: bionet.software Subject: Re: Alignment Soft. on Internet Date: 2 Jul 1995 05:25:10 GMT Organization: Lombardi Cancer Center Lines: 4 Message-ID: <3t5ajm$gva@ari.net> References: NNTP-Posting-Host: pppaiks.ari.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:Pine.ULT.3.91.950701125448.15053B-100000@hisar.cc.boun.edu.tr Why not use shareware MACAW (both for Mac and Windows), which is super, on your PC? From owner-software@net.bio.net Sat Jul 01 23:00:00 1995 Path: biosci!rutgers!gatech!news.uoregon.edu!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: Sequence Analysis -- Linux Binaries? Date: 2 Jul 1995 07:02:21 GMT Organization: University of Washington Genetics Lines: 18 Message-ID: <3t5g9t$1h3@nntp3.u.washington.edu> References: <3snb8g$95f@mark.ucdavis.edu> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: PHYLIP can easily be compiled on Linux Keywords: Linux, sequence analysis, phylogenies, PHYLIP In article <3snb8g$95f@mark.ucdavis.edu>, Alan Williams wrote: >I'm interested in any sites that have linux binaries for doing DNA/RNA >sequence analysis (ie GDE, fsap, blast, plasmid mapping, ....) Thanks alot. As far as I know, PHYLIP binaries for Linux are not available by ftp (and I wouldn't particularly encourage it because the endlessly changing Linux library versions make it hard to be widely compatible). But PHYLIP does compile "out of the box" on Linux with gcc. Just uncompress and un-tar our archive into a directory, and type "make all". So you make your own binaries with no difficulties. It has to work on Linux because I have Linux on my laptop. ----- Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!europa.chnt.gtegsc.com!news.sprintlink.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!swrinde!news.uh.edu!jane.uh.edu!biolfc From: biolfc@jane.uh.edu (Chang, Yu Y) Newsgroups: bionet.software Subject: Re: Alignment Soft. on Internet Date: 3 Jul 1995 15:46 CDT Organization: University of Houston Lines: 17 Distribution: world Message-ID: <3JUL199515464668@jane.uh.edu> NNTP-Posting-Host: jane.uh.edu News-Software: VAX/VMS VNEWS 1.41 >I am looking for a common-share program on the internet that can do >on-line sequence alignment by E.mail ( using Lynx, Mosaic,... ), It does >not have to be free of charge ! > >Osman El-maarri >Bogazici University >Department of Molecular Biology and Genetics >Bebek 80815, Istanbul, Turkey For multiple sequence alignment, check out the URL using Netscape (or some Web browser that supports forms): http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html Mick From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!biosci!not-for-mail From: bbrush@unixg.ubc.ca (Brad Brush) Newsgroups: bionet.software Subject: Bioscan on disk info wanted Date: 3 Jul 1995 14:28:11 -0700 Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 6 Sender: biohelp@net.bio.net Distribution: world Message-ID: <3t3tas$4bh@interchg.ubc.ca> NNTP-Posting-Host: net.bio.net I am considereing buying Bioscan on disk, a reference source for biotechnology companies ($1000 US). I have seen the hard copy (10kg) and I have inquired regarding the program's ability to export into a DBF format. The company seems very fuzzy on that. Does anyone have any experience with this program. We cannot afford to send away almost $1500 Cdn and not have a working program. From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!biosci!not-for-mail From: billh@lisboa.ks.uiuc.edu (William F. Humphrey) Newsgroups: bionet.announce,bionet.software Subject: Announcing the Program namd Date: 3 Jul 1995 14:13:14 -0700 Organization: University of Illinois at Urbana Lines: 91 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <3t4uve$kba@vixen.cso.uiuc.edu> NNTP-Posting-Host: net.bio.net Keywords: molecular dynamics Xref: biosci bionet.announce:2251 bionet.software:12577 Announcing the Program namd --------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability the program namd, a new package for high performance parallel molecular dynamics simulations. This software is being made available to the structural biology research community free of charge, and includes the source code for namd, documentation, and precompiled binaries for various parallel platforms The documentation, in postscript form, includes a programmers guide and a users guide. Obtaining namd ------------- A more complete description of namd is available via the namd WWW home page: http://www.ks.uiuc.edu:1250/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd Features -------- namd is a molecular dynamics program designed to provide high performance simulations for large biological molecular systems. Specifically, namd achieves high performance by exploiting the power of parallel computers and by providing a modular design that facilitates the implementation of new algorithms. A high degree of modularity is obtained by using an object-oriented design and implementation in C++. namd uses spatial decomposition coupled with a multithreaded, message-driven design, which provides a scalable, efficient parallel framework. namd also incorporates the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the Scientific Computing group at Duke University, which allows full electrostatic force evaluation in O(N) time. As part of the MDScope system, namd is connected via the communication system MDComm to the molecular graphics program VMD (also developed by the Theoretical Biophysics group) to provide such an interactive system where researchers can view and interact with a running simulation. The program has many features, which include: o Input and output file compatibility with X-PLOR o CHARMM19 and CHARMM22 parameter support o Support for traditional MD functions such as energy minimization, velocity rescaling, harmonic boundary conditions, harmonic atom restraints, etc. o Full electrostatic evaluation using DPMTA from Duke University integrated using a multiple timestep integration scheme. For more information on DPMTA, see the Scientific Computing home page at: http://www.ee.duke.edu/Research/SciComp.html o Spatial decomposition for O(N/P) scalability of memory, computation, and communication. o Message-driven, multithread design for high performance parallel execution. o Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure. o Portable parallelism provided by PVM and Charm++ communication systems o Integration with the program VMD, a molecular graphics program developed in the Theoretical Biophysics Group at the University of Illinois. See the VMD WWW home page for more info: http://www.ks.uiuc.edu:1250/Research/vmd VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communications package (called MDComm) constitute the 'MDScope' environment. Availability ------------ namd should run on any parallel platform with a C++ compiler and PVM version 3.3.6 or later. Tested Makefiles are included for clusters of HP, SGI, and IBM workstations, Cray T3D, and Convex Exemplar. Precompiled binaries are provided for HP and SGI workstations. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. This project is funded by the National Institutes of Health and the National Science Foundation. -- /* Bill Humphrey (billh@ks.uiuc.edu) */ /* Theoretical Biophysics | Nothing matters but */ /* University of Illinois | the weekend, from a */ /* 3117 Beckman Institute _______| Tuesday point of view */ /* 405 North Matthews | phone: (217) 244-1851 */ /* Urbana, IL 61801 | fax: (217) 244-6078 */ From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!biosci!not-for-mail From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: embnet.general,bionet.software.gcg,bionet.software,bionet.general,bionet.announce Subject: Announcement: EGCG 8.0 (beta) release Date: 3 Jul 1995 14:13:35 -0700 Organization: The Sanger Centre Lines: 128 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software.gcg:1286 bionet.software:12578 bionet.general:16019 bionet.announce:2254 EGCG 8.0 ======== Introduction ============ The EGCG package of entensions to the GCG (Wisconsin) sequence analysis package is now available as a beta release. A report on EGCG 8.0 is included in the latest issue of embnet.news, available from the following sources: URL http://www.sanger.ac.uk/~pmr/egcg.html (EGCG article) URL http://www.dl.ac.uk/embnet.news/vol2_2/contents.html (vol 2, no. 2) Throughout the development of the EGCG package, there have been excellent collaborations with the EMBnet community. Academic software such as EGCG, developed for a limited number of users, cannot under normal circumstances be maintained to a sufficient standard for reliable public use. Only the large number of EMBnet users, and the efforts of the EMBnet support personnel, have made it possible to produce a robust package. In return, we receive many suggestions for further developments which we can provide and test locally and then easily incorporate into the next release. The EGCG team have fixed the major problems reported by the pre-beta testers. The beta release should work correctly on Irix 5.2, OSF/1 V3.0, Solaris 2.3 and OpenVMS-AXP V6.1 systems. Distribution ============ EGCG is no longer distributed with GCG. We prefer to distribute the package directly to users through FTP, allowing us to more rapidly provide new programs and updates, and to keep control of our own software. The EGCG programs are distributed freely to academic users throughout the world. The only requirement is that users must have a valid GCG licence to build the programs. We have a new E-mail address for support. All questions and comments about EGCG can now be sent to egcg@embnet.org . The main distribution site is at The Sanger Centre, Hinxton, UK. Anonymous FTP: ftp.sanger.ac.uk directory: pub/pmr/egcg8 (main distribution in .tar.Z format) directory: pub/pmr/egcg8vms (.bck format for for VMS sites) The EGCG programs can be installed as a single copy on a mixed unix or VMS cluster. Separate directories are used for the system-specific files (object files and image files). Release Notes ============= EGCG 8.0 supports GCG release 8.0. The Unix and VMS sources are identical. Many programs have been significantly improved since the last Unix and VMS releases of EGCG 7. We are working on full release notes to document the changes. Highlights of EGCG 8.0 include: * All programs now run on Unix and VMS (many were VMS only in EGCG 7). These include MAPSELECT which creates local enzyme data files; PEPCOIL which identifies coiled-coil regions and leucine zippers; NEWFEATURES which analyses and edits the EMBL feature table; TPROFILESEARCH which compares protein profiles to DNA databases; and PEPALLWINDOW which plots hydrophobicity for aligned sequences. * New programs in release 8.0 include POLAND which simulates transition curves for DNA and RNA; PRETTYBOX which produces shaded sequence alignments; and STSSEARCH which searches a DNA database for matches to primer pairs * The EQuickSearch programs remain fully supported and enhanced in EGCG. * PRETTYBOX is now an EGCG program. * Colour options are added to PRETTYPLOT and several other programs. * Single source version for Unix and VMS to make code management easier. * EGCG procedure libraries EGENLIB and EGENAPPLIB. * Standardized user prompts in all programs. * Full command line control. * All programs can be run in batch (postponed until GCG 8.1 is released). * Standardized and simplified graphics routines. * E-mail support from the EGCG team egcg@embnet.org Into the Future =============== Since EGCG was first released with GCG, it has become very popular at a number of sites around the world. We now have a backlog of program submissions to include in EGCG which we plan to add as soon as the C interface to the procedure library is in place. Contributing authors in the backlog include William Pearson and Rainer Fuchs. Additional contributions are always welcome. Acknowledgements ================ We are very grateful to (in alphabetical order) Rein Aasland, Wilhelm Ansorge, Peer Bork, Thure Etzold, Toby Gibson, Tom Kristensen, David Mathog, Franc Pattus, Kate Rice, Christian Schwager, Peter Sibbald, Julie Thompson, Hartmut Voss, Gert Vriend and Rick Westerman for their many contributions and critical comments as users of the EGCG Programs. We are also deeply indebted to the staff of GCG Inc. who provided rapid and helpful answers to our many questions during the development of the programs. Many thanks to Irv Edelman, Maggie Smith, Donald Katz, Michael Hogan, Joseph King, Lynn Miller, Mary Schulz and especially John Devereux. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 From: Gleason.Pace@f37.n105.z1.fidonet.org (Gleason Pace) Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!psgrain!armon!jina!fredmail Newsgroups: bionet.software Subject: Plasmid drawing software Message-ID: <804802529.AA00159@jina.rain.com> Date: Sun, 02 Jul 1995 11:32:00 -0800 X-FTN-To: Mike Holloway Lines: 40 Hello Mike! 01 Jul 95 20:36, Mike Holloway wrote to All: >> WHY DO PEOPLE WANT SUPERB, FEATURE-RICH SOFTWARE BUT DON'T >> EXPECT TO PAY FOR IT??? MH> I don't think anyone is suggesting that someone doing good work MH> shouldn't be allowed to make a living. That's not the issue in MH> this recurring problem, which isn't going away, and will only get MH> worse as the federal budget is cut. The problem is that we can't MH> afford to pay, yet we need the software. Mol bio software, often MH> buggy as hell, limited in function, and with difficult to use MH> interfaces, seem always priced just out of our reach. MH> Individual labs simply do not have the budgets for it. >> So, if you want someone to creeate this >> great software, remember that they will need to do it full-time, >> and they'll need to get paid. MH> Seems to me that NCBI tried doing something about it, organizing MH> software development, AND employing programmers. They COULD MH> budget for supporting programmers. But the programmers cried MH> bloody murder and put a stop to it. The field sure has taken off MH> since then hasn't it? Yup. MH> It should be plain to everyone by now. Individual labs can not MH> support the development of the kind of software we need. This is MH> not going to change any time in the future. My, this is a familiar discussion. Also very close to interests of mine since I am a shareware author and a possesor of BA & BS in biological fields which doesn't put me on the same level as some of you, I know. Also I am speaking to you from the Land of Fido. But enough of disclaimer. *:-> The fact is that some generous souls have written quality software of one sort or another and just given it away. I suspect that these people often are well situated enough that they can well aford it, playful enough to enjoy the considerable work that certainly is involved and humble enough to remember times when they dearly appreciated such things. Some of us really do appreciate. But the tendency of the mass is to think that if some can do it, why can't most or even all? On the other hand, nobody expects computer hardware to be free, or lab equipment. By the way, there is a university that I know of where the professors all donate their time; wouldn't you like to come teach there.... Limited budgets? Sure, but it's also a matter of priority isn't it? Gleason From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!sal!akkiraju From: akkiraju@sal.cs.uiuc.edu (Nataraj Akkiraju) Newsgroups: bionet.software Subject: Software for computing Solv. Acc. Surf. Area derivatives Date: 3 Jul 1995 20:09:41 GMT Organization: University of Illinois at Urbana Lines: 20 Message-ID: <3t9iq5$1bj@vixen.cso.uiuc.edu> NNTP-Posting-Host: sal.cs.uiuc.edu I am looking for some publicly available software for computing solvent accessible surface area derivatives. I am aware that 2 programs ANAREA and MSEED do this. I am interested in getting a copy of ANAREA that computes solvent accessible surface area derivatives. If you have any information about this, please send me some mail at akkiraju@cs.uiuc.edu I do not read this newgroup regularly, so I would appreciate an email response. Nataraj. From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!europa.chnt.gtegsc.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!bloom-beacon.mit.edu!news.bu.edu!news3.near.net!saturn.caps.maine.edu!dartvax.dartmouth.edu!usenet From: Matthew Koff Newsgroups: bionet.software Subject: Re: Bibliographic software Date: 3 Jul 1995 18:48:05 GMT Organization: Dartmouth Medical School Lines: 6 Message-ID: <3t9e15$ajv@dartvax.dartmouth.edu> References: <3t11ec$ka3@ecnits.ecn.nl> NNTP-Posting-Host: kip-dms-79.dartmouth.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:3t11ec$ka3@ecnits.ecn.nl I have used Reference Manager and EndNote. I like them both.. They both work beautifully. Unfortunately they are not freeware! Matt From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!seunet!news2.swip.net!plug.news.pipex.net!pipex!dish.news.pipex.net!pipex!edi.news.pipex.net!pipex!europa.chnt.gtegsc.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!bloom-beacon.mit.edu!news.bu.edu!news3.near.net!saturn.caps.maine.edu!dartvax.dartmouth.edu!usenet From: Matthew Koff Newsgroups: bionet.software Subject: (no subject) Date: 3 Jul 1995 18:22:26 GMT Organization: Dartmouth Medical School Lines: 17 Message-ID: <3t9ch2$ajv@dartvax.dartmouth.edu> NNTP-Posting-Host: kip-dms-79.dartmouth.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.software I would appreciate any advice on software to use for sequence alignment. Looking to align gene sequences ranging from 100-8,000 kb. I have used GCG in the past to do this, and don't have access to the program.. Are there any shareware programs that could do this and give me a percent similarity between molecules? Any suggestions would be greatly appreciated. Thanks are extended in advance!! Please post or E-Mail me directly.. mkoff@coos.dartmouth.edu Thanks again- Matt Koff From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!biosci!not-for-mail From: thompson@carbo.vadms.wsu.edu (Steve Thompson) Newsgroups: bionet.announce,bionet.biology.computational,bionet.molbio.evolution,bionet.molbio.bio-matrix,bionet.software,bionet.software.gcg Subject: Final Call for Participation: BioComputing Education Workshop @ PSBI Date: 3 Jul 1995 14:13:04 -0700 Organization: WSU VADMS Center Lines: 236 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: Reply-To: thompson@ribozyme.vadms.wsu.edu NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:2249 bionet.biology.computational:691 bionet.molbio.evolution:3074 bionet.molbio.bio-matrix:591 bionet.software:12576 bionet.software.gcg:1285 Dear Colleague, Please find enclosed the final "Call for Papers, Demonstrations and Participation" for the upcoming workshop on Biocomputing Education: Challenges and Opportunities to be held as part of the First Pacific Symposium on Biocomputing (PSB-I), the agenda of which can be found following the Call. We are excited about this meeting and the workshop. To the best of our knowledge (and please correct us if you have knowledge that we are wrong), this will be the first time that a forum on educational issues will be included in a meeting on computational approaches to molecular biology. We would especially like your comments regarding what you think are the most important issues in biocomputing education. Plan to submit a paper if you can, but at least mark the meeting on your calendar and consider joining us in Hawaii next year. Regards, Susan J. Johns Steven M. Thompson A. Keith Dunker +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ CALL FOR PAPERS, DEMONSTRATIONS AND PARTICIPATION Biocomputing Education: Challenges and Opportunities First Pacific Symposium on Biocomputing Ritz Carlton Hotel, Big Island, Hawaii --- January 3-6, 1996 Susan J. Johns, Steven M. Thompson, and A. Keith Dunker Visualization, Analysis and Design in the Molecular Sciences (VADMS) and the Department of Biochemistry and Biophysics Washington State University Pullman, WA 99164-1224 & 4660 Phone: (509) 335-0424 & 335-5322 FAX: (509) 335-0540 & 335-9688 E-mail: prcadms@jaguar.csc.wsu.edu thompson@jaguar.csc.wsu.edu dunker@jaguar.csc.wsu.edu The need for a forum on educational issues: Philosophically, we have come to the view that computer science is to molecular biology as calculus is to physics, yet at present there is really no well defined curriculum for computational molecular biology. Although specific individuals have developed courses or workshops, educational materials such as textbooks or laboratory exercises based on existing courses or workshops are not widely available. In addition to the absence of formal materials, there is also a lack of communication among those of us who are now teaching courses in this domain. Correcting the deficiencies regarding the lack of educational materials and the lack of communication on educational issues represents both a challenge and an opportunity for the community of scientists who are currently doing research in biocomputing. A workshop: Recognizing the need for the development of an educational forum, the Pacific Symposium on Biocomputing (PSB) has included our workshop on biocomputing education as part of its overall program. Our hope is that this workshop on biocomputing education will become an important node with regard to the dissemination of educational materials, information, and approaches in this field. To the end of improving communication, we encourage your formal or informal participation at our workshop on educational issues. Bring your course outlines, syllabi, laboratory exercises, videotapes, CD-ROMS or whatever educational materials you have developed or that you use for teaching computational approaches to biology, especially molecular biology. We hope to have a very open discussion about what works and what does not and what needs to be done in the future. Submission of papers: We also encourage you to submit full technical papers or abstracts for posters on biocomputing education to be included in the general refereeing process. We envision that such papers could range from philosophical discussions on biocomputing education to the nuts-and-bolts of particular courses or workshops that are enjoying significant success. Given a sufficient number of refereed papers submitted on biocomputing education, additional time will be allocated by the PSB organizers for their presentation. Submitted papers and abstracts will be carefully peer reviewed by at least 3 independent referees for publication in an archival proceedings. Publication of a full paper is required for oral presentation. Submissions from researchers who desire to present their work at the conference without the publication of a full paper are eligible for exhibition space in the poster and demonstration sessions. Publication: In addition to traditional print options, PSB is exploring the possibility of publishing its proceedings as the first in a series of peer-reviewed electronic conference publications from a major scientific publisher. Authors would have the ability to include extensive color graphics, animations, datasets and source code in papers published electronically and to obtain printed versions of individual papers by facsimile. The publisher would offer attractive licensing arrangements for the series, intending to insure the greatest possible availability in libraries and other institutions. Whether we opt for electronic publication or not, we hope to have the contents of the proceedings indexed in Medline and elsewhere. PSB is also exploring the possibility of CD-ROM distribution, as well as a follow-up book with extended versions of the best papers. We hope that these forward-looking publication efforts will encourage you to submit your best upcoming work to this conference. Key dates: week of July 2 -- Feedback from us on abstracts July 27 -- Full papers due September 11 -- Notification of acceptance, with comments October 2 -- Final, revised manuscripts due Conference registration for authors is required along with the submission of the final paper on October 2. There will be an early registration discount for people who register on or before that date. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ First Pacific Symposium on Biocomputing (PSB-I) Ritz Carlton Hotel, Big Island, Hawaii --- January 3-6, 1996 The conference will consist of several tracks: # The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution Chairs: Richard A. Goldstein & Russ B. Altman Contact: altman@camis.stanford.edu # Interactive Molecular Visualization Chairs: Michael Teschener and Chris Henn Contact: micha@basel.sgi.com # Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics Chairs: Tom Head, Takashi Yokomori, Katsumi Nitta & Kiyoshi Asai Contact: tom@math.binghamton.edu # Discovering, Learning, Analyzing and Predicting Protein Structure Chairs: Richard H. Lathrop & A. Keith Dunker Contact: dunker@jaguar.csc.wsu.edu minitracks: # Population Modeling Chair: John Conery Contact: conery@cs.uoregon.edu # Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution Chairs: Martin Field & Jiali Gao contact: mjfield@ibs.fr # Models of Control Systems in Biology Chair: Seth Michelson contact: seth.michelson@syntex.com # Computational Studies on the Design of Protease Inhibitors Chair: C. N. Hodge Contact: hodgecn@lldmpc.dnet.dupont.com and workshops: # Internet Tools for Computational Biology Chair: Reinhard Doelz Contact: doelz@ubaclu.unibas.ch # Biocomputing Education: Challenges and Opportunities Chairs: Susan J. Johns, Steven M. Thompson & A. Keith Dunker Contact: thompson@jaguar.csc.wsu.edu For questions, or for information about submissions of papers, posters or demonstrations that do not fit into any of the above sessions, contact the conference co-chairs: Dr. Teri Klein Computer Graphics Laboratory University of California, San Francisco San Francisco, CA 94143-0446 USA phone: +1 (415) 476-0663 fax: +1 (415) 502-1755 email: klein@cgl.ucsf.edu or Dr. Lawrence Hunter Lister Hill Center National Library of Medicine Bldg. 38A, MS-54 8600 Rockville Pike Bethesda, MD 20894 USA phone: +1 (301) 496-9300 fax: +1 (301) 496-0673 email: hunter@nlm.nih.gov +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Registration Details The registration costs for this year's PSB conference is $375 (due in part, to the generous support of DOE). The hotel room cost is $130 per day double occupancy plus tax. The registration costs includes continental breakfasts, some lunches, and three receptions. There will be an additional charge for participants who would like the proceedings in hardcopy. Abstracts of all papers and posters will be provided in the registration materials. We are anticipating the cost of the proceedings to be in the neighborhood of $50-$75, but we won't have a signed contract with the publishers until the second week of July. The PSB web page is located at http://cgl.ucsf.edu:80/psb. A registration web page link will be available shortly. For further registration and site information, contact the PSB conference coordinator: Sharon Surles PSB Conference Coordinator IS, Inc., Suite 203 5330 Carroll Canyon Rd San Diego, CA 92121 USA phone: +1 (619) 658-9782 Please refer to the web site listed above for more details and/or contact the participating section chairs or Drs. Hunter and Klein directly. From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!psgrain!iafrica.com!ticsa.com!cstatd.cstat.co.za!ucthpx!wabe.csir.co.za!pukrs7.puk.ac.za!mbpc20.uovs.ac.za!thanh From: thanh@wwg3.uovs.ac.za Newsgroups: bionet.software Subject: Colonia counter Date: Mon, 3 Jul 1995 13:54:57 GMT Organization: Fun company Lines: 6 Message-ID: NNTP-Posting-Host: mbpc20.uovs.ac.za Hi, I need a program which can count amount of colonia in image of Petri dish. Does anyone know where I can get the program or it's name? Thanks T. Vu Nguyen From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!derijkp From: derijkp@reks.uia.ac.be (Peter.DeRijk) Subject: Re: Sequence Analysis -- Linux Binaries? Message-ID: <1995Jul3.103318.1331@reks.uia.ac.be> Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 References: <3snb8g$95f@mark.ucdavis.edu> Date: Mon, 3 Jul 1995 10:33:18 GMT Lines: 15 Alan Williams (ez005401@rocky.ucdavis.edu) wrote: : I'm interested in any sites that have linux binaries for doing DNA/RNA : sequence analysis (ie GDE, fsap, blast, plasmid mapping, ....) Thanks alot. : : -- : ********************************************************************** : Alan Williams : University of California, Davis "Where observation is concerned, : Plant Biology Section chance favors the prepared mind." : ajwilliams@ucdavis.edu -- Louis Pasteur : ********************************************************************** : tkDCSE is now available for Linux. See my announcement for more information, or check out the DCSE home page at URL: http://www-rrna.uia.ac.be/~peter/dcse/ From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!derijkp From: derijkp@reks.uia.ac.be (Peter.DeRijk) Subject: tkDCSE alignment editor available for Linux Message-ID: <1995Jul3.103027.1085@reks.uia.ac.be> Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 Date: Mon, 3 Jul 1995 10:30:27 GMT Lines: 211 tkDCSE for Linux is finally available. Version 3.4 is mainly for the Linux port, and is not available for the other platforms. Maybe it will be when I get the time to make new distributions. You can get the package via WWW and anonymous ftp. Read the appended readme file for more details. For those who don't know Linux (is this possible?): it is a great free Unix clone, including X-Windows, which runs on plain PC's. Regards, Peter De Rijk ---- Peter De Rijk derijkp@reks.uia.ac.be Peter To achieve the impossible, one must think the absurd. to look where everyone else has looked, but to see what no one else has seen. DCSE v3.4 for X-Windows ----------------------- The homepage for DCSE is available on our WWW server http://www-rrna.uia.ac.be/~peter/dcse/index.html). You can look there for more info. What is DCSE v3 (tkDCSE) ------------------------ DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment. It is written in C, and it uses dynamic memory for most things. This means you can almost edit any size of alignment with it. It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system, checking of incorporated RNA structure, on-line hypertext help, macros, and a lot more. This new version of DCSE has an easy to use, yet flexible and programmable X-windows interface provided by the Tcl/Tk language. A complete on-line hypertext help system is provided. Although DCSE v3 is compatible with version 2 of DCSE, its implementation is completely different. The core of DCSE is implemented as an object which can be controlled by giving commands to it from the Tcl language, an easy to learn, yet flexible, interpreted language. The interface is written as a Tcl program. This way the program can be easily customized, and batch jobs are even possible. This approach has several advantages: - the user can adapt the interface of DCSE completely to his own liking. - It is easy to create macros or programs wich extend DCSE. - external programs can also be controlled in Tcl, and seamlessly integerated. - Tcl/Tk exists for a great variety of computers, so porting should be simplified. Convers is a complementary program to DCSE which does things like converting between different file-formats. The new version has been written a set of commandline programs, which are controlled by a Tcl/Tk interface. What is new in v3.4 ------------------- This release is mainly for the port to Linux. Dynamic loading is not available on Linux DCSE. Its main executable has the necessary extensions statically linked. This might change once ELF is commonly available on Linux systems. The descriptions in the help pages can be somewhat inaccurate about this (They are the same as those for SGI and Sun systems, which do support dynamic loading. Some other changes are: - plugins: external programs/extensions to DCSE can be installed/deinstalled by adding or removing a directory in the plugins subdir. - Unpatched Tcl and Tk libraries are now used: The problem of getting one environment variable TCL_LIBROOT do everything is solved by calling tkstartup.tcl directly, and hacking the info command using tcl code (in tclstartup.tcl) - Standard installation now does not give group write permissions (was a possible security hole) - dnapro and prodna added to Convers: used to translate a DNA alignment into a protein alignment, and vice versa. The original DNA sequences are recovered from the reference file when using prodna. - several bugfixes Getting the package ------------------- You can get the package by anonymous ftp to www-rrna.uia.ac.be. It is under the directory pub/dcse. You can also get the distribution via WWW from the DCSE home page on the following URL http://www-rrna.uia.ac.be/~peter/dcse/index.html The package is split in two parts, so that they fit on diskettes. tkdcse-linux-3.4.tar.gz: contains everything to run DCSE tcltkman-linux.tar.gz: contains the manual pages for Tcl/Tk, these are not necessary, but can be useful when programming in Tcl. Installing the package ---------------------- Uncompress and untar the distribution in a suitable directory. This will produce a directory called tkdcse_home. The man pages for Tcl/Tk are not in this distribution (so it fits on a floppy when compressed). If you want to include these (only needed for programming), you should also get the file tcltkman-linux.tar.gz, and uncompress it in the tkdcse_home directory before installing. Go into the directory tkdcse_home, and start the program install. Then follow directions. tar xvvzf tkdcse-linux-3.4.tar.Z cd tkdcse_home ./install The install program will give you more info on what to do to install DCSE. The programs can be started by typing 'tkdcse' or 'tkconvers' in a shell window. tkdcse for Linux notes ---------------------- Many of the key combinations used in dcse (Alt-arrows, Control-arrows, Alt-Control-arrows) are by default used by the pager in fvwm. You can remove these by commenting out the following lines in the /usr/X11/lib/X11/fvwm/system.fvwmrc file (system wide) or in your personal .fvwmrc file: #Key Left A M Scroll -10 +0 #Key Right A M Scroll +10 +0 #Key Up A M Scroll +0 -10 #Key Down A M Scroll +0 +10 # press shift arrow + control anywhere, and move the pointer by 1% of a page #Key Left A SC CursorMove -1 0 #Key Right A SC CursorMove +1 +0 #Key Up A SC CursorMove +0 -1 #Key Down A SC CursorMove +0 +1 # press shift arrow + meta key, and move the pointer by 1/10 of a page #Key Left A SM CursorMove -10 +0 #Key Right A SM CursorMove +10 +0 #Key Up A SM CursorMove +0 -10 #Key Down A SM CursorMove +0 +10 Dynamic loading of modules is not yet supported by tkDCSE for Linux. There is one executable containing Tcl/Tk, BLT, Itcl, expect, and my own extensions extraL and desc. This executable is called desc. The help pages might not always be correct about this. Bugs ---- If you are having problems with the program contact me. I will do my best to get it fixed. Please report any bugs you have found. If possible, state your machine's hardware and software configurations. Sending me a full description of the circumstances in which the bug occurs, possibly with the data it happened on, will help me tracking down a bug. If you have any suggestions, you can also make them to me. Citation -------- A paper has been written about DCSE and this is submitted to and accepted by CABIOS. If you have used the program to obtain results in a paper you've written, please cite the following reference: Peter De Rijk and Rupert De Wachter DCSE v2.54, an interactive tool for sequence alignment and secondary structure research. Comput. Applic. Biosci. Reprints of articles in which DCSE is mentioned would be welcomed. How to contact me ----------------- I will do my best to reply as fast as I can to any problems, etc. However, unfortunately the development of DCSE is not my only task, which is why my response might not be always as fast as you would like (although I get a very good average). Peter De Rijk University of Antwerp (UIA) Department of Biochemistry Universiteitsplein 1 B-2610 Antwerp tel.: 32-03-820.23.16 fax: 32-03-820.22.48 E-mail: derijkp@reks.uia.ac.be Legalities ---------- DCSE is Copyright Peter De Rijk, University of Antwerp (UIA), 1993 You may give this application to anyone, via any medium, so long as it is delivered with ALL the supplied files and UNALTERED, and it is not supplied on a disc you are charging for (except for media and postage costs). I maintain copyright on all the material supplied and reserve the right to amend these conditions in cases where I deem misuse. Disclaimer This application is supplied free to everyone 'as is', I do not give any guarantee that it is free of bugs, or supply any warranty about its suitability for use. No liability will be accepted for any damage to or loss of data as a result of using this application. However, if there are any problems with it and you notify me of them, I will probably do my best to rectify them. From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.nic.surfnet.nl!ecnits.ecn.nl!usenet From: veltman@ecn.nl (veltman) Newsgroups: bionet.software Subject: Re: Bibliographic software Date: 3 Jul 1995 11:19:31 GMT Organization: Netherlands Energy Research Foundation ECN Lines: 32 Message-ID: <3t8jo3$92e@ecnits.ecn.nl> References: <3t11ec$ka3@ecnits.ecn.nl> NNTP-Posting-Host: ecp387.ecn.nl X-Newsreader: WinVN 0.90.3 In article <3t11ec$ka3@ecnits.ecn.nl>, veltman@ecn.nl (veltman) says: > > >Hello everyone, > >Bibliographic software is what I am looking for to store >references to journal articles etc. >Anybody knows a pointer? >I'd be very glad to receive some suggestions. > >Arie Veltman Two pointers came back on my request for bibliographic software: ---- Try Refs by Tim Cutts. Easy-to-use, Unix-Refer-Style files (ascii). Great shareware. ftp://cyclin.zoo.cam.ac.uk/pub/refs/refs772.zip ---- & ---- I use Reference Manager for Windows, and like it very much. It has many export filters to automatically format your levenswerk for the journal of your choice, without destroying your original masterpiece. Contact Research information systems at risinfo@ris.risinc.com ---- If anyone has more, please let us know. Arie Veltman From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!scripps.edu!usenet From: Massimo Delledonne Newsgroups: bionet.software Subject: Re: Plasmid drawing software Date: 3 Jul 1995 05:49:43 GMT Organization: The Scripps Research Institute, La Jolla, CA Lines: 84 Message-ID: <3t80dn$bpn@riscsm.scripps.edu> References: <3sm623$jh2@mira.sara.nl> <1995Jun27.113413.96456@kuhub.cc.ukans.edu> <3t484n$9rm@warp.cris.com> NNTP-Posting-Host: nb40ppp4.salk.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) >pgegen@DawnTreader.bio.ukans.edu (Peter Gegenheimer) wrote: > >>WHY DO PEOPLE WANT SUPERB, FEATURE-RICH SOFTWARE BUT DON'T EXPECT TO PAY FOR >>IT??? > Ok, that's a good question ..... Money problem I think .... But there are several things programmers should consider .... There are several good shareware programs out there in any field .... I don't think I need to remind you how many megabites of windows or mac or unix or dos programs people wrote, and also for molecular biology I can use several good FREE or shareware programs that help me in my work .. What I don't have yet is a simple program that help me drawing plasmids for presentation or pubblications ... I'm not looking for a big program that allow me to handle ANY kind of sequence or piece of DNA or protein and so on ... I already pay an annual fee to use GCG and that's enough for my budget .... I think a lot of people out there is not looking for a program that draw a plasmid from a sequence (using may be one of those (in my opinion) TERRIBLE programs that require a key in the parallel port to works, making impossible keep a copy of the program in my notebook. ( I pay for GCG, but I can connect to my GCG from everywhere in the world via internet, I'm not forced to use it only from the computer I have in the lab) So far I'm using HG for Windows, but I have to draw a circle, draw some arcs and so on ... pretty painfull but I don't have anything else ..... I don't think big groups like NCBI or EMBL or some computing groups wouldn't be able of give us a so simple program ..... >So, if you want someone to creeate this >great software, remember that they will need to do it full-time, and >they'll need to get paid. > Ok, but I don't pay for my Netscape client .... That company made a very smart job giving for free the program to universities and research centers ... A company could make a good program and sell it to Biotech companies (usually with less money problems then univerities) and give it for a nominal fee (or better for free) to people like me .... and ... let me say .... when I put a sequence in the database ..... I don't ask for money ..... but I'm working all the day too! I mean, the scientific comunity is pretty big .. somebody works on DNA, somebody on protein, somebody on HIV ...... somebody develope software ... All these guys get public money .... Why should I pay if they develop a program that allow me to simplify my work? (not the business, the research work) For what I know, I don't have to pay if I use technology and material patented for some reason till I stay in the research field ... I don't pay fees when I clone something, even if all the cloning process have been patented long time ago ...... Please consider in a different way research center and Company ...... Several programmers already consider it, but none of them think (or have time to spend) about a very simple plasmid drawing program for windows platform .... Also a restriction site analysis program would be VERY nice :-) Just my tought ... Massimo delledonne ========================================================================= ========= Massimo Delledonne, PhD permanent address: Istituto di Genetica Vegetale Universita' Cattolica S.Cuore, 29100 Piacenza ITALY Ph. (+39) 523-599209 Fax (+39) 523-599283 internet: delle@pc.unicatt.it PLEASE NOTE: From 3/95 to 12/95 at The Salk Institute for Biological Studies, La Jolla, CA (USA) Fax (619) 558-6379 internet: delledonne@sc2.salk.edu (I read Email from my italian address anyway) The Salk Institute for Biological Studies La Jolla, CA From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!CAMD2.KKPCR.RE.KR!ccheon From: ccheon@CAMD2.KKPCR.RE.KR Newsgroups: bionet.software Subject: DNA strider Date: 2 Jul 1995 20:35:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9507030326.AA27762@camd2.kkpcr.re.kr> NNTP-Posting-Host: net.bio.net Dear Netters: Could anyone tell me where I can ftp old version (free) of DNA strider--maybe v. 1.0? Thanks in advance. Choong-Ill ccheon@camd2.kkpcr.re.kr From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!CAMD2.KKPCR.RE.KR!ccheon From: ccheon@CAMD2.KKPCR.RE.KR Newsgroups: bionet.software Subject: motif search Date: 2 Jul 1995 20:33:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9507030324.AA27758@camd2.kkpcr.re.kr> NNTP-Posting-Host: net.bio.net Dear Netters: I am trying to find a software for "Shotgun alignment" which is to build a consensus sequence from a large set of DNA sequences. Any of you can tell me which program is proper to use? Thanks. CIC From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!noc.netcom.net!ixnews.netcom.com!netnews From: shelbyb@ix.netcom.com (Harold Boxenbaum) Newsgroups: bionet.software Subject: Re: ImageCalc available? Date: 3 Jul 1995 02:46:54 GMT Organization: Netcom Lines: 38 Distribution: world Message-ID: <3t7lmu$9ji@ixnews6.ix.netcom.com> References: <3sfdma$r2n@warp.cris.com> NNTP-Posting-Host: ix-dc17-05.ix.netcom.com In <3sfdma$r2n@warp.cris.com> mike.holloway@stjude.org (Mike Holloway) writes: > >The June '95 issue of Biotechniques has an article about a Windows image >analysis program called ImageCalc. The author apparently wants to >distribute it by having people mail him a formatted disk and a postage >paid envelope. Is this guy for real? Does anyone know of a site that >carries the program? It's not in IU. > >====================================================================== == >Mike Holloway |* On average, 8 people a day on the waiting list >mike.holloway@stjude.org | for a transplant die for lack of a donor. >____________________________|* The end-stage diseases treated by transplant > do not recognize age, race, nationality or pocketbook. >* There is no justifiable reason to deny organ donation, but many myths and > misunderstandings. >* Next of kin must allow donation. Your family must know your wishes. >* Only a small fraction of the next of kin of potential donors allow > donation to take place. >* In general, medical professionals do not recognize their obligation to > support and promote donation. >Questions? See FAQ: >http://www.lib.ox.ac.uk/internet/news/faq/bit.listserv.transplant.html >or >ftp://rtfm.mit.edu/pub/usenet/bit.listserv.transplant/ >====================================================================== == What does the program do? What is the address? How can you go wrong, for an investment of about 2 dollars? Harold. From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!gatech!news.uoregon.edu!vixen.cso.uiuc.edu!news.ecn.bgu.edu!psuvax1!rutgers!oitnews.harvard.edu!fas-news.harvard.edu!lipid!robison From: robison@lipid.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: motif search Date: 3 Jul 1995 15:01:44 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 27 Distribution: world Message-ID: <3t90oo$j6t@decaxp.harvard.edu> References: <9507030324.AA27758@camd2.kkpcr.re.kr> NNTP-Posting-Host: lipid.harvard.edu X-Newsreader: TIN [version 1.2 PL2] ccheon@CAMD2.KKPCR.RE.KR wrote: : Dear Netters: : I am trying to find a software for "Shotgun alignment" which is to build : a consensus sequence from a large set of DNA sequences. : Any of you can tell me which program is proper to use? You might try Gary Gryan's FALCON (Fast Assembly of Large CONtigs), which is available from ftp.rascal.med.harvard.edu or via the Church Lab WWW page at http://twod.med.harvard.edu/ FALCON is capable of assembling multiple-megabase shotgun projects on desktop workstations in a matter of days, and cosmid-sized projects in about 10 minutes. Enjoy! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!biosci!not-for-mail From: thompson@carbo.vadms.wsu.edu (Steve Thompson) Newsgroups: bionet.announce,bionet.biology.computational,bionet.molbio.evolution,bionet.molbio.bio-matrix,bionet.software,bionet.software.gcg Subject: Final Call for Participation: BioComputing Education Workshop @ PSBI Date: 3 Jul 1995 16:36:42 -0700 Organization: WSU VADMS Center Lines: 236 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: Reply-To: thompson@ribozyme.vadms.wsu.edu NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:2257 bionet.biology.computational:694 bionet.molbio.evolution:3075 bionet.molbio.bio-matrix:592 bionet.software:12582 bionet.software.gcg:1287 Dear Colleague, Please find enclosed the final "Call for Papers, Demonstrations and Participation" for the upcoming workshop on Biocomputing Education: Challenges and Opportunities to be held as part of the First Pacific Symposium on Biocomputing (PSB-I), the agenda of which can be found following the Call. We are excited about this meeting and the workshop. To the best of our knowledge (and please correct us if you have knowledge that we are wrong), this will be the first time that a forum on educational issues will be included in a meeting on computational approaches to molecular biology. We would especially like your comments regarding what you think are the most important issues in biocomputing education. Plan to submit a paper if you can, but at least mark the meeting on your calendar and consider joining us in Hawaii next year. Regards, Susan J. Johns Steven M. Thompson A. Keith Dunker +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ CALL FOR PAPERS, DEMONSTRATIONS AND PARTICIPATION Biocomputing Education: Challenges and Opportunities First Pacific Symposium on Biocomputing Ritz Carlton Hotel, Big Island, Hawaii --- January 3-6, 1996 Susan J. Johns, Steven M. Thompson, and A. Keith Dunker Visualization, Analysis and Design in the Molecular Sciences (VADMS) and the Department of Biochemistry and Biophysics Washington State University Pullman, WA 99164-1224 & 4660 Phone: (509) 335-0424 & 335-5322 FAX: (509) 335-0540 & 335-9688 E-mail: prcadms@jaguar.csc.wsu.edu thompson@jaguar.csc.wsu.edu dunker@jaguar.csc.wsu.edu The need for a forum on educational issues: Philosophically, we have come to the view that computer science is to molecular biology as calculus is to physics, yet at present there is really no well defined curriculum for computational molecular biology. Although specific individuals have developed courses or workshops, educational materials such as textbooks or laboratory exercises based on existing courses or workshops are not widely available. In addition to the absence of formal materials, there is also a lack of communication among those of us who are now teaching courses in this domain. Correcting the deficiencies regarding the lack of educational materials and the lack of communication on educational issues represents both a challenge and an opportunity for the community of scientists who are currently doing research in biocomputing. A workshop: Recognizing the need for the development of an educational forum, the Pacific Symposium on Biocomputing (PSB) has included our workshop on biocomputing education as part of its overall program. Our hope is that this workshop on biocomputing education will become an important node with regard to the dissemination of educational materials, information, and approaches in this field. To the end of improving communication, we encourage your formal or informal participation at our workshop on educational issues. Bring your course outlines, syllabi, laboratory exercises, videotapes, CD-ROMS or whatever educational materials you have developed or that you use for teaching computational approaches to biology, especially molecular biology. We hope to have a very open discussion about what works and what does not and what needs to be done in the future. Submission of papers: We also encourage you to submit full technical papers or abstracts for posters on biocomputing education to be included in the general refereeing process. We envision that such papers could range from philosophical discussions on biocomputing education to the nuts-and-bolts of particular courses or workshops that are enjoying significant success. Given a sufficient number of refereed papers submitted on biocomputing education, additional time will be allocated by the PSB organizers for their presentation. Submitted papers and abstracts will be carefully peer reviewed by at least 3 independent referees for publication in an archival proceedings. Publication of a full paper is required for oral presentation. Submissions from researchers who desire to present their work at the conference without the publication of a full paper are eligible for exhibition space in the poster and demonstration sessions. Publication: In addition to traditional print options, PSB is exploring the possibility of publishing its proceedings as the first in a series of peer-reviewed electronic conference publications from a major scientific publisher. Authors would have the ability to include extensive color graphics, animations, datasets and source code in papers published electronically and to obtain printed versions of individual papers by facsimile. The publisher would offer attractive licensing arrangements for the series, intending to insure the greatest possible availability in libraries and other institutions. Whether we opt for electronic publication or not, we hope to have the contents of the proceedings indexed in Medline and elsewhere. PSB is also exploring the possibility of CD-ROM distribution, as well as a follow-up book with extended versions of the best papers. We hope that these forward-looking publication efforts will encourage you to submit your best upcoming work to this conference. Key dates: week of July 2 -- Feedback from us on abstracts July 27 -- Full papers due September 11 -- Notification of acceptance, with comments October 2 -- Final, revised manuscripts due Conference registration for authors is required along with the submission of the final paper on October 2. There will be an early registration discount for people who register on or before that date. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ First Pacific Symposium on Biocomputing (PSB-I) Ritz Carlton Hotel, Big Island, Hawaii --- January 3-6, 1996 The conference will consist of several tracks: # The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution Chairs: Richard A. Goldstein & Russ B. Altman Contact: altman@camis.stanford.edu # Interactive Molecular Visualization Chairs: Michael Teschener and Chris Henn Contact: micha@basel.sgi.com # Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics Chairs: Tom Head, Takashi Yokomori, Katsumi Nitta & Kiyoshi Asai Contact: tom@math.binghamton.edu # Discovering, Learning, Analyzing and Predicting Protein Structure Chairs: Richard H. Lathrop & A. Keith Dunker Contact: dunker@jaguar.csc.wsu.edu minitracks: # Population Modeling Chair: John Conery Contact: conery@cs.uoregon.edu # Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution Chairs: Martin Field & Jiali Gao contact: mjfield@ibs.fr # Models of Control Systems in Biology Chair: Seth Michelson contact: seth.michelson@syntex.com # Computational Studies on the Design of Protease Inhibitors Chair: C. N. Hodge Contact: hodgecn@lldmpc.dnet.dupont.com and workshops: # Internet Tools for Computational Biology Chair: Reinhard Doelz Contact: doelz@ubaclu.unibas.ch # Biocomputing Education: Challenges and Opportunities Chairs: Susan J. Johns, Steven M. Thompson & A. Keith Dunker Contact: thompson@jaguar.csc.wsu.edu For questions, or for information about submissions of papers, posters or demonstrations that do not fit into any of the above sessions, contact the conference co-chairs: Dr. Teri Klein Computer Graphics Laboratory University of California, San Francisco San Francisco, CA 94143-0446 USA phone: +1 (415) 476-0663 fax: +1 (415) 502-1755 email: klein@cgl.ucsf.edu or Dr. Lawrence Hunter Lister Hill Center National Library of Medicine Bldg. 38A, MS-54 8600 Rockville Pike Bethesda, MD 20894 USA phone: +1 (301) 496-9300 fax: +1 (301) 496-0673 email: hunter@nlm.nih.gov +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Registration Details The registration costs for this year's PSB conference is $375 (due in part, to the generous support of DOE). The hotel room cost is $130 per day double occupancy plus tax. The registration costs includes continental breakfasts, some lunches, and three receptions. There will be an additional charge for participants who would like the proceedings in hardcopy. Abstracts of all papers and posters will be provided in the registration materials. We are anticipating the cost of the proceedings to be in the neighborhood of $50-$75, but we won't have a signed contract with the publishers until the second week of July. The PSB web page is located at http://cgl.ucsf.edu:80/psb. A registration web page link will be available shortly. For further registration and site information, contact the PSB conference coordinator: Sharon Surles PSB Conference Coordinator IS, Inc., Suite 203 5330 Carroll Canyon Rd San Diego, CA 92121 USA phone: +1 (619) 658-9782 Please refer to the web site listed above for more details and/or contact the participating section chairs or Drs. Hunter and Klein directly. From owner-software@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!biosci!not-for-mail From: billh@lisboa.ks.uiuc.edu (William F. Humphrey) Newsgroups: bionet.software,bionet.biology.computational,bionet.molec-model Subject: Announcing the Program VMD, Version 1.0 Date: 3 Jul 1995 14:28:15 -0700 Organization: University of Illinois at Urbana Lines: 88 Sender: biohelp@net.bio.net Approved: comp-bio-moderator@net.bio.net Distribution: world Message-ID: <3t4tvg$ipt@vixen.cso.uiuc.edu> NNTP-Posting-Host: net.bio.net Keywords: molecular graphics, molecular dynamics Xref: biosci bionet.software:12581 bionet.biology.computational:692 bionet.molec-model:478 Announcing the Program VMD, Version 1.0 --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability of version 1.0 of the program VMD, a new package for the graphical display and visualization of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and a precompiled binary for Silicon Graphics workstations running version 5 or later of the IRIX operating system. The documentation, in postscript form, includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer such as Mosaic or Netscape. Obtaining VMD ------------- A more complete description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu:1250/Research/vmd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd (please see the README file in this directory for the latest version info) Features -------- VMD is designed for the visualization of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o Many molecular rendering and coloring methods. o Stereo display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, and Raster3D. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu:1250/Research/namd VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment. Availability ------------ VMD runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library (a commercial port of the SGI GL library, available from Portable Graphics, Inc.) is available on your system. Two versions of the distribution are available, one including the complete VMD source code, and one which just includes a precompiled VMD executable for SGI IRIX version 5. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. This project is funded by the National Institutes of Health and the National Science Foundation. -- /* Bill Humphrey (billh@ks.uiuc.edu) */ /* Theoretical Biophysics | Nothing matters but */ /* University of Illinois | the weekend, from a */ /* 3117 Beckman Institute _______| Tuesday point of view */ /* 405 North Matthews | phone: (217) 244-1851 */ /* Urbana, IL 61801 | fax: (217) 244-6078 */ From owner-software@net.bio.net Mon Jul 03 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!uunet!in1.uu.net!dockmaster.phantom.com!rg From: goldstei@phantom.com (Richard A Goldstein) Newsgroups: bionet.software Subject: Re: winplas and genbank files? Date: Mon, 03 Jul 95 01:47:24 GMT Organization: [MindVox] / Phantom Access Technologies / (+1 [212] 989-2418) Lines: 37 Distribution: world Message-ID: <3t7i77$iai@dockmaster.phantom.com> References: <3sv4fp$eq4@vixen.cso.uiuc.edu> <1995Jun30.154402.2194@alw.nih.gov> NNTP-Posting-Host: rg.phantom.com X-Newsreader: News Xpress Version 1.0 Beta #2 >> i downloaded the demo copy of winplas. i'm trying to import genbank >> files into new documents. that works without a problem but the >> software cannot recognize the special features listed in the file. >> this function works with the pbr322.gb_ included with the demo but >> not on the ones i download. i assume i'm downloading them correctly >> because the software recognizes the sequence and can perform a >> restriction analysis. >> thanks for any help >> >I was just talking to Rich Goldstein a few minutes ago and he says that >this is a known problem with the Demo but has been fixed in the commercial >version. He also says that he has added the ability to cope with ambiguous >bases, which is also a handy feature. > This is a really nice program and, at ca. $270 - 300 a copy, is not >too expensive. The only dislike I have so far is that the commercial version >relies on a hardware key for copy protection. > Actually, the problem has been fixed in the Demo as well, which is available from the Web Site, http://www.phantom.com/~goldstei/winplas.html or currently in the /Incoming directory at IUBio as /Incoming/WinPlasD.Zip (Note the prior version, WinPlasD.EXE at the same site, has the bug) The problem involved ambiguity with the "source" feature key, and removing "source" features from the GenBank files _should_ solve the problem for those using the buggy Demo. Ambiguous base handling is available in the commercial version. Please address any questions, comments, suggestions, or problems to Rich Goldstein, Goldstein Software goldstei@phantom.com All mail promptly answered! From owner-software@net.bio.net Mon Jul 03 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!europa.chnt.gtegsc.com!library.ucla.edu!news.bc.net!rover.ucs.ualberta.ca!news.sas.ab.ca!freenet.edmonton.ab.ca!erinb From: erinb@freenet.edmonton.ab.ca () Newsgroups: bionet.software Subject: *.mov??? How do I view? Date: 4 Jul 1995 06:03:39 GMT Organization: Edmonton Freenet, Edmonton, Alberta, Canada Lines: 6 Message-ID: <3taljr$u96@news.sas.ab.ca> NNTP-Posting-Host: freenet.edmonton.ab.ca X-Newsreader: TIN [version 1.2 PL2.3] Does anyone have a URL for software that will let me view a .mov file? I am running windows...but the media player does not recognize the format of this file. Any help will be very appreciated! Thanks in advance Erin From owner-software@net.bio.net Mon Jul 03 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!europa.chnt.gtegsc.com!library.ucla.edu!news.bc.net!torn!newshost.uwo.ca!jkiernan.anatomy.uwo.ca!jkiernan From: jkiernan@julian.uwo.ca (J. A. Kiernan) Newsgroups: bionet.software Subject: Re: Bibliographic software Date: Mon, 3 Jul 1995 20:11:18 GMT Organization: ITS, University of Western Ontario Lines: 14 Message-ID: References: <3t11ec$ka3@ecnits.ecn.nl> <3t8jo3$92e@ecnits.ecn.nl> NNTP-Posting-Host: jkiernan.anatomy.uwo.ca In article <3t8jo3$92e@ecnits.ecn.nl> veltman@ecn.nl (veltman) writes: >Subject: Re: Bibliographic software >In article <3t11ec$ka3@ecnits.ecn.nl>, veltman@ecn.nl (veltman) says: >> >>Bibliographic software is what I am looking for to store >>references to journal articles etc. >>Anybody knows a pointer? >>I'd be very glad to receive some suggestions. I use Papyrus, and am very happy with it. It's much cheaper than Ref.Man., does all the same things, and can import pretty well any other refs database - even my old home-made one. From owner-software@net.bio.net Mon Jul 03 23:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!europa.chnt.gtegsc.com!news.sprintlink.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunic!sunic.sunet.se!news.uni-c.dk!news From: Jan Hansen Newsgroups: bionet.software Subject: ANNOUNCEMENT OF O-GLYCOSYLATION PREDICTION SERVER Date: 4 Jul 1995 07:23:15 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 228 Message-ID: <3taq93$mjo@news.uni-c.dk> NNTP-Posting-Host: dna.cbs.dtu.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP22) X-URL: news:bionet.software *************** NetOglyc Mail Server V1.0 *************** Prediction of Mucin type O-glycosylation of mammalian proteins Center for Biological Sequence Analysis The Technical University of Denmark DK-2800 Lyngby, Denmark DESCRIPTION: The NetOglyc mail server is a service producing neural network predictions of mucin type O-glycosylation sites in mammalian proteins as described in: J.E. Hansen, O. Lund, J. Engelbrecht, H. Bohr, J.O. Nielsen, J-E.S. Hansen and S. Brunak, Prediction of O-glycosylation of mammalian proteins: Specificity patterns of UDP-GalNAc:polypeptide N-acetylgalac- tosaminyltransferase. The Biochemical Journal, 308, 801-813, 1995. ABSTRACT: The specificity of the enzyme(s) catalyzing the covalent link between the hydroxyl side-chains of serine or threonine and the sugar moiety GalNAc is unknown. Pattern recognition by artificial neural networks and weight matrix algorithms was performed to determine the exact position of in vivo O-linked GalNAc glycosylated serine and threonine residues from the primary sequence exclusively. The acceptor sequence context for O-glycosylation of serine was found to differ from that of threonine and the two types were therefore treated separately. The context of the sites showed a high abundance of proline, serine and threonine extending far beyond the previously reported region covering positions -4 through +4 relative to the glycosylated residue. The O-glycosylation sites were found to cluster and to have a high abundance in the amino-terminal part of the protein. The sites were also found to have an increased preference for three different classes of beta-turns. No simple consensus like rule could be deduced for the complex glycosylation sequence acceptor patterns. The neural networks were trained on the hitherto largest data material consisting of 48 carefully examined mammalian glycoproteins comprising 264 O-glycosylation sites. For detection neural network algorithms were much more reliable than weight matrices. The networks correctly found 60-95% of the O-glycosylated serine/threonine residues and 89-97% of the non-glycosylated residues in two independent test sets of known glycoproteins. A computer server using E-mail for prediction of O-glycosylation sites has been implemented and made publicly available. FURTHER INFORMATION: The NetOglyc server returns a help file if the submitted file contains the word `help'. CONFIDENTIALITY Your submitted sequences will be deleted automatically immediately after processing by NetOglyc. PAPER TO REFERENCE IN REPORTING RESULTS: Jan E. Hansen, Ole Lund, Jacob Engelbrecht, Henrik Bohr, Jens O. Nielsen, John-E.S. Hansen, and Soren Brunak. Prediction of O-glycosylation of mammalian proteins: Specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase. Biochemical Journal 308, 801-813, 1995. COMMENTS AND SUGGESTIONS: Since an expanded data set with additional O-glycosylated sequences would increase the performance of the network, we are very interested in receiving such material. If you have knowledge of experimentally determined O-glycosylation sites in glycoproteins not already in the data set (see reference Biochem. J. 308, 801-813, 1995.) we would like to include them. Any other comments regarding the predictions or the data may be sent to: Jan Hansen (janhan@cbs.dtu.dk) Center for Biological Sequence Analysis The Technical University of Denmark Building 206 DK-2800 Lyngby Denmark Tel: +45 45252485 Fax: +45 45934808 PROBLEMS: Should be addressed to: Kristoffer Rapacki (rapacki@cbs.dtu.dk) or Karsten Dalsgaard (karsten@cbs.dtu.dk) Center for Biological Sequence Analysis The Technical University of Denmark Building 206 DK-2800 Lyngby Denmark Tel: +45 45252477 Fax: +45 45934808 ----------------------------------------------------------------------- INSTRUCTIONS for using the NetOglyc mail server: In order to use the mail server for prediction on amino acid sequences: 1) Prepare a text file including one or more sequences. The sequences must be preceded by a first line starting by the symbol > followed by a name (identifier) of the sequence. Next line contain the sequence. There must be at least one character at each line of each sequence. Note: Any character after the symbol > will be interpreted as sequence. The sequences must be submitted using the one letter abbreviations for the amino acids: `acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY'. N.B. Other characters will be accepted, but not encoded in the network window, when making the prediction. Example: Create a text file: `sequence.txt' using an editor, the syntax of the file may look like this: >seq_name1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVY GETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASG NNFVECT >seq_name2 TELKAVAHQPTGYTMVPFRVDPPNEVTVEDKDRMTLEKVVFESHKCVVLGSHIVHAKMEVGDLAATKG GHAWAMGFAETIPMYFEIAYAETPKSANAAVIYPKGD 2) Mail the text file to NetOglyc@cbs.dtu.dk: In the UNIX environment you may mail the text file `sequence.txt' to NetOglyc@genome.cbs.dtu.dk by typing: mail NetOglyc@.cbs.dtu.dk < sequence.txt 3) You will receive a mail containing the prediction, or possibly error messages from the server. If the file contains the word `help', this help file will be returned. Response time depends on system load. 4) A www server: http://www.cbs.dtu.dk/netOglyc/cbsnetOglyc.html may also be used. -------------------------------------------------------------------------------- FORMAT OF NetOglyc PREDICTION OUTPUT: IDENTIFIER: LENGTH: DISTRIBUTION: SSTTGVAMHTSTSSSVTKSYISSQT s........s.s.....s..s... SINGLE RESIDUE ACTIVITIES: ID POSITION RESIDUE ASSIGNMENT ACTIVITY -------------------------------------------------------------------------------- EXAMPLE OF OUTPUT OF PREDICTION OF seq_name1 mentioned above. NetOglyc Mail Server Output Prediction for: THREONINE RESIDUES Message 1/1 From NetOglyc mail server Jun 26 '95 at 12:27 pm 120 IDENTIFIER: seq_name1 LENGTH: 143 DISTRIBUTION: t: 1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYGETVGSNSYPHK YNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT ................t.............................................................. .............................................................. SINGLE RESIDUE ACTIVITIES: (ID, POSITION, RESIDUE, ASSIGNMENT, ACTIVITY) seq_name1 5 T . 0.150 seq_name1 18 T t 0.522 seq_name1 32 T . 0.283 seq_name1 71 T . 0.376 seq_name1 130 T . 0.188 seq_name1 132 T . 0.312 seq_name1 143 T . 0.157 NetOglyc Mail Server Output Prediction for: SERINE RESIDUES IDENTIFIER: seq_name1 LENGTH: 143 DISTRIBUTION: s: 1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYGETVGSNSYPHK YNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT ............................................................................... ....................s......................................... SINGLE RESIDUE ACTIVITIES: (ID, POSITION, RESIDUE, ASSIGNMENT, ACTIVITY) seq_name1 8 S . 0.243 seq_name1 12 S . 0.181 seq_name1 13 S . 0.290 seq_name1 14 S . 0.404 seq_name1 17 S . 0.043 seq_name1 35 S . 0.186 seq_name1 37 S . 0.227 seq_name1 51 S . 0.089 seq_name1 53 S . 0.087 seq_name1 54 S . 0.046 seq_name1 63 S . 0.390 seq_name1 64 S . 0.075 seq_name1 74 S . 0.077 seq_name1 76 S . 0.203 seq_name1 90 S . 0.089 seq_name1 92 S . 0.087 seq_name1 93 S . 0.046 seq_name1 102 S s 0.618 seq_name1 103 S . 0.177 seq_name1 108 S . 0.202 seq_name1 111 S . 0.197 seq_name1 135 S . 0.120 -------------------------------------------------------------------------------- CURRENT NETWORK The network will be updated and predictions can alter due to different versions. The network is balanced to give optimal predictions whether you submit sequences with no homology to the known O-glycosylated proteins or not. If however the submitted sequence is identical to the sequences in our training dataset, we will notify you by sending you both the assigment of the identical sequence in our data set and the prediction. From owner-software@net.bio.net Mon Jul 03 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Re: Bibliographic software Date: 4 Jul 1995 07:21:36 GMT Organization: University of Cambridge, England Lines: 34 Message-ID: <3taq60$1lt@lyra.csx.cam.ac.uk> References: <3t11ec$ka3@ecnits.ecn.nl> <3t8jo3$92e@ecnits.ecn.nl> NNTP-Posting-Host: mole.bio.cam.ac.uk veltman@ecn.nl (veltman) writes: >In article <3t11ec$ka3@ecnits.ecn.nl>, veltman@ecn.nl (veltman) says: >> >> >>Hello everyone, >> >>Bibliographic software is what I am looking for to store >>references to journal articles etc. >>Anybody knows a pointer? >>I'd be very glad to receive some suggestions. >> >>Arie Veltman >Two pointers came back on my request for bibliographic software: >---- >Try Refs by Tim Cutts. >Easy-to-use, Unix-Refer-Style files (ascii). >Great shareware. >ftp://cyclin.zoo.cam.ac.uk/pub/refs/refs772.zip If anyone is trying to download Refs (I am the author) my apologies for the erratic availability of the server. cyclin is the machine Refs is developed on, and I can't develop and run an ftp server simultaneously (the ftp server runs under Linux, and I develop under OS/2). I am doing a *lot* of Refs work at the moment, preparing it for a port to Windows 95 and/or OS/2 as soon as is practically feasible. Regards, Tim. From owner-software@net.bio.net Mon Jul 03 23:00:00 1995 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!waikato!canterbury.ac.nz!MANUKA.lincoln.ac.nz!pc090163.lincoln.ac.nz!mclachla From: mclachla@tui.lincoln.ac.nz (Andrew McLachlan) Newsgroups: bionet.software Subject: Re: Bibliographic software Date: Tue, 4 Jul 1995 00:12:57 GMT Organization: Lincoln University, New Zealand Lines: 44 Message-ID: References: <3t11ec$ka3@ecnits.ecn.nl> <3t8jo3$92e@ecnits.ecn.nl> NNTP-Posting-Host: pc090163.lincoln.ac.nz In article <3t8jo3$92e@ecnits.ecn.nl> veltman@ecn.nl (veltman) writes: >In article <3t11ec$ka3@ecnits.ecn.nl>, veltman@ecn.nl (veltman) says: >> >> >>Bibliographic software is what I am looking for to store >>references to journal articles etc. >>Anybody knows a pointer? >>I'd be very glad to receive some suggestions. >> >>Arie Veltman >Two pointers came back on my request for bibliographic software: >---- >Try Refs by Tim Cutts. >Easy-to-use, Unix-Refer-Style files (ascii). >Great shareware. >ftp://cyclin.zoo.cam.ac.uk/pub/refs/refs772.zip >---- >& >---- >I use Reference Manager for Windows, and like it very much. It has >many export filters to automatically format your levenswerk for the >journal of your choice, without destroying your original masterpiece. >Contact Research information systems at risinfo@ris.risinc.com >---- >If anyone has more, please let us know. Also try Papyrus 7.0. I use it to paste references into my document, then have Papyrus scan the document and generate a reference list according to the journal style that you want. I particularly like the data entry of Papyrus. Email Dave Goldman at rsd@teleport.com for more details. Papyrus (still) costs US$99 for the full package (no additional modules needed). Cheers Andrew McLachlan mclachla@tui.lincoln.ac.nz From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!elroy.jpl.nasa.gov!lll-winken.llnl.gov!noc.near.net!news3.near.net!saturn.caps.maine.edu!dartvax.dartmouth.edu!usenet From: Bob.Gross@dartmouth.edu (Robert H. Gross) Newsgroups: bionet.software Subject: Re: Plasmid drawing software Date: 5 Jul 1995 16:12:13 GMT Organization: Dartmouth College, Hanover, NH Lines: 13 Sender: Robert.H.Gross@dartmouth.edu Message-ID: <3tedkt$ce8@dartvax.dartmouth.edu> References: <3sm623$jh2@mira.sara.nl> <1995Jun27.113413.96456@kuhub.cc.ukans.edu> <3t484n$9rm@warp.cris.com> <3t80dn$bpn@riscsm.scripps.edu> NNTP-Posting-Host: at-1-sn-50.dartmouth.edu X-Posted-From: InterNews 1.0.6@dartmouth.edu In article <3t80dn$bpn@riscsm.scripps.edu> Massimo Delledonne writes: > What I don't have yet is a simple program that help me drawing > plasmids for presentation or pubblications Try contacting Textco at 603-643-1471. The Gene Construction Kit runs on a Mac and will do what you want. It was reviewed recently in Biotechnology Software Journal. Bob Gross Dept. of Biology, Dartmouth College bob.gross@dartmouth.edu From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!gatech!concert!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (Bill Pearson) Subject: FASTA20x1 available for DOS X-Nntp-Posting-Host: dayhoff.med.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Date: Wed, 5 Jul 1995 13:58:33 GMT Lines: 25 Xref: biosci bionet.software:12602 bionet.molbio.genbank:2060 bionet.molbio.embldatabank:522 bionet.molbio.proteins:4987 The current version of the FASTA package has been ported to "DOS" using the Borland C++ 4.51 compiler. It is available from ftp.virginia.edu in "pub/fasta/dos". This release has not been tested extensively. Fortunately, the changes required to move the unix/mac version to DOS were modest (most changes involved changes from int to long and some work with "far" pointers). At the moment, there is no "Windows" or "Win32S" version of FASTA. If you have any problems with the program, please send me email. The FASTA package is not in the public domain. It is copyrighted by William R. Pearson and the University of Virginia. You are welcome to download the program from ftp.virginia.edu, but please do not offer it for redistribution without contacting me first. Bill Pearson -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!dish.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!is.bbsrc.ac.uk!pc0519.ri.bbsrc.ac.uk!user From: Andy.Law@bbsrc.ac.uk (Andy Law (Big Nose)) Newsgroups: bionet.software Subject: Re: ncbi server at nih.gov down? Date: Wed, 05 Jul 1995 17:20:38 +0000 Organization: Roslin Institute Lines: 24 Distribution: world Message-ID: References: NNTP-Posting-Host: pc0519.ri.bbsrc.ac.uk X-Newsreader: Value-Added NewsWatcher 2.0b24.0+ In article , fsl@psu.edu (Daniel Cosgrove) wrote: > RE: > >Since 6/29/95 approx 10pm I have not been able to get responses from the > >BLAST server. Is this a separate problem, or another aspect of the > >"transatlantic" problem? Are other users in US having the same problem? Is > >there an alternative way of accessing BLAST? > >Gregory M. Acland > > > I too have been waiting for a reply from the BLAST server at > blast@ncbi.nlm.nih.gov, for 2 days. Anyone know what is going on, and is > there an alternative server?? > I don't know about the rest of the folks that were having problems, but I can now get at the BLAST servers again from here in the UK. The problem seemed to be fixed sometime over the weekend. I've just pinged cruncher to make sure it is still there and I got responses. -- Andy Law ( Andy.Law @ bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!demon!uknet!daresbury!not-for-mail From: RAFFAELE CALOGERO Newsgroups: bionet.software Subject: info about GROMOS licencing conditions Date: 4 Jul 1995 15:56:55 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3tbkrn$2la@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Dear Netters, I am playing arround with the WHATIF molecular modelling program and I am interested to implement the GROMOS program in it. Does any body knows the E_MAIL address of Prof. W. van Gunsteren Dept of ........, ETH Zurich Switzerland? I need to contact him to get information on the licencing conditions for non profit organizations. Thank you Raffaele Calogero calogero@chemna.dichi.unina.it Dipartimento di Genetica, Biologia Generale e Molecolare, via Mezzocannone 8 80134 Napoli (Italy) Tel ++39 81 55 26 208 Fax ++39 81 55 27 950 From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!cam.news.pipex.net!pipex!dish.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!newsfeed.ACO.net!fstgds15.tu-graz.ac.at!usenet From: "Sepp D. Kohlwein" Newsgroups: bionet.software Subject: Re: Microscopy News Groups Date: 4 Jul 1995 16:08:27 GMT Organization: Dept. Biochemistry, Technical University Graz Lines: 40 Message-ID: <3tbp1r$c1h@fstgds15.tu-graz.ac.at> References: <3tb68s$jfa@ccuf.wlv.ac.uk> NNTP-Posting-Host: fbiocm201.tu-graz.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: mike@sass2.wlv.ac.uk X-URL: news:3tb68s$jfa@ccuf.wlv.ac.uk Mike J Adams wrote: > >Does anyone know of any newsgoups relating to microscopy >and / or image anaylsis of cells. Are any companies in >that field on the Net ? I haven't been able to find >anything of much use yet. If anyone knows of any sites, >newsgroups or home pages I would be very grateful if you >could post them at this newsgroup. > > Thanks in advance. > > Hi Mike, check out the following sites: http://www.cs.ubc.ca/spider/ladic/confocal.html http://www.spie.org/ confocal newsgroup: confocal@ubvm.cc.buffalo.edu (send "help" to listserv@ubvm.cc.buffalo.edu for info) other newsgroups: sci.image.processing sci.techniques.microscopy Hope this helps ! Good luck Sepp D. Kohlwein *********************************************************************** Sepp D. Kohlwein, PhD Genetics and Molecular Biology Group Department of Biochemistry and Food Chemistry Technical University Graz phone: ++43 (316) 873-6456 Petersgasse 12 fax: ++43 (316) 810-599 A 8010 Graz, Austria e-mail kohlwein@fscm1.dnet.tu-graz.ac.at *********************************************************************** From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!fauern!lrz-muenchen.de!news.informatik.uni-muenchen.de!jaeger From: jaeger@informatik.uni-muenchen.de (Jochen Jaeger) Newsgroups: bionet.software Subject: wanted: datastructure of aminoacids and proteins Date: 4 Jul 1995 11:26:11 GMT Organization: Institut fuer Informatik der Universitaet Muenchen Lines: 24 Distribution: world Message-ID: <3tb8gj$11d@arcadia.informatik.uni-muenchen.de> NNTP-Posting-Host: gefjon.cip.informatik.uni-muenchen.de Originator: jaeger@gefjon.cip.informatik.uni-muenchen.de hello, we are beginning a project in which we want to apply graph. theoretical algorithms to the analysis of protein structures. For that we need a formal description and datastructure of amino acids and proteins, which has to include: - atoms - bonds - conformations - interactions and everything else of relevance. Who has already worked on datastructures or can provide some information on what has been done previously? Sincerely, J. Jaeger -- E-Mail: jaeger@informatik.uni-muenchen.de From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!CORNELL.EDU!gma2 From: gma2@CORNELL.EDU (Gregory M. Acland) Newsgroups: bionet.software Subject: Re: ncbi server at nih.gov down? Date: 4 Jul 1995 06:56:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: RE: >NCBI's servers are all up. The problem appears limited to some transatlantic >connections that travel by way of SPRINT, a commercial Internet provider. >We have been providing 'traceroute' information to our Internet provider >(SURANET) and they are working with SPRINT to isolate the problem. Since 6/29/95 approx 10pm I have not been able to get responses from the BLAST server. Is this a separate problem, or another aspect of the "transatlantic" problem? Are other users in US having the same problem? Is there an alternative way of accessing BLAST? Gregory M. Acland (607) 256-5684 [phone] Center for Canine Genetics & Reproduction (607) 256-5689 [fax] James A. Baker Institute for Animal Health gma2@cornell.edu College of Veterinary Medicine Cornell University Hungerford Hill Rd, Ithaca, New York 14853 From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.nic.surfnet.nl!rl0001.rulimburg.nl!rlmatvx1.rulimburg.nl!Harry.Wandler From: Harry.Wandler@bw.rulimburg.nl Newsgroups: bionet.software Subject: Re: Anatomy graphics Date: Tue, 4 Jul 1995 11:21:47 GMT Organization: Rijksuniversiteit Limburg Lines: 33 Distribution: world Message-ID: References: <3r51gu$fmp@acme.freenet.columbus.oh.us> <3r5c6m$15fe@msunews.cl.msu.edu> <3s0f18$6v7@ixnews3.ix.netcom.com> <3smurl$mst@agate.berkeley.edu> <3t2bl1$bv4@ixnews3.ix.netcom.com> NNTP-Posting-Host: 137.120.26.91 X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #9] In article <3t2bl1$bv4@ixnews3.ix.netcom.com> shelbyb@ix.netcom.com (Harold Boxenbaum) writes: >From: shelbyb@ix.netcom.com (Harold Boxenbaum) >Subject: Re: Anatomy graphics >Date: 1 Jul 1995 02:24:33 GMT >In <3smurl$mst@agate.berkeley.edu> berk@uclink.berkeley.edu (Berkeley >Nguyen Limketkai) writes: >> >>: > hcampbel@freenet.columbus.oh.us says... >> >>: > I have downloaded what is termed raw graphic data from the Visible >> >>: > Human Data Set at the National Library of Medicine. It is located >at the >>: > This material consists of digitized >>: > cross-sections of an actual human and CAT/MRI data as well. >> >>: > I would like to incorporate this material into tutorial programs >> >>Are these, however, copyrighted images? >No, nothing from the federal government is copyrighted, unless they >specifically indicate it is. But I've never seen anything copyrighted. >Harold. Missed the first note. Could you tell me at which site these images are found? I'd like to take a look at them.... Thanks, RvD From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!warwick!bham!bcs177.bham.ac.uk!s.m.williams.bcm From: s.m.williams.bcm@bham.ac.uk (Stephen Williams) Newsgroups: bionet.software Subject: Re: *.mov??? How do I view? Date: Tue, 4 Jul 1995 12:08:12 Organization: The University of Birmingham Lines: 24 Distribution: world Message-ID: References: <3taljr$u96@news.sas.ab.ca> NNTP-Posting-Host: bcs177.bham.ac.uk X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <3taljr$u96@news.sas.ab.ca> erinb@freenet.edmonton.ab.ca () writes: >From: erinb@freenet.edmonton.ab.ca () >Subject: *.mov??? How do I view? >Date: 4 Jul 1995 06:03:39 GMT >Does anyone have a URL for software that will let me view a .mov file? I >am running windows...but the media player does not recognize the format >of this file. Any help will be very appreciated! >Thanks in advance >Erin Try my WEB page. The programme Graphics workshop is supposed to be able to display MOV files whn you download the quicktime MCI drivers too. I've not tried to view MOV files with it though. The URL for my page is:- http://sun1.bham.ac.uk/s.m.williams.bcm/images/viewers.html I will be putting up links to other programmes that will definately view MOV files, hopefully next week. I'm a bit busy with work at the momment though. Steve From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!warwick!news.wlv.ac.uk!usenet From: Mike J Adams Newsgroups: bionet.software Subject: Microscopy News Groups Date: 4 Jul 1995 10:47:56 GMT Organization: University of Wolverhampton, U.K. Lines: 11 Message-ID: <3tb68s$jfa@ccuf.wlv.ac.uk> NNTP-Posting-Host: sass2.wlv.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Does anyone know of any newsgoups relating to microscopy and / or image anaylsis of cells. Are any companies in that field on the Net ? I haven't been able to find anything of much use yet. If anyone knows of any sites, newsgroups or home pages I would be very grateful if you could post them at this newsgroup. Thanks in advance. From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!agate!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!cosgrove--1!fsl From: fsl@psu.edu (Daniel Cosgrove) Newsgroups: bionet.software Subject: Re: ncbi server at nih.gov down? Date: Wed, 5 Jul 1995 15:52:12 GMT Organization: CAC Lines: 13 Distribution: world Message-ID: References: NNTP-Posting-Host: cosdan.bio.psu.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] RE: >Since 6/29/95 approx 10pm I have not been able to get responses from the >BLAST server. Is this a separate problem, or another aspect of the >"transatlantic" problem? Are other users in US having the same problem? Is >there an alternative way of accessing BLAST? >Gregory M. Acland I too have been waiting for a reply from the BLAST server at blast@ncbi.nlm.nih.gov, for 2 days. Anyone know what is going on, and is there an alternative server?? Dan Cosgrove From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!dish.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!is.bbsrc.ac.uk!news From: Mathew Woodwark Newsgroups: bionet.software Subject: Re: Plasmid drawing software Date: 5 Jul 1995 09:27:10 GMT Organization: Biotechnology and Biological Sciences Research Council Lines: 84 Message-ID: <3tdlte$7gn@is.bbsrc.ac.uk> References: <3sm623$jh2@mira.sara.nl> <1995Jun27.113413.96456@kuhub.cc.ukans.edu> <3t484n$9rm@warp.cris.com> <3t80dn$bpn@riscsm.scripps.edu> NNTP-Posting-Host: pc0547.cc.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Massimo Delledonne wrote: >>pgegen@DawnTreader.bio.ukans.edu (Peter Gegenheimer) wrote: >> >>>WHY DO PEOPLE WANT SUPERB, FEATURE-RICH SOFTWARE BUT DON'T EXPECT TO PAY FOR >>>IT??? >> > >Ok, that's a good question ..... Money problem I think .... >But there are several things programmers should consider .... >There are several good shareware programs out there in any field .... >I don't think I need to remind you how many megabites of windows or mac >or unix or dos programs people wrote, and also for molecular biology I >can use several good FREE or shareware programs that help me in my work >.. What I don't have yet is a simple program that help me drawing >plasmids for presentation or pubblications ... I'm not looking for a big >program that allow me to handle ANY kind of sequence or piece of DNA or >protein and so on ... I already pay an annual fee to use GCG and that's >enough for my budget .... I think a lot of people out there is not >looking for a program that draw a plasmid from a sequence (using may >be one of those (in my opinion) TERRIBLE programs that require a key in >the parallel port to works, making impossible keep a copy of the program >in my notebook. ( I pay for GCG, but I can connect to my GCG from >everywhere in the world via internet, I'm not forced to use it only from >the computer I have in the lab) >So far I'm using HG for Windows, but I have to draw a circle, draw some >arcs and so on ... pretty painfull but I don't have anything else ..... > >I don't think big groups like NCBI or EMBL or some computing groups >wouldn't be able of give us a so simple program ..... > > If you have a license for GCG, why not use PLASMIDMAP. I know its not the prettiest graphics in the world, but it does the job. If you run mapsort/plasmid, you can edit the resultant tick file like so: Original: Name From To Strand Color Fromsymbol Tosymbol Style .. eco0109I 392 392 . green . . tick eco0190I 513 513 . green . . tick haeI 844 844 . black . . tick haeI 972 972 . black . . tick hin41 536 536 . black . . tick hin41 722 722 . black . . tick edited: eco0190I 392 513 - green > > range haeI 844 972 + black | > range hin41 536 722 + black . . block (stuff deleted) This gives you an output in blocks and ranges and restriction sites of enzymes for your plasmid. I know its not windows, but it does the job. >========================================================================= >========= >Massimo Delledonne, PhD > >permanent address: Istituto di Genetica Vegetale > Universita' Cattolica S.Cuore, 29100 Piacenza ITALY > Ph. (+39) 523-599209 Fax (+39) 523-599283 > internet: delle@pc.unicatt.it > (more stuff deleted so I can post this message) Cheers Mathew -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr Mathew Woodwark mathew.woodwark@bbsrc.ac.uk Molecular Biology Software Support Tel: 01582 762271 BBSRC Computing Centre Fax: 01582 761710 West Common, Harpenden Hertfordshire, AL5 2JE, UK +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!hrz-ws11.hrz.uni-kassel.de!hrz-ws41.hrz.uni-kassel.de!bartke From: bartke@hrz-ws41.hrz.uni-kassel.de (C. R. Bartke) Newsgroups: bionet.software Subject: Q: RasMol pictures (cytochrome) in TIBS 20, p. 217 - HOW? Followup-To: bionet.software Date: 4 Jul 1995 16:01:58 GMT Organization: Kassel University, Germany Lines: 24 Distribution: world Message-ID: <3tbolm$qeq@hrz-ws11.hrz.uni-kassel.de> Reply-To: bartke@hrz.uni-kassel.de NNTP-Posting-Host: hrz-ws41.hrz.uni-kassel.de Hello there! After reading the article "Cytochrome f revealed" (Prince, GR and George, GN) in TIBS 20, pages 217 f., I tried (as an exercise) to visualise the cytochromes given in Fig. 1 exactly the same way as they did it. I used RasMol 2.5 (Unix). It worked fine except for the fact that I was not able to get the "connections" between the two amino acids and the Fe-ion and the Heme-Group respectively. Is there any way in RasMol (or RasWin) to make use of the CONECT-field in the PDB-File (e.g. 1CYO)? The ATOMNOs of the involved atoms do show up in these fields, but have found no way to use that info. Any suggestions? Thanks for consideration, Cornelius ___________________________________________________________________ Cornelius R. Bartke Student der Biologie im FB 19 Hauffstrasse 16 Gesamthochschule Universit„aet Kassel 34246 Vellmar Kassel - Germany Fon&Fax: ++49/561/823330 e-mail: bartke@hrz.uni-kassel.de From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!gatech!europa.chnt.gtegsc.com!howland.reston.ans.net!swrinde!dish.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!brenner From: brenner@mole.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Re: How can I buy PDB CD? Date: 5 Jul 1995 19:34:29 GMT Organization: University of Cambridge, England Lines: 21 Message-ID: <3tepg5$m2d@lyra.csx.cam.ac.uk> References: <9507050701.AA29396@camd2.kkpcr.re.kr> NNTP-Posting-Host: mole.bio.cam.ac.uk yskim@CAMD2.KKPCR.RE.KR writes: >Dear Netters: >Recently our institute bought a program for molecular simulation. >In order to use that program, we need PDB files. >But as you know, the PDB is largest. So we want to buy CD containing >PDB files. Please inform me Company, Price, and Fax or internet ID >and so on. There is an order form in the PDB newsletter at: http://www.pdb.bnl.gov/newslttr.txt Each release is $300.00. Steve -- Steven E. Brenner | S.E.Brenner@bioc.cam.ac.uk MRC Laboratory of Molecular Biology | Hills Road | Office: +44 1223 402221 Cambridge CB2 2QH, UK | Fax: +44 1223 213556 From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!venus.sun.com!nntp-hub2.barrnet.net!news3.near.net!saturn.caps.maine.edu!maine.maine.edu!io00865 Organization: University of Maine System Date: Wed, 5 Jul 1995 13:53:02 EDT From: Ethan Strauss Message-ID: <95186.135303IO00865@MAINE.MAINE.EDU> Newsgroups: bionet.software,bionet.molbio.genbank Subject: Can I filter random matches due to aa composition? Lines: 16 Xref: biosci bionet.software:12606 bionet.molbio.genbank:2062 Hi all, I have a bunch of very "T" rich amino acid sequences. When I send them to the BLAST server I get lots of matches with mucins and other sticky proteins. I found this very strange as I don't think the virus I have sequenced is likely to encode mucins. I randomized the order of the amino acids in the sequence and sent that to BLAST. I found a very similar set of matches to the real sequence. So my question is what can I do about it? Is there some way to filter out the matches which are due only to aa composition? It seems like I should randomize a bunch of times, send all the randomized sequences to BLAST and then exclude everything which shows up with the random sequences. Is there a program which will do this for me? Any suggestions would be appreciated. Ethan Strauss IO00865@maine.maine.edu Dept. Plant Biology & Pathology 74 N. Main St. Apt#1 University of Maine at Orono 04469 Orono ME, 04473 207-581-2994 207-866-5935 From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!dish.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!hgmp.mrc.ac.uk!news From: n.j.lindsey@hgmp.mrc.ac.uk (Dr. N.J. Lindsey) Newsgroups: bionet.software Subject: Re:Antibody Modelling software Date: 5 Jul 1995 17:58:59 GMT Organization: UK HGMP Resource Centre Lines: 10 Message-ID: <3tejt3$35h@mercury.hgmp.mrc.ac.uk> References: <3tbolm$qeq@hrz-ws11.hrz.uni-kassel.de> Reply-To: n.j.lindsey@Bradford.ac.uk NNTP-Posting-Host: iron.hgmp.mrc.ac.uk I am interesting in modelling antibody structures and am interested in any programs that anyone might recommend Please rely to me directly as I don't often have the time to view the list Nigel Lindsey N.J.Lindsey@Bradford.ac.uk From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Newsgroups: bionet.general,bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: CALL FOR PAPERS: Internet/Biology Message-ID: <1995Jul5.180227.13284@comp.bioz.unibas.ch> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Nntp-Posting-Host: biox.embnet.unibas.ch Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Date: Wed, 5 Jul 1995 18:02:27 GMT Lines: 82 Xref: biosci bionet.general:16044 bionet.software:12604 Pacific Symposium on Biocomputing Kohala Coast, Island of Hawaii - January 3-6, 1996 http://cgl.ucsf.edu/psb/psb.html Workshop: Internet Tools for Computational Biology C A L L F O R P A P E R S http://www.ch.embnet.org/psb =============================================================== We would like to invite paper submissions in this exciting field of interdisclipinary research. The development is currently progressing rapidly. In particular, the development of more sophisticated client/server technology to overcome less refined features of the generic http protocol, including authorisation, state, security, synchronisation issues Biological applications start to become indispensible, in particular database retrieval sophisticated program input linkage analysis gene (exon) prediction 3D modelling: MIME types 3D modelling: VRML The most important development 'backstage' is to expand server-server communication for data update and data presentation issues. We welcome papers describing results from a wide range of possible methodologies, including access to, and analyses of the databases of biomolecular sequences and structures, simple conceptual and computational evolutionary models, and success/quality/accessibility reports. Reports on molecular modelling via internet tools and special user group communication, such as MOO interlinking, as well as generic methods for maintenance of information are welcome. Current plans are for electronic publication of the papers by the MIT Press, in both HTML and postscript. People wishing to present posters without publishing a full paper may submit an abstract. Preregistration for the conference is required for the inclusion of a paper in the conference proceedings. IMPORTANT DATES Paper submissions due: July 27, 1995 Notification of paper acceptance: September 11, 1995 Final paper deadline October 2, 1995 Early registration deadline October 2, 1995 More information: Pacific Symposium on Biocomputing Kohala Coast, Island of Hawaii - January 3-6, 1996 http://cgl.ucsf.edu/psb/psb.html Workshop: Internet Tools for Computational Biology http://www.ch.embnet.org/psb =============================================================== R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!CAMD2.KKPCR.RE.KR!yskim From: yskim@CAMD2.KKPCR.RE.KR Newsgroups: bionet.software Subject: How can I buy PDB CD? Date: 5 Jul 1995 01:16:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9507050701.AA29396@camd2.kkpcr.re.kr> Dear Netters: Recently our institute bought a program for molecular simulation. In order to use that program, we need PDB files. But as you know, the PDB is largest. So we want to buy CD containing PDB files. Please inform me Company, Price, and Fax or internet ID and so on. Thanks in advances. Kim, Yong-Sig Internet:yskim@camd2.kkpcr.re.kr From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Newsgroups: bionet.software Path: biosci!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Subject: Re: ncbi server at nih.gov down? Message-ID: <1995Jul5.214115.2122@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] References: Date: Wed, 5 Jul 95 21:41:15 GMT Lines: 39 Sprint notified us this afternoon the router problem was corrected over the weekend and we've verified that the machines in the UK that we had trouble connecting with are now reachable. The BLAST e-mail server machine did have a problem processing e-mail requests on 6/29 -6/30. If you sent an e-mail request in that time frame and haven't gotten a response, you should re-send. Dennis Benson NCBI Andy Law (Big Nose) (Andy.Law@bbsrc.ac.uk) wrote: > In article , fsl@psu.edu (Daniel Cosgrove) wrote: > > RE: > > >Since 6/29/95 approx 10pm I have not been able to get responses from the > > >BLAST server. Is this a separate problem, or another aspect of the > > >"transatlantic" problem? Are other users in US having the same problem? Is > > >there an alternative way of accessing BLAST? > > >Gregory M. Acland > > > > > > I too have been waiting for a reply from the BLAST server at > > blast@ncbi.nlm.nih.gov, for 2 days. Anyone know what is going on, and is > > there an alternative server?? > > > I don't know about the rest of the folks that were having problems, but I > can now get at the BLAST servers again from here in the UK. The problem > seemed to be fixed sometime over the weekend. I've just pinged cruncher to > make sure it is still there and I got responses. > -- > Andy Law > ( Andy.Law @ bbsrc.ac.uk ) > ( Big Nose in Edinburgh ) From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!demon!uknet!daresbury!not-for-mail From: P.Clifford@Queens-Belfast.AC.UK Newsgroups: bionet.software Subject: Flowering in Soya Bean Date: 6 Jul 1995 16:05:57 +0100 Lines: 3 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3tgu4l$bvl@mserv1.dl.ac.uk> Original-To: BIO-SOFT@dl.AC.uk I wish to get hold of some software that went 'out of print' in 1988. It's Flowering in Soya Bean by Longman Micro Software made in 1983. I need it in PC version. Can anyone help? Email P.CLIFFORD@QUB.QC.UK From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!dish.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!ws41.cnusc.fr!UNIX13.U-3MRS.FR!news From: Daniel GAUTHERET Newsgroups: bionet.software Subject: Help in interpreting LALIGN results (FASTA package) Date: 6 Jul 1995 15:24:17 GMT Organization: Centre de Calcul de Saint Jerome Lines: 35 Message-ID: <3tgv71$cfh@unix13.u-3mrs.fr> NNTP-Posting-Host: dali.cnrs-mrs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software I am getting results I don't understand when running a DNA sequence through LALIGN (FASTA 2.0 package) against its own reverse- complement: The fragments that get the best scores are very often self-complementary (at least 80% of them in average). For example, in a sequence of length 1000, many of the best scores look like this one: 66.7% identity in 30 nt overlap; score: 64 943 972 | 950 960 970 | +STRD GGGGAGGGATTCCGGCCGAATGCCGTCCCC <- original seq ::::: :: : :::::: : :: ::::: -STRD GGGGACGGCATTCGGCCGGAATCCCTCCCC <- reverse complement | 40 50 | 29 58 . where the bottom fragment (reverse complement: 29-58) is actually (943-972) read backward, that is the top fragment. Thus this fragment matched its own reverse complement, or in other words, the match is on the diagonal of the matrix. How comes this can occur as often as in 80-100% of the solutions? I thought it could be a specificity of my DNA sequence, but I get the same thing with random sequences. Does LALIGN favor matches on the diagonal? Or is it another artifact that escaped me? Thanks for your help, Daniel GAUTHERET Universite Aix-Marseille II From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!EU.net!Austria.EU.net!newsfeed.ACO.net!fstgds15.tu-graz.ac.at!fochsg01!zuegg From: zuegg@fochsg01 (Johannes Zuegg) Newsgroups: bionet.software Subject: Announcement: Enantioselectivity Calc/Displ Programs Date: 6 Jul 1995 09:46:26 GMT Organization: Graz University of Technology, Austria Lines: 93 Message-ID: <3tgbdi$eo7@fstgds15.tu-graz.ac.at> NNTP-Posting-Host: fochsg01.tu-graz.ac.at Keywords: Enantioselectivity, Program X-Newsreader: TIN [version 1.2 PL1] ------------------------------------------------------------------------------- Selectivity 1.0 for Mac and Windows by: K. Faber, H. Hoenig and A. Kleewein; Copyright (C) December 1994. ------------------------------------------------------------------------------- Description This program can be used for the calculation of the selectivity - expressed as the Enantiomeric Ratio E - of a kinetic resolution of enantiomers for irreversible reactions. A short description how to operate it is included in the main window. More detailed information on the theoretical background and of the merits and limits of the method is described in the help-file. A detailed paper on this topic will be published in Preparative Biotransformations , S. M. Roberts (Ed.), Wiley, 1995. The program may be freely given away but must not be sold. As this program is still under development, any suggestions and comments for improvements, corrections, desired additional features or hard- and software incompatibilities are highly welcome. Please use the contact adress given below. ------------------------------------------------------------------------------- Programs * Mac - Version 1.0 The program runs under system 6.X or higher and any standard Macintosh configuration should be compatible. The program is available on our site: Http://www-orgc.tu-graz.ac.at/programs/enantio/mac The program selectiv.hqx and the help-file selhelp.hqx (MS-Word document) can be obtained in BinHex-form by clicking on the name. There are no preferences to be installed. For the decoding we recommend any application from the Stuff/Unstuff-family. * Windows - Version 1.0 The program is written in VBasic 3.0 and runs with Windows 3.1 or higher. The program is available as a self extracting file or as compressed Zip file on our site: Http://www-orgc.tu-graz.ac.at/programs/enantio/win Please transfer the program selectiv.exe by clicking on the name and then start the program in a local directory on your site. The program will create the installation files. The selectiv.zip must be uncompressed with pkunzip and includes the same files as the selfextracting file. (!) In case you encounter a problem or when you need the program on disc or via email please contact the adress given below by phone, letter, fax or e-mail. ------------------------------------------------------------------------------- Contact Kurt Faber (for Mac-Version) E-Mail:faber@orgc.tu-graz.ac.at Phone:++43-316-873-8254 Helmut Hoenig (for Windows-Version) E-Mail:hoenig@orgc.tu-graz.ac.at Phone:++43-316-873-8246 Institute for Organic Chemistry at Technical University of Graz Stremayrgasse 16, A-8010 Graz, AUSTRIA Fax: ++43-316-811-057 ------------------------------------------------------------------------------- Enjoy the program Johannes Zuegg --------------------------------------------------------------------- Institute for Organic Chemistry Tel : +43 [0]316 873-8246 University of Technology Graz 6387 Stremayrgasse 16 Fax : +43 [0]316 815710 A-8010 Graz (Austria) EMail: Zuegg@orgc.tu-graz.ac.at --------------------------------------------------------------------- From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.chnt.gtegsc.com!casaba.srv.cs.cmu.edu!das-news2.harvard.edu!fas-news.harvard.edu!nucleus!robison From: robison@nucleus.harvard.edu (Keith Robison) Newsgroups: bionet.software,bionet.molbio.genbank Subject: Re: Can I filter random matches due to aa composition? Followup-To: bionet.software,bionet.molbio.genbank Date: 6 Jul 1995 13:03:48 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 42 Message-ID: <3tgmvk$gme@decaxp.harvard.edu> References: <95186.135303IO00865@MAINE.MAINE.EDU> NNTP-Posting-Host: nucleus.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:12612 bionet.molbio.genbank:2063 Ethan Strauss (IO00865@MAINE.MAINE.EDU) wrote: : Hi all, : I have a bunch of very "T" rich amino acid sequences. When I send : them to the BLAST server I get lots of matches with mucins and : other sticky proteins. I found this very strange as I don't think the : virus I have sequenced is likely to encode mucins. I randomized : the order of the amino acids in the sequence and sent that to BLAST. : I found a very similar set of matches to the real sequence. So my : question is what can I do about it? Is there some way to filter out : the matches which are due only to aa composition? It seems like I should : randomize a bunch of times, send all the randomized sequences to BLAST : and then exclude everything which shows up with the random : sequences. Is there a program which will do this for me? : Any suggestions would be appreciated. This is what the XNU and SEG filter options to BLAST do -- they mask out low-complexity (composition-biased) sequence segments prior to your search. You can also get these programs from NCBI in order to mask queries for other programs (the masking is quite literal -- amino acid characters in low-complexity region are replaced with X's). How you invoke these filters depends on how you are accessing the BLAST server, but you should be able to find them in the documentation. The theory & bibliography on these beasts is well explained in Altschul et al. Nature Genetics 6:119-129. 1994 Enjoy! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!sol.ctr.columbia.edu!news.mtu.edu!msunews!harbinger.cc.monash.edu.au!bruce.cs.monash.edu.au!not-for-mail From: lloyd@bruce.cs.monash.edu.au (Lloyd Allison) Newsgroups: bionet.software Subject: Re: Sequence alignment significance? Date: 6 Jul 1995 00:01:52 GMT Organization: Computer Science, Monash University, Australia Lines: 20 Message-ID: <3tf95g$jib@harbinger.cc.monash.edu.au> References: <3sms8d$hf2@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: dec31.cs.monash.edu.au X-Newsreader: TIN [UNIX 1.3 941213BETA PL0] Cornelius Krasel (phak004@wrzx12.rz.uni-wuerzburg.de) wrote: ... : contains two gaps. We now would like to find out if this aligment : bears any statistical significance (even better would be to know if : the alignment bears biological significance, but I doubt programs : are able to find this out :-). The fasta package contains several ... we have a significance test (i) for an alignment and (ii) for the hypothesis that 2 seq's are related - for a given model of course. NB. (i) and (ii) are not the same thing. http://www.cs.monash.edu.au/~lloyd/tildeStrings/index.html Lloyd ALLISON Dept. of Computer Science, Monash University, Clayton, Victoria 3168, AUSTRALIA tel: 61 3 905 5205 fax: 61 3 905 5146 email: lloyd@cs.monash.edu.au LA home From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!torn!newshost.uwo.ca!ustilago.plantsci.uwo.ca!aday From: aday@julian.uwo.ca (Alan Day) Newsgroups: bionet.software Subject: LATEST VERSIONS OF GENETICS TEACHING SOFTWARE Date: Wed, 5 Jul 1995 15:46:22 GMT Organization: ITS, UWO Lines: 70 Message-ID: NNTP-Posting-Host: ustilago.plantsci.uwo.ca Keywords: Genetics, molecular biology , teaching software X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] ANNOUNCEMENT - Latest Versions of Visual Genetics/The Virtual Genetics Lab. Leading Teaching software for introductory Genetics, Biochemistry, Molecular Biology courses - now used by over 120 institutions in >15 countries - much acclaimed by students. 1. Version 2.0 of 'Visual Genetics' now has 68 long full screen animations (each a 10 - 20 min lesson) on key classical and molecular genetics topics) Typical animation-lessons include:- DNA Fingerprinting Replication at the Replication fork Holliday and other Molecular models of Recombination Chromosomal inversions Translation DNA Repair Lac operon DNA Sequencing.......and many more. The program also includes 180 multiple choice and 72 problem-solving questions with EXPLAINED answers, diagrams to label etc. Requires Windows but all animations available separately for DOS only or MAC QuickTime computers. Animations available as complete, partial or custom sets. 2. Version 2.0 of The 'Virtual Genetics Lab' now ships with 2 options - the standard version for student self-directed learning of lab experiments in classical genetics, and a new 'Print Report' version which can be used for graded tutorials etc. These programs simulate on screen the steps that would be taken to:- 1. Isolate and identify 3 fungal auxotrophic mutants 2. Classify 10 apparently identical auxotrophs for allelism - based on pathway analysis 3. Classify 10 apparently identical auxotrophs for allelism - based on complementation test analysis 4. Map 3 auxotrophic mutations via random spore analysis 5. Map 3 auxotrophic mutations and a colour mutation via tetrad analysis 6. Map 3 auxotrophic mutations, a drug resistance mutation and a colour mutation via mitotic recombination. 7. Then combine mapping data into one map Requires Windows. DEMOS and Further enquiries DEMOS on the 'NET' WWW access: http://www.inform.umd.edu/EdRes/Topic/AgrEnv/Biotech/Software/bio-anim Gopher Access: gopher gopher.nalusda.gov -Information Centers -Biotechnology Information Center -Software -GENETICS & MOLECULAR BIOLOGY PROGRAMS BY BIO-ANIMATE PRODUCTIONS Please read the text file that comes with these demos for full information on installation, running, pricing etc. If problems with downloading or further info needed contact aday@julian.uwo.ca Enquiries re ordering incl. low cost network rates, system requirements etc to Bio-Animate Productions, 28 Askin St London, Ont, Canada (519-432-5800) From owner-software@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!asuvax!noao!CS.Arizona.EDU!news.Arizona.EDU!champlin From: champlin@GAS.UUG.Arizona.EDU (Jacob B Champlin) Newsgroups: bionet.software Subject: Database search program? Date: 6 Jul 1995 06:57:24 GMT Organization: The University of Arizona Lines: 22 Message-ID: <3tg1gk$7no@news.ccit.arizona.edu> NNTP-Posting-Host: helium.gas.uug.arizona.edu X-Newsreader: TIN [version 1.2 PL2] I am looking for a program that will go through the yeast gene database and retrieve this information: 1.