From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!xmission!news.cc.utah.edu!zifi.genetics.utah.edu!zinc From: zinc@zifi.genetics.utah.edu (zinc) Newsgroups: bionet.software Subject: Re: rasmol on linux Date: 2 Nov 1995 02:26:27 GMT Organization: assorted dsRNAs and lotsa zinc Lines: 34 Message-ID: <479a8j$brr@news.cc.utah.edu> References: <477sma$3v0@reeve.research.aa.wl.com> NNTP-Posting-Host: zifi.genetics.utah.edu -----BEGIN PGP SIGNED MESSAGE----- In article <477sma$3v0@reeve.research.aa.wl.com>, Brian Moldover wrote: >I'm unable to get Rasmol 2.5 or 2.6 to compile under Linux. It complains about >header files missing in xwin11.c. Does anyone have any tips, or failing that, a >precompiled version? Thanks! Rasmol v2.5 compile just fine on my linux box. i compiled it before i moved to ELF, so i've just got the a.out executable. i'd be happy to mail it to you if you'd like. - -pjf -----BEGIN PGP SIGNATURE----- Version: 2.6.2 Comment: Auto-signed with Bryce's Auto-PGP v1.0beta3 iQCVAwUBMJgsSU3Qo/lG0AH5AQFxMgP/V/QZFI+CCaR2w0baEJP1uScRuXIrVmdh 0vxf4w0iaaucliYwj79aBpPqBEA0xkiHhDuJWqonJYkQEHkm/yVmBUvQc2fUasnI nhHkGZRvcSe+n/jDW9bMSYUrl8/aEq/vJ+wIir8/8EPW2ixkwEPWHPeR45pQpdfl T0YlyVwXQnI= =CchJ -----END PGP SIGNATURE----- -- patrick finerty = zinc@zifi.genetics.utah.edu = pfinerty@nyx.cs.du.edu U of Utah biochem grad student in the Bass lab - zinc fingers + dsRNA! ** FINGER zinc-pgp@zifi.genetics.utah.edu for pgp public key - CRYPTO! zifi runs LINUX 1.2.11 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!biosci!not-for-mail From: hunter@work.nlm.nih.gov (Larry Hunter) Newsgroups: bionet.announce,bionet.biology.computational,bionet.general,bionet.info-theory,bionet.molbio.bio-matrix,bionet.molec-model,bionet.population-bio,bionet.software,bionet.women-in-bio Subject: Pacific Symposium on Biocomputing -- Program & Final Announcement Date: 1 Nov 1995 16:14:34 -0800 Organization: National Library of Medicine Lines: 322 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: Reply-To: Hunter@nlm.nih.gov NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:2592 bionet.biology.computational:811 bionet.general:18239 bionet.info-theory:3710 bionet.molbio.bio-matrix:666 bionet.molec-model:648 bionet.population-bio:1630 bionet.software:13801 bionet.women-in-bio:3264 **** PSB '96 FINAL ANNOUNCEMENT **** This is the program of the Pacific Symposium on Biocomputing to be held on the Big Island of Hawaii, January 3-6, 1996. For symposium registration information and forms, please see our web site at http://cgl.ucsf.edu/psb or send email to psb@intsim.com INVITED PRESENTATIONS: Minoru Kanehisa, Kyoto University: Logical Simulation of Biomolecular Information Pathways David Weininger, DAYLIGHT Chemical Information Systems. CEX and the Single Chemist SESSION TOPICS: * Internet Tools for Computational Biology * Biocomputing Education: Challenges and Opportunities * Interactive Molecular Visualization * Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics * The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution * Discovering, Learning, Analyzing and Predicting Protein Structure * Population Modelling * Models of Control Systems in Biology * Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution * Computational Studies on the Design of Protease Inhibitors ORAL PRESENTATIONS Tatsuya Akutsu and Hiroshi Tashimo, "Protein structure comparison using representation by line segment sequences" Kurt Albrect, John Hart, Alex Shaw and A. Keith Dunker, "Quaternion Contact Ribbons: a New Tool for Visualizing Intra- and Inter-molecular Interactions in Proteins." Nickolai N. Alexandrov, Ruth Nussinov and Ralk M. Zimmer, "Fast Protein Fold Recognition via Sequence to Structure Alignment and Contact Capacity Potentials." Russ B. Altman and John Koza, "A Programming Course in Bioinformatics for Computer and Information Science Students." Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnord and David Whitmire "Massively Parallel Simulated Annealing Algorithms for Chromosome Reconstruction via Clone Ordering." Erich Bornberg-Bauer, "Structure Formation of Biopolymers is Complex, Their Evolution may be Simple." Michael Brown and Charles Wilson, "RNA Pseudoknot Modeling Using Intersections of Stochastic Context Free Grammars with Applications to Database Search." Su Yun Chung and S. Subbiah, "How similar must a template protein be for homology modeling by side-chain packing methods?" Steven A. Corcelli, Joel D. Kress, Lawrence R. Pratt and Gregory Tawa, "Mixed Direct-Iterative Methods for Boundary Integral Formulations of Dielectric Solvation Models." Gordon Crippen and Vladimir Maiorov, "All possible protein folds at low resolution." Erzsbet Csuhaj-Varj, Rudolf Freund, Lila Kari and Gheorghe P un, "DNA Computing Based on Splicing: Universarity Results." Ewa Deelman, Thomas Caraco, and Boleslaw K. Szymanski, "Parallel Discrete Event Simulation of Lyme Disease" Francisco M. De La Vega, Robert Giegerich and Georg Fuellen, "Distance Education through the Internet: The GNA-VSNS Biocomputing Course" T. Gregory Dewey and Bonnie J. Strait, "Multfractals, Encoded Walks and the Ergodicity of Protein Sequences." Reinhard Doelz and Florian Eggenberger, "List Update Processing (LUP) - Solving the database update problem" David L. Dowe, Lloyd Allison, Trevor Dix, Lawrence Hunter, Chris S. Wallace and Timothy Edgoose, "Circular Clulstering of Protein Dihedral Angles by Minimum Message Length." Keith Downing, "An Object-Oriented Data-Driven Migration Model." Herbert Edelsbrunner, Michael Facello and Jie Liang, "On the Definition and the Construction of Pockets in Macromolecules." C. Ferretti and S. Kobayashi , "DNA Splicing Systems and Post Systems." Daniel Fischer, Arne Elofsson, Danny Rice and David Eisenberg, "Assessing the performance of fold recognition methods by means of a comprehensive benchmark." Bruno A. Gaeta, Carolyn A. Bucholtz, Rowena Campbell, Camson Huynh, Stephanie Kim, and Alex H. Reisner, "Biocomputing Education by the Australian National Genomic Information Service." K.M. Gernert, L.D. Bergman, B.D. Thomas, J.C. Plurad, J.S. Richardson, D.C. Richardson and L.D. Bergman, "Puzzle Pieces Defined: Locating Common Packing Units in Tertiary Protein Contacts" Brad Gulko and David Haussler, "Using Multiple Alignments and Phylogenetic Trees to Detect RNA Secondary Structure." Paul Horton, " A Branch and Bound Algorithm for Local Multiple Alignment" Wolf-Dietrich Ihlenfeldt and Johann Gasteiger, "Beyond the Hyperactive Molecule: Search, Salvage and Visualization of Chemical Information from the Internet." Susan J. Johns, Steve M. Thompson, and A.Keith Dunker, "An Introductory Course in Computational Molecular Biology: Rationale, History, Observations and Course Description." A. Peter Johnson and Zsolt Zsoldos, "Visualisation in the SPROUT molecular design program." Richard Judson, "Computational Evolution of a Model Polymer that Folds to a Specified Target Conformation" Peter Karp, "A Protocol for Maintaining Multidatabase Referential Integrity" Andrzej Kolinski, Jeffrey Skolnick and Adam Godzik, "An algorithm for prediction of structural elements in small proteins" Eugene Kolker and Edward Trifonov, "Sequence Sizes of Eukaryotic Enzymes" Y. Komeiji, H. Yokoyama, M. Uebayasi, M. Taiji, T. Fukushige, D. Sugimoto, R.Takata, A Shimizu and K. Itsukashi, "A high performance system for molecular dynamics simulations of biomolecules using a special-purpose computer" J. M. Koshi and R. A. Goldstein, "Correlating Mutation Matrices with Physical-Chemical Properties" John R. Koza and David Andre, "A Case Study Where Biology Inspired a Solution to a Computer Science Problem." H. Matsua, "Protein Phylogenetic Inference using Maximum Likelihood with a Genetic Algorithm" Richard P. Muller and Arieh Warshel, "Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution: Proton Transfer in [FHF]-" . Nickolai N. Alexandrov, Ruth Nussinov, and Ralf M. Zimmer, "Fast protein fold recognition via sequence to structure alignment and contact capacity potentials" Jiann-Jong Pan and Jenn-Kang Hwang, "Mixed Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution and in Enzymes by the Classical Trajectory Mapping Approach" . Andrew Pohorille, Christophe Chipot, Michael H. New, and Michael A. Wilson, "Molecular Modeling of Protocellular Functions" Stephen D. Rufino, Luis E. Donate, Luc Canard, and Tom L. Blundell, "Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structure" E. Swanson and T. P. Lybrand, "Computational Biology Instruction at the University of Washington Center for Bioengineering" Erika Tateishi and Satoru Miyano, "A Greedy Strategy for Finding Motifs from Yes-No Examples" A. Tropsha, R. K. Singh, I. I. Vaisman and W. Zheng, "Statistical Geometry Analysis of Proteins: Implications for inverted structure prediction" David Van Der Spoel and Herman J.C. Berendsen, "Determination of Proton Transfer Rate Constants Using Ab Initio, Molecular Dynamics and Density Matrix Evolution Calculations" Gennady Verkhivker, "Empirical Free Energy Calculations of Human Immunodeficiency Virus Type 1 Protease Crystallographic Complexes. II. Knowledge-Based Ligand-Protein Interaction Potentials Applied to the Thermodynamic Analysis of Hydrophobic Mutations" Michal Vieth, Andrzej Kolinski, Charles L. Brooks, III, and Jeffrey Skolnick, "Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants" H. Vollhardt and J. Brickmann, "3D Molecular Graphics on the World Wide Web" Cathy H. Wu, Hsi-Lien Chen, Chin-Ju Lo and Jerry W. McLarty, "Motif Identification Neural Design for Rapid and Sensitive Protein Family Search" Tetsushi Yada, Masato Ishikawa, Hidetoshi Tanaka and Kiyoshi Asai, "Extraction of Hidden Markov Model Representations of Signal Patterns in DNA Sequences" POSTER PRESENTATIONS (including live poster demonstrations): Tatsuya Akutsu, "A Simple Alignment Algorithm for Three-dimensional Protein Structures." Russ B. Altman and Steven C. Bagley, "Conserved biochemical features among four protease molecules with not structural or sequential homology." Russ B. Altman, Robert Schmidt and Mark Gerstein, "A library of low-variance cores for protein families." Paul Bieganski, John Riedl, John Carlis and Ernest F. Retzel, "Motif Explorer P A tool for interaction exploration of Amino Acid Sequence Motifs." GeneQuiz II: Automatic Function Asignment for Genome Sequence Analysis." Fancisco M. De La Vega, Carlos Cerpa, Gabriel Guarneros and Robert M. Farber, "A Mutal Information Analysis of tRNA seqeuence and modification patterns distinctive of species and phylogentic domain. P. De Rijk and R. De Wachter, "tkDCSE, The dedicated comparitive sequence editor." Yukiko Fujiwara, Minoru Asogawa and Akihiko Konagaya, "Motif extraction using an improved iterative duplication method for HMM topology learning." K.M. Gernert, J.S. Richardson and D.C. Richardson, "MAGE as a teaching tool." Andrei Grigoriev, Richard Mott and Hans Lehrach, "Handling experimental noise and integrating different types of data in genomic mapping." X. Guan and E. Uberbacher, "A fast lookup algorithm for detecting repetitive DNA sequences." Chris Henn and Michael Teschner, "Molecular Inventor: Discovering novel compounds in a collaborative environment." C. N. Hodge, Z.W. Wasserman, P.F.W. Stouten, B.A. Luty and C. Liang, "Fitting Flexible ligands into flexible active sites." Conrad C. Huang, Gregory S. Couch, Eric F. Pettersen and Thomas E. Ferrin, " Chimera: An extensible molecular modelling application constructed using standard components." Peter D. Karp and Suzanne M. Paley, "Retrofitting existing applications and authoring new applications for the World Wide Web." Ajay Jain, "Flexible Molecular Docking: Scoring, Site Identification and Database Searching." F. Lebon, "Strategy for de novo computational drug design of HIV-1 PR inhibitors." J.E. Marstaller and M. D. Zorn, "An electronic laboratory notebook based on the World Wide Web." H. Matsuda, F. Taniguchi and A. Hashimoto, "A notation of amino acid conformations for exploring similar protein structures." Seth Michelson, "Biological control in tumor growth." Arthur J. Olson and Bruce S. Duncan, "Protein-protein docking using parametric surface representations." Martin G. Reese, Nomi L. Harris and Frank H. Eeckman, "Large scale sequencing specific neural networks for promotor and splice site recognition." B. A. Reva, A. V. Finkelstein, D. S. Rykunov and A. J. Olson, "Building of self-avoidingt lattice models of proteins using a SCF-optimization" Michel F. Sanner, Boris A. Reva, Alexei V. Finkelstein and Arthur J. Olson, "Increasing accuracy of energy calculations of lattice models by adjusting the potentials." R. K. Singh, D. L. Hoffman and A. Tropsha, "Rapid comparison and classification of protein 3D structures using one-dimensional structure profiles. Wayne E. Steinmetz, Steve Cotton and Cynthia D. Selassie, "A CoMFA analysis of the elastase catalyzed hydrolysis of glycine esters." Hideaki Sugawara, Junko Shimura, Satoru Miyazaki, Yoshihiro Masuda and Yasuhiro Ishitobi, "Application of a new data model and visualization to systematics." Barnabas Takacs, "A parallel computational model of attention and saccade generation in the human visual system." Hidetoshi Tanaka, "An automatic configuration algorithm of discrete hidden Markov models for amino acid sequences." Holly Tao, Zhen Tao Chu and Arieh Warshel, "Quantitative studies of ligand-receptor interactions: A rapid evaluation of binding free energies of endothiapepsin to its inhibitors." Excited states of the chromophores of the photosynthetic reaction center >From Rhodopseudomonas viridis: A QM/MM study that includes MM polarization." Iosif I. Vaisman, "Virtual communities at interdisciplinary boundaries." -- Lawrence Hunter, PhD. National Library of Medicine phone: +1 (301) 496-9300 Bldg. 38A, 9th floor fax: +1 (301) 496-0673 Bethesda. MD 20894 USA email: hunter@nlm.nih.gov PGP 2.62 public key from http://www-swiss.ai.mit.edu/~bal/pks-toplev.html From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!news.belwue.de!news.uni-konstanz.de!schink From: Andreas.Brune@uni-konstanz.de (Andreas Brune) Newsgroups: bionet.software Subject: Re: reference manager/bibliography freeware (or shareware) Date: Thu, 02 Nov 95 07:29:32 GMT Organization: Universitaet Konstanz Lines: 12 Distribution: world Message-ID: <479s0t$bsg@eurybia.rz.uni-konstanz.de> References: <478q32$di6@taco.cc.ncsu.edu> NNTP-Posting-Host: schink.biologie.uni-konstanz.de X-Newsreader: News Xpress Version 1.0 Beta #4 In article <478q32$di6@taco.cc.ncsu.edu>, Susan Jane Hogarth wrote: >I'm looking for freeware/shareware to manage my references. Try REFS by Tim Cutts. http://chiark.chu.cam.ac.uk:81/refs/refs.html Really nice shareware program. Dr. Andreas Brune Phone: +49-7531-883282 Mikrobielle Oekologie Fax: +49-7531-882966 Universitaet Konstanz E-mail: Andreas.Brune@uni-konstanz.de From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!CONTI3.SCI.UNIROMA1.IT!aureli From: aureli@CONTI3.SCI.UNIROMA1.IT ("aureli@conti3.sci.uniroma1.it") Newsgroups: bionet.software Subject: looking for reference manager software Date: 2 Nov 1995 03:10:48 -0800 Organization: Dept.Chemistry-Univ. "La Sapienza" Rome (Italy) Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511021108.AA16187@itaca.caspur.it> I'm looking for freeware/shareware to manage my reference. It'd be able to import references from different sources (i.e.medline). I'm a Mcintosh user, so does anyone know where I can find something? Thanks Tommaso Aureli Dipartimento di Chimica Universita' "La Sapienza" P.le Aldo Moro 5, 00185 Roma (Italy) aureli@conti3.sci.uniroma1.it From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!ts16-12.wla.ts.ucla.edu!dtyyu From: dtyyu@ucla.edu (David Tak Yan Yu) Newsgroups: bionet.software Subject: Using NIH-Image with window3.1 Date: Thu, 2 Nov 1995 12:47:21 Organization: UCLA Lines: 5 Distribution: world Message-ID: NNTP-Posting-Host: ts16-12.wla.ts.ucla.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I wish to use the NIH-Image to measure density of SDS-PAGE bands. However, that program is for Mac. How can I use it in my own PC with window3.1? David Yu dtyyu@ucla.edu From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!usenet From: Robert Russell Newsgroups: bionet.molbio.proteins,bionet.software,bionet.structural-nmr,bionet.xtallography Subject: ANNOUNCE- *** PROTEIN 3D STRUCTURE ALIGNMENT SOFTWARE - STAMP v4.0 *** Date: 2 Nov 1995 18:18:48 GMT Organization: Imperial Cancer Research Fund Lines: 41 Message-ID: <47b228$b0d@charlie.lif.icnet.uk> NNTP-Posting-Host: bonsai.lif.icnet.uk 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) To: gjb@bioch.ox.ac.uk X-URL: news:bionet.molbio.proteins Xref: biosci bionet.molbio.proteins:6167 bionet.software:13809 bionet.structural-nmr:868 bionet.xtallography:2137 NEW RELEASE OF STAMP (Structural Alignment of Multiple Proteins) Version 4.0 STAMP is a package comprising 15 programs for alignment and analysis of protein three-dimensional structures. The major features are: 1) Fast alignment and superimposition of two or more protein structures 2) Generation and display superimposed protein 3D structures and sequence alignments 3) Comparison of a protein 3D structure to a database of other 3D structures 4) Direct interface to MOLSCRIPT and ALSCRIPT drawing programs 5) A clear method for assigning which regions within a family of proteins are structurally equivalent, without the need for graphical intervention. STAMP is available free of charge to non-profit organisations, and to others for a fee. A license must be completed by all prospective users. Users of previous versions of STAMP can obtain the new version with the same license. The new version (4.0) has corrected several bugs, ontains a much improved manual and includes several new programs, including those for the generation of MOLSCRIPT input, and for the generation of averaged structures. For further details as to the program and licenses, see: WWW http://geoff.biop.ox.ac.uk/ FTP ftp://geoff.biop.ox.ac.uk/README ftp://geoff.biop.ox.ac.uk/STAMP.LIC or contact Geoff Barton via mailto:gjb@bioch.ox.ac.uk Robert B. Russell Biomolecular Modelling, Imperial Cancer Research Fund 44 Lincoln's Inn Fields, P.O. Box 123, London, WC2A 3PX, U.K. Tel: 44 171 269 3583 FAX: 44 171 269 3479 mailto:russell@icrf.icnet.uk WWW http://bonsai.lif.icnet.uk/people/rob/rob.html From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!sundog.tiac.net!usenet From: "Richard J. Resnick" Newsgroups: bionet.software Subject: Primerv2.2 port to Macintosh Date: 2 Nov 1995 16:56:25 GMT Organization: Apple Pi Consulting Lines: 25 Message-ID: <47at7p$4uf@sundog.tiac.net> NNTP-Posting-Host: applepi.tiac.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.software Hello, I'm the author of Primer v2.2, in the middle of a port to the Macintosh. I wanted to post on this group to listen to what folks have to say about Primer v2.2, to ask what features they would like to see in a Mac ver- sion, and in general to just get some feedback. Currently, Primer v2.2 runs on UNIX machines, as well as the World Wide Web (http://www-genome.wi.mit.edu/cgi-bin/primer2.2/primer_front). Comments would be most helpful around issues of I/O, that is: how would you like to input sequences? What sorts of output should there be? Printable? Networkable? Output to screen vs. file? User interface comments are also highly desirable. Thanks in advance for your suggestions. Drop me a line if you'd like to be on the mailing list for the Macintosh version of Primers. Richard Resnick Director, Chief Engineer Apple Pi rjr@applepi.com http://www.applepi.com/users/rjr/index.html (under construction) From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news.sprintlink.net!news.computek.net!news From: mjimenez@computek.net (Martin Jimenez) Newsgroups: bionet.software Subject: CASE FAQ Date: 2 Nov 1995 08:20:45 GMT Organization: Compu-Net Lines: 7 Message-ID: <479v0t$n1@news.computek.net> NNTP-Posting-Host: 205.241.169.13 Mime-Version: 1.0 X-Newsreader: WinVN 0.99.2 I am looking for information about CASE tools. I need to know what CASE is, what are its parts, etc. Please email me info. Thanks ! From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!waikato!comp.vuw.ac.nz!canterbury.ac.nz!MANUKA.lincoln.ac.nz!pc090222.lincoln.ac.nz!mclachla From: mclachla@tui.lincoln.ac.nz (Andrew McLachlan) Newsgroups: bionet.software Subject: Re: reference manager/bibliography freeware (or shareware) Date: Thu, 2 Nov 1995 23:40:52 GMT Organization: Lincoln University, New Zealand Lines: 18 Message-ID: References: <478q32$di6@taco.cc.ncsu.edu> NNTP-Posting-Host: pc090222.lincoln.ac.nz Susan Jane Hogarth writes: >I'm looking for freeware/shareware to manage my references. >It'd be nice to have something that would work with Windows, >but DOS is OK, too. I'd even be interested in hearing recomendations >about commercial programms, especially if they have demo versions >to try. I can recommend a commercial program, Papyrus. There is a demo available. Email Dave Goldman at rsd@teleport.com and he will help you (he is the president of the software company that make Papyrus). Papyrus is a DOS program, but works well under Windows (it can paste references directly to the Windows clipboard). It costs $99 US plus some postage. Cheers Andrew McLachlan mclachla@tui.lincoln.ac.nz From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!news.rediris.es!obelix.cica.es!obelix.cica.es!not-for-mail From: claros@obelix.cica.es (Manuel G. CLAROS) Newsgroups: bionet.software Subject: Staden pack Date: 2 Nov 1995 15:35:00 +0100 Organization: La Magnanima Universidad de Malaga, y el CICA en su nombre Lines: 25 Message-ID: <47akuk$9ci@obelix.cica.es> NNTP-Posting-Host: obelix.cica.es X-Newsreader: TIN [version 1.2 PL0] [ Article crossposted from bionet.molbio.methds-reagnts ] [ Author was Manuel G. CLAROS (claros@ccuma.uma.es) ] [ Posted on 2 Nov 1995 15:33:56 +0100 ] I would like to have some information of how to purchase the Staden pack of programs. I tried to find his e-mail or something and I did not find anything. Could someone give some light about this? Thanks Please, e-mail me the reply... It is a little urgent and news arrive several days later. -- Manuel G. CLAROS -. .-. .-. .-. . -> claros@ccuma.uma.es <- Biologia Molecular ||X|||\ /|||X|||\ /| Facultad Ciencias |/ \|||X|||/ \|||X|| Siempre nos quedara Paris E-29071 Malaga ' `-' `-' `-' `- (Casablanca) -- Manuel G. CLAROS -. .-. .-. .-. . -> claros@ccuma.uma.es <- Biologia Molecular ||X|||\ /|||X|||\ /| Facultad Ciencias |/ \|||X|||/ \|||X|| Siempre nos quedara Paris E-29071 Malaga ' `-' `-' `-' `- (Casablanca) From owner-software@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.connectnet.com!usenet From: cis@cheminnovation.com Newsgroups: bionet.software Subject: Re: s'ware to convert MOL to graphics Date: Wed, 01 Nov 95 19:51:47 PST Organization: CONNECTnet Internet Network Services (service provider) Lines: 36 Message-ID: <479fcg$on8@news.connectnet.com> References: <46uos4$n83@caesar.ultra.net> NNTP-Posting-Host: henryl.connectnet.com Mime-Version: 1.0 X-Newsreader: WinVN 0.93.6 In article <46uos4$n83@caesar.ultra.net>, kbrady@kbrady@ultranet.com says... > >I have a library of chemical MOL files which I would like to convert to >graphics which I could easily import into a PC-based word-processor (BMP >is easiest). Can anyone point me to some software that does this (batch- >mode please - I have hundreds of files!) > >Thanks in advance.. >kbrady@ultranet.com Chemistry 4-D Draw can do exactly what you want to do. There is a special version that allows you to type "*.mol" as input files and the program will read all of the specified files and convert them into Metafiles or bitmap files. Chemistry 4-D Draw is a new drawing program which understands IUPAC nomenclature rules. It allows you to create high-quality structures simply by entering molecular names. It includes a full set of intelligent tools for drawing, text and structure editing, and labeling. Features include: * Create/Edit structures in 2D, 3D or 4D (Name space) * Import/Export MDL MOL files * Export publication quality graphics using OLE-2 technologies (Drag&Drop) * Save fragments with your own "trivial names" Chemistry 4-D Draw is available on ALL major PC platforms: Windows 95, Windows 3.1, Windows NT, Macintosh, OS/2 For more information, please see http://www.cheminnovation.com or contact ChemInnovation Software at Tel (619)566-2846 Fax (619)566-4138 E-mail: cis@cheminnovation.com From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!xmission!news.cc.utah.edu!zifi.genetics.utah.edu!zinc From: zinc@zifi.genetics.utah.edu (zinc) Newsgroups: bionet.software Subject: Re: Using NIH-Image with window3.1 - try a Mac emulator - Executor Date: 3 Nov 1995 05:44:25 GMT Organization: assorted dsRNAs and lotsa zinc Lines: 73 Message-ID: <47ca7p$8ac@news.cc.utah.edu> References: NNTP-Posting-Host: zifi.genetics.utah.edu -----BEGIN PGP SIGNED MESSAGE----- In article , David Tak Yan Yu wrote: >I wish to use the NIH-Image to measure density of SDS-PAGE bands. >However, that program is for Mac. How can I use it in my own PC with >window3.1? David, first off, i have zero to do with this company. i am simply a VERY satisfied customer and wish to see them succeed. you should try out a program called Executor. this is a Macintosh emulator that runs under DOS, Linux, and NextStep. it is pretty nice and runs NIH Image quite well. although this is a commercial program, you can obtain a demo copy via anonymous ftp or the WWW at a couple of locations. the demo will run for 10 minutes as a fully functional program at which point it exits. this is sufficient time for you to decide if you think it will be useful for you at which point you can license it from ARDI. currently, it is fairly inexpensive to license executor, but they will be going to press with a CD soon and the price will go up considerably. if i were you, i'd check it out quickly... this site is very slow, only connected via a 28.8 K modem http://www.ardi.com/ vorlon is pretty fast... http://vorlon.mit.edu/arditop.html currently, the most up to date version of executor is 1.99p5. YOU MUST INSTALL 1.99p first before installing p5!!! you can find this here; ftp://ftp.ardi.com/pub/BleedingEdge/DOS/ additionally, an HFV file containing NIH image can be obtained from this site; ftp://vorlon.mit.edu/pub/ardi/HFV/science/nihimage.hfv i have been using it on my linux computer for some time now and i have to say it's pretty damn cool. there's no other Mac emulator available. - -pjf -----BEGIN PGP SIGNATURE----- Version: 2.6.2 Comment: Auto-signed with Bryce's Auto-PGP v1.0beta3 iQCVAwUBMJmsO03Qo/lG0AH5AQGnRwP/QTlgQUoa8ANxf2kHW/oEitN176/VLlmN sosrDWLLpOOyCc8mm9mRlifwZK4z6YsAoLhS+RV98mI+kyBEFbCpvW78fgF9Ut73 1dmERYofhRpOdVkKVDk1C6EmELt4jXm/P26LigoTH4+wAAUbGigemF1Zq6b5HO2A 5/lg83oJgKA= =Aral -----END PGP SIGNATURE----- -- patrick finerty = zinc@zifi.genetics.utah.edu = pfinerty@nyx.cs.du.edu U of Utah biochem grad student in the Bass lab - zinc fingers + dsRNA! ** FINGER zinc-pgp@zifi.genetics.utah.edu for pgp public key - CRYPTO! zifi runs LINUX 1.2.11 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!waikato!comp.vuw.ac.nz!canterbury.ac.nz!chmeds.ac.nz!mkennedy From: mkennedy@chmeds.ac.nz (Martin Kennedy) Newsgroups: bionet.software Subject: Re: reference manager/bibliography freeware (or shareware) Message-ID: <1995Nov3.143033.457@chmeds.ac.nz> Date: 3 Nov 95 14:30:33 +1200 References: <478q32$di6@taco.cc.ncsu.edu> <479s0t$bsg@eurybia.rz.uni-konstanz.de> Distribution: world Lines: 28 In article <479s0t$bsg@eurybia.rz.uni-konstanz.de>, Andreas.Brune@uni-konstanz.de (Andreas Brune) writes: > In article <478q32$di6@taco.cc.ncsu.edu>, > Susan Jane Hogarth wrote: >>I'm looking for freeware/shareware to manage my references. > > Try REFS by Tim Cutts. > http://chiark.chu.cam.ac.uk:81/refs/refs.html > Really nice shareware program. > Dr. Andreas Brune Phone: +49-7531-883282 > Mikrobielle Oekologie Fax: +49-7531-882966 > Universitaet Konstanz E-mail: Andreas.Brune@uni-konstanz.de I'll second that; Tim is also close to a release of a Win95 version. You can demo a fully fucntional version which handles a couple of hundred (or therabouts) references; full functionality requires registration and payment (I think this is about 80 pounds Sterling). -- Cheers, Martin NNNN NN Martin A Kennedy (E-mail = mkennedy@chmeds.ac.nz) ZZZZZZZ NN NN NN Cytogenetic and Molecular Oncology Unit ZZZ NN NN NN Christchurch School of Medicine ZZZ NN NNNN Christchurch, New Zealand ZZZZZZZ Phone (64-3)364-0880 Fax (64-3)364-0750 From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: timc@chiark.chu.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: reference manager/bibliography freeware (or shareware) Date: 03 Nov 1995 08:22:35 +0000 (GMT) Organization: Linux Unlimited Lines: 24 Message-ID: References: <478q32$di6@taco.cc.ncsu.edu> <479s0t$bsg@eurybia.rz.uni-konstanz.de> <1995Nov3.143033.457@chmeds.ac.nz> NNTP-Posting-Host: chiark.chu.cam.ac.uk Originator: timc@chiark.chu.cam.ac.uk (UNIX:@[127.0.0.1]) In article <1995Nov3.143033.457@chmeds.ac.nz>, Martin Kennedy wrote: >In article <479s0t$bsg@eurybia.rz.uni-konstanz.de>, Andreas.Brune@uni-konstanz.de (Andreas Brune) writes: >> In article <478q32$di6@taco.cc.ncsu.edu>, >> Susan Jane Hogarth wrote: >>>I'm looking for freeware/shareware to manage my references. >> >> Try REFS by Tim Cutts. >> http://chiark.chu.cam.ac.uk:81/refs/refs.html >> Really nice shareware program. > >I'll second that; Tim is also close to a release of a Win95 >version. You can demo a fully fucntional version which handles a >couple of hundred (or therabouts) references; full functionality >requires registration and payment (I think this is about 80 >pounds Sterling). 30 pounds, actually. However, the original poster was asking about Macintosh software, and Refs is only available for the various flavours of Windows. Tim. From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!dziuxsolim.rutgers.edu!er7.rutgers.edu!not-for-mail From: nlandau@eden.rutgers.edu (Nicholas Landau) Newsgroups: bionet.software Subject: Biological WordPerfect Dictionary? Date: 3 Nov 1995 01:22:21 -0500 Organization: Rutgers University Lines: 6 Message-ID: <47ccet$smb@er7.rutgers.edu> NNTP-Posting-Host: er7.rutgers.edu Keywords: wordperfect biology Is it possible to be get spelling dictionaries for WordPerfect (both Mac and IBM) which include biological jargon (especially taxonomic names?) I'm just tired of the speller hitting every other word, and would be willing to pay to make this problem go away. From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dish.news.pipex.net!pipex!news00.sunet.se!sunic!news99.sunet.se!umdac!news From: Ingvar Holm Newsgroups: bionet.software Subject: Re: DNA Strider 1.2 or 2.0 somewhere? Date: 3 Nov 1995 09:58:32 GMT Organization: University of Umea, Sweden Lines: 27 Message-ID: <47cp48$64b@studium.student.umu.se> References: NNTP-Posting-Host: mac22.zoofys.umu.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; PPC) To: foisys@tornade.ere.umontreal.ca X-URL: news:foisys-2810950900360001@192.0.194.1 Hi, I purchased version 1.2 of DNA Strider from Christian Marck a year ago or so. The price then was FF 1500. It works fine on almost any Mac, although you may want a bigger screen than what you get on the Plus, SE/30 etc. There are some improvements in the program compared to ver. 1.0.1 that I used previously. I hav not heard of any more recent version ("2.0" or so). The address to the author as printed on the manual is: Christian Marck Service de Biochimie et de Genetique Moleculaire Bat.142 Centre d'Etudes de Saclay 91191 Gif-Sur-Yvette Cedex France No fax-, telephone- or e-mail available. Hope this information is of any use to you, Ingvar Holm Dept. Cell. Dev. Biol. Umea University S-901 87 Umea Sweden From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!enews.sgi.com!decwrl!news-server.ncren.net!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.software Subject: Re: reference manager/bibliography freeware (or shareware) Date: 3 Nov 1995 21:15:47 GMT Organization: North Carolina State University Lines: 26 Message-ID: <47e0q3$953@taco.cc.ncsu.edu> References: <478q32$di6@taco.cc.ncsu.edu> <479s0t$bsg@eurybia.rz.uni-konstanz.de> <1995Nov3.143033.457@chmeds.ac.nz> NNTP-Posting-Host: sparc5c-2203gardnr.ppath.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) X-URL: news:Vzz*srNjm@chiark.chu.cam.ac.uk timc@chiark.chu.cam.ac.uk (Tim Cutts) wrote: >In article <1995Nov3.143033.457@chmeds.ac.nz>, >Martin Kennedy wrote: >>In article <479s0t$bsg@eurybia.rz.uni-konstanz.de>, Andreas.Brune@uni-konstanz.de (Andreas Brune) writes: >>> In article <478q32$di6@taco.cc.ncsu.edu>, >>> Susan Jane Hogarth wrote: >>>>I'm looking for freeware/shareware to manage my references. >>> >>> Try REFS by Tim Cutts. >>> http://chiark.chu.cam.ac.uk:81/refs/refs.html >>> Really nice shareware program. >> >>I'll second that; Tim is also close to a release of a Win95 >>version. You can demo a fully fucntional version which handles a >>couple of hundred (or therabouts) references; full functionality >>requires registration and payment (I think this is about 80 >>pounds Sterling). > >30 pounds, actually. However, the original poster was asking about >Macintosh software, and Refs is only available for the various >flavours of Windows. > Actually, I *was* looking for DOS/Win software - you must have me confused with someone else. I've downloaded this program, and it looks very nice. Haven't had much chance to play with it yet, but I'm looking forward to it.... From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!news-server.ncren.net!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.software Subject: Re: Biological WordPerfect Dictionary? Date: 3 Nov 1995 21:16:58 GMT Organization: North Carolina State University Lines: 14 Message-ID: <47e0sa$953@taco.cc.ncsu.edu> References: <47ccet$smb@er7.rutgers.edu> NNTP-Posting-Host: sparc5c-2203gardnr.ppath.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) X-URL: news:47ccet$smb@er7.rutgers.edu nlandau@eden.rutgers.edu (Nicholas Landau) wrote: > >Is it possible to be get spelling dictionaries for WordPerfect (both >Mac and IBM) which include biological jargon (especially taxonomic names?) >I'm just tired of the speller hitting every other word, and would be >willing to pay to make this problem go away. > Can't you make custom dictionaries in WordPerfect? You can with Word.... -- Susan Jane Hogarth Charter member, PETA (People for Eating Tasty Animals) From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!lll-winken.llnl.gov!uwm.edu!vixen.cso.uiuc.edu!rs6000.cmp.ilstu.edu!rs6000.cmp.ilstu.edu!ajotsuka From: ajotsuka@rs6000.cmp.ilstu.edu (Anthony Otsuka) Subject: Re: Macvector contact address, suggested alternatives ? Sender: news@rs6000.cmp.ilstu.edu (News Admin.) Message-ID: <1995Nov3.042148.68262@rs6000.cmp.ilstu.edu> Date: Fri, 3 Nov 1995 04:21:48 GMT References: Organization: Illinois State University X-Newsreader: TIN [version 1.2 PL2] Lines: 42 Adrian Walden (waldena@tawa.fri.cri.nz) wrote: : Hi, I require a contact address for the producers of the Macvector : software package. Furthermore I am interested in suggestions for : alternatives to this package. I wish to carry out sequence analysis as : featured in the GCG package (not available at this institute). : Thanks : Adrian Hi, The address for Kodak which sells MacVector is: Scientific Imaging Systems Eastman Kodak Company 25 Science Park New Haven, CT 06511 Tel: (800)225-5352 or (716)588-2572 Part of the reason I responded is that I would like to know if anyone has had any luck with the BandScanner software to read gels scanned with flatbed scanner. We find that the software is (in our hands) pretty much useless as it picks up too many faint background bands, and the resulting data needs to edited heavily. The other software, MacVector and AssemblyLign, works pretty good. My only complaints are that there are some sequence length limits in MacVector and that when searching ENTREZ EST's you have to manually switch between disks 3 and 4 for as many sequences as you requested. This can be avoided by using two CD-ROM drives or by copying the data to the hard disk. I like the alignment scheme using different colors in AssemblyLign, but I don't like the fact that you can't lock the relative positions of gels so that when new data is added in the middle of a gel, the remaining gels would shift to the right. In Staden's software this is automatic. If you are sequencing 30 kb pieces with repetitive sequences, you can spend a considerable amount of time manually shifting gels into alignment. The best we could to to avoid this is to work with contigs that contain only part of our sequence (up to about 5 kb at a time) and stitch the consensus sequences together at the end. Good luck, A. Otsuka From owner-software@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Claude Gronfier" Newsgroups: bionet.software Subject: HELP for Winchat Date: 3 Nov 1995 17:28:10 -0000 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47djfa$iss@mserv1.dl.ac.uk> Reply-To: claude.gronfier@c-strasbourg.fr Comments: Authenticated sender is X-mailer: Pegasus Mail for Windows (v2.10) Original-To: bio-soft@dl.ac.uk I have recently received a new computer with the WINDOWS95 system. However, I have not the WINCHAT accessory, so useful to communicate with others computers connected on the internal net of my company. I have copied the winchat.exe, the winchat.in and the winchat.gid from another computer but Winchat doesn't work !!! Help! Thank you for sending me necessary files or indicate me ftp/http site where I could find them Eagerly... Claude Gronfier. From owner-software@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!agate!fruitfly.berkeley.edu!gregg From: gregg@fruitfly.berkeley.edu (Gregg Helt) Newsgroups: bionet.software Subject: bioTkperl software now available (beta) Date: 3 Nov 95 19:23:23 Organization: University of California, Berkeley Lines: 72 Distribution: world Message-ID: NNTP-Posting-Host: fruitfly.berkeley.edu A beta release of bioTkperl is now available for distribution. This is a port of David Searls' bioTk Tcl/Tk widgets to Tk/Perl, with some enhancements. Not all of the components have been ported yet, but the ones that have are pretty stable. --------------------------------------------------------------------------- What is bioTk? From the bioTk home page (http://www.cbil.upenn.edu/~dsearls/bioTk.html): "bioTk is a library of widgets and utilities designed to support the creation of graphical user interfaces in the domain of computational biology and genome informatics. The overarching philosophy behind bioTk is componentry: that is, the creation of adaptable, reusable software, deployed in modules that are easily incorporated in a variety of applications, and in such a way as to promote interaction between those applications." The original implementation of bioTk was in Tcl, and is now at release 1.3. A new release is being worked on. See the above URL for details. --------------------------------------------------------------------------- What is bioTkperl? bioTkperl is a port of the bioTk widgets/components to Tk/Perl, along with some enhancements. Also, the bioTk components have been reimplemented as Perl classes, so most procedures from the Tcl version have been replaced with method calls on objects. However, particular care was taken to keep the bioTk API compatible between the Tcl and Perl implementations. The current version is bioTkperl0.8, which includes a full Tk/Perl implementation of the bioTk Sequence widget (for displaying DNA sequences), and an almost complete implementation of the bioTk Map widget (for displaying genomic maps), along with some added features. It requires perl version 5.001m or higher and the Tk/Perl extension version b6 or higher (if you only have access to an earlier version of Tk/Perl, see the README for needed modifications). --------------------------------------------------------------------------- Where can you download bioTkperl? Via anonymous ftp from fruitfly.berkeley.edu, in /pub/bioTk/bioTkperl0.8.tar.gz. --------------------------------------------------------------------------- How about documentation and demos? The Tcl version of bioTk includes extensive documentation, which applies equally to the Perl version (the parts that have been ported), except for differences noted in the README. The latest Tcl version can be found via anonymous ftp at cbil.humgen.upenn.edu, under /pub/bioTk.tar.Z. Ports of several tutorials/demos from the Tcl version (bioTk1.3) are included in the distribution. The best way to get a feel for the differences in using the Perl version is to look through the tutorial demos, and compare them to sequence.tut and map.tut in the Tcl version. In addition I have included a demo version of an application I have been working on called AnnotP1. This has served both as a testbed for bioTkperl and as a useful lab tool for analysis of P1 clones being sequenced here at the Berkeley Drosophila Genome Center. --------------------------------------------------------------------------- Please feel free to send me comments, bug reports, etc. Gregg Helt gregg@fruitfly.berkeley.edu From owner-software@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!gatech!usenet.eel.ufl.edu!news.uoregon.edu!chi-news.cic.net!news.compuserve.com!news.production.compuserve.com!news From: Dmitri Davvydov <73522.3465@CompuServe.COM> Newsgroups: bionet.molbio.proteins,bionet.software Subject: CARY VARIAN OS/2 SOFTWARE Date: 4 Nov 1995 07:38:52 GMT Organization: Institute of Biomedical Chemistry, Moscow Lines: 75 Message-ID: <47f5ac$sno$1@mhade.production.compuserve.com> Xref: biosci bionet.molbio.proteins:6192 bionet.software:13832 In his message Manoj Ramjee wrote: > Our lab has a Cary 1E and we are looking to update. At the > moment the offers are whether we stay with the DOS version of > the software or whether we 'upgrade' to OS/2 ? We are getting > a Pentium machine to run the Cary but the software issue has > not been solved. Apart from the Varian WWW site info > (http://www.varian.com), I would welcome additional comments > on the following please. > 1. Does anyone use this system and do you like it ? > 2. What are the prolems encountered ? > 3. What is OS/2 like ? (It takes up around 80 MB on the HD and > 12 MB RAM to run!) > 4. Is there a Win95 version on the horizon ? > 5. Anything else you think we should know before going on. 1. I've some experience using Cary 3E with both DOS and OS/2 software. OS/2 version is much more user friendly, flexible and convenient. In fact, it isn't a version, it is entirely new software package. It looks very close to my idea of normal instrument control program which I've in mind. If the principles of DOS version are somewhat archaic, OS/2 mouse-and-window-oriented, multitasking program is one of the best instrument-controlling programs I've ever seen (however, when I start to work with it, knowing clumsy and unconvenient DOS version, I had a very sceptic mood). The program appears just like usual Windows-oriented programs and takes few tenths of minuts to be familiar with it. The program gives you nice abilities of spectra overlapping, mathematical operations on spectra, export and import your data in ASCII using user-specified delimiters; you can save and retreive your methods, etc. 2. Hovewer, the program is a little bit underdone. As usually, it has some bugs. However, these bugs are never fatal. They appears usually after few hours of work, when the program is saturated with your data. These bugs leads to some messages like "Can't retrive method", "Can't open window", etc. It's a bit annoying, but still tolerable (you can simply reboot the system). But what is important - you never loose your data. On my opinion an amount of bugs here is well reasonable for so large program. 3. OS/2 is true multitasking operating system. Only Windows-95 approaches this lewel. User interface of OS/2 is Windows- or Macintosh-alike. However, OS/2 is totally compatible with DOS- and Windows. Almost all DOS- and Windows-oriented programs work well under OS/2. OS/2 is multitasking operating system. Many programs can work simultaneously and share data at the same time in your system. You can easily jump between windows of OS/2, Windows- and DOS-based applications. Actually you don't need Windows (even W95) if you have OS/2 on your computer. However, to have the best results you should be carefull choosing instalation options. The best way is to replace DOS by OS/2, instead of creating a multisystem computer. Since OS/2 well emulates DOS, you will still have ability to run all DOS-oriented programs in DOS environment. Windows you don't need here - OS/2 totally replaces it for Windows-oriented programs. Just try OS/2 - you can see that it's a nice alternative to W95. Since of multitasking nature of OS/2 you can combine Varian software with your favorite data-fitting programs at the same time. For example, we have adapted our DOS-oriented data fitting and handling software SpectraLab (see Miniprint suppl. to our paper in Arch.Biochem.Biophys., v. 320(2) 330-344 (1995)) to work with Varian software, so we can make fitting of kinetic curves, spectra decomposition, SVD-analysis (principal component anlysis) by runing both programs together and sharing the data area. Testing the Varian OS/2 software for the first time I did not believed that it's realy suitable for work. I've never seen something really good for an instrument control before. Actually, I do prefer to adapt my own program (SpectraLab) to work with any instrument I use. But working with OS/2 version of Varian software I've found that it's well tolerable, so I can save my time and work using this program instead of adapting my own software. Feel free to ask more questions, if necessary. Dr. Dmitri Davydov, Institute of Biomedical Chemistry, Russian Acad. of Medical Science, Moscow. -- From owner-software@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!c-strasbourg.fr!claude.gronfier From: claude.gronfier@c-strasbourg.fr ("Claude Gronfier") Newsgroups: bionet.software Subject: HELP for Winchat Date: 3 Nov 1995 21:38:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <47djk6$j29@mserv1.dl.ac.uk> Reply-To: claude.gronfier@c-strasbourg.fr NNTP-Posting-Host: net.bio.net I have recently received a new computer with the WINDOWS95 system. However, I have not the WINCHAT accessory, so useful to communicate with others computers connected on the internal net of my company. I have copied the winchat.exe, the winchat.in and the winchat.gid from another computer but Winchat doesn't work !!! Help! Thank you for sending me necessary files or indicate me ftp/http site where I could find them Eagerly... Claude Gronfier. From owner-software@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.infi.net!news.infi.net!not-for-mail From: tmeade@infi.net (Medical Services 2001) Newsgroups: bionet.software Subject: Patient Accounting For Health Care Providers Date: 4 Nov 1995 12:34:11 -0500 Organization: InfiNet Lines: 10 Sender: tmeade@news.infi.net Distribution: usa Message-ID: NNTP-Posting-Host: larry.infi.net If your practice is in need of an affordable, full featured patient accounting program, we can help. We offer programs for the medical, dental, and mental health fields. For details Email tmeade@infi.net and in the subject indicate your field. -- Tony Meade tmeade@infi.net MEDICAL SERVICES 2001 Phone: (804)-471-5385 Fax: (804)-471-5663 From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!simtel!zombie.ncsc.mil!admaix.sunydutchess.edu!ub!newserve!npnews!usenet From: James Garbarsky Newsgroups: bionet.software Subject: HP Cable Date: 6 Nov 1995 01:19:47 GMT Organization: SUNY New Paltz Lines: 5 Message-ID: <47jnrj$l45@motss.newpaltz.edu> NNTP-Posting-Host: sah.eelab.newpaltz.edu Mime-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4c) X-URL: file:/home/garbar69/web/ad1 HOT DEALS!!! Data Transfer Cable for HP Calculators, Electronic Organizers and other graphing calculators. HP - PC Data w/ FREE SOFTWARE Only $12.95. Others Only $7.95. Send E-mail to garbar69@eelab.newpaltz.edu From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!PEASTMS.PKU.EDU.CN!lxzyx From: lxzyx@PEASTMS.PKU.EDU.CN Newsgroups: bionet.software Subject: How can I get pc-software for .pdb database Date: 5 Nov 1995 19:45:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511060310.AA02901@peastms.pku.edu.cn> I have used insightII for SGI to view 3D structure of proteins before. However, Someguys told me that a pc-software can also do the same work. Can you tell me how can I get it? Chunhui Mo From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.ios.com!ppp-17.ts-5.nyc.idt.net!user From: Efrain@soho.ios.com (Efrain Gonzalez) Newsgroups: bionet.software Subject: Protein Sequence Analysis Date: 6 Nov 1995 17:34:22 GMT Organization: Internet Online Services Lines: 11 Message-ID: NNTP-Posting-Host: ppp-17.ts-5.nyc.idt.net Can anyone reccommend a powerful protein sequence analysis program for Mac or Power Mac. I have heard of MAcvector, but I am having trouble contacting International Biotechnologies, Inc. Please E-mail any responses. Thank you for your help. -- ---- Efrain@soho.ios.com From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!ihnp4.ucsd.edu!agate!ames!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!torn!watserv3.uwaterloo.ca!inniss2 From: awgumley@sciborg.uwaterloo.ca (Andrew Gumley) Subject: Primer software Message-ID: Sender: news@watserv3.uwaterloo.ca Nntp-Posting-Host: inniss2.uwaterloo.ca Organization: University of Waterloo X-Newsreader: News Xpress Version 1.0 Beta #3 Date: Mon, 6 Nov 1995 16:23:12 GMT Lines: 7 Is there shareware for primer design? If so, could I get the address. Andrew awgumley@sciborg.uwaterloo.ca From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!cmir.arnes.si!senca.mf.uni-lj.si!senca.mf.uni-lj.si!nntp Newsgroups: bionet.software Subject: Re: reference manager/bibliography freeware (or shareware) Message-ID: <309E914C.3E01@ibmi.mf.uni-lj.si> From: Lovro Stanovnik Date: Mon, 06 Nov 1995 14:50:52 -0800 References: <478q32$di6@taco.cc.ncsu.edu> Organization: Dept. Pharmacology, MF Nntp-Posting-Host: stanovnik-pc.mf.uni-lj.si X-Mailer: Mozilla 2.0b2 (Windows; I; 16bit) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 9 Hi, 'Reference Manager' from Research Information systems is very powerful reference management software, it is rather expensive :-( They also have a demo version (for Windows and DOS). You can reach them at: rminfo@ris.risinc.com Refs is also OK thou much less powerful but much cheaper. Lovro From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!psinntp!psinntp!psinntp!psinntp!pubxfer.news.psi.net !usenet From: robert@symbolic.com (Robert Wheeler) Newsgroups: bionet.software Subject: Need Computer Asset Control Software Date: 6 Nov 1995 15:22:13 GMT Organization: Symbolic Systems, Inc. Lines: 14 Message-ID: <47l975$p51@pubxfer4.news.psi.net> NNTP-Posting-Host: www.symbolic.com Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 I am looking for Computer Asset Control Software for the windows enviroment. This software should be for the sole purpose of keeping track of Computer Licenses and agreements. Pleasde contact me asap, with any information. Thank you for your time, Robert Wheeler Robert@symbolic.com From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!news2.acs.oakland.edu!cwis-20.wayne.edu!cmb.biosci.wayne.edu!dwomble From: dwomble@cmb.biosci.wayne.edu (David Womble) Newsgroups: bionet.software Subject: Re: Sequencher Software Phone #? Date: 6 Nov 1995 13:50:39 GMT Organization: Wayne State University Lines: 16 Message-ID: <47l3rf$6ku@cwis-20.wayne.edu> References: Reply-To: dwomble@cmb.biosci.wayne.edu NNTP-Posting-Host: cmb.biosci.wayne.edu X-Newsreader: TIN [version 1.2 PL2] Mary P. Remington (mremingt@umabnet.ab.umd.edu) wrote: : Does anyone have a phone # for GeneCode. I think they are the company : that sells the software. Please email me as I am anxious to find out : about this software. Thanks, Mary This is the info I found: Howard Cash: Phone 313-769-4192 e-mail to howardc@genecodes.com -- David D. Womble Center for Molecular Medicine and Phone: 313-577-2374 Genetics, Wayne State University Fax: 313-577-6200 5047 Gullen Mall, Detroit, MI 48202 E-mail: dwomble@cmb.biosci.wayne.edu From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.tamu.edu!bloom-beacon.mit.edu!spool.mu.edu!torn!news.bc.net!news.sfu.ca!news From: Evan Cooch Newsgroups: bionet.software Subject: new SigmaPlot for Win Date: 6 Nov 1995 04:17:53 GMT Organization: Simon Fraser University Lines: 20 Message-ID: <47k29h$hgp@morgoth.sfu.ca> NNTP-Posting-Host: cooch.biol.sfu.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 32bit) I have been a dedicated user of SigmaPlot for years, most recently with the various Windows flavours. I just purchased the upgrade to 3.0. However, I have noticed that it has one major problem (at least for me) - it absolutely refuses to print on my HP 4M PostScript printer. Has anyone else out there who has upgraded had this problem? I'm on the verge of sending it back. I might even be willing to ignore the fact it takes 45 seconds to just load it on my hot-rod machine if I could get it to print! :-) -- _/_/_/_/ _/_/_/_/_/ _/ _/ Evan Cooch _/ _/ _/ _/ Department of Biological Sciences _/_/_/_/ _/_/_/ _/ _/ Simon Fraser University _/ _/ _/ _/ Burnaby, British Columbia V5A 1S6 _/_/_/_/ _/ _/_/_/_/ cooch@fraser.sfu.ca From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!zoo337.zoo.unibas.ch!user Newsgroups: bionet.software Subject: Re: Macvector contact address, suggested alternatives ? Message-ID: From: flook@ubaclu.unibas.ch (Paul Flook) Date: Mon, 06 Nov 1995 17:42:12 +0200 References: <1995Nov3.042148.68262@rs6000.cmp.ilstu.edu> Organization: Zoologisches Institut Basel Nntp-Posting-Host: zoo337.zoo.unibas.ch Lines: 40 In article <1995Nov3.042148.68262@rs6000.cmp.ilstu.edu>, ajotsuka@rs6000.cmp.ilstu.edu (Anthony Otsuka) wrote: >..... > Part of the reason I responded is that I would like to know if > anyone has had any luck with the BandScanner software to read gels > scanned with flatbed scanner. We find that the software is > (in our hands) pretty much useless as it picks up too many faint > background bands, and the resulting data needs to edited heavily. > The other software, MacVector and AssemblyLign, works pretty good. >...... We purchased the BandScanner software at the beginning of this year and have had mixed fortunes. In its favour, this Software is one of the less expensive alternatives currently available and used in combination with Assemblylign it is an improvement on manual entry of gels. In particular the ability to locate and view conflicting base positions quite quickly is obviously a big advantage. HOWEVER, the technical support from IBI is just about non-existent, and Anthony Otsuka is right to say that the sequences sometimes need a lot of editing. I have found the same problem that he reports - too many background bands - but I think with experience it's possible to overcome this problem without too much difficulty. I should add though that we are accumulating data from large numbers of homologous sequences and insertions/deletions are very conspicuous when we come add sequences to our existing alignments. Therefore I am confident that after a relatively small amount of editing it's possible to get very accurate sequences. If you were to use this software for sequencing long clones of undetermined homology you would have to sequence both strands completely and have lots of long overlaps in order to get accurate sequences. -- Paul Flook Zoologisches Institut Rheinsprung 9 Basel CH-4051 Switzerland Tel. : (+41) 061 267 3496 Fax. : (+41) 061 267 3457 Email : Flook@UBACLU.UNIBAS.CH From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Newsgroups: embnet.general,bionet.software,bionet.software.gcg Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!in2p3.fr!oleane!jussieu.fr!citi2.fr!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Remote Access to BioComputing Basel Message-ID: <1995Nov1.165627.2142@comp.bioz.unibas.ch> Followup-To: embnet.general,bionet.software,bionet.software.gcg Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <1995Oct26.203721.19775@comp.bioz.unibas.ch> <474svp$g8d@news.Belgium.EU.net> Date: Wed, 1 Nov 1995 16:56:27 GMT Lines: 20 Xref: biosci bionet.software:13837 bionet.software.gcg:1451 Planet Internet Guest (visitor@planet.iocom.be) wrote: : jgjlfijbjm Thanks for the input ... I forgot to mention that Hassle5 documentation on HTML basis is available from bioftp.unibas.ch://bioftp-sw/hassledoc/relase/JAMINX.HTML and the corresponding SWITCH mirror. Printed documentation can be ordered from the publisher (FAX +41 61 263 0642) - fax an information inquiry in order to get details. Regards Reinhard Doelz EMBnet Switzerland -- 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 Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!newsflash.concordia.ca!not-for-mail From: cl_andr@alcor.concordia.ca (Christopher Andrews) Newsgroups: bionet.software Subject: Sequence-matching software? Date: 6 Nov 1995 22:43:37 GMT Organization: Concordia University, Montreal, Canada Lines: 12 Message-ID: <47m32p$2av@newsflash.concordia.ca> NNTP-Posting-Host: alcor.concordia.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII NNTP-Posting-User: cl_andr X-Newsreader: WinVN 0.99.6 Hey folks! Does anyone know of a software app that would allow me to input my E. coli DNA fragment restriction pattern and would return a match on the E. coli chromosome? This would help me tremendously. Please reply by e-mail. Christopher Andrews cl_andr@alcor.concordia.ca http://alcor.concordia.ca/~cl_andr From owner-software@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!chi-news.cic.net!brutus.bright.net!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!sd1 From: sd1@mole.bio.cam.ac.uk (Sandy Dickin (Zoology)) Newsgroups: bionet.software Subject: Deletion breakpoint analysis? Date: 6 Nov 1995 14:07:46 GMT Organization: University of Cambridge, England Lines: 13 Message-ID: <47l4ri$33f@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk I am looking for software (for any platform, but preferably Unix or Macintosh), which will help me locate the endpoints of deletions in plasmids. I have sequenced these endpoints, and I wish to find their location in the original plasmid sequence. I have tried this using various programs; staden (fasta, gap and bestfit), and gcg. These only seem capable of finding the first breakpoint, not the second. Am I doing something wrong, or is there a specific program available that could help me in my quest? Thanks for any and all help! Sandy. From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!howland.reston.ans.net!blackbush.xlink.net!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.rhrz.uni-bonn.de!news.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!infosrv.rz.uni-kiel.de!usenet From: stu30244@mail.uni-kiel.d400.de (Bert Schinkel) Newsgroups: bionet.software Subject: software help ????? Date: 7 Nov 1995 07:04:52 GMT Organization: Universitaet Kiel Lines: 16 Message-ID: <47n0ek$spr@infosrv.rz.uni-kiel.de> NNTP-Posting-Host: pc1630.dial.uni-kiel.de Mime-Version: 1.0 X-Newsreader: WinVN 0.93.10 Well, i am deeply depressed, because i am now have searched for days through several ftp-servers and htmls to find infos/software to be able to use my "OAK technology Mozart OPL3" sound card under WIN95. My search has been....oh,well. Thus I hope to find someone to help me. A short info would be that great.... THANKS Bert Schinkel From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!alpha2.csd.uwm.edu!yanliu From: Yan Q Liu Newsgroups: bionet.software Subject: Help needed Date: Tue, 7 Nov 1995 08:23:54 -0600 Organization: University of Wisconsin - Milwaukee Lines: 3 Message-ID: NNTP-Posting-Host: 129.89.169.2 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I need to do a little work with Pasecal compiler on my PC, would anyone know that where I can find a freeware or shareware from internet to download the program compiler? Your help will be greatly appreciated. From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: tinker@ Newsgroups: bionet.software.contrib,bionet.software.pc,bionet.software Subject: GREGOR (genetic simulation) v. 1.5 Date: 7 Nov 1995 22:14:28 GMT Organization: Plant Science, McGill University, Montreal, Canada Lines: 12 Distribution: world Message-ID: <47olo4$8nn@sifon.cc.mcgill.ca> Reply-To: tinker@agradm.lan.mcgill.ca NNTP-Posting-Host: qtl.agrenv.mcgill.ca X-Newsreader: IBM NewsReader/2 v1.2 GREGOR is a free software package for performing genetic simulation on a PC computer. Version 1.5 has just been placed on our ftp site: gnome.agrenv.mcgill.ca in /pub/genetics/software/GREGOR Nick Tinker From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!spool.mu.edu!news.cs.indiana.edu!umn.edu!newsstand.tc.umn.edu!usenet From: danp@biosci.cbs.umn.edu (Dan S. Prestridge, Ph.D.) Newsgroups: bionet.software Subject: PROMOTER SCAN 1.50 release Date: Tue, 07 Nov 1995 20:56:32 GMT Organization: University of Minnesota Lines: 53 Message-ID: <47oh4i$gf1@epx.cis.umn.edu> NNTP-Posting-Host: dialup-10-a-16.gw.umn.edu X-Newsreader: Forte Free Agent v0.55 ANNOUNCING THE AVAILABILITY OF PROMOTER SCAN version 1.50 for UNIX: PROMOTER SCAN Version 1.50 for UNIX is now available. The program for IBM PCs is NOT YET READY, and will be announced at a later date. Improvements in version 1.50 (over version 1.00) are: 1) The correction of the over-prediction of TATA boxes (a bug reported by Dr. James Fickett at Los Alamos National Lab). 2) An 2/3rds reduction in the number of false positives reported by the program. Previously PROMOTER SCAN reported one false positive in about 5600 bases; PROMOTER SCAN version 1.5 reports about one false positive in 17,200 bases (while recognizing about 70% of promoter sequences). If you are interested in getting a copy of the program, send E-mail to danp@biosci.cbs.umn.edu for instructions. PROMOTER SCAN is designed to find putative eukaryotic Pol II promoter sequences in primary DNA sequence data. This program is experimental in nature, and should be used as an experimental tool. PROMOTER SCAN is best used to locate regions in primary DNA sequence that might be good candidate regions to further test for promoter functionality. At this time, based upon test promoter and non-promoter sequence sets, the program recognizes approximately 70% of all EPD primate promoter sequences, with a false positive rate of about one in every 17,200 bases. Please refer to: Prestridge, D.S. (1995). Predicting Pol II Promoter Sequences Using Transcription Factor Binding Sites. J Mol Biol 249(5):923-932. If you have any additional questions, please let me know. When requesting further information on how to obtain PROMOTER SCAN, PLEASE SPECIFY UNIX OR IBM PC. Sincerely, Dan S. Prestridge ___________________________________________________________________________ Dan S. Prestridge, Ph.D. E-mail: DANP@BIOSCI.UMN.EDU Director Telephone: (612) 625-3744 Advanced Biosciences Computing Center Fax: (612) 625-5780 University of Minnesota 1479 Gortner Ave. St. Paul, MN 55108 ___________________________________________________________________________ From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!usc!news.cerf.net!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: Sequencher Software Phone #? Date: 7 Nov 1995 18:14:35 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 13 Message-ID: <47o7mb$94m@gap.cco.caltech.edu> References: Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article , "Mary P. Remington" writes: >Does anyone have a phone # for GeneCode. I think they are the company >that sells the software. Please email me as I am anxious to find out >about this software. Thanks, Mary > The number I have for GeneCodes is (313) 769-7249 Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software,embnet.general Subject: Re: [Q] Molscript Postscript problem: Printers stuck Date: 7 Nov 1995 18:13:35 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 51 Message-ID: <47o7kg$94m@gap.cco.caltech.edu> References: <1995Oct31.121039.45581@yogi.urz.unibas.ch> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <1995Oct31.121039.45581@yogi.urz.unibas.ch>, doelz@ubaclu.unibas.ch (R.Doelz,Biocomputing Basel;+41 61 267 22 47) writes: > > >Dear colleagues, > >We run Molscript 1.4 on a DEC 1152 printer and encounter problems >to print once a single plot has completed - the postscript >output will block the printer for further requests. Hmm, we have not seen that one. We print Molscript output through Impressario to an HP Deskjet 550c, or via lpr to an LPD on our OpenVMS system, and out from there through DCPS to a Printserver. In neither case does a print job jam the printer. On the other hand, we're still using Molscript 1.2. The two possibilities are: 1. Something funny about the postscript from molscript. 2. Something funny about the postscript driver. 3. Combination of 1 and 2. "1" would seem to be discounted by DCPS sending it successfully to the LPS20. A good test would be, assuming you've got lpr via Multinet or some such on the VMS platform, to send that to the HP5 LaserJet. If it prints from the VMS side, but not the Unix side, then it is a Unix problem, not a file problem. Another test that would be easy to perform would be to move the 1152 to a serial line on the VMS system, set that up as a print queue, and see if printing through it jams. What happens when you print two *text* postscript jobs to the 1152, does the first jam the second? If not, then that suggests case "3", a combination of postscript and printer problems. Take a look at the postscript output, does it have these as the last few lines: grestore stroke MolScriptPlotSave restore showpage %%Trailer %%BoundingBox: 49 99 551 701 %%EOF The most likely culprit would seem to be a missing %%EOF - easy to see how that might jam the printer. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.dfn.de!fu-berlin.de!zrz.TU-Berlin.DE!sandmann.prz.tu-berlin.de!cs.tu-berlin.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!news.th-darmstadt.de!News.Uni-Marburg.DE!usenet From: becker@ps1515.chemie.uni-marburg.de (Anderas Becker) Newsgroups: bionet.software Subject: Re: Primer software Date: 6 Nov 1995 23:18:59 GMT Organization: FB Chemie/Biochemie, Universtity, Marburg, Germany Lines: 23 Message-ID: <47m553$1sp@surz03.HRZ.Uni-Marburg.DE> References: NNTP-Posting-Host: nnex04.ppp.uni-marburg.de X-Newsreader: WinVN 0.92.6+ In article , awgumley@sciborg.uwaterloo.ca (Andrew Gumley) says: > >Is there shareware for primer design? If so, could I get the address. > > >Andrew > > >awgumley@sciborg.uwaterloo.ca There is a lot even for different systems. Take a look at my home page: http://www.chemie.uni-marburg.de/~becker Andreas ---------------------------------------------------------------------- Andreas Becker Arbeitskreis Prof. Kadenbach, FB Chemie/Biochemie, Hans- Meerwein-Strasse, Philipps-Universitaet, 35043 Marburg, Germany Phone: privat +49 6421 47304 Labor +49 6421 28 -5721 Fax -2191 eMail: BECKER@ps1515.Chemie.Uni-Marburg.De WWW : http://www.chemie.uni-marburg.de/~becker From owner-software@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-konstanz.de!news From: Marcus Macht Newsgroups: bionet.software Subject: Re: How can I get pc-software for .pdb database Date: 7 Nov 1995 11:08:32 GMT Organization: Universitaet Konstanz Lines: 12 Distribution: world Message-ID: <47neng$hr3@eurybia.rz.uni-konstanz.de> References: <199511060310.AA02901@peastms.pku.edu.cn> NNTP-Posting-Host: sg17.chemie.uni-konstanz.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; IRIX 5.3 IP22) To: lxzyx@PEASTMS.PKU.EDU.CN X-URL: news:199511060310.AA02901@peastms.pku.edu.cn Hello Chunhui, for displaying of protein structures you can use the RasMol program which is available by ftp from ftp.dcs.ed.ac.uk. It is public domain and exists for PC, Mac and Unix (Linux). I hope I could help you, yours sincerely Marcus Macht Faculty of Chemistry University of Constance Germany From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.gryffin.com!news.ece.uc.edu!babbage.ece.uc.edu!root From: "Jeffrey L. Nauss" Newsgroups: bionet.software Subject: Re: Papyrus software? Date: 8 Nov 1995 14:38:33 GMT Organization: Dept. Chemistry, Univer. Cincinnati Lines: 43 Message-ID: <47qfd9$i6e@babbage.ece.uc.edu> References: <47p04a$qtf@news2.cts.com> NNTP-Posting-Host: ucmodl.che.uc.edu 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) To: sorind@crash.cts.com X-URL: news:47p04a$qtf@news2.cts.com sorind@crash.cts.com (Sorin Damian) wrote: >I'm posting this question for a friend of mine... >He was talking >about something new (or newer) by the name "Papyrus". Is anybody willing >to help him in obtaining this software package. Papyrus version 7.0 can be obtained from: Research Software Design 2718 SW Kelly Street, Suite 181 Portland, OR 97201 (503) 796-1368 FAX: (503) 241-4260 e-mail: RSD@applelink.apple.com The full program is available for $99 and runs on DOS or in a DOS-window with Windows 3.1. I don't know for sure if it will work in Windows 95 but I believe it will. A demo is available for $25 (I think that is the cost) which will be applied towards the purchase price of the complete program. The demo is fully functional but with a reduced size for the database. Nevertheless, it certainly will allow you to appreciate the full potential for the program. I have used Papyrus for over five years now and am extremely happy with it. I highly recommend it. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!daresbury!yama.mcc.ac.uk!news.lancs.ac.uk!news From: R.Lauder@lancaster.ac.uk (B Lauder) Newsgroups: bionet.software Subject: Re: new SigmaPlot for Win Date: 8 Nov 1995 13:50:43 GMT Organization: Lancaster University Lines: 31 Message-ID: <47qcjj$stg@info1.lancs.ac.uk> References: <47k29h$hgp@morgoth.sfu.ca> NNTP-Posting-Host: bsa046000002.lancs.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 In article <47k29h$hgp@morgoth.sfu.ca>, cooch@fraser.sfu.ca says... SIGMA-PLOT >I just purchased the upgrade to 3.0. However, I have noticed that it has >one major problem (at least for me) - it absolutely refuses to print on >my HP 4M PostScript printer. Has anyone else out there who has upgraded >had this problem? I'm on the verge of sending it back. Well I'm using V1.02 and have had no printer problems until I installed a new HP 850C - Now the output is screwed up totally :-( I have no idea what causes this problem as the printer behaves fine otherwise. If I try to print across the network onto another printer (BJ-200) the output is also screwed up. However, if I go to the machine to which the BJ-200 is attached and open up the *.spw file (still on my machine in a shared dir) I can output fine. I'd be grateful for any inout on this. >I might even be willing to ignore the fact it takes 45 seconds to just >load it on my hot-rod machine if I could get it to print! :-) Mmmm - Slow is it :-( - I'm thinking of making the upgrade to 3 recomend it? ======================================================== Bob Lauder Biological Sciences, University of Lancaster, UK Home page - http://bssv01.lancs.ac.uk/gig/ppl/bob/home.htm From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!rutgers!gatech!usenet.eel.ufl.edu!warwick!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!news From: Christopher Spry Newsgroups: bionet.software Subject: Re: Lotus ? Date: 8 Nov 1995 09:11:16 GMT Organization: St. George's Hospital Medical School Lines: 10 Message-ID: <47ps7k$rer@mercury.hgmp.mrc.ac.uk> References: <47pqgm$5c7@mserv1.dl.ac.uk> NNTP-Posting-Host: sprysgi.sghms.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) X-URL: news:47pqgm$5c7@mserv1.dl.ac.uk Lotus had a server at: http://www.support.lotus.com Lines from the UK are so bad at present that we have 100% packet loss from that address, but you may do beter from the States. It should be what you are looking for. -- Christopher Spry. cspry@sghms.ac.uk From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: suleyman aydin Newsgroups: bionet.software Subject: Lotus ? Date: 8 Nov 1995 08:41:58 -0000 Organization: Anadolu University, Eskisehir-TURKEY Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47pqgm$5c7@mserv1.dl.ac.uk> X-Acknowledge-To: Original-To: bio-soft@dl.ac.uk We are seeking the new version of Lotus-Manuscript word proccesor But we do not know if it (later than v.2.00) exists and if there is an e-mail address of LOTUS... Any help is appreciated. .... Suleyman AYDIN (Ph.D. student of pharmacology) d31@vm.baum.anadolu.edu.tr From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!usc!newshub.cts.com!crash!sorind From: sorind@crash.cts.com (Sorin Damian) Newsgroups: bionet.software Subject: Papyrus software? Date: 8 Nov 1995 01:11:38 GMT Organization: CTS Network Services (CTSNET), San Diego, CA Lines: 9 Message-ID: <47p04a$qtf@news2.cts.com> NNTP-Posting-Host: crash-i2.cts.com I'm posting this question for a friend of mine which needs to put order in his references. He is using a speciealized database which is obsolete by now (can make searches by name, author, keyword, etc.). He was talking about something new (or newer) by the name "Papyrus". Is anybody willing to help him in obtaining this software package. Any other feedback on any reference organizer will be much appreciated. thank you damian From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!ames!waikato!celebrian.otago.ac.nz!usenet From: Gunn@Otago.ac.nz (Derek Gunn) Newsgroups: bionet.software,bionet.general,sci.bio.misc Subject: SKIS - Biodiversity Checklisting Program Date: 8 Nov 1995 22:36:40 GMT Organization: University of Otago Lines: 38 Sender: -Not-Authenticated-[4796] Message-ID: <47rbdo$fjt@celebrian.otago.ac.nz> NNTP-Posting-Host: mac240042.otago.ac.nz X-Posted-From: InterNews 1.0.6@mac240042.otago.ac.nz Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.software:13869 bionet.general:18373 sci.bio.misc:1013 Soon we'll be sending a notice this way about a software system that is pretty basic to biology. The SKI-System (SKIS) creates and manages taxonomic checklists. The 700K free start-up pack contains the fully functional checklisting program (SKI_IN). Included are read-only input data files covering Birds, Mammals and Plants. Some additional, and also free, input files contain a full range of Families for all six Kingdoms. So all named species can be checklisted with menu support to Family- level. Then there are species-level input data files... What's not for free is a high-level version of the program suitable for project management. It can import foreign taxonomic files and update the Classification in SKI-files; it's currently working at Family level. SKIS aims to make taxonomic problems a thing of the past for anyone whose interest is "just" to use taxonomy as a means to other ends - eg, people working in conservation and ecology. We're interested in how group specialists, especially the modern breed of taxonomists, will take to SKIS. And we also want to know what software specialists and IT types make of it. We think the System has some revolutionary new ways of making life easier for lots of people. Try it; eg, see what use you might have for 'user-defined standard taxonomies' (a flexible tool rather than a straight jacket). Your responses will be much appreciated. Watch this space. Stan Woods, Derek Gunn SKS-Information From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!async15-11.remote.ualberta.ca!user From: rmh@gpu.srv.ualberta.ca (Robert Hornbeck) Newsgroups: bionet.software Subject: DNA Reading Frame Analysis Date: Wed, 08 Nov 1995 08:35:33 -0700 Organization: Braintwitch Iching Inc. Lines: 11 Message-ID: NNTP-Posting-Host: async15-11.remote.ualberta.ca X-Newsreader: Yet Another NewsWatcher 2.0b30 I am in search of some software that will extract or predict the reading frames in a DNA sequence. I know that DNA Strider performs this task but I can not afford the $200 USD for it. I am an undergrad working on a little phylogenetics and it is tough predicting this sort of thing with out software. If any one has any recommendations I would appreciated it. I am using a Macintosh LC630 but I do have access to othe computers as well, although I would prefer macintosh format. You can send your replies to: "rmh@gpu.srv.ualberta.ca". Thank You For Your Time David Frederiksen From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!usenet From: Thomas Poppe Newsgroups: bionet.software Subject: Re: Logitech Trackball drivers Date: 8 Nov 1995 17:14:06 GMT Organization: Katholieke Universiteit Leuven Lines: 7 Message-ID: <47qogu$t9@chaos.kulnet.kuleuven.ac.be> Reply-To: THOMAS.POPPE@student.kuleuven.ac.be NNTP-Posting-Host: ipv13235.cc.kuleuven.ac.be X-Newsreader: WinVN 0.92.6+ Can someone tell me where I can find drivers for my Logitech Trackball (I lost my disk), or can someone somhow upload them to me? I would realy appreciate this. Thomas From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: Patrick R. Jones <102570.2734@CompuServe.COM> Newsgroups: bionet.software,bionet.xtallography Subject: Research help - Free Date: 7 Nov 1995 19:13:41 GMT Organization: Personal Lines: 22 Message-ID: <47ob55$j3n$2@mhafc.production.compuserve.com> Xref: biosci bionet.software:13866 bionet.xtallography:2154 I am a biology undergraduate biology student and I am looking for a project to work on. I am not going to school winter quarter ( out of money, you know ) and I need something to keep my brain tuned into biology. I can’t take an internship or something like a internship because I have a family and a job; the job has nothing to do with biology. I would like to help someone or group do something. I am interested in biochemistry, DNA sequencing, biocomputing, etc. I would do work on a project for no charge. In return the work has to be the kind on which a paper could be written and I would like to be a co-author. In other words I help you with some research and you help me with my career. Unless you are in the Salt Lake City, Utah area this work should be something that can be done over the Internet or phone. Going to another location, unless your willing to pay, is not an option ( remember I am poor ). Please respond by e-mail; my address is 102570.2734@CompuServe.COM Thank you for your time. Patrick R. Jones -- <> From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: Patrick R. Jones <102570.2734@CompuServe.COM> Newsgroups: bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.software Subject: Help with research - Free!!! Date: 7 Nov 1995 19:12:22 GMT Organization: Personal Lines: 23 Message-ID: <47ob2m$j3n$1@mhafc.production.compuserve.com> Xref: biosci bionet.cellbiol:3389 bionet.general:18365 bionet.molbio.methds-reagnts:36084 bionet.molbio.proteins:6226 bionet.software:13865 I am a biology undergraduate biology student and I am looking for a project to work on. I am not going to school winter quarter ( out of money, you know ) and I need something to keep my brain tuned into biology. I can’t take an internship or something like a internship because I have a family and a job; the job has nothing to do with biology. I would like to help someone or group do something. I am interested in biochemistry, DNA sequencing, biocomputing, etc. I would do work on a project for no charge. In return the work has to be the kind on which a paper could be written and I would like to be a co-author. In other words I help you with some research and you help me with my career. Unless you are in the Salt Lake City, Utah area this work should be something that can be done over the Internet or phone. Going to another location, unless your willing to pay, is not an option ( remember I am poor ). Please respond by e-mail; my address is 102570.2734@CompuServe.COM. I would have posted my resume, but the software I am using won't let me. Thank you for your time Patrick R. Jones -- <> From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: IUBio archive mirror sites Date: 8 Nov 1995 22:28:49 GMT Organization: Biology, Indiana University - Bloomington Lines: 29 Message-ID: <47rav1$p8k@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu I know the trans-atlantic net connections are bad these days. These are the IUBio mirror sites that I am aware of. If anyone else is maintaining a public mirror of IUBio sections, please let me know. If anyone would like to do so, also let me know. Note that the full http and gopher services of FlyBase at IUBio now can be mirrored. Contact me for details. -- Don FTP file mirrors: ftp://ftp.gdbnet.ad.jp/ftpsync/ftp.bio.indiana.edu/ -- full mirror of iubio ftp://ftp.ddbj.nig.ac.jp/pub/mirror/IUBIO/molbio -- /molbio section " /IUBIO/flybase -- /flybase data section ftp://ftp.funet.fi/pub/sci/molbio/iubiomolbio -- mirrors the /molbio section ftp://ftp.sunet.se/ ?? -- I couldn't get a look here due to net time-outs FlyBase database only: http://www.embl-ebi.ac.uk:7081/ -- full mirror of IUBio Flybase WWW services gopher://www.embl-ebi.ac.uk:7071/ -- full mirror of IUBio Flybase Gopher services -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.software Subject: Positions on protein analysis available Date: 8 Nov 1995 09:19:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511081724.AA04275@urano.mia.uv.mx> Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:41 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) oct. issue. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!agate!darkstar.UCSC.EDU!usenet From: Kimmen Voronov Sjolander Newsgroups: bionet.software Subject: Dirichlet mixture paper available via ftp and on the web Date: 9 Nov 1995 01:42:03 GMT Organization: University of California, Santa Cruz Lines: 44 Message-ID: <47rm9b$5k6@darkstar.UCSC.EDU> NNTP-Posting-Host: pomo.cse.ucsc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 4.1.4 sun4c) X-URL: news://darkstar/bionet.software The Computational Biology group at the University of California, Santa Cruz, is pleased to announce the following paper available via ftp and on the web. ------------------------------------ ``Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology", Sjolander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I.S., and Haussler, D. ------------------------------------ URL: http://www.cse.ucsc.edu/research/compbio/dirichlet.html ftp: ftp.cse.ucsc.edu pub/protein/dirichlet/dirichlet.jnl.ps.Z (A nine-component Dirichlet mixture estimated on the Blocks database is also available at this site.) ------------------------------------ Abstract: This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a protein family or domain are known. We present a method for condensing the information in a protein database into a mixture of Dirichlet densities. These mixtures are designed to be combined with observed amino acid frequencies, to form estimates of expected amino acid probabilities at each position in a profile, hidden Markov model, or other statistical model. These estimates give a statistical model greater generalization capacity, such that remotely related family members can be more reliably recognized by the model. Dirichlet mixtures have been shown to outperform substitution matrices and other methods for computing these expected amino acid distributions in database search, resulting in fewer false positives and false negatives for the families tested. This paper corrects a previously published formula for estimating these expected probabilities, and contains complete derivations of the Dirichlet mixture formulas, methods for optimizing the mixtures to match particular databases, and suggestions for efficient implementation. From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.dacom.co.kr!simtel!news.sprintlink.net!connix.com!news From: jbriasco@connix.com (Joseph A. Briasco) Newsgroups: bionet.software Subject: FS Windows NT 3.51 Date: 9 Nov 1995 03:33:43 GMT Organization: Mercury Global Technologies Lines: 2 Message-ID: <47rsqn$kof@comet.connix.com> NNTP-Posting-Host: mgt.connix.com X-Newsreader: OUI TE 1.0.0.1 I currently own an extra copy of NT 3.51 CD-ROM upgrade, unopened and still sealed in it's original packaging. I will sell it to the best offer and will ship it however you choose, COD. Please E-Mail jbriasco@connix.com. From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!AXP3400.KYUNGPOOK.AC.KR!z8913017 From: z8913017@AXP3400.KYUNGPOOK.AC.KR (Oh Ki Won) Newsgroups: bionet.software Subject: (none) Date: 8 Nov 1995 18:28:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511090226.LAA06121@axp3400.kyungpook.ac.kr> NNTP-Posting-Host: net.bio.net unsubscribe From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!AXP3400.KYUNGPOOK.AC.KR!z8913017 From: z8913017@AXP3400.KYUNGPOOK.AC.KR (Oh Ki Won) Newsgroups: bionet.software Subject: (none) Date: 8 Nov 1995 20:03:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511090401.NAA21456@axp3400.kyungpook.ac.kr> NNTP-Posting-Host: net.bio.net mailx bio-soft@net.bio.net unsubscribe From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!news.bc.net!malun1.mala.bc.ca!mala.bc.ca!howesan From: howesan@mala.bc.ca Newsgroups: bionet.software Subject: How to get blast post Date: 9 Nov 95 10:21:55 -0700 Organization: Malaspina University-College Lines: 61 Message-ID: <1995Nov9.102155@malins.mala.bc.ca> NNTP-Posting-Host: malins.mala.bc.ca How can I get a copy of the Blast sequence comparison program? I would like to set up my own data base any compare the sequences in this data base only. Any suggestions about what data base would be of great help as well. Thanks in advance. Andrew From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.u.washington.edu!root From: "Peter J. Myler" Newsgroups: bionet.software Subject: Re: Text file to reference manager (mac) Date: Thu, 09 Nov 1995 09:34:45 -0800 Organization: Seattle Biomedical Research Institute Lines: 24 Message-ID: <30A23BB5.1F53@u.washington.edu> References: NNTP-Posting-Host: cs104-8.u.washington.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b2a (Windows; I; 16bit) >Fellow Researchers, > Does anyone know of a macintosh program that will convert a text file >of references (bibliography) into a generally accepted commercial format >(Medline, etc.) so it can be imported by a commercial reference program >(Reference Manager)? >Thanks, >Mike Kennedy >Dept. Biochemistry/Molecular Biology >Mayo Foundation Mike: Reference Manager has a Cpature Definition Editor which will allow you to make a capture definition for importing referecnes in just about any format. Contact RIS (1-(800)-722-1227) for more details. Peter =================================================================== Peter J. Myler Seattle Biomedical Research Institute Associate Scientist 4 Nickerson Street, Seattle, WA 98109-1651 phone: (206) 284-8846x332 FAX: (206) 284-0313 e-mail: MYLERPJ@U.WASHINGTON.EDU =================================================================== From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!mayonews.mayo.edu!kennedymi.mayo.edu!user From: kennedym@mayo.edu (Mike Kennedy) Newsgroups: bionet.software Subject: Text file to reference manager (mac) Date: 9 Nov 1995 16:46:01 GMT Organization: Dept. Biochemistry, Mayo Fdn. Lines: 11 Message-ID: NNTP-Posting-Host: kennedymi.mayo.edu X-Newsreader: Value-Added NewsWatcher 2.0b27.1+ Fellow Researchers, Does anyone know of a macintosh program that will convert a text file of references (bibliography) into a generally accepted commercial format (Medline, etc.) so it can be imported by a commercial reference program (Reference Manager)? Thanks, Mike Kennedy Dept. Biochemistry/Molecular Biology Mayo Foundation (kennedym@mayo.edu) "See this quarter? It used to be a nickel!" From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sgigate.sgi.com!sgiblab!news.cs.indiana.edu!umn.edu!newsstand.tc.umn.edu!usenet From: danp@biosci.cbs.umn.edu (Dan S. Prestridge, Ph.D.) Newsgroups: bionet.software Subject: IBM version of PROMOTER SCAN 1.5 is ready Date: Thu, 09 Nov 1995 14:53:55 GMT Organization: University of Minnesota Lines: 60 Message-ID: <47t4kh$789@epx.cis.umn.edu> NNTP-Posting-Host: dialup-12-c-41.gw.umn.edu X-Newsreader: Forte Free Agent v0.55 ANNOUNCING THE AVAILABILITY OF PROMOTER SCAN version 1.50 for IBM DOS: PROMOTER SCAN Version 1.50 for IBM DOS is now available, and also available for UNIX machines (works on Sun, SGI, DEC Alpha, IBM RS6000, and others). The IBM DOS version is identical to the UNIX version, except it uses a little fancier text graphics and can only handle sequences up to 10kb (the UNIX version will handle up to 50kb presently - and can be boosted if needed). Improvements in version 1.50 (over version 1.00) are: 1) The correction of the over-prediction of TATA boxes (a bug reported by Dr. James Fickett at Los Alamos National Lab). 2) An 2/3rds reduction in the number of false positives reported by the program. Previously PROMOTER SCAN reported one false positive in about 5600 bases; PROMOTER SCAN version 1.5 reports about one false positive in 17,200 bases (while recognizing about 70% of promoter sequences). If you are interested in getting a copy of the program, send E-mail to danp@biosci.cbs.umn.edu for instructions. PROMOTER SCAN is designed to find putative eukaryotic Pol II promoter sequences in primary DNA sequence data. This program is experimental in nature, and should be used as an experimental tool. PROMOTER SCAN is best used to locate regions in primary DNA sequence that might be good candidate regions to further test for promoter functionality. At this time, based upon test promoter and non-promoter sequence sets, the program recognizes approximately 70% of all EPD primate promoter sequences, with a false positive rate of about one in every 17,200 bases. Please refer to: Prestridge, D.S. (1995). Predicting Pol II Promoter Sequences Using Transcription Factor Binding Sites. J Mol Biol 249(5):923-932. If you have any additional questions, please let me know. When requesting further information on how to obtain PROMOTER SCAN, PLEASE SPECIFY UNIX OR IBM PC. Sincerely, Dan S. Prestridge ___________________________________________________________________________ Dan S. Prestridge, Ph.D. E-mail: DANP@BIOSCI.UMN.EDU Director Telephone: (612) 625-3744 Advanced Biosciences Computing Center Fax: (612) 625-5780 University of Minnesota 1479 Gortner Ave. St. Paul, MN 55108 ___________________________________________________________________________ From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!csn!nntp-xfer-2.csn.net!tali.UCHSC.edu!essex.UCHSC.edu!woodr From: Rebecca Wood Newsgroups: bionet.software Subject: help finding data management program Date: Thu, 9 Nov 1995 15:07:34 -0700 Organization: University of Colorado, Health Sciences Center Lines: 8 Message-ID: NNTP-Posting-Host: essex.uchsc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looking for a software program that will manage assay results for about 20,000 samples with varying types of assays, and that may do some of the common calculations on raw data, and will print reports to clients. Something similar to a LIMBS system (but not so expensive) may work. Does anyone have any suggestions? Thanks From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!UCDAVIS.EDU!wbkim From: wbkim@UCDAVIS.EDU (Woon-Bong Kim) Newsgroups: bionet.software Subject: Re: Text file to reference manager (mac) Date: 9 Nov 1995 13:40:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 9 Nov 1995, Mike Kennedy wrote: > Fellow Researchers, > Does anyone know of a macintosh program that will convert a text file > of references (bibliography) into a generally accepted commercial format > (Medline, etc.) so it can be imported by a commercial reference program > (Reference Manager)? > Thanks, > > Mike Kennedy > Dept. Biochemistry/Molecular Biology > Mayo Foundation > (kennedym@mayo.edu) "See this quarter? It used to be a nickel!" > > Try EndLink. From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.u.washington.edu!root From: Colleen O'Rork Newsgroups: bionet.software Subject: LOOKING FOR OLIGO DATABASE SOFTWARE Date: 9 Nov 1995 21:04:19 GMT Organization: University of Washington Lines: 6 Message-ID: <47tqcj$f16@nntp3.u.washington.edu> NNTP-Posting-Host: 128.95.211.29 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.software We're a lab looking for a way to organize a database of our oligos that can cross reference by various subjects (date, temp, plasmid) AND to scan the sequences as well for short areas of homology. We're Macintosh based. Anyone have anything that might work? From owner-software@net.bio.net Wed Nov 08 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!unixg.ubc.ca!van-bc!news.rmii.com!newsjunkie.ans.net!news.ptd.net!news From: tacohead@postoffice.ptd.net (Tacohead) Subject: Moneymaking Software : Quick Cash D/L = Wincash[1\1] - wincash.zip [2/9] X-Nntp-Posting-Host: cs1-02.iro.ptd.net Content-Type: message/partial; id="815957377@Tacohead"; number=2; total=9 Message-ID: Sender: news@postoffice.ptd.net (News Master) Organization: Your Organization X-Newsreader: WinVN 0.99.5 Mime-Version: 1.0 Date: Thu, 9 Nov 1995 20:05:26 GMT Lines: 964 MG3VZtjzGetyETwVoUOa7aib8CulagCVSw7SzED2CqpL4WhpFSJd4H6VtoEF Q7Xp+mZG+BlU9EBxmMZdoHE1qk3lNJLoFWoJ0yGi0T0vavbZ2Pe6WUgJlXUD E8HLhyHntnTu29y2STxx6L4Md5pTqKkmdy/K3I8kNOMsOlaNe3depmkvK5QC 8FLp/GHM+XoCnWGPpS6xT3EdvmNIT0OPoUYzJ/+ADiaVPOmqeZWThydojm/l QsW22tmyxokOaYG7PdhMxdopn2la0oDHd4XcUqPXpLiPWNyH5Uk6443sINBg 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