From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Murray-Rust Dr P Newsgroups: bionet.software Subject: Collaborative BioMolecular Tools Date: 2 Mar 1994 13:37:10 -0000 Lines: 137 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2l24q6$96k@mserv1.dl.ac.uk> Original-To: "Bionet.software" As a result of the encouragement from members of this newsgroup I shall shortly (2-3 weeks) be posting a URL-tree at Daresbury on this topic. I attach the present home page as a guide as to its contents. At present I am not looking for contributions across the whole range of subjects, since that could be overwhelming (!). I am particularly keen that the tools should map onto data wherever possible and I would very much appreciate contributions in the two areas below. It is essential that the source of the data is verifiable and that there are no copyright problems with its appearing on a public noticeboard. PLEASE DO NOT MAIL ME DATA AT PRESENT; I would, however, be most grateful for URL's. Failing that, a brief statement about where the data are, their accessibility, etc. Reference data -------------- I would like pointers to machine-readable high-quality, read-only data of *fundamental and lasting importance* in the area of sequences and structure. Examples would be: Genetic code(s), chemical formulae (if possible with stereochemistry) of amino acids and nucleotides, atomic weights, ASCII characters, spacegroups (which I have already been given, thanks). File Formats ------------ It is critical that standards are developed for files, even if "de facto". I would like pointers to descriptions of the file formats, especially as URL's. (For example the SWISS-PROT manual is described under http://expasy.hcuge.ch/txt/userman.txt - if there is a URL, this is all that is necessary.). C++ beta-testing ---------------- I am putting the C++ library out for beta-testing. If there is anyone who would be interested in helping with this, I'd be happy to hear from them. It will help if they have a /ftp/incoming where I can ftp the tar.Z file since I cannot yet mount it for them to download. (ca 1.5Mbytes). TIA P. ------------------------------------------------------------------------- Collaborative BioMolecular Tools Home Page ------------------------------------------------------------------------- Collaborative BioMolecular Tools is an new venture in molecular computing, fuelled by the need for robust tools and made possible by the collaborative approach of the scientific community. In this spirit CBMT is offered as a nucleus for the development of a communal resource. The reason for CBMT Much of the software used in presently was developed in an era when there was little formal support for programming and the pioneers in this area built programs and databases with what tools they had. Often programs evolved with each generation of students and postdocs passing through, which made maintenance, documentation and navigation problematic. Today we have access to more powerful technology, in particular: Object-Oriented programming, scripts and filters, hypertext, networking and the international community, standards (such as CIF and ASN.1), and GUI's. These systems, if used at full potential, will revolutionise molecular computing, allowing scientists to put their ideas into programs in a few days or even hours. But the tools are not yet there, there is a severe "learning curve", and considerable investment is needed. Bioinformatics and Molecular computing is an extremely diverse area with many mature and expanding disciplines. Many of these have data, algorithms, and programs which are developed in differing cultures and are only barely compatible. Terminology is a problem and information is often lost when transferring from one area to another. What is CBMT? CBMT is composed of donated software components which, are developed so as to interact and interface as smoothly as possible. With a sufficient critical mass of tools, it becomes much more efficient to construct a "program" out of the tools rather than writing it from scratch. The diversity and complexity means that good navigation tools are essential and this has been given very high priority in CBMT. A user should be able to find out in a few hours: what a set of tools does, whether they are relevant to her problem, how long the learning curve is, and what are the alternatives. This should include reading critical reports on the tools, and also building a sample program and running it. CBMT philosophy Understanding the philosophy is central to the success of the venture and to the use of the tools. Some of the key principles are: relevance and usefulness portability and robustness extensibility and further development validation of methods and data protection and management of the namespace education further building of the international and interdisciplinary community appropriate recognition of the contributions of donors The components The components can be any unit which will interface with other units and which is sufficiently general to have a clear purpose. At present (February 1994) I envisage: A C++ class library A library of filters/scripts (e.g. *.csh, *.tcl, *.com, etc) GUI components (and possibly some GUI's) Reference data for file formats and other standards CIF's and their use both in crystallography and elsewhere Critical appraisals of tools and data Reference data (e.g. Atomic data, Amino Acid properties) Tools for navigation (e.g. markup scripts, browsers) A newsgroup PM-R> ------------------------------------------------------------------------------ (Disclaimer: this is a personal activity, and is not (yet) sponsored by any of: Glaxo Research and Development (my employers), Birkbeck College (where I lecture, and for which course I developed much of the material), and Daresbury (who have been kind enough to find me some space)). ------------------------------------------------------------------------------ Peter Murray-Rust | "Nothing exists except atoms and empty pmr1716@ggr.co.uk | space; all else is opinion" (Democritos). Protein Structure Group, Glaxo Group Research, Greenford, MIDDX, UB6 0HE, UK ------------------------------------------------------------------------------ From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Newsgroups: bionet.software,comp.sys.mac.scitech Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!MathWorks.Com!transfer.stratus.com!noc.near.net!news.cs.brandeis.edu!ahouse From: ahouse@hydra.rose.brandeis.edu. (Jeremy Creighton Ahouse) Subject: MAC program that will recognize areas? Message-ID: <1994Mar2.140415.4083@news.cs.brandeis.edu> X-Posted-From: InterNews 1.0@80.1.64.129.in-addr.arpa. Lines: 13 Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University - Biology Date: Wed, 2 Mar 1994 14:04:15 GMT Lines: 14 Xref: biosci bionet.software:7441 comp.sys.mac.scitech:875 I am looking for a MAC program that will recognize areas on maps and calculate their area. We can scan the images in. Evidently photoshop will recognize outlined regions but does not have the capacity to calculate areas. The Morphosys system on PCs (by Duncan and Meacham), would work, but that would constrain us to a computer system that we have limited access to. Do you all know of any program for a MAC that can be used for this purpose? Jeremy Creighton Ahouse Biology and Center for Complex Systems Brandeis University Waltham, MA 02254-9110 ahouse@hydra.rose.brandeis.edu From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.software Subject: Re: Help searching databases = ACNUC Date: 2 Mar 1994 07:43:18 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 58 Distribution: world Message-ID: <2l1g2m$nfs@cismsun.univ-lyon1.fr> References: <2l1fhv$nfs@cismsun.univ-lyon1.fr> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr Xref: biosci bionet.molbio.embldatabank:295 bionet.molbio.genbank:1552 bionet.software:7438 >I need some help in searching through the sequence data bases for splice >junctions. >I am trying to look at sequences next to splice junctions >but in the EXON. M. Gouy has developped a database named ACNUC that allows such request (ref). ACNUC A RETRIEVAL SYSTEM FOR GENBANK, EMBL, AND NBRF/PIR ACNUC is a retrieval system for the nucleotide sequence databases GenBank or EMBL and for the protein sequence data base NBRF/PIR. ACNUC allows to select sequences from many criteria (keyword, taxonomy, bibliography, sequence length, molecule type, organelle etc...) from these 3 data bases, to translate protein-coding genes in protein, and to extract selected sequences in user files. ACNUC is unique in providing direct access to coding regions (e.g. protein coding regions, tRNA or rRNA coding regions) of DNA fragments present in GenBank and in EMBL (introns, exon, CDS, 3'UTR, mRNA, 5'UTR, tRNA, etc... described on the FEATURES). Notably, ACNUC allows to extract fragments adjacent to the extremities of a subsequence (CDS, intron, tRNA, exon, etc...). Therefore it is possible to systematically extract, for example, 50 nt downstream of introns end of human protein encoding genes (or according to any other criteria). ACNUC is known to run on Sun (SunOs or Solaris), IBM Risc workstations, SGI computers, Dec-alpha systems, and VAX/VMS systems. It should be easily installed on most unix platforms. Contact M. Gouy for help for other unix systems. ACNUC is distributed by anonymous ftp from the internet address: biom3.univ-lyon1.fr or, numerically, 134.214.92.37 The directory there is /pub/acnuc ref: M. Gouy et al. (1985) CABIOS 3:167-172 M. Gouy et al. (1984) Nucl. Acids Res. 12:121-127 Contact = M. Gouy: mgouy@evomol.univ-lyon1.fr Laurent Duret Laboratoire de Biometrie, Genetique et Biologie des Populations URA CNRS 243 Universite Claude Bernard - Lyon I 43, Bd du 11 Novembre 1918 F-69622 Villeurbanne cedex Tel: +33 72.44.81.42 E-mail: duret@biomserv.univ-lyon1.fr From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Newsgroups: bionet.software Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Subject: Re: nucleotide sequence searching via the Internet Message-ID: <1994Mar2.034454.1729@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: Tin 1.1 PL4 References: <9403012358.AA27630@green.dfci.harvard.edu> Distribution: bionet Date: Wed, 2 Mar 94 03:44:54 GMT Lines: 675 agustin@GREEN.DFCI.HARVARD.EDU writes: : I'm highly interested in these : e-mail methods you mentioned in your e-mail. : It would be great if you could tell me where these *help-files* : are that you mentioned. Dear Agustin Amos Bairoch put together a wonderful list of all these servers, I append it below. This document includes the procedure to get the help information for each of these servers. In most cases it simply involves just sending the word 'help' in the body of the text. best of luck, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov ============================================================================== Name : serv_ema.txt Version: 1.70 / December 10, 1993 Concern: List of molecular biology email servers Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva bairoch@cmu.unige.ch ============================================================================== ----------------------------------------------------------------------------- FEEDBACK IN THE FORM OF CORRECTIONS, ADDITIONS, ETC ARE MORE THAN WELCOME !!! ----------------------------------------------------------------------------- A) INTRODUCTION =============== A1) General introduction ------------------------ This document briefly describes the various email servers that are available to molecular biologists. The servers described in this document generally fall into one of the following two categories: 1) Servers that provide an analytical function. You need to provide to such a server nucleic acid or protein sequence(s), the server sends back the result of an analysis (for example a similarity search) carried out on the sequences(s). 2) Servers that allow you to retrieve all or part of a database. Note that some servers can fall into both categories. We do not describe here the sites that allows the transfer of files by what is known as anonymous "ftp" (File transfer protocol), nor do we describe the BIOSCI electronic newsgroup system or the other bulletin boards that are available to molecular biologist. These services are described in the following documents: serv_ftp.txt: For a list of molecular biology FTP servers for databases and software. serv_bbo.txt: For a list of bulletin boards services for molecular biologists. A2) Some tips ------------- 1) Except when noted otherwise all the servers listed in this document will send you a full description of the service that they offer and the syntax that they support if you send a message containing only the word: help to the correct email address of the server. As the services offered by most of these servers generally evolve and get expanded, it is a good idea to request, every six months or so, the help documentation files of the servers that you are using. 2) Most of these servers provide an email address where you can reach a human interlocutor to report problems. Before you send mail to such an address, make sure that the current version of the help documentation file does not already provide the answer to your question(s) !! 3) Please be patient !!! Some of the servers described in this document are accessed by many users and the response time can vary with the load. In addition network trafic has a significant impact on the transit time for an email message. So if you have submitted a request to a server you should at least wait 48 hours before taking any further step. At that point you should not directly resubmit your request, but send a message to the address used to reports problems so as to inquire on the status of the server. A3) MAILFASTA ------------- MAILFASTA is a UNIX shell script which will take a DNA or PROTEIN sequence and will reformat it and mail it to any or all of the following email servers (which are all described in section B below): BLAST, BLITZ, BLOCKS, FASTA, Geneid, GRAIL, PredictProtein, and Pythia. MAILFASTA is a public domain program developed by Thon de Boer of the Department of Microbiological Physiology at the Vrije universiteit in Amsterdam Holland. He can be contacted at: deboer@bio.vu.nl The current version of the program is: 3.2 of July 1993 The program can be downloaded from various ftp sites such as at EMBL (ftp. embl-heidelberg.de) or at the iubio archive site (iubio.bio.indiana.edu). And its can also be obtained by email from the EMBL Network File Server (see the description in section B below). MAILFASTA is packed as an shell archive. It contains : mailfasta : The UNIX shell script cid.c : A small c program which will determine if the sequence is DNA or protein. getentry : A shell script which can be used to retrieve entries of interest mailfasta.doc : The documentation file mailfasta.changes : A file stating the changes since version 2.1 Warning: MAILFASTA makes use of the program 'readseq' for file conversion. This program MUST be present and is NOT included with the shell archive, you must also get it by ftp or by email. A4) Acknowledgments ------------------- Many thanks to all those who provided me information that was used in compiling this file, especially to Bob Harper (harper@convex.csc.fi) and Tan Tin Wee (bchtantw@nuscc.nus.sg) who forwarded or provided me with lots of information. A5) Additional references ------------------------- A very good summary of what you can do with electonic mail servers has been recently published: Henikoff S. Sequence analysis by electronic mail server. Trends Biochem. Sci. 18:267-268(1993). A6) Where can you find this file and the other serv_xxx files ------------------------------------------------------------- The latest version of the serv_ema.txt, serv_ftp.txt and serv_bbo.txt files are always available, by anonymous FTP, on the following server: expasy.hcuge.ch (129.195.254.61) These files are in the directory: /databases/info ============================================================================== B) LIST OF EMAIL SERVERS ------------------------ Total number of servers listed: 31 ------------------------------------------------------------------------------ Entry : EMS0029 Name : BioSCAN Organiz. : Department of Computer Science / University of North Carolina Chapel Hill / U.S.A. Type : ANALYSIS Description: Allows users to send a nucleotide or protein query sequence to the BioSCAN server (which use a special-purpose hardware accelerator) to do a similarity search with an algorithm similar to BLAST. The search can be done on SWISS-PROT, PIR, or GenBank. Address : bioscan@cs.unc.edu Contact : To report problems: bioscan-info@cs.unc.edu Status : Tested (29 Oct 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0025 Name : BIOSCI waismail server Organiz. : BIOSCI / IntelliGenetics Inc / Mountain View / USA Type : RETRIEVAL Description: This server can be used for text searching of the following two BIOSCI WAIS archives: biosci (complete archive of BIOSCI/bionet postings) and biology-journal-contents (archive of BIO-JOURNAL/ bionet.journals.contents table of contents postings). Address : waismail@net.bio.net Contact : To report problems: biosci@net.bio.net Status : Tested (11 May 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0001 Name : BIOSERVE Organiz. : Group T-10 / Los Alamos National Laboratory / USA Type : RETRIEVAL Description: Allows the retrieval of: documents concerning GenBank (feature table, flatfile format, submission form, transaction protocol, etc.); the LiMB database; a number of software packages (alpar, alwin, score, signal-scan, trna-scan, etc.). You can also use this server to retrieve a GenBank entry or to be aware of any overlap in sequencing effort with other investigators (cdna- inform). Address : bioserve@temin.lanl.gov Contact : To report problems: michael@genome.lanl.gov Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0002 Name : BLAST e-mail server Organiz. : National Center for Biotechnology Information National Library of Medicine / NIH / Bethesda / USA Type : ANALYSIS Description: The BLAST algorithm is a heuristic for finding ungapped, locally optimal sequence alignments.The BLAST family of programs employs this algorithm to compare an amino acid query sequence against a protein sequence database or a nucleotide query sequence against a nucleotide sequence database, as well as other combinations of protein and nucleic acid searches. Address : blast@ncbi.nlm.nih.gov Contact : To report problems: blast-help@ncbi.nlm.nih.gov Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0014 Name : BLITZ electronic mail server (MPsrch) Organiz. : Edinburgh University Biocomputing Research Unit (BRU) / U.K. and European Molecular Biology Laboratory / Heidelberg / Germany Type : ANALYSIS Description: Email server for the MPsrch program from the BRU. MPsrch allows you to perform sensitive and extremely fast comparisons of your protein sequences against the Swiss-Prot database using the Smith and Waterman best local similarity algorithm. Runs on the MasPar family of massively parallel machines. MPsrch is the fastest implementation of the SW algorithm currently available on any machine. Address : blitz@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (29 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Name : BLOCKS e-mail searcher Organiz. : Fred Hutchinson Center / Seattle / USA Type : ANALYSIS and RETRIEVAL Description: Compares a protein or DNA sequence to the current database of protein blocks. Blocks are short multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. The BLOCKS database has been constructed by successive application of the automated PROTOMAT system to individual entries in the PROSITE catalog of protein groups keyed to the SWISS-PROT protein sequence database. You can also use this server to retrieve specifics blocks and PROSITE entries. Address : blocks@howard.fhcrc.org Contact : To report problems: jorja@sparky.fhcrc.org Status : Tested (3 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0003 Name : DAPMAIL Organiz. : Edinburgh University Biocomputing Research Unit (BRU) / U.K. Type : ANALYSIS Description: Fast sequence database searching programs that runs on an Active Memory Technology Distributed Array Processor AMT DAP. Address : dapmail@ed.ac.uk Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0004 Name : Darwin Organiz. : Computational Biochemistry Research Group (CBRG) ETH / Zurich / Switzerland Type : ANALYSIS Description: Give access to various analytical functions implemented in the Darwin sequence analysis package; such as: PepPepSearch: search a protein sequence against the SWISS-PROT database using Smith-Waterman's version of dynamic programming. NuclPepSearch: search a nucleotide sequence directly against the entire SWISS-PROT database using the algorithm by Knecht and Gonnet. PepNuclSearch: search a protein sequence directly against the entire EMBL nucleotide database using the algorithm by Knecht and Gonnet. MassSearch: search the SWISS-PROT database for sequences which when digested by the given enzyme will match the given set of weights. Address : cbrg@inf.ethz.ch Contact : To report problems: knecht@inf.ethz.ch Status : Tested (29 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0027 Name : dFLASH server Organiz. : IBM Research Division's Thomas J. Watson Research Center Yorktown Heights / USA Type : ANALYSIS Description: "Homologous sequence retrieval" program for protein sequences based on the FLASH algorithm (Fast-Lookup Algorithm for Sequence Homology). Currently operates with SWISS-PROT; will soon also allows searches in GenBank. Address : dflash@watson.ibm.com Contact : To report problems: dflash@watson.ibm.com; the "Subject" line should contain the word "comments". Note : To get help send a message with the word "dFLASH" in the "Subject" line a body containing the words "send help". Status : Tested (28 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0005 Name : EMBL Network File Server Organiz. : European Molecular Biology Laboratory (EMBL) Heidelberg / Germany Type : RETRIEVAL Description: This server allows the retrieval via email of EMBL and SWISS-PROT entries as well as a wide variety of databases. It also allows the retrieval of public domain software for MS-DOS computers, the Apple Macintosh, DEC VAX/VMS, and UNIX. The programs are distributed in a form that is first compressed and then converted from binary to a printable ASCII text file. Note : You can also obtain all of these databases and software by FTP. If you have access to FTP you should use that method rather than use the email file server. The EMBL anonymous FTP server is described in the "serv_ftp.txt" file. Address : netserv@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0006 Name : EMBL Mail-FASTA Server Organiz. : European Molecular Biology Laboratory (EMBL) Heidelberg / Germany Type : ANALYSIS Description: Allows to perform fast and sensitive comparisons of nucleic acid or protein sequences against various databases. Mail-FASTA is based on the FASTA program developed by Pearson and Lipman (PNAS 85:2444-2448(1988)) as implemented in the GCG package. The EMBL database is updated daily. [The purpose and use of this server is identical to that of the GENIUSnet Mail-Fasta Service (entry EMS0010)] Address : fasta@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0007 Name : EST Report Mail Server Organiz. : National Center for Biotechnology Information National Library of Medicine / NIH / Bethesda / USA Type : RETRIEVAL Description: Allows the retrieval of Expressed Sequence Tag (EST) sequences from the dbEST collection. You can request ESTs by specifying either their NCBI id or their GenBank AC numbers, GDB ids, etc. Address : est_report@ncbi.nlm.nih.gov Contact : To report problems: carolyn@ncbi.nlm.nih.gov Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0008 Name : Flat DB E-Mail Network Server Organiz. : Faculty of Technology / Gunma University / Japan Type : RETRIEVAL AND ANALYSIS Description: Allows to retrieve entries from sequence databases using various text search parameters. This server gives you access to GenBank, EMBL, SWISS-PROT, PIR, GenPept, and PRF. Give access to the following analysis functions: generate complementary strands of DNA sequences; scan databases using the various FASTA programs (fasta, tfasta, lfasta); evaluate statistical significance of sequence matching (RDF2, RDF2G, etc.). Address : flat-netserv@smlab.eg.gunma-u.ac.jp Contact : To report problems: smiyazaw@smlab.eg.gunma-u.ac.jp Status : Tested (31 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0009 Name : Geneid Organiz. : Molecular Biology Computer Research Resource (MBCRR) Boston / USA Type : ANALYSIS Description: Artificial intelligence system for analyzing vertebrate genomic DNA and for the prediction of exons and gene structure as described in J. Mol. Biol. 226:141-157(1992). Address : geneid@darwin.bu.edu Contact : To report problems: steen@darwin.bu.edu Note : To get help send "geneid info" instead of "help". Status : Tested (4 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0010 Name : GENIUSnet Mail-Fasta Service Organiz. : German Cancer Research Centre (DKFZ) / Heidelberg / Germany Type : ANALYSIS Description: Allows to perform fast and sensitive comparisons of nucleic acid or protein sequences against various databases. Mail-FASTA is based on the FASTA program developed by Pearson and Lipman (PNAS 85:2444-2448(1988)) as implemented in the GCG package. [The purpose and use of this server is identical to that of the the EMBL Mail-FASTA Server (entry EMS0006)] Address : mfasta@genius.embnet.dkfz-heidelberg.de Contact : To report problems: dok248@genius.embnet.dkfz-heidelberg.de Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0011 Name : GENIUSnet sequence-server Organiz. : German Cancer Research Centre (DKFZ) / Heidelberg / Germany Type : RETRIEVAL Description: Allows to retrieve entries from the EMBL, GenBank, SWISS-PROT and PIR sequence databases using either the entry name or the accession number. The sequences returned are in the GCG format. Address : netserv@genius.embnet.dkfz-heidelberg.de Contact : To report problems: dok248@genius.embnet.dkfz-heidelberg.de Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0012 Name : GenMark Organiz. : Georgia Tech School of Applied Biology and Office of Information Technology / USA Type : ANALYSIS Description: System for predicting protein coding regions in E. coli and closely related species. It is based on a special type of Markov chain model of coding and noncoding nucleotide sequences. Address : genmark@ford.gatech.edu Contact : To report problems: mb56@hydra.gatech.edu Note : To get help you need to send "instructions" as the subject line of your message. Status : Tested (30 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0013 Name : GRAIL (Gene Recognition and Analysis Internet Link) Organiz. : Oak Ridge National Laboratory / USA Type : ANALYSIS Description: System for predicting protein coding regions in human DNA sequences using a neural network approach as described in PNAS 88:11261-11265(1991). Address : grail@ornl.gov Contact : To report problems: grailmail@ornl.gov Status : Tested (4 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0028 Name : MOWSE Organiz. : Imperial Cancer Research Fund and SERC Daresbury Laboratory / UK Type : ANALYSIS Description: Peptide mass fingerprint email server service. MOWSE allows the identification of known proteins from a set of molecular weights (mass spec) determined after proteolytic digests. Address : mowse@dl.ac.uk Contact : To report problems: mbdpn@s-crim1.dl.ac.uk Status : Tested (2 Sep 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0015 Name : NetGene mail server Organiz. : Department of Physical Chemistry Technical University of Denmark Lyngby / Denmark Type : ANALYSIS Description: Produce neural network predictions of splice sites in vertebrate genes as described in J. Mol. Biol. 220:49-65(1991). Address : netgene@virus.fki.dth.dk Contact : To report problems: engel@virus.fki.dth.dk Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0030 Name : nnpredict Organiz. : University of California - San Francisco (UCSF) / USA Type : ANALYSIS Description: Analyze a protein sequence and sends back a prediction of the secondary structure using a two-layer, feed-forward neural network method. Address : nnpredict@celeste.ucsf.edu Contact : To report problems: nnpredict-request@celeste.ucsf.edu Status : Tested (7 Dec 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0016 Name : PDB e-mail file server Organiz. : Protein Data Bank / Brookhaven National Laboratory / USA Type : RETRIEVAL Description: Provides PDB general information and documentation files. Address : fileserv@pb1.pdb.bnl.gov Note : To get help send a message containing the following type of line: send info your_e-mail_address. Contact : To report problems: skora@bnl.gov Status : Tested (7 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0017 Name : PredictProtein Organiz. : Protein Design Group European Molecular Biology Laboratory (EMBL) Heidelberg / Germany Type : ANALYSIS Description: Analyze a protein sequence and sends back a multiple sequence alignment performed by a weighted dynamic programming method (MaxHom) and a secondary structure prediction produced by a profile network method (PHD). Address : predictprotein@embl-heidelberg.de Contact : To report problems: predict-help@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0018 Name : PIR Network Request Service Organiz. : Protein Information Resource National Biomedical Research Foundation Washington, DC / USA Type : RETRIEVAL AND ANALYSIS Description: General purpose server that allows the retrieval of entries from sequence databases using various text search parameters. This server gives you access to PIR, NRL_3D, PATCHX, GenBank and EMBL. You can also use it for FASTA searches of protein or nucleotide sequences (which will be translated in its six reading frames) against the PIR, NRL_3D, and PATCHX databases. Address : fileserv@gunbrf.bitnet or fileserv@nbrf.georgetown.edu Contact : To report problems: postmaster@gunbrf.bitnet or postmaster@nbrf.georgetown.edu Status : Tested (4 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0019 Name : Pythia Organiz. : Biological and Medical Research Division Argonne National Laboratory / Argonne / USA Type : ANALYSIS Description: Allows the identification of human repetitive DNA elements such as L1, MERx, LTR, etc. Can also be used to identify the presence of Alu sequences and to classify them into subfamilies. Address : pythia@anl.gov Contact : To report problems: pythia-admin@anl.gov Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0020 Name : EMBL Mail-QUICKSEARCH server Organiz. : European Molecular Biology Laboratory (EMBL) Heidelberg / Germany Type : ANALYSIS Description: Service based on the QUICKSEARCH and QUICKSHOW programs developed by J. Devereux as implemented in the GCG package. It allows to perform very rapid comparisons of a nucleic acid sequence against the EMBL and GenBank databases. It answers the question: does this sequence already occur in the database (with a small number of mismatches) ? The databases are updated daily. Address : quick@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0026 Name : RDP mail server Organiz. : Ribosomal Database Project / University of Illinois Type : RETRIEVAL Description: Access to data and software relative to ribosomal RNA sequences. Address : server@rdp.life.uiuc.edu Contact : To report problems: rdp@phylo.life.uiuc.edu Status : Tested (29 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0021 Name : RETRIEVE E-Mail Server Organiz. : National Center for Biotechnology Information National Library of Medicine / NIH / Bethesda / USA Type : RETRIEVAL Description: Allows to retrieve entries from sequence databases using various text search parameters. This server gives you access to GenBank, EMBL, SWISS-PROT, PIR, GenPept, Kabat, etc. Address : retrieve@ncbi.nlm.nih.gov Contact : To report problems: retrieve-help@ncbi.nlm.nih.gov Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0031 Name : SBASE Organiz. : International Centre for Genetic Engineering and Biotechnology (ICGEB) / Trieste / Italy Type : ANALYSIS Description: Will do a search (using Blast) of a protein sequence agains the SBASE database of protein sequence domains. Address : sbase@icgeb.trieste.it Contact : To report problems: sbase-comment@icgeb.trieste.it Status : Tested (9 Dec 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0023 Name : Springer Journals Preview Service Organiz. : Springer Verlag, Dept. New Technologies Type : RETRIEVAL Description: Distribution of the table of contents and abstracts for selected life sciences journals published by Springer Verlag. The table of contents are free, but there is a charge of 20$ per year for abstracts. Address : svjps@dhdspri6.bitnet Contact : To report problems: springer@dhdspri6.bitnet Status : Tested (12 Mar 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0024 Name : TM7 file server. Organiz. : European Molecular Biology Laboratory (EMBL) Heidelberg / Germany Type : RETRIEVAL Description: The aim is to have all data relevant to G protein-coupled receptors that possess the 7 transmembrane helical motif. Address : tm7@embl-heidelberg.de Contact : To report problems: vriend@embl-heidelberg.de Status : Tested (30 Mar 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0022 Name : University of Houston Gene-Server Organiz. : University of Houston / USA Type : RETRIEVAL Description: Allows to retrieve entries from the GenBank and PIR sequence databases using various text search parameters. It also allows the retrieval of public domain software for MS-DOS computers, the Apple Macintosh, DEC VAX/VMS, and UNIX as well as additional text files such as the BIO-Matrix newsletters. Address : gene-server@bchs.uh.edu Contact : To report problems: gene-server-management@evolution.bchs.uh.edu Status : Tested (7 Jan 1993). ------------------------------------------------------------------------------ // ============================================================================== =End=of=document============================================================== -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!MARISTB.MARIST.EDU!KS7S From: KS7S@MARISTB.MARIST.EDU ("Barrett, Paul A.") Newsgroups: bionet.software Subject: EPO publications Date: 2 Mar 1994 02:21:04 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01MAR94.23002189.0061.MUSIC@MARISTB> NNTP-Posting-Host: net.bio.net I'm looking for any recent publications on results of experimentation dealing with the hormone erythropoitien. Please send any information that you have to me at the address 'ks7s@musicb.marist.edu' or through the bio-net service. Thanks. From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!phibred.com!news From: Glenn Brooke, Ph.D. Subject: phylogenetic trees Message-ID: X-Xxdate: Wed, 2 Mar 94 15:21:02 GMT Sender: news@phibred.com (USENET News System) Organization: Pioneer Hi-bred International, Inc. X-Useragent: Version 1.1.3 Date: Wed, 2 Mar 1994 21:22:56 GMT Lines: 8 Aside from the program suite PHYLIP, does anyone have suggestions for software to take short (<150) nucleotide sequences and create phylogenetic trees? Preferred platform in Macintosh, but we have unix and PCs available. Thanks in advance, Glenn Brooke, Ph.D. Pioneer Hi-Bred International, Inc. brookerg@phibred.com From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Adam Sartiel Newsgroups: bionet.software Subject: Contig mapping software Date: 2 Mar 1994 20:39:55 -0000 Lines: 22 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2l2tir$emg@mserv1.dl.ac.uk> Reply-To: Adam Sartiel Original-To: bio-soft@dl.ac.uk In our mapping efforts, we try to determine the correct order of markers using YAc clones, in the final purpose of getting a full contig. A typical marker record consists of '+' and '-' for the corresponding positive and negative clones. The desired output would be something like this: ++++++ ++++++++ ++++ +++++ etc. Can anybody suggest software which might aid us in computing the optimal arrangement and presenting it nicely (on Unix, DOS, Mac or MS-Windows)? Thank you, Adam Sartiel From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Newsgroups: bionet.software,comp.sys.mac.scitech Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!noc.near.net!news.cs.brandeis.edu!ahouse From: ahouse@hydra.rose.brandeis.edu. (Jeremy Creighton Ahouse) Subject: Re: MAC program that will recognize areas? Message-ID: <1994Mar2.195102.9847@news.cs.brandeis.edu> X-Posted-From: InterNews 1.0@80.1.64.129.in-addr.arpa. Lines: 10 Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University - Biology References: <1994Mar2.140415.4083@news.cs.brandeis.edu> <1994Mar2.162932.27304@sifon.cc.mcgill.ca> Date: Wed, 2 Mar 1994 19:51:02 GMT Lines: 10 Xref: biosci bionet.software:7444 comp.sys.mac.scitech:881 Thank you all, The consensus seems to be NIH image. One of you did mention that Canvas could do this. Jeremy Creighton Ahouse Biology and Center for Complex Systems Brandeis University Waltham, MA 02254-9110 From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!HOBBES.KZOO.EDU!deal From: deal@HOBBES.KZOO.EDU ("Ralph M. Deal") Newsgroups: bionet.software Subject: Re: Computer algebra system Date: 2 Mar 1994 17:26:47 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199403021731.MAA00274@hobbes> NNTP-Posting-Host: net.bio.net In response to: > I'm looking for a fairly simple and low cost computer algebra system > to analyze and manipulate math functions. Would like it to display > graphs of polynomials and to handle matrix and vector operations. > Also it should run on an IBM compatible 486DX with 8MB RAM and Windows > 3.1. Any suggestions? I believe Mathematica will be too much. > I recommend MatLAB by MathWorks which works on many platforms, including 486. I use it on a Mac and find it extremely useful for just these tasks. Note that it is NOT a symbolic manipulator like Mathematica or maple. It is an elegant front end for the LINPAK and EISPAK routines (plus more now of course). Ralph M. Deal Chemistry Dept. Kalamazoo College, Kalamazoo, MI 49006 DEAL@KZOO.EDU -- From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Newsgroups: bionet.software,comp.sys.mac.scitech Path: biosci!bcm!cs.utexas.edu!math.ohio-state.edu!cyber2.cyberstore.ca!nntp.cs.ubc.ca!utcsri!newsflash.concordia.ca!sifon!norton.geog.mcgill.ca!zak From: zak@norton.geog.mcgill.ca (Zachary James) Subject: Re: MAC program that will recognize areas? Message-ID: <1994Mar2.162932.27304@sifon.cc.mcgill.ca> Originator: zak@norton.geog.mcgill.ca Sender: news@sifon.cc.mcgill.ca Organization: McGill University References: <1994Mar2.140415.4083@news.cs.brandeis.edu> Date: Wed, 2 Mar 1994 16:29:32 GMT Lines: 14 Xref: biosci bionet.software:7442 comp.sys.mac.scitech:877 From article <1994Mar2.140415.4083@news.cs.brandeis.edu>, by ahouse@hydra.rose.brandeis.edu. (Jeremy Creighton Ahouse): > I am looking for a MAC program that will recognize areas on maps and > calculate their area. We can scan the images in. Evidently photoshop > will recognize outlined regions but does not have the capacity to > calculate areas. The Morphosys system on PCs (by Duncan and Meacham), > would work, but that would constrain us to a computer system that we > have limited access to. Do you all know of any program for a MAC that > can be used for this purpose? NIH Image (available via anon FTP from zippy.nimh.nih.gov) will do this. Zak JAMES GIS Technician McGill U. Geography From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!math.fu-berlin.de!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.cellbiol,bionet.software Subject: How to find pleckstrin domains? Date: 2 Mar 1994 21:18:40 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 61 Message-ID: <2l2vrgINNpkb@sat.ipp-garching.mpg.de> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Xref: biosci bionet.cellbiol:348 bionet.software:7447 Hello fellow netters, I would like to generate a profile which can be used to test new sequences for the occurence of a pleckstrin domain. I have tried to generate a profile with the GCG program PROFILESEARCH, using the alignments given in Musacchio et al., Trends Biochem. Sci. 18, 343-348, 1993. Since the authors have used a different program which they claim to be superior, I have started with aligning a few sequences according to the paper and using these to find new members of the pleckstrin domain family. Unfortunately, I find that there is no really good way to discriminate true positives from false hits. I have started with the sequences marked in table I as members of the first profile. The profilesearch of SwissProt gives the following result (I have changed the output for brevity): Orig. Sequence with description 20.99 SWISS:GTPA_HUMAN Ras GAP (member of original profile) 20.98 SWISS:GTPA_BOVIN Ras GAP 19.13 SWISS:GNRP_RAT Guanine nucleotide releasing protein (member of original profile) 17.89 SWISS:OXYB_HUMAN Oxysterol-binding protein (member of original profile) 17.74 SWISS:OXYB_RABIT Oxysterol-binding protein 17.33 SWISS:DYN1_RAT Dynamin-1 (member of original profile) 17.18 SWISS:SOS_DROME Son of sevenless protein (member of original profile) 16.21 SWISS:P47_HUMAN Pleckstrin (member of original profile) 15.32 SWISS:DYN_DROME Dynamin = shibire protein 13.01 SWISS:SPCB_DROME Spectrin beta chain 12.57 SWISS:TYK2_HUMAN Non-receptor tyrosine-protein kinase tyk2 12.56 SWISS:PIP2_HUMAN PLC-gamma 12.34 SWISS:PIP2_BOVIN PLC-gamma 12.22 SWISS:ARK1_RAT beta-adrenergic receptor kinase 1 12.19 SWISS:ARK1_BOVIN beta-adrenergic receptor kinase 1 12.19 SWISS:ARK1_HUMAN beta-adrenergic receptor kinase 1 12.15 SWISS:RRPB_IBVB RNA-directed RNA polymerase (from a virus) 12.13 SWISS:PIP2_RAT PLC-gamma 12.12 SWISS:ACHG_CHICK Acetylcholine receptor, gamma chain precursor 12.06 SWISS:ARK2_RAT beta-adrenergic receptor kinase 2 12.05 SWISS:SDHD_ECOLI D-serine dehydratase 12.05 SWISS:PIP4_HUMAN PLC-IV 11.90 SWISS:PIP4_RAT PLC-IV 11.86 SWISS:ENV_SIVAT gp160 precursor .. Two things confuse me: a) All of the sequences which score obviously high are already member of the profile or very related to a member of the profile. b) While most of the top-scoring sequences are considered by Musacchio et al. to be a member of the pleckstrin domain-containing group of proteins, there are some which do not, e.g. Serine dehydratase from E. coli or the RNA polymerase. How can these proteins for sure be excluded from the pleckstrin family? --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Newsgroups: sci.chem,sci.physics,sci.bio,sci.comp-aided,bionet.software Path: biosci!daresbury!trane.uninett.no!news.eunet.no!nuug!news.eunet.fi!news.funet.fi!luotsi.uku.fi!mesaani.uku.fi!perch From: perch@mesaani.uku.fi (Perch-projekti) Subject: PERCH, semi-commercial NMR software, new demo Summary: tools for analysing and interpreting NMR data Sender: news@luotsi.uku.fi Message-ID: Date: 2 Mar 94 10:14:41 GMT Organization: University of Kuopio, Finland Keywords: NMR software, spectra simulation, analysis ___ / _____/ ___ / _____/ / / / / / / / / / / _____/ _____/ __ / / ____ / / / / | / / / __/ ______/ __/ __| ______/ __/ __/ P E A K R E S E A R C H Lines: 20 Xref: biosci sci.chem:9476 sci.physics:31205 sci.bio:7132 sci.comp-aided:302 bionet.software:7439 PERCH provides many sophisticated tools for analysing and interpreting 1D-NMR data in general and spectral analysis in particular. PERCH very well suites to NMR-teaching as well. PERCH takes advantage of 32bit code and is running on IBM/PC under DOS and Windows. PERCH is developed and distributed by the University of Kuopio, Finland. The plain simulation/iteration modules are stand alone and free (QCPE), the additional graphics and tools are charged. A new demo is available via anonymous ftp from ftp.funet.fi under pub/sci/chem/nmr. Read PERCH.TXT for download instructions. For further information, please contact: PERCH Project phone: + 358 71 163242 University of Kuopio, POB 1627 telefax: + 358 71 163259 FIN-70211 Kuopio, FINLAND e-mail: perch@mesaani.uku.fi Copyright 1993-1994 PERCH Project, University of Kuopio, Finland. All rights reserved. From owner-software@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!nedcu0!mbegger From: Louis.Egger@bota.unine.ch (Louis Egger) Newsgroups: bionet.software Subject: Software for MPN estimation? Message-ID: <1994Mar2.221421.2168@nedcu0> Date: 2 Mar 94 22:14:20 MET Organization: University of Neuchatel, Switzerland Lines: 10 Our Lab is about to do enumeration of bacterial groups in soils. We plan to estimate the cell numbers using the method of MOST-PROBABLE-NUMBER (MPN). Thus, we would like to find a program for PC instead of using the traditional tables. Who knows if such a program extits (commercial or share-ware) and where we could get it? Please E-mail your comments to egger@bota.unine.ch. Thanks a lot! Louis From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!torn!utnut!utcsri!newsflash.concordia.ca!CC.UMontreal.CA!megasun.BCH.UMontreal.CA!tim From: tim@megasun.BCH.UMontreal.CA (Tim Littlejohn) Subject: Re: sequence/contig assembly Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal References: <2kv4lc$o3c@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 3 Mar 1994 05:01:47 GMT Lines: 59 >One of the best (if not the best) sequence assembly software comes in Roger Staden's package. If you are a research institute, it's around a mere hundred pounds sterlimg, and it is excellent. > >If you have X-windows, its even better. > >It is very simple, though can appear complicated to a non-computer user. > >Unfortunately, I cant find his e-mail address. Enquiries about obtaining the Staden package can be directed to Roger Staden at: rs@mrc-lmb.cam.ac.uk Furthermore, there is a prototype bionet newsgroup dedicated to this package. The function of this group is to act as a forum of news and idea exchange between the users of the package and the developers. To subscribe to this group send a mail message to the Internet address: biosci-server@net.bio.net Leave the Subject: line of the message blank and enter the following line into the body of the mail message: subscribe staden-users This message will be automatically read by our computer and your e-mail address will be extracted from the mail header and added to the list. A repository of informaton on the package can be browsed through Gopher at: megasun.bch.umontreal.ca select the menu item labelled: Computational Molecular Biology- programs, documents, help then Staden Package If you have any questions about any of this, just send me an email at: tim@bch.umontreal.ca Tim Littlejohn -- ============================================================================== Tim Littlejohn E-mail: tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, succursale A, Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!UTMSI.ZO.UTEXAS.EDU!CURTIS From: CURTIS@UTMSI.ZO.UTEXAS.EDU Newsgroups: bionet.software Subject: re: Software for MPN estimation? Date: 3 Mar 1994 00:48:29 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <940302184858.1189@UTMSI.ZO.UTEXAS.EDU> NNTP-Posting-Host: net.bio.net A program in BASIC that can be used to calculate MPNs and confidence intervals is found in: Hurley and Roscoe (1983) J. Appl. Bacteriol. 55:159 We use it routinely with good success. It is particularly attractive because one is not constrained by a fixed number of dilutions, a fixed number of replicates at each dilution, or dilution by a fixed amount. It also provides confidence intervals about the estimates. Curtis Suttle Marien Science Inst. Univ. Texas, Austin From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!ee.und.ac.za!inet.up.ac.za!ccnet.up.ac.za!fourie From: fourie@ccnet.up.ac.za (Fourie Joubert) Newsgroups: bionet.software Subject: Sparcclassic for Molecular Biology? Date: Thu, 3 Mar 1994 08:51:41 GMT Organization: University of Pretoria Lines: 19 Message-ID: NNTP-Posting-Host: 137.215.128.62 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi We are thinking of buying a system for molecular biology, but can only afford a Sparcclassic (Over here we have to multiply the $ price by 8). Is there anyone out there using the Classic for sequence analysis, etc? I would appreciate some comments about what workload this system can handle. Please mail, thank a lot! __________________________________________________________________________ _/_/_/_/ _/_/_/_/_/ Fourie Joubert _/ _/ Department of Biochemistry _/ _/ University of Pretoria _/_/_/_/ _/ South Africa _/ _/ fourie@ccnet.up.ac.za _/ _/_/_/_/ Disclaimer: "Fourie who?" __________________________________________________________________________ From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: DCLAP, C++ class application library source (cross-platform) available Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington Date: Thu, 3 Mar 1994 16:58:46 GMT Lines: 67 Don's Class Application (DCLAP) library is a C++ class library for building applications on the common windowing operating systems (Macintosh, MS-Windows, XWindow-Motif and possibly others). This is built on the cross-platform toolkit from National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM), called NCBI toolkit, and especially the Vibrant window system subset, plus the corelib subset. This toolkit is written in ANSI C, and compiles on a variety of systems. The source for NCBI tools is available for anonymous ftp from ncbi.nlm.nih.gov as /toolbox/ncbi_tools/ncbi.tar.Z DCLAP is still very preliminary. There is yet no detailed documentation for it. It is based loosely on the MacApp and TCL application class libraries available on Macintosh, but is structured to use the available Vibrant toolkit methods. The only platforms I've tested it with are Macintosh-Think C 6-Symantec C++, Sun-GCC/G++-Motif, and MS Windows-Borland C++. Source and updates will be available thru ftp/gopher at ftp.bio.indiana.edu, /util/dclap... Currently there are these sets of source required to compile dclap applications: dclap.tar.Z -- general application framework classes source dbio.tar.Z -- biosequence specific classes source dmake.tar -- compiling instructions & compiler make documents ncbi.tar.Z -- NCBI's toolkit source ncbi.diff -- any patches to NCBI's toolkit needed for dclap See the /util/dclap/utils section for Mac and MSWin tar and compress programs to open the unix standard .tar.Z files. Current applications written w/ Dclap include GopherPup -- Internet gopher+ client SeqPup -- biosequence editor and analysis platform MyApp -- demonstration program StripPS -- simple filter program (postscript to plain text) MailHelp -- simple email-to-help-desk app I'd like to thank Jonathan Kans, primary author of NCBI's Vibrant user-interface, both for making this very useful code available to the community, and for his efforts to incorporate changes for DCLAP into it. DCLAP is copyrighted 1994 by Don Gilbert. You may use it in non-commercial software without asking additional permission, and you may freely redistribute it. See Copyright.dclap document for details. For DCLAP bug reports, comments, etc., email to dclap@bio.indiana.edu If you are working in the biocomputing/computational biology field and want help w/ dclap, please ask. Contributions to dclap source are welcome. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: SeqPup, biosequence editor & analysis, crossplatform available Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington Date: Thu, 3 Mar 1994 16:56:15 GMT Lines: 67 SeqPup is a biological sequence editor and analysis program usable on the common computer systems including Macintosh, Motif/X-Windows and MS-Windows. It includes, or will, links to network services and external analysis programs. Features multiple sequence alignment editor single sequence editor window read and write several sequence file formats consensus,reverse,complement,degap operations automatic preference saving internet send mail internet sequence analysis services and more NOTICE: This release is still unfinish, and has bugs. Please careful of trusting important data to it. It may be useful to some of you as is. SeqPup is being written by Don Gilbert using DCLAP, a C++ Class Application framework, and founded on the NCBI Toolkit, especially it's Vibrant user-interface section written by Jonathan Kans. You can obtain this release thru anonymous ftp or gopher to ftp.bio.indiana.edu, in folder /molbio/seqpup, as seqpup.hqx (Macintosh), seqpup.zip (MS Windows), seqpup-sun-static.tar.Z (SunOS Sparcstation), and perhaps other binaries. There may be additional distribution software, data or information in this /molbio/seqpup folder. See the Readme files in it for details. See also /util/dclap for source code. Comments, bug reports and suggestions for new features (see below) may be addressed via e-mail to SeqPup@Bio.Indiana.Edu SeqApp/SeqPup was started Sept. 1990 as MacApp sequence editor/analysis platform on which analysis programs from other authors could be easily incorporated into a useable interface. 1 Mar 94: First public release of SeqPup, version -1. It has plenty of bugs and missing features, including: no Undo (this is a real bite to those used to it) mostly no cut/copy/paste/clear limited printing of documents or views mostly no align-view manipulations (move,cut/copy,edit in place, shift, ...) no pretty print views no restriction maps no dot plots no ... problems w/ window display & keeping track of active window (x,mswin) I'll be adding back many of these features from the Macintosh SeqApp as time permits. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!crcnis1.unl.edu!unlinfo.unl.edu!dwoodman From: dwoodman@unlinfo.unl.edu (david woodman) Newsgroups: bionet.software Subject: TWINSPAN Date: 3 Mar 1994 15:55:29 GMT Organization: University of Nebraska--Lincoln Lines: 4 Message-ID: <2l519h$k3s@crcnis1.unl.edu> NNTP-Posting-Host: unlinfo2.unl.edu X-Newsreader: TIN [version 1.2 PL2] A colleague of mine is enquiring of a program named "TWINSPAN" (apparently from Cornell U) and would like to obtain a source for the same. It, apparently, examines species distributions and looks for patterns of the same. Thanks. From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!usenet.ins.cwru.edu!agate!msuinfo!netnews.upenn.edu!amalthea.humgen.upenn.edu!tisdall From: tisdall@amalthea.humgen.upenn.edu (James Tisdall) Newsgroups: bionet.software Subject: Re: Searching GenBank for nucleotide repeats Date: 3 Mar 1994 13:46:45 GMT Organization: University of Pennsylvania Lines: 383 Message-ID: <2l4po5$kls@netnews.upenn.edu> References: NNTP-Posting-Host: amalthea.humgen.upenn.edu In article keith@bones.biochem.ualberta.ca (Keith Robinson) writes: >A staff member here wants to search all of the rodent cDNA sequences in >GenBank to get an idea of the frequency of occurence of: > > - Single base repeats (e.g. GGGGGG) of lengths 6 to 20 inclusive > for all 4 possible combinations > > - double-base repeats (e.g. GAGAGAGAGAGA) of length 6 to 20, for > all 16 possible combinations > > - triple-base repeats (e.g. GATGATGATGATGATGAT) of length 6 to 20, > for all 64 possible combinations > >We use GCG here, and it is possible to perform this search with GCG's >"findpatterns" command (e.g. searching for G repeats can be done with >the pattern ~GG{6,20}~G), but this is time consuming (human and computer), >and processing the resulting output file is rather tedious. Before >attempting to write our own program, does anyone know of any software >which would make setting up and interpreting results of these searches >easier? > > Keith Robinson Dept. of Biochemistry > The University of Alberta Edmonton, Alberta Canada This was relatively straightforward using "DNA WorkBench", from ftp site cbil.humgen.upenn.edu:/pub/dnaworkbench I used the Unix version. I've appended the output of the program, followed by the program. I put the program in a file called "repeats" and executed the command dnaworkbench -q -f repeats The program included some start and end timing information - it took about an hour and a half to run. If the last line of the program is uncommented, by removing the leading "#" character, the program runs and leaves you in interactive mode, with all the search results available for further processing. (By length 6 to 20, I assume you want that number of repeats of the groups, not nucleotide length - e.g. the set of trinucleotides acg repeated 6 to 20 times, would not include "acgacgacg" of length 9. If I am assuming incorrectly, and you wanted the length of each search string to be between 6 and 20 nucleotides in length, just edit the program so that the dinucleotides are in the form e.g. (AT){3,10} and the trinucleotides are in the form e.g. (ATG){2,7}.) I extract the GenBank cDNA sequences by simply searching for the string cDNA (or c-DNA) over the gbrod.seq library; then for each set of hits on a given repeat sequence, I take the intersection of the hits with the cDNA set. My simple method of extracting the cDNA sequences no doubt includes some false positives, and may be missing some cDNA's as well - but to "get an idea of the frequency of occurence" of these repeats in rodent cDNA, I expect it's fairly accurate. It often is not necessary to search for all e.g. 64 trinucleotide repeats. For instance, AAA is already a repeat, and will be found by finding repeats of A. Also, ACT and CTA and TAC are "rotations" of each other, so you only really have to look for one of them. Following are the "interesting" repeats up to length 3 (send me mail for a program that calculates these, up to length 8). Note that there are only 30 of these, as opposed to 4+16+64= 84 of all permutations. Of course, it depends on how exact you're trying to be - you may find some sequences for which there are e.g. AAG repeats of length 6 which are not GAA repeats of length 6. Also, it is sometimes only necessary to search for just one of a pair of complementary fragments such as ACT and TGA. ### Table of non-periodic strings over {a,c,g,t} modulo rotations, up to ### length 3. A C G T AC AG AT CG CT GT AAC AAG AAT ACC ACG ACT AGC AGG AGT ATC ATG ATT CCG CCT CGG CGT CTG CTT GGT GTT Jim ====================================================================== James Tisdall Departments of Genetics and Computer and Information Science Computational Biology and Informatics Laboratory, Human Genome Project University of Pennsylvania tisdall@cbil.humgen.upenn.edu 215-573-3113 fax 215-573-3111 Biocomputing Associates (610) 933-9266 ====================================================================== #####Cut here: start of program output######## Wed Mar 2 19:11:55 EST 1994 Wed Mar 2 20:53:37 EST 1994 "HELP SEARCHES" for instructions to LOAD, SAVE, WRITE, and RETRIEVE To combine searches use "HELP" for INTERSECTION UNION DIFFERENCE SEARCHES Size Number Command _____________________________________ 8158 1 text c-?dna (in gbrod) 5268 2 sequence A{6,20} (in gbrod) 2368 3 intersect 1 $ 2818 4 sequence C{6,20} (in gbrod) 1257 5 intersect 1 $ 3027 6 sequence G{6,20} (in gbrod) 1232 7 intersect 1 $ 4365 8 sequence T{6,20} (in gbrod) 1789 9 intersect 1 $ 1162 10 sequence (AA){6,20} (in gbrod) 562 11 intersect 1 $ 519 12 sequence (AC){6,20} (in gbrod) 114 13 intersect 1 $ 248 14 sequence (AG){6,20} (in gbrod) 66 15 intersect 1 $ 191 16 sequence (AT){6,20} (in gbrod) 61 17 intersect 1 $ 525 18 sequence (CA){6,20} (in gbrod) 117 19 intersect 1 $ 141 20 sequence (CC){6,20} (in gbrod) 37 21 intersect 1 $ 17 22 sequence (CG){6,20} (in gbrod) 2 23 intersect 1 $ 244 24 sequence (CT){6,20} (in gbrod) 65 25 intersect 1 $ 247 26 sequence (GA){6,20} (in gbrod) 57 27 intersect 1 $ 18 28 sequence (GC){6,20} (in gbrod) 3 29 intersect 1 $ 121 30 sequence (GG){6,20} (in gbrod) 30 31 intersect 1 $ 535 32 sequence (GT){6,20} (in gbrod) 106 33 intersect 1 $ 196 34 sequence (TA){6,20} (in gbrod) 62 35 intersect 1 $ 248 36 sequence (TC){6,20} (in gbrod) 65 37 intersect 1 $ 546 38 sequence (TG){6,20} (in gbrod) 117 39 intersect 1 $ 663 40 sequence (TT){6,20} (in gbrod) 239 41 intersect 1 $ 483 42 sequence (AAA){6,20} (in gbrod) 240 43 intersect 1 $ 14 44 sequence (AAC){6,20} (in gbrod) 4 45 intersect 1 $ 24 46 sequence (AAG){6,20} (in gbrod) 16 47 intersect 1 $ 15 48 sequence (AAT){6,20} (in gbrod) 4 49 intersect 1 $ 14 50 sequence (ACA){6,20} (in gbrod) 4 51 intersect 1 $ 32 52 sequence (ACC){6,20} (in gbrod) 15 53 intersect 1 $ 1 54 sequence (ACG){6,20} (in gbrod) 0 55 intersect 1 $ 2 56 sequence (ACT){6,20} (in gbrod) 1 57 intersect 1 $ 24 58 sequence (AGA){6,20} (in gbrod) 16 59 intersect 1 $ 57 60 sequence (AGC){6,20} (in gbrod) 33 61 intersect 1 $ 49 62 sequence (AGG){6,20} (in gbrod) 18 63 intersect 1 $ 2 64 sequence (AGT){6,20} (in gbrod) 1 65 intersect 1 $ 15 66 sequence (ATA){6,20} (in gbrod) 4 67 intersect 1 $ 8 68 sequence (ATC){6,20} (in gbrod) 0 69 intersect 1 $ 6 70 sequence (ATG){6,20} (in gbrod) 2 71 intersect 1 $ 19 72 sequence (ATT){6,20} (in gbrod) 4 73 intersect 1 $ 14 74 sequence (CAA){6,20} (in gbrod) 4 75 intersect 1 $ 33 76 sequence (CAC){6,20} (in gbrod) 15 77 intersect 1 $ 55 78 sequence (CAG){6,20} (in gbrod) 30 79 intersect 1 $ 9 80 sequence (CAT){6,20} (in gbrod) 1 81 intersect 1 $ 28 82 sequence (CCA){6,20} (in gbrod) 12 83 intersect 1 $ 15 84 sequence (CCC){6,20} (in gbrod) 3 85 intersect 1 $ 13 86 sequence (CCG){6,20} (in gbrod) 8 87 intersect 1 $ 26 88 sequence (CCT){6,20} (in gbrod) 5 89 intersect 1 $ 0 90 (CGA){6,20} (in gbrod) 0 91 intersect 1 $ 18 92 sequence (CGC){6,20} (in gbrod) 9 93 intersect 1 $ 14 94 sequence (CGG){6,20} (in gbrod) 7 95 intersect 1 $ 0 96 (CGT){6,20} (in gbrod) 0 97 intersect 1 $ 2 98 sequence (CTA){6,20} (in gbrod) 1 99 intersect 1 $ 24 100 sequence (CTC){6,20} (in gbrod) 4 101 intersect 1 $ 44 102 sequence (CTG){6,20} (in gbrod) 15 103 intersect 1 $ 15 104 sequence (CTT){6,20} (in gbrod) 4 105 intersect 1 $ 24 106 sequence (GAA){6,20} (in gbrod) 16 107 intersect 1 $ 2 108 sequence (GAC){6,20} (in gbrod) 0 109 intersect 1 $ 50 110 sequence (GAG){6,20} (in gbrod) 20 111 intersect 1 $ 10 112 sequence (GAT){6,20} (in gbrod) 6 113 intersect 1 $ 56 114 sequence (GCA){6,20} (in gbrod) 30 115 intersect 1 $ 19 116 sequence (GCC){6,20} (in gbrod) 10 117 intersect 1 $ 15 118 sequence (GCG){6,20} (in gbrod) 7 119 intersect 1 $ 38 120 sequence (GCT){6,20} (in gbrod) 13 121 intersect 1 $ 51 122 sequence (GGA){6,20} (in gbrod) 18 123 intersect 1 $ 20 124 sequence (GGC){6,20} (in gbrod) 10 125 intersect 1 $ 13 126 sequence (GGG){6,20} (in gbrod) 4 127 intersect 1 $ 12 128 sequence (GGT){6,20} (in gbrod) 1 129 intersect 1 $ 3 130 sequence (GTA){6,20} (in gbrod) 1 131 intersect 1 $ 0 132 (GTC){6,20} (in gbrod) 0 133 intersect 1 $ 11 134 sequence (GTG){6,20} (in gbrod) 1 135 intersect 1 $ 25 136 sequence (GTT){6,20} (in gbrod) 10 137 intersect 1 $ 15 138 sequence (TAA){6,20} (in gbrod) 4 139 intersect 1 $ 2 140 sequence (TAC){6,20} (in gbrod) 1 141 intersect 1 $ 2 142 sequence (TAG){6,20} (in gbrod) 1 143 intersect 1 $ 19 144 sequence (TAT){6,20} (in gbrod) 4 145 intersect 1 $ 9 146 sequence (TCA){6,20} (in gbrod) 1 147 intersect 1 $ 26 148 sequence (TCC){6,20} (in gbrod) 5 149 intersect 1 $ 1 150 sequence (TCG){6,20} (in gbrod) 0 151 intersect 1 $ 15 152 sequence (TCT){6,20} (in gbrod) 4 153 intersect 1 $ 9 154 sequence (TGA){6,20} (in gbrod) 5 155 intersect 1 $ 38 156 sequence (TGC){6,20} (in gbrod) 12 157 intersect 1 $ 12 158 sequence (TGG){6,20} (in gbrod) 2 159 intersect 1 $ 25 160 sequence (TGT){6,20} (in gbrod) 10 161 intersect 1 $ 19 162 sequence (TTA){6,20} (in gbrod) 4 163 intersect 1 $ 15 164 sequence (TTC){6,20} (in gbrod) 4 165 intersect 1 $ 26 166 sequence (TTG){6,20} (in gbrod) 9 167 intersect 1 $ 189 168 sequence (TTT){6,20} (in gbrod) 49 169 intersect 1 $ #####Cut here: end of program output######## #####Cut here: start of DNA WorkBench program ######## date text c-?dna gbrod sequence A{6,20} gbrod ; intersection 1 $ sequence C{6,20} gbrod ; intersection 1 $ sequence G{6,20} gbrod ; intersection 1 $ sequence T{6,20} gbrod ; intersection 1 $ sequence (AA){6,20} gbrod ; intersection 1 $ sequence (AC){6,20} gbrod ; intersection 1 $ sequence (AG){6,20} gbrod ; intersection 1 $ sequence (AT){6,20} gbrod ; intersection 1 $ sequence (CA){6,20} gbrod ; intersection 1 $ sequence (CC){6,20} gbrod ; intersection 1 $ sequence (CG){6,20} gbrod ; intersection 1 $ sequence (CT){6,20} gbrod ; intersection 1 $ sequence (GA){6,20} gbrod ; intersection 1 $ sequence (GC){6,20} gbrod ; intersection 1 $ sequence (GG){6,20} gbrod ; intersection 1 $ sequence (GT){6,20} gbrod ; intersection 1 $ sequence (TA){6,20} gbrod ; intersection 1 $ sequence (TC){6,20} gbrod ; intersection 1 $ sequence (TG){6,20} gbrod ; intersection 1 $ sequence (TT){6,20} gbrod ; intersection 1 $ sequence (AAA){6,20} gbrod ; intersection 1 $ sequence (AAC){6,20} gbrod ; intersection 1 $ sequence (AAG){6,20} gbrod ; intersection 1 $ sequence (AAT){6,20} gbrod ; intersection 1 $ sequence (ACA){6,20} gbrod ; intersection 1 $ sequence (ACC){6,20} gbrod ; intersection 1 $ sequence (ACG){6,20} gbrod ; intersection 1 $ sequence (ACT){6,20} gbrod ; intersection 1 $ sequence (AGA){6,20} gbrod ; intersection 1 $ sequence (AGC){6,20} gbrod ; intersection 1 $ sequence (AGG){6,20} gbrod ; intersection 1 $ sequence (AGT){6,20} gbrod ; intersection 1 $ sequence (ATA){6,20} gbrod ; intersection 1 $ sequence (ATC){6,20} gbrod ; intersection 1 $ sequence (ATG){6,20} gbrod ; intersection 1 $ sequence (ATT){6,20} gbrod ; intersection 1 $ sequence (CAA){6,20} gbrod ; intersection 1 $ sequence (CAC){6,20} gbrod ; intersection 1 $ sequence (CAG){6,20} gbrod ; intersection 1 $ sequence (CAT){6,20} gbrod ; intersection 1 $ sequence (CCA){6,20} gbrod ; intersection 1 $ sequence (CCC){6,20} gbrod ; intersection 1 $ sequence (CCG){6,20} gbrod ; intersection 1 $ sequence (CCT){6,20} gbrod ; intersection 1 $ sequence (CGA){6,20} gbrod ; intersection 1 $ sequence (CGC){6,20} gbrod ; intersection 1 $ sequence (CGG){6,20} gbrod ; intersection 1 $ sequence (CGT){6,20} gbrod ; intersection 1 $ sequence (CTA){6,20} gbrod ; intersection 1 $ sequence (CTC){6,20} gbrod ; intersection 1 $ sequence (CTG){6,20} gbrod ; intersection 1 $ sequence (CTT){6,20} gbrod ; intersection 1 $ sequence (GAA){6,20} gbrod ; intersection 1 $ sequence (GAC){6,20} gbrod ; intersection 1 $ sequence (GAG){6,20} gbrod ; intersection 1 $ sequence (GAT){6,20} gbrod ; intersection 1 $ sequence (GCA){6,20} gbrod ; intersection 1 $ sequence (GCC){6,20} gbrod ; intersection 1 $ sequence (GCG){6,20} gbrod ; intersection 1 $ sequence (GCT){6,20} gbrod ; intersection 1 $ sequence (GGA){6,20} gbrod ; intersection 1 $ sequence (GGC){6,20} gbrod ; intersection 1 $ sequence (GGG){6,20} gbrod ; intersection 1 $ sequence (GGT){6,20} gbrod ; intersection 1 $ sequence (GTA){6,20} gbrod ; intersection 1 $ sequence (GTC){6,20} gbrod ; intersection 1 $ sequence (GTG){6,20} gbrod ; intersection 1 $ sequence (GTT){6,20} gbrod ; intersection 1 $ sequence (TAA){6,20} gbrod ; intersection 1 $ sequence (TAC){6,20} gbrod ; intersection 1 $ sequence (TAG){6,20} gbrod ; intersection 1 $ sequence (TAT){6,20} gbrod ; intersection 1 $ sequence (TCA){6,20} gbrod ; intersection 1 $ sequence (TCC){6,20} gbrod ; intersection 1 $ sequence (TCG){6,20} gbrod ; intersection 1 $ sequence (TCT){6,20} gbrod ; intersection 1 $ sequence (TGA){6,20} gbrod ; intersection 1 $ sequence (TGC){6,20} gbrod ; intersection 1 $ sequence (TGG){6,20} gbrod ; intersection 1 $ sequence (TGT){6,20} gbrod ; intersection 1 $ sequence (TTA){6,20} gbrod ; intersection 1 $ sequence (TTC){6,20} gbrod ; intersection 1 $ sequence (TTG){6,20} gbrod ; intersection 1 $ sequence (TTT){6,20} gbrod ; intersection 1 $ date searches #perl $Quiet=0; $Commandline=0; #remove first '#' to stay in interactive mode #####Cut here: end of DNA WorkBench program ######## From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Jeroen Coppieters Newsgroups: bionet.software Subject: Re: phylogenetic trees Date: 3 Mar 1994 09:32:07 -0000 Lines: 40 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2l4aqn$omf@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk On Wed, 2 Mar 1994 Glenn.Brooke@dl.ac.uk wrote: > Aside from the program suite PHYLIP, does anyone have suggestions > for software to take short (<150) nucleotide sequences and create > phylogenetic trees? Preferred platform in Macintosh, but we have > unix and PCs available. Thanks in advance, > > Glenn Brooke, Ph.D. > Pioneer Hi-Bred International, Inc. > brookerg@phibred.com > The program ClustalV (Higgins and Sharp) runs on PC,UNIX,VAX and Mac (although not very Mac-like). It can create multiple alignments and uses the Neighbor Joining method of Saitou and Nei (1987) to create trees. Only it has no feature to display the resulting tree graphically. It has the possiblility of writing out the results in a number of formats that can be used as input for other programs (like PHYLIP) You can ftp the program from ftp@embl-heidelberg.de and possibly from other places as well. Jeroen Ref Higgins, D.G. and Sharp, P.M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5, 151-153. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol.Biol.Evol. 4, 406-425. ===================================================================== jecop@gengenp.rug.ac.be / Jeroen Coppieters \ \ /\/\ /\/ Lab of Genetics \ \ / /\ \/ /\ University of Gent. \ /\/ \/\/ \ /\ AG GC C Ledeganckstraat 35 \ / \ T A G A A B-9000 Gent (Belgium) \/ A AA GA 32-9-2645189 ===================================================================== From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!news.Brown.EDU!noc.near.net!news.tufts.edu!opal.tufts.edu!etsang From: etsang@opal.tufts.edu Subject: Program to calculate RIAs ????? Message-ID: <1994Mar3.162115.1@opal.tufts.edu> Lines: 14 Sender: news@news.tufts.edu (USENET News System) Organization: Tufts University - Medford, MA Date: Thu, 3 Mar 1994 21:21:15 GMT *** HELP *** Is there anyone out there who can tell me where I can find a computer program (IBM or Mac) for calculating radioimmunoassays (RIA). I am particularly interested in cyclic AMP RIAs. Since I rarely read the newsgroup, please send replies to: ryip@umassmed.ummed.edu Any information will be appreciated. Thanks!! Rupert Yip 508-856-2334 / 508-792-6796 From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.msfc.nasa.gov!cs.utk.edu!stc06r.CTD.ORNL.GOV!esdwmp.esd.ornl.gov!wmp From: wmp@esdwmp.esd.ornl.gov (Wilfred M. Post) Newsgroups: bionet.software Subject: Re: TWINSPAN Date: 3 Mar 1994 21:32:01 GMT Organization: ORNL-ESD Earth Sciences Modeling Center Lines: 19 Distribution: world Message-ID: <2l5l0h$fa7@stc06r.CTD.ORNL.GOV> References: <2l519h$k3s@crcnis1.unl.edu> NNTP-Posting-Host: esdwmp.esd.ornl.gov TWINSPAN is available in souce code and as an IBM-PC executable from Multivariate Analysis on the PC-ORD System August 1993 Version Bruce McCune Department of Botany & Plant Pathology Oregon State University Cordley Hall Corvallis Oregon 97331-2902 Orders: 503-737-1733 e-mail: mccuneb@bcc.orst.edu ------- W. M. Post wmp@ornl.gov From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!ysics.physics.sunysb.edu!news From: mhollowa@epo.som.sunysb.edu Newsgroups: bionet.software Subject: Windows Mosiac Help? Date: 3 Mar 1994 20:54:30 GMT Organization: SUNY@Stony Brook Lines: 18 Distribution: world Message-ID: <2l5iq6$la6@ysics.physics.sunysb.edu> NNTP-Posting-Host: cloner.pediatrics.sunysb.edu X-Newsreader: Since the folks distributing Windows Mosiac version 2 don't seem to be able to respond to user problems, I hoped that one of the bionauts pushing WWW could help with what, I assume, must be a fairly common problem. Mosiac crashes my system faster than anything I've ever experienced. Makes my head spin and its very frustrating. Trying to access the Blast server, for instance, brings an instant crash. Windows reports errors in various running applications and then in user.exe. Removing the applications doesn't help. Very large sound files produce a blank screen and complete hang up. Everything seems to be set up correctly. Wnqvt and Hgopher work fine. I'm running Trumpet Winsock 1a, latest version. As far as I can tell, Windows Mosiac is useless. I can't see or access anything past a few gopher sites or homepages. Mike Holloway mhollowa@epo.som.sunysb.edu From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!GREEN.DFCI.HARVARD.EDU!agustin From: agustin@GREEN.DFCI.HARVARD.EDU Newsgroups: bionet.software Subject: AA --> pI ? Date: 3 Mar 1994 19:00:56 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403031901.AA02704@green.dfci.harvard.edu> NNTP-Posting-Host: net.bio.net Dear fellow Networkers, Does anybody know a program (for DOS/Windows, Mac or UNIX) that calculates with a given amino acid sequence the pI ? Thanks a lot! Agustin =================================================== Agustin de la Calle Dana-Farber Cancer Institute Harvard Medical School agustin@green.dfci.harvard.edu =================================================== From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!bembidion.agforbes.arizona.edu!user From: dmaddsn@ccit.arizona.edu (David R. Maddison) Newsgroups: bionet.software Subject: Re: phylogenetic trees Followup-To: bionet.software Date: 3 Mar 1994 17:53:13 GMT Organization: University of Arizona Lines: 34 Message-ID: References: NNTP-Posting-Host: bembidion.agforbes.arizona.edu In article , Glenn Brooke, Ph.D. wrote: > Aside from the program suite PHYLIP, does anyone have suggestions > for software to take short (<150) nucleotide sequences and create > phylogenetic trees? Preferred platform in Macintosh, but we have > unix and PCs available. Thanks in advance, > Some of the software you might consider on the Mac is: * PAUP (parsimony & Lake's Invariants, diverse array of features, by far the most comprehensive of parsimony-based tree inference programs) Author: David Swofford Contact: paup@onyx.si.edu. (I think distribution is still in limbo) * MacClade (parsimony based, intended less for tree inference and more for examining character evolution, manipulating trees, entering data, producing graphics, etc.) Authors: Wayne Maddison & David Maddison Contact: biology@world.std.com (Sinauer Associates) On the PC side I would consider looking at MEGA (various distance methods, parsimony) HENNIG86 (parsimony based; very fast but fewer features) CLADOS (parsimony based, more for looking at character evolution and graphics) NTSYS (various distance methods) COMPONENT (various important tree analyses; not for tree inference) There's more but these are the more widely distributed ones that come to mind at the moment. Check out the PHYLIP documentation for more details. From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Subject: Re: Phone number Message-ID: <1994Mar3.162524.4514@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: Tin 1.1 PL4 References: <9403030115.AA01685@speedy.speedy.coacade.uv.mx> Distribution: bionet Date: Thu, 3 Mar 94 16:25:24 GMT Lines: 26 evargas@SPEEDY.COACADE.UV.MX (Enrique Vargas) writes: : Hi! : I want to know if somebody can send me the Tai Te Wu, George Johnson : or the Kabat database administrators phone number for ask them: : When this database is available again by INTERNET? : Thanks in advance. : ******************************************************************************* : * Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * : ******************************************************************************* : * Laboratorio de Biologia Molecular * Phone number: (28)125757 * : * e Inmunologia Teorica. * FAX number: (28)125757 * : ******************************************************************************* : * Instituto de Investigaciones Biologicas * Universidad Veracruzana * : * * Xalapa, Veracruz; Mexico. * : ******************************************************************************* The Kabat database is available by anonymous FTP to: ncbi.nlm.nih.gov Change to the directory 'repository'. The Kabat files are under the subdirectory 'kabat'. Regards, Dennis Benson NCBI From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!zorzal.edu.ar!bd4a From: bd4a@zorzal.edu.ar (Diego M.Burrieza LU 674/90) Newsgroups: bionet.software Subject: Symphony ---> 123 Converter Date: 3 Mar 1994 22:26:59 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Hi all, I am writing this in behalf of a friend. She has got a disk full of files made with Symphony. Her hard drive crashed down two days ago, and when she went to re-install the program, she realized that the #*&$^$@# of his brother had erased them. She need to use the files urgently and she has no way of getting Symphony soon. She has 123, Quattro Pro and Excel. If you know about a ShareWare file converter from Symphony format to one of the mentioned, I'm sure that she will be very pleased. If you consider appropriate to zip and uuencode, you can send it to my Email box. Since now, thank you for your time and good will. I remain, sincerely yours, Diego M. Burrieza Undergraduate Student Faculty of Exact and Natural Sciences University of Buenos Aires Argentina InterNet: bd4a@zorzal.edu.ar From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!SPEEDY.COACADE.UV.MX!evargas From: evargas@SPEEDY.COACADE.UV.MX (Enrique Vargas) Newsgroups: bionet.software Subject: Phone number Date: 3 Mar 1994 01:08:54 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403030115.AA01685@speedy.speedy.coacade.uv.mx> NNTP-Posting-Host: net.bio.net Hi! I want to know if somebody can send me the Tai Te Wu, George Johnson or the Kabat database administrators phone number for ask them: When this database is available again by INTERNET? Thanks in advance. ******************************************************************************* * Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * ******************************************************************************* * Laboratorio de Biologia Molecular * Phone number: (28)125757 * * e Inmunologia Teorica. * FAX number: (28)125757 * ******************************************************************************* * Instituto de Investigaciones Biologicas * Universidad Veracruzana * * * Xalapa, Veracruz; Mexico. * ******************************************************************************* From owner-software@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!dockmaster.phantom.com!scorpion From: scorpion@mindvox.phantom.com (Ernesto Alvarez) Newsgroups: bionet.software Subject: program looking for Date: Thu, 03 Mar 94 16:45:38 EST Organization: [MindVox] / Phantom Access Technologies / (+1 800-MindVox) Lines: 5 Distribution: world Message-ID: NNTP-Posting-Host: mindvox.phantom.com Originator: scorpion@mindvox Hi anyone knows a program the name I think is [QUIZ] in some Temp agencies they used this program to test people in diferent areas like in wordperfect and speed etc, I would like to find this program so I can test my self thanks to every one From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!news-feed-2.peachnet.edu!emory!nigel.msen.com!math.fu-berlin.de!GSF.DE From: WJST@GSF.DE (Matthias Wjst) Subject: Re: Symphony ---> 123 Converter Message-ID: <19940304102410.WJST@GSF.DE> Sender: news@math.fu-berlin.de (Math Department) Nntp-Posting-Host: 146.107.56.73 Organization: All opinions are my own, not by the GSF X-Newsreader: FTPNuz (DOS) v1.0 References: Date: Fri, 4 Mar 1994 09:24:00 GMT Lines: 93 In Article "bd4a@zorzal.edu.ar (Diego M.Burrieza LU 674/90)" says: > Hi all, > I am writing this in behalf of a friend. She has got a disk full > of files made with Symphony. Her hard drive crashed down two days ago, and > when she went to re-install the program, she realized that the #*&$^$@# of > his brother had erased them. She need to use the files urgently and she has > no way of getting Symphony soon. She has 123, Quattro Pro and Excel. If you > know about a ShareWare file converter from Symphony format to one of the > mentioned, I'm sure that she will be very pleased. If you consider > appropriate to zip and uuencode, you can send it to my Email box. > Since now, thank you for your time and good will. > I remain, sincerely yours, > There is an ultimative software package for file conversion, called DBMSCOPY. It is sold by Conceptual Software, Inc., P.O. Box 56627, Houston, TX 77256 (713) 667-4222 or (713) 667-3FAX, however, not free :-( The following formats are supported (Sept 1990): wks lotus 1 a 3 1 1-2-3 (.WKS) wk1 lotus 1 a 3 1 1-2-3 V2 (.WK1) dif dif 1 a 3 1 DIF xls excel 1 a 3 1 Excel slk sylk 1 a 3 1 Multiplan SYLK Files wkq lotus 1 a 3 1 Quattro (.WKQ) wrk lotus 1 a 3 1 Symphony V1 (.WRK) wr1 lotus 1 a 3 1 Symphony V1.1 (.WR1) dbf db3sq 1 b 3 1 Alpha IV Database clarion clarion 1 b 3 1 Clarion dbf db3sq 1 b 3 1 Clipper dease dease 1 b 3 0 DataEase (System/Form) dbm dease 1 b 3 0 DataEase (Forms Direct) 2.5 dbm4 dease 1 b 3 0 DataEase (Forms Direct) 4.0 dbase2 db3sq 1 b 3 1 dBase II dbf db3sq 1 b 3 1 dBase III dbase4 db3sq 1 b 3 1 dBase IV dbf db3sq 1 b 3 1 dBXL dbf db3sq 1 b 3 1 FoxBASE db paradox2 1 b 3 1 Paradox dta pcfile 1 b 3 1 PC-File pfs pfs 1 b 1 1 PFS:File dbs prodassq 1 b 3 1 PRODAS rbf rbase 1 b 3 0 Rbase V rxd reflex 1 b 3 1 Reflex ssd saspc 1 b 3 1 SAS/PC smartdb smartdb 1 b 3 1 Smartware Database ab6 abstat 1 c 3 1 ABstat (.AB6) ab8 abstat 1 c 3 1 ABstat (.AB8) across across 1 c 2 1 Across bass bass 1 c 3 1 Bass bmdp bmdp 1 c 3 1 BMDP css css 1 c 3 1 CSS bdf egret 1 c 3 1 EGRET rec epiinfo 1 c 3 1 EpiInfo gauss gauss 1 c 3 1 Gauss glm glim 1 c 2 1 Glim mii msii 1 c 3 1 MicroStat-II mtw minitab 1 c 3 1 Minitab ncss solo 1 c 3 0 NCSS dbs prodassq 1 c 3 1 PRODAS ssd saspc 1 c 3 1 SAS/PC sca sca 1 c 3 1 SCA solo solo 1 c 3 1 Solo spss spss 1 c 3 1 SPSS/PC stata stata 1 c 3 1 Stata asf stsc 1 c 3 1 StatGraphics statpac statpac 1 c 3 1 StatPac stp statplan 1 c 3 1 StatPlan III systat systat 1 c 3 1 SYSTAT ystat ystat 1 c 3 1 YStat datalex datalex 1 d 1 1 Datalex EntryPoint 90 dcs act 1 e 1 1 ACT! Activity Files lcs act 1 e 1 1 ACT! History Files 4c$ 4cast2 1 f 3 0 4CaST/2 autobox autobox 1 f 2 0 Autobox autocast 4cast2 1 f 3 0 Autocast uni forecast 1 f 3 0 Forecast Pro probe probe 1 f 3 0 Probe rat rats 1 f 3 0 Rats sal soritec 1 f 3 0 Soritec sasport5 sasport5 1 g 3 1 SAS Transport V5 sasport sasport 1 g 3 1 SAS Transport V6 sascomp sasport 1 g 3 1 SAS Transport V6 Compressed gra sigmaplo 1 h 3 1 SigmaPlot jbd sigmaplo 1 h 3 1 SigmaScan sygraph systat 1 h 3 1 SYGRAPH inform informix 0 i 3 0 Informix ingres ingres 0 i 3 0 Ingres oracle oracle 0 i 3 0 Oracle ascii2 ascii 1 j 3 1 ASCII Character Files ascii ascii 1 z 3 1 ASCII --Regards, Matthias From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Subject: Re: want software ideas Message-ID: Keywords: n Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia References: <2kp61f$ln0@ysics.physics.sunysb.edu> Date: Sun, 27 Feb 1994 17:10:17 GMT Lines: 24 In article <2kp61f$ln0@ysics.physics.sunysb.edu>, wrote: > >... It >wouldn't even have to be the mega-package they're selling for > $1000. I >suspect that for every lab that's going to spend $1000 on a multifunction >package there will be more than 10 labs that will spend $100 on a part of >that package, or on something that hasn't cost the programer as much to >produce. Look at the numbers. The NIH gives out about 25,000 grants total every year. I doubt whether 20% of those are to molecular biologists, but lets assume that's the number. That's 5000 potential US customers - max - at market saturation (which will never happen). Consider the costs for programmers, secretary, advertising, possible sales force, etc and the maximum $500,000 that you would get from your $100 package disappears very quickly. And then, what about year 2? The only sophisticated software products on the market that cost < $500 sell in the 1,000,000's of units. Almost any product that sells in the 1,000's of units, requires substantial support and sophisticated programming sells for > $10,000. Bill Pearson From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!pipex!uknet!lyra.csx.cam.ac.uk!pavo.csi.cam.ac.uk!camcus!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Subject: Re: AA --> pI ? Message-ID: <1994Mar4.100854.881@infodev.cam.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: grus.cus.cam.ac.uk Organization: U of Cambridge, England References: <9403031901.AA02704@green.dfci.harvard.edu> Distribution: bionet Date: Fri, 4 Mar 1994 10:08:54 GMT Lines: 36 In article <9403031901.AA02704@green.dfci.harvard.edu>, agustin@GREEN.DFCI.HARVARD.EDU writes: |> Dear fellow Networkers, |> |> Does anybody know a program (for DOS/Windows, Mac or UNIX) that |> calculates with a given amino acid sequence the pI ? |> Thanks a lot! |> Agustin |> |> =================================================== |> |> Agustin de la Calle |> Dana-Farber Cancer Institute |> Harvard Medical School |> |> agustin@green.dfci.harvard.edu |> =================================================== You can do it with the gcg package - isolectric does it well, with a PS file output: " Isoelectric plots the charge as a function of pH for any peptide sequence. " Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!caen!usenet.coe.montana.edu!netnews.nwnet.net!ns1.nodak.edu!plains!mcclean From: mcclean@plains.NoDak.edu (Phillip McClean) Subject: Re: Mac tto PC shareware? Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Thu, 3 Mar 1994 19:03:09 GMT References: <2kt68f$apt@canopus.cc.umanitoba.ca> Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 31 Andre Hamel (hamel@cc.umanitoba.ca) wrote: : I have some Mac written text files sent to me from a colleague, but I have : MSDOS based PC. What software to use? Where can I get shareware for this : purpose? ... ftp sites? ... program name for me to search via archie or : gopher? : thanks much in advance : ******************** : Andre Hamel email: hamel@cc.umanitoba.ca : Manitoba Government Veterinary Services lab tel.: (204) 945-7630 : 545 University Crescent, FAX: (204) 945-8062 : Winnipeg, Manitoba, : CANADA R3T 5S6 ******************** You can obtain a program from ftp.cica.indiana.edu via anonymous ftp called MACSEE that will do exactly what you want. The directory location is pub/pc/win3/util The name of the file is macsee3d.zip. You will need to unzip it when you received the program. I believe it also comes packaged with a DOS version. Phil McClean mcclean@plains.nodak.edu If From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.belwue.de!news.uni-ulm.de!news From: S_DOLLINGE@rzmain.rz.uni-ulm.de (Dollinger Juergen) Newsgroups: bionet.software Subject: Re: Postscript Converter Date: 4 Mar 1994 23:10:18 GMT Organization: University of Ulm, Germany Lines: 11 Distribution: world Message-ID: <2l8f4q$9nh@wega.rz.uni-ulm.de> References: <2kkvss$o9d@mserv1.dl.ac.uk> NNTP-Posting-Host: main01.rz.uni-ulm.de X-News-Reader: VMS NEWS v1.25 In-Reply-To: mbkxb@s-crim1.dl.ac.uk's message of 25 Feb 1994 13:53:32 GMT mbkxb@s-crim1.dl.ac.uk writes: > Does anybody know of a program to convert a postscript file into a graphical > format file of some kind (TIFF, PICT etc). I'd prefer if it ran on a > Mac, but at my current stage of frustration, any platform will do. On Unix/X I use xv. Its a fine image viewer and converter for gif, Postscript, pbm, bmp, tiff, jpeg and a few other formats. You can get it via anonymous ftp from a lot of sites including info.rz.uni-ulm.de : /pub/misc/xv3.00.tar.z From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.software From: Duncan@genesys.demon.co.uk (Duncan Clark) Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!pipex!uknet!demon!genesys.demon.co.uk!Duncan Subject: Re: want software ideas Distribution: world References: Organization: GeneSys Ltd. Reply-To: Duncan@genesys.demon.co.uk X-Newsreader: Simple NEWS 1.90 (ka9q DIS 1.21) Lines: 19 Date: Fri, 4 Mar 1994 14:42:49 +0000 Message-ID: <762792169snz@genesys.demon.co.uk> Sender: usenet@demon.co.uk In article wrp@dayhoff.med.Virginia.EDU writes: > The only sophisticated software products on the market that >cost < $500 sell in the 1,000,000's of units. Almost any product that >sells in the 1,000's of units, requires substantial support and >sophisticated programming sells for > $10,000. I disagree. Graphit as sold by Sigma and direct from Erithacus Software sells for roughly $500 on quantities of a maybe 300-400 per year. The author is a one-man company doing it in his spare time (away from his lectureship). It is a very sophisticated windows program and is rated very highly. I have no financial interest in this company. Duncan -- ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys.demon.co.uk GeneSys Ltd. | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uknet!gdt!bsmail!irix!andmp From: andmp@irix.bris.ac.uk (David Pickles) Subject: Re: Symphony ---> 123 Converter Message-ID: Sender: usenet@info.bris.ac.uk (Usenet news owner) Nntp-Posting-Host: irix.bris.ac.uk Reply-To: D.M.Pickles@bristol.ac.uk Organization: University of Bristol, England X-Newsreader: TIN [version 1.2 PL1] References: Distribution: bionet Date: Fri, 4 Mar 1994 18:19:12 GMT Lines: 16 On 3 Mar 1994 22:26:59 -0000 Diego M.Burrieza LU 674/90 (bd4a@zorzal.edu.ar) wrote: |> no way of getting Symphony soon. She has 123, Quattro Pro and Excel. If you |> know about a ShareWare file converter from Symphony format to one of the |> mentioned, I'm sure that she will be very pleased. If you consider Well, this should be an easy one... my version of 123 (v2.4) comes with a Translate utility (access from the startup menu) which allows interconversion between Symphony (v1.0 - 2.2) and 123 amongst others. Regards David Pickles ----------------------------------------------------------------------------- JANET: D.M.Pickles@uk.ac.bristol INTERNET: D.M.Pickles@bristol.ac.uk ----------------------------------------------------------------------------- From owner-software@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!torn!utnut!utcsri!newsflash.concordia.ca!canopus.cc.umanitoba.ca!hamel From: hamel@cc.umanitoba.ca (Andre Hamel) Newsgroups: bionet.software Subject: Re: Mac tto PC shareware? Date: 4 Mar 1994 16:51:25 GMT Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 9 Message-ID: <2l7oud$m2o@canopus.cc.umanitoba.ca> References: <2kt68f$apt@canopus.cc.umanitoba.ca> NNTP-Posting-Host: castor.cc.umanitoba.ca Thanks to all who emailed & posted replies. ******************** Andre Hamel email: hamel@cc.umanitoba.ca Manitoba Government Veterinary Services lab tel.: (204) 945-7630 545 University Crescent, FAX: (204) 945-8062 Winnipeg, Manitoba, CANADA R3T 5S6 ******************** From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!cs.utexas.edu!swrinde!emory!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!gamera.umd.edu!carlf-mac.umd.edu!user From: fitz@cbl.umd.edu (Carl Fitz) Newsgroups: bionet.software Subject: Re: Windows Mosiac Help? Followup-To: bionet.software Date: Sat, 05 Mar 1994 10:23:33 -0500 Organization: Chesapeake Biol. Lab Lines: 18 Distribution: world Message-ID: References: <2l5iq6$la6@ysics.physics.sunysb.edu> NNTP-Posting-Host: carlf-mac.umd.edu In article <2l5iq6$la6@ysics.physics.sunysb.edu>, mhollowa@epo.som.sunysb.edu wrote: ...descriptions of computer crashing deleted.... > > As far as I can tell, Windows Mosiac is useless. I can't see or access > anything past a few gopher sites or homepages. > I'm sorry to hear that you're having such problems with Windows Mosaic. We run a mac version of Mosaic which is truly a great tool, without problems. Hopefully they will provide Windows fixes in the future, but Mosaic itself is a very nice concept and implementation - aside from Windows problems. -- H. Carl Fitz MIIEE, Univ. of Maryland fitz@cbl.umd.edu From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!lyra.csx.cam.ac.uk!pavo.csi.cam.ac.uk!mole.bio.cam.ac.uk!seb1005 From: seb1005@mole.bio.cam.ac.uk (Steven Brenner) Subject: Re: Best of WWW 94 Message-ID: <1994Mar5.011053.13215@infodev.cam.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: mole.bio.cam.ac.uk Organization: U of Cambridge, England References: <2kfnc4$dt8@mserv1.dl.ac.uk> Distribution: bionet Date: Sat, 5 Mar 1994 01:10:53 GMT Lines: 36 robison1@husc10.harvard.edu (Keith Robison) writes: >Murray-Rust Dr P writes: >> - HTML pages often tree structured and a user may wish to >>download the whole tree (this would be the case for a manual, for >>example). Is there a tool that does this, or does the implementer have >>to provide a (continuously updated) *.tar.Z of the whole resource? >There are some tools for this; unfortunately they are hard to find. >The lists of misc. tools at CERN & NCSA seem to be out of date. >There are some perl programs out there to fetch URLs -- they could >be built into such a "whole-tree fetcher" with a bit of work. >(Of course, if you are into truely baroque methods you could do >it all with the remote-control features of Mosaic!) A tree-fetcher (called w3get) was recently posted to comp.infosystems.www, and I think I have a copy of it. Note, however, that using such a system is very dangerous, as most-nontrivial trees on the net are in fact general webs which will eventuall point to virtually every other site. --- Perhaps the easiest way to get "text-only" versions of a given WWW page (other than using the save command in an interactive session of Mosaic or lynx) is to use "lynx -dump "; this sends the formatted page to stdout. Steven -- Steven E. Brenner | Department of Biochemistry S.E.Brenner@bioc.cam.ac.uk | University of Cambridge Lab +44 223 333671 | Tennis Court Road Fax +44 223 333345 | Cambridge CB2 1QW, UK From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!usc!usc!not-for-mail From: mkido@hsc.usc.edu (Mitsuru Kido) Newsgroups: bionet.software Subject: Help!, Re: Intron Splicing Rule Date: 4 Mar 1994 19:21:33 -0800 Organization: University of Southern California, Los Angeles, CA Lines: 11 Sender: mkido@hsc.usc.edu Distribution: usa Message-ID: <2l8trt$s8i@hsc.usc.edu> NNTP-Posting-Host: hsc.usc.edu Keywords: Intron, Splicing Hi, netter. In this newsgroup, somebody was looking for a software to predict exon-intron boundary from cDNA several month ago. Replying his request, a certain professor of Medical Genetics Department at Harvard University cited a reference, which describes detail rules of intron-splicing. Does somebody remember the reference? Might be Nucleic Acid Research. Mitsuru Kido mkido@hsc.usc.edu From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!nobody From: noronha@umbc.edu (Santosh Noronha) Newsgroups: bionet.software Subject: ESSYNS Date: 4 Mar 1994 23:45:36 -0500 Organization: University of Maryland, Baltimore County Lines: 13 Distribution: bionet Message-ID: <2l92pgINNs0l@umbc7.umbc.edu> NNTP-Posting-Host: umbc7.umbc.edu Hi! I'm looking for a piece of software called ESSYNS (evaluation and simulation of synergistic systems) used to model metabolic fluxes. I have been unable to locate it in the standard ftp sites. This package was developed for a PC by Dr. Douglas Irvine (Univ Colorado, Boulder), and i've been unable to contact him too. Has anybody seen that package out there or would anybody know how to get in touch with him? Thanx! Santosh Noronha noronha@coe1.engr.umbc.edu From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.dfn.de!gwdu03.gwdg.de!lince.mpib-tuebingen.mpg.de!user From: casal@mpbvax.mpib-tuebingen.mpg.de (Jose Casal) Subject: Re: phylogenetic trees Message-ID: Followup-To: bionet.software Sender: news@gwdu03.gwdg.de (USENET News System) Nntp-Posting-Host: lince.mpib-tuebingen.mpg.de Organization: MPI f. Entwicklungsbiologie References: Date: Fri, 4 Mar 1994 19:10:31 GMT Lines: 13 In article , Glenn Brooke, Ph.D. wrote: > Aside from the program suite PHYLIP, does anyone have suggestions > for software to take short (<150) nucleotide sequences and create > phylogenetic trees? Preferred platform in Macintosh, but we have > unix and PCs available. Thanks in advance, > Maybe you can try an E-mail server instead. Send a HELP message to CBRG@INF.ETHZ.CH. The PhyloTree and RootedTree outputs are postscript files that you can print using Apple's Laser Writer Utility. Good luck! From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!sol.ctr.columbia.edu!ucsnews!newshub.sdsu.edu!nic-nac.CSU.net!csulb.edu!paris.ics.uci.edu!news.claremont.edu!nntp-server.caltech.edu!imppig!ranabir From: ranabir@imppig.caltech.edu (Ranabir Sinha-Roy) Newsgroups: bionet.software Subject: CD deconvoluting software Date: 4 Mar 1994 18:56:06 GMT Organization: California Institute of Technology, Pasadena Lines: 12 Message-ID: <2l8086$osi@gap.cco.caltech.edu> NNTP-Posting-Host: imppig.caltech.edu X-Newsreader: NN version 6.5.0 #10 (NOV) Sorry if this is yet another FAQ. I need software that can deconvolute CD spectra of small peptides (15-20 mers) and return me a percentage of secondary structure contribution (x% helix, y% sheet etc.). I have used the LINCOMB package but was wondering if there is anything else in the PC/Mac/SGI shareware/commercial domain. I am interested in programs that use a decent basis set. Thanx in advance, Ranabir Sinha Roy p.s. Thanx to all who responded to my earlier post on ribbons. Molscript is up and running great! From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!usenet.ins.cwru.edu!neur21812.NEUR.CWRU.Edu!hxm8 From: hxm8@po.cwru.edu (Harry Menegay) Newsgroups: bionet.software Subject: Re: Windows Mosiac Help? Date: Sat, 5 Mar 1994 16:17:12 Organization: Case Western Reserve University - Dept of Neuroscience Lines: 30 Distribution: world Message-ID: References: <2l5iq6$la6@ysics.physics.sunysb.edu> NNTP-Posting-Host: neur21812.neur.cwru.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article fitz@cbl.umd.edu (Carl Fitz) writes: >From: fitz@cbl.umd.edu (Carl Fitz) >Subject: Re: Windows Mosiac Help? >Date: Sat, 05 Mar 1994 10:23:33 -0500 >In article <2l5iq6$la6@ysics.physics.sunysb.edu>, >mhollowa@epo.som.sunysb.edu wrote: >...descriptions of computer crashing deleted.... >> >> As far as I can tell, Windows Mosiac is useless. I can't see or access >> anything past a few gopher sites or homepages. >> >I'm sorry to hear that you're having such problems with Windows Mosaic. We >run a mac version of Mosaic which is truly a great tool, without problems. >Hopefully they will provide Windows fixes in the future, but Mosaic itself >is a very nice concept and implementation - aside from Windows problems. This is really a configuration problem, not a windows problem. I have been using Mosaic for Windows for a few months. It reqired only a few minutes to set up and has run without flaw on my machine. I don't think the software needs a re-write. I think that the configuration on that poster's machine had just not been set correctly. Harry Menegay Dept. of Neuroscience, CWRU hxm8@po.cwru.edu From owner-software@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!darkstar.UCSC.EDU!ra.UCSC.EDU!stefan From: stefan@ra.UCSC.EDU (Stefan Engstrom) Newsgroups: bionet.software Subject: Re: Postscript Converter Date: 5 Mar 1994 03:08:43 GMT Organization: UCO/Lick Observatory Lines: 22 Distribution: world Message-ID: <2l8t3r$ocu@darkstar.UCSC.EDU> References: <2kkvss$o9d@mserv1.dl.ac.uk> <2l8f4q$9nh@wega.rz.uni-ulm.de> NNTP-Posting-Host: ra.ucsc.edu X-Newsreader: TIN [version 1.2 PL2] Dollinger Juergen (S_DOLLINGE@rzmain.rz.uni-ulm.de) wrote: > mbkxb@s-crim1.dl.ac.uk writes: > > Does anybody know of a program to convert a postscript file into a graphical > > format file of some kind (TIFF, PICT etc). I'd prefer if it ran on a > > Mac, but at my current stage of frustration, any platform will do. > On Unix/X I use xv. Its a fine image viewer and converter for gif, Postscript, > pbm, bmp, tiff, jpeg and a few other formats. > You can get it via anonymous ftp from a lot of sites including > info.rz.uni-ulm.de : /pub/misc/xv3.00.tar.z If xv won't do that for you, try ghostscript! It will produce portable format pixmaps for you. -- / ( ? O stefan@lick.ucsc.edu (Stefan Engstrom) o ) () / || From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!ysics.physics.sunysb.edu!NewsWatcher!user From: sbbiovm.sunysb.edu (Ing-Nang Wang) Newsgroups: bionet.software Subject: Re: ESSYNS Followup-To: bionet.software Date: Sun, 06 Mar 1994 10:15:52 -0500 Organization: Dept. of Ecology and Evolution Lines: 27 Distribution: bionet Message-ID: References: <2l92pgINNs0l@umbc7.umbc.edu> NNTP-Posting-Host: 129.49.19.31 In article <2l92pgINNs0l@umbc7.umbc.edu>, noronha@umbc.edu (Santosh Noronha) wrote: > Hi! > I'm looking for a piece of software called ESSYNS (evaluation and > simulation of synergistic systems) used to model metabolic fluxes. I have > been unable to locate it in the standard ftp sites. This package was > developed for a PC by Dr. Douglas Irvine (Univ Colorado, Boulder), and i've > been unable to contact him too. Has anybody seen that package out there or > would anybody know how to get in touch with him? > Thanx! > Santosh Noronha > noronha@coe1.engr.umbc.edu I don't think ESSYSN is freely available on the net. You have to purchase it from Dr. M.A. Savageau, who is in Department of Microbiology (?), University of Michigan, Ann Arbor. Check out the apendix of "Control of metabolic processes" ed. by A. Cornish-Bowden and M. L. Cardenase (1990) for details. cheers, -- Ing-Nang Wang ingnang@sbbiovm.sunysb.edu Dept. Ecology and Evolution SUNY-Stony Brook Stony Brook, NY 11974 From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!LAS.SINICA.EDU.TW!mbyhsun%ccvax.dnet From: mbyhsun%ccvax.dnet@LAS.SINICA.EDU.TW Newsgroups: bionet.software Subject: help on BinHex Date: 6 Mar 1994 06:35:19 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403062236.AA18220@las.sinica.edu.tw> NNTP-Posting-Host: net.bio.net Dear Netters: I have ftp some .hqx files (text mode) through our campus computer center, then kermit to my Mac. When I use BinHex to decode, I got the message: CRC($0000) error. What is wrong? Please help. Henry Sun From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!ysics.physics.sunysb.edu!news From: mhollowa@epo.som.sunysb.edu Newsgroups: bionet.software Subject: Re: Windows Mosiac Help? Date: 6 Mar 1994 03:24:40 GMT Organization: SUNY@Stony Brook Lines: 23 Distribution: world Message-ID: <2lbido$62b@ysics.physics.sunysb.edu> NNTP-Posting-Host: cloner.pediatrics.sunysb.edu X-Newsreader: In article hxm8@po.cwru.edu (Harry Menegay) writes: >I don't think the software >needs a re-write. I think that the configuration on that poster's machine had >just not been set correctly. Well, I don't know what's going on, but I don't think that there's anything necessarily wrong with the way I set up the packet drivers and Winsock. Why would wnqvt and hgopher be working so well? No, this is Mosiac specific. You implied in your mail message that you don't use Novell odi. What packet driver are you using? I could try to use the Microsoft TCP/IP winsock with the Novell odinsup and see how that fares. Maybe Mosiac is balking at something having to do with the combination of Trumpet Winsock and Novell drivers. Is there anyone out there using odi and Trumpet Winsock? I can't believe that I'm the first to try this combination. Thanks for any clues, Mike Holloway mhollowa@epo.som.sunysb.edu From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!darwin.sura.net!nuance.com!not-for-mail From: krc@moontarz.nuance.com (King Research Corporation) Newsgroups: bionet.software Subject: Database access Date: 5 Mar 1994 17:33:52 -0600 Organization: Nuance Network Services, Huntsville, AL Lines: 14 Message-ID: <2lb4t0$a4e@moontarz.nuance.com> NNTP-Posting-Host: moontarz.nuance.com Keywords: Database access, SQL, internet I am trying to find out what access methods are possible for the various genome databases on the internet. I know GDB has a database server but I'm not sure about the others. Anyone who has any information that you could send me, it would be greatly appreciated. Please mail any info to krc@nuance.com Thanks, Bill Chandler -- **************************************************************************** * Bill Chandler King Research Corporation * * Email: krc@nuance.com * **************************************************************************** From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!batcomputer!cornell!newsstand.cit.cornell.edu!root From: douglas l feinstein Newsgroups: bionet.software Subject: Enzyme Kinetics Modelling Date: 6 Mar 1994 21:10:26 GMT Organization: cornell university medical college Lines: 13 Distribution: world Message-ID: <2ldgs2INNcat@newsstand.cit.cornell.edu> NNTP-Posting-Host: guru.med.cornell.edu X-UserAgent: Version 1.1.3 X-XXDate: Sun, 6 Mar 94 16:12:02 GMT Is there any Mac (preferrably), or DOS software available to determine Km and Vmax values for various enzyme systems? In particular user defined systems fairly more complicated than the typical M-M equation. We need to model a 2 enzyme, 2 product system in which product 1 is the substrate for enzyme 2, and we can measure all substrates and products. Any help grately appreciated. dlf Doug Feinstein | Voice: 212 570-2900 Dept Neurobiology | Fax: 212 988-3672 Cornell University Medical College | E-mail: dlfeins@cumc.cornell.edu We're not the best at what we do, but we're the only ones who do it... From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!ihnp4.ucsd.edu!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!chih-che From: chih-che@cae.wisc.edu (Chih-Che Lin) Newsgroups: bionet.software Subject: Software Idea wanted Date: 6 Mar 1994 21:11:31 GMT Organization: U of Wisconsin-Madison College of Engineering Lines: 20 Sender: chih-che@cae.wisc.edu (Chih - Che Lin) Distribution: world Message-ID: <2ldgu3$83v@news.doit.wisc.edu> NNTP-Posting-Host: sun-37.cae.wisc.edu Hi netters, We want to do some simulations in tRNA by using Smirnov statistic based on the paper by Hugh B. Nicholas Jr and Spencer B. Graves, Clustering of Transfer RNAs by Cell Type and Amino Acid Specificity. Is there anyone out there having some ideas about software that regarding Smirnov statistic? ------------------------------------------------------------------------ | Chih-Che (Gary) Lin | | Dept. of Bacteriology | | University of Wisconsin -- Madison | | E-mail: chih-che@cae.wisc.edu | | | ------------------------------------------------------------------------ From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uwm.edu!fnnews.fnal.gov!att-in!news.cs.indiana.edu!lynx.unm.edu!carina.unm.edu!news-user From: tmalecki@unm.edu (tinalyn marie malecki) Newsgroups: bionet.software,comp.edu,sci.edu,sci.stat.edu Subject: scientific graphing software Date: 6 Mar 1994 13:56:39 -0700 Organization: University of New Mexico, Albuquerque Lines: 19 Distribution: na Message-ID: <2ldg27$anr@carina.unm.edu> NNTP-Posting-Host: carina.unm.edu Xref: biosci bionet.software:7491 comp.edu:2364 sci.edu:2065 sci.stat.edu:840 Hello! I am looking for a software package that has scientific graphing capabilities (e.g., varied charts and diagram types with labeling options, font variation, size variation, data range varation, etc.). I have looked at Mathematica and it looks promising, yet, being familiar with QuatroPro, Mathematica's graphing capabilities fall far short of those of Quatro Pro's. Can anyone direct me to a scientific--or scientific-like--software package that has robust graphing abilities? Is f(g)scholar such a package? Any advice will be appreciated. Thank you! Best wishes, From owner-software@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!saimiri.primate.wisc.edu!caen!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.belwue.de!news.uni-ulm.de!news From: S_DOLLINGE@rzmain.rz.uni-ulm.de (Dollinger Juergen) Newsgroups: bionet.software Subject: Re: Multiple choice marking software Date: 6 Mar 1994 20:19:41 GMT Organization: University of Ulm, Germany Lines: 14 Distribution: world Message-ID: <2lddst$5ul@wega.rz.uni-ulm.de> References: <2kkugm$nqt@mserv1.dl.ac.uk> NNTP-Posting-Host: main01.rz.uni-ulm.de X-News-Reader: VMS NEWS v1.25 In-Reply-To: bssjrb@midge.bath.ac.uk's message of 25 Feb 1994 13:29:58 -0000 In <2kkugm$nqt@mserv1.dl.ac.uk> bssjrb@midge.bath.ac.uk writes: > descriminate. At present we have to edit the data files on the PC, transfer > them to the mainframe and then use a most unfriendly and inflexible > program to analyse the data. What kind of operating system do you use on your PC? Linux?, OS/2?, Windows NT? What should the