From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!bcm!jpower From: jpower@kiwi.imgen.bcm.tmc.edu (Joanna L. Power) Newsgroups: bionet.molbio.gdb,bionet.software Subject: GDB frontend software Keywords: gdb x interface Message-ID: <211pon$erq@gazette.bcm.tmc.edu> Date: 2 Jul 93 17:03:19 GMT Organization: Molecular Biology Information Resource, Baylor College of Medicine, Houston, Tx Lines: 36 Xref: biosci bionet.molbio.gdb:75 bionet.software:5384 NNTP-Posting-Host: kiwi.imgen.bcm.tmc.edu Originator: jpower@kiwi.imgen.bcm.tmc.edu Is anyone out there successfully using the gdb frontend software on xterms? I am having a bizarre problem with the DISPLAY variable. First, DISPLAY must be set as an IP address instead of as a machine name. I can handle that. The second problem is more troublesome, as our goal is to set this up for users who may be intimidated by the process in general. The problem: After I set DISPLAY in the initialization script, the user must still select "Change Terminal Environment" from the main menu, then "Change $DISPLAY Variable" from the next menu. The variable I set in the initialization script is there as the default, but it is not actually set until the user accepts it. My goal is to arrange it so that the user does not have to navigate through these menus merely to hit return and accept the proper value for DISPLAY. Any ideas? Please feel free to reply be e-mail if this request does not seem of general enough interest. -- Joanna Power Genome Center Informatics Core | jpower@bcm.tmc.edu Baylor College of Medicine | 1 Baylor Plaza | voice: 713-798-4689 Houston, TX 77030 | fax: 713-798-5386 -- -- Joanna Power From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software Subject: Re: Molecular Weight search software wanted Message-ID: Date: 3 Jul 93 00:09:07 GMT References: <1993Jun30.165111.27075@comp.bioz.unibas.ch> Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 759 NNTP-Posting-Host: s-crim1.dl.ac.uk In-reply-to: doelz@comp.bioz.unibas.ch's message of Wed, 30 Jun 1993 16:51:11 GMT Reinhard asked a question about molecular weight searching. Such software is available on the UK EMBnet node and will be made available via an email server in the next few days. I append a software description below. Details of the software can be found in the last issue of Current Biology Rgds Alan Bleasby ?RC Daresbury Laboratory Warrington WA4 4AD UK Daresbury is the UK EMBnet national node. MOWSE MANUAL Version 1.0 D.J.C.Pappin and A.J.Bleasby [1] Introduction: [2] Construction of the MOWSE database. [2.1] Source database. [2.2] Calculation of Molecular weight fragments. [2.3] MOWSE database structure. [2.4] The MW primary fragment molecular weight file. [2.5] The MDX file OWL entry index. [2.6] The SMW whole sequence molecular weight file. [2.7] Program Requirements. [2.8] MOWSE Scoring scheme. [2.9] Simulation studies. [3] References. [4] Running database searches. [4.1] Mw data file. [4.2] Running the program. [5] Results listing. [5.1] Specified search parameters. [5.2] Short 'hit' listing. [5.3] Detailed 'hit' listing. [5.4] Example of output listing. [1] Introduction: Determination of molecular weight has always been an important aspect of the characterization of biological molecules. Protein molecular weight data, historically obtained by SDS gel electrophoresis or gel permeation chromatography, has been used to establish purity, detect post-translational modification (such as phosphorylation or glycosylation) and aid identification. Until just over a decade ago, mass spectrometric techniques were limited to relatively small biomolecules, as proteins and nucleic acids were too large and fragile to withstand the harsh physical processes required to induce ionization. This began to change with the development of 'soft' ionization methods such as fast atom bombardment (FAB)[1], electrospray ionisation (ESI) [2,3] and matrix-assisted laser desorption ionisation (MALDI)[4], which can effect the efficient transition of large macromolecules from solution or solid crystalline state into intact, naked molecular ions in the gas phase. As an added bonus to the protein chemist, sample handling requirements are minimal and the amounts required for MS analysis are in the same range, or less, than existing analytical methods. As well as providing accurate mass information for intact proteins, such techniques have been routinely used to produce accurate peptide molecular weight 'fingerprint' maps following digestion of known proteins with specific proteases. Such maps have been used to confirm protein sequences (allowing the detection of errors of translation, mutation or insertion), characterise post-translational modifications or processing events and assign disulphide bonds [5,6]. Less well appreciated, however, is the extent to which such peptide mass information can provide a 'fingerprint' signature sufficiently discriminating to allow for the unique and rapid identification of unknown sample proteins, independent of other analytical methods such as protein sequence analysis. The following text describes the construction and development of the MOWSE peptide mass database (for MOlecular Weight SEarch) at the SERC Daresbury Laboratory. Practical experience has shown that sample proteins can be uniquely identified using as few as 3- 4 experimentally determined peptide masses when screened against a fragment database derived from over 50,000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino acid composition or linear sequence, peptide masses can clearly provide a set of determinants sufficiently unique to identify or match unknown sample proteins. Peptide mass fingerprints can prove as discriminating as linear peptide sequence, but can be obtained in a fraction of the time using less material. In many cases, this allows for a rapid identification of a sample protein before committing to protein sequence analysis. Fragment masses also provide structural information, at the protein level, fully complementary to large-scale DNA sequencing or mapping projects [7,8,9]. [2] Construction of the MOWSE database. [2.1] Source database. MOWSE was created from the OWL non-redundant composite protein sequence database [10,11]. The latest release (version 18.1) contains 51,093 protein entries (comprising some 15,956,287 residues), derived from: Residues Entries SWISSPROT Rel 22 25044 8375696 NBRF Rel 33(PIR 1) 942 374576 NBRF Rel 33(PIR 2) 4660 1122905 NBRF Rel 33(PIR 3) 7688 2200541 GenBank Rel 72 8200 2601590 NRL_3D Rel 9 (June 1992) 1352 224520 [2.2] Calculation of Molecular weight fragments. For each entry in the source OWL database, MOWSE derives both whole sequence molecular weight and calculated peptide molecular weights for complete digests using the range of cleavage reagents and rules detailed in Table 1. Cleavage is disallowed if the target residue is followed by proline (except for CNBr or Asp N). Glu C (S. aureus V8 protease) cleavages are also inhibited if the adjacent residue is glutamic acid. Peptide mass calculations are based entirely on the linear sequence and use the average isotopic masses of amide-bonded amino acid residues (IUPAC 1987 relative atomic masses). To allow for N-terminal hydrogen and C-terminal hydroxyl the final calculated molecular weight of a peptide of N residues is given by the equation: N S residue mass + 18.0153 n=1 Molecular weights are rounded to the nearest integer value before being entered into the database. Cysteine residues are calculated as the free thiol, anticipating that samples are reduced prior to mass analysis. CNBr fragments are calculated as the homoserine lactone form. Information relating to post- translational modification (phosphorylation, glycosylation etc.) is not incorporated into calculation of peptide masses. Reagent no. Reagent Cleavage rule Total peptides 1 Trypsin C-term to K/R 1711729 2 Lys C C-term to K 922337 3 Arg C C-term to R 835392 4 Asp N N-term to D 835002 5 Glu C (Bicarbonate) C-term to E 915708 6 " (Phosphate) C-term to E/D 1793285 7 Chymotrypsin C-term to F/W/Y/L/M 3047947 8 CNBr C-term to M 392924 Table 1: Cleavage reagents modelled by MOWSE. [2.3] MOWSE database structure. The database consists of three binary files: i) MOWSE.MW The primary file containing the fragment molecular weights. ii) MOWSE.MDX Index file relating OWL identifier codes to the molecular weight information in the primary Mw file. iii) MOWSE.SMW Calculated molecular weights of intact OWL sequences. The query program accesses the binary information transparently from the user viewpoint. In the internal representation the molecular weight (and other) integers are stored as 4-byte machine specific quantities. The binary files can be transferred between machines of the same 'endian' nature, but 'cross-endian' transfer is not possible. The MOWSE software allows recreation of the files on any platform supporting a standard C language compiler. The organisation of the database files is described below. [2.4] The MW primary fragment molecular weight file. Fragment molecular weight entries in this file map sequentially to the order of entries within the source (OWL) protein sequence file. Each MW file entry consists of 4 blocks and are shown below. The MW entries are catenated. Block 1 OWL Entry Code 20 bytes Block 2 OWL Title Line 80 bytes Block 3 Reagent Table 80 bytes Block 4 Reagent 1 4 byte Reag From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!redid.org.do!indotec!frichard From: indotec!frichard@redid.org.do ("Frank Richardson") Newsgroups: bionet.software Subject: looking for algae culture media software Message-ID: <2c344ad0._indotec@indotec.redid.org.do> Date: 2 Jul 93 15:29:09 GMT Sender: daemon@net.bio.net Reply-To: "Frank Richardson" Distribution: bionet Lines: 19 -------------------- Is there any software available (database) that allow me to find specific culture media for algae. The software should be able to run on IBM compatibles. I need it in order to find a selective culture media for Chroococcus sp., an sphaerical non colonial blue green. Frank Frank Richardson Phone : (809) 566-8121 (ext 264) indotec!frichard@redid.org.do Home : (809) 596-6801 Fax : (809) 540-2808 or 2809 Address: INDOTEC, attn: Frank Richardson P.O. Box 329-2, Sto. Dgo. DOMINICAN REPUBLIC From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: Sebastian.Bunka@vu-wien.ac.at (Bunka Sebastian) Newsgroups: bionet.software Subject: RE: database for clones Message-ID: <1993Jul2.131719.15700@gserv1.dl.ac.uk> Date: 2 Jul 93 12:43:31 GMT Sender: I102PC1@at.ac.vu-wien.edvznovell2 Distribution: bionet Organization: Vet.Med.Uni Wien Lines: 51 Original-To: bio-soft@uk.ac.daresbury Priority: normal X-Mailer: WinPMail v1.0 (R1) >Newsgroups: bionet.software >Path: alijku05!alijku11!news.univie.ac.at!paladin.american.edu!howland.resto n.ans.net!sol.ctr.columbia.edu!news.columbia.edu!cubmol!pw >From: pw@cubmol.bio.columbia.edu (Paul Wakenight) >Subject: database for strains, etc? >Message-ID: <1993Jun29.000050.2164@news.columbia.edu> >Sender: usenet@news.columbia.edu (The Network News) >Nntp-Posting-Host: cubmol.bio.columbia.edu >Organization: Columbia University, Dept. of Biological Sciences. >Distribution: bionet.software >Date: Tue, 29 Jun 1993 00:00:50 GMT >Lines: 8 >Is there any software available ( database ) that would allow one to >keep track of cell lines, etc. etc. >Thanks much. >Paul there are some good PD programs available: FTP felix.embl-heidelberg.de somewhere in PUB/MSDOS filename dnaclone.uaa update 16-Mar-1990 version 1.1 size 190 k compressed PAK ASCII conversion UUE (split; 3 parts: .UAA to .UAC) author Roy T. K. description Management of clones, strains, libraries etc. databases literature CABIOS 5 (1989), 321-322 an other file is clones.uaa... If you need a copy, I can send it to you by e-mail file attachment ... ps. you need the uudecode programs ! SB +------------------------------------------------------------------+ |Dr. Sebastian Bunka Email: Sebastian.Bunka@vu-wien.ac.at | |Inst.f.Bakteriologie | |Vet.Med.Uni Wien Phone: +43-1-71155/261 | |Linke Bahngasse 11 Fax: +43-1-71 49 110 | |A-1030 Wien | +------------------------------------------------------------------+ From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: JRAMON@mvax.fmed.uam.es Newsgroups: bionet.software Subject: Re: Digital Signature Standard Message-ID: <1993Jul2.094024.11798@gserv1.dl.ac.uk> Date: 2 Jul 93 11:41:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 181 X-Organization: Universidad Autonoma de Madrid (UAM) X-Envelope-To: bio-software@daresbury.ac.uk Original-To: bio-software@uk.ac.daresbury X-Vms-To: IN"bio-software@daresbury.ac.uk" Comments: Pasarela de correo electronico local Internet<->DECnet de la UAM With respect to the problem of the Digital Signature Standard, while it concerns mainly the USA (.gov and .people), I'd like to add some comments of my own. First, I'm not too literate on encription algorithms, neither the legal issues concerning them abroad the USA. But may this affect me, it interests me. >... >Several years ago, Congress directed the NIST (National Institute of >Standards and Technology, formerly the National Bureau of Standards) >to choose a single digital signature algorithm as a standard for the >US. > >In 1992, two algorithms were under consideration. One had been >developed by NIST with advice from the NSA (National Security Agency), >which engages in electronic spying and decoding. There was widespread >suspicion that this algorithm had been designed to facilitate some >sort of trickery. > >The fact that NIST had applied for a patent on this algorithm >engendered additional suspicion,... IMHO, governments shouldn't interfere with individual rights, but if they must guarantee them they must have the right to *some times* ***violate*** them (e.g. depriving criminals of liberty). It is the role of the people to control the government so that it doesn't make bad use of its powers. However, there still remains the moral issue of what happens when the gov. is stronger than the people. For instance in many underdevelopped countries *ultimately owned* by another country or commercial company. >... >On June 8, NIST published a new plan which combines the worst of both >worlds: to adopt the suspect NIST algorithm, and give PKP, Inc. an >*exclusive* license to the patent for it. This plan places digital >signature use under the control of PKP through the year 2010. >... And this is even more appealing. I can never trust a private company. You can't often trust the public institutions (or politics), but they are -in democratic countries- under your control. You can't in any way direct the personal politics of a private party. Which is the same to say as that you are *absolutely* in their hands and can only relay in their *good volunteer* if such a thing can be expected from anyone that works only for his/her own interest. And were it such good- ness, you must take into account other third parties. Any entity whose life is threatened by another one will use anything at its reach to defend itself, i.e. a threatened company could chose to rise its royalties as much as needed and charge any additional royalties it needed. >... > ** The following notice was published in the Federal Register, Vol. > 58, No. 108, dated June 8, 1993 under Notices ** > >National Institute of Standards and Technology > >Notice of Proposal for Grant of Exclusive Patent License > >This is to notify the public that the National Institute of >Standards and Technology (NIST) intends to grant an exclusive >world-wide license to Public Key Partners of Sunnyvale, California ================== >to practice the Invention embodied in U.S. Patent Application No. >07/738.431 and entitled "Digital Signature Algorithm." A PCT >application has been filed. The rights in the invention have been >assigned to the United States of America... (my underlining, some stuff deleted) More on the same, but now this not only affects the USA. Since most USA standards become world standards, and since many under- developed countries relay on US technologies, now the problem extends to us all. >Appendix "A" > >... some stuff deleted ... > >It is PKP's intent to make practice of the DSA royalty free for ============^^^^^^ >personal, noncommercial and U.S. Federal, state and local >government use. As explained below, only those parties who enjoy >commercial benefit from making or selling products, or certifying >digital signatures, will be required to pay royalties to practice >the DSA. My underlining again. Aha! so all you (and maybe us) have is a declaration of principles or intentions. Which in principle sound quite well. But no assurance you won't get later surprises. Let's see... Uh? Am I paranoic?... I remember the LZW compression algorithm issue. Wasn't too enforced till it went a de-facto standard. Oh, and wasn't it similar with the Backing-Store algorithm? Freely used in X-windows, which was developed with public resources, until X became a standard -mainly por its public accessibility-, and then after several years, the patent comes suddenly into light! And what happened with the threats to the Univ. of Wisconsin GCG package last summers? Wasn't it that it was threatened because of commercial companys pressure on the politicians or so? >Having stated these intentions, PKP now takes this opportunity to >publish its guidelines for granting uniform licenses to all parties >having a commercial interest in practicing this technology: Well, well, all of them sound quite senseful. Do they? >Fourth, PKP's royalty rates for the right to make or sell products, >subject to uniform minimum fees, will be no more than 2 1/2% for >hardware products and 5% for software, with the royalty rate >further declining to 1% on any portion of the product price >exceeding $1,000. These royalty rates apply only to noninfringing >parties and will be uniform without regard to whether the licensed >product creates digital signatures, verifies digital signatures or >performs both. Now if I want to make, say, a new program, using a few standards for it to be useful, say I use encryption, I pay 5%, say I use X with Backing-Store (which pays royalties), which draws an X-Or cursor (which is also patented), and compresses the messages with LZ, and uses a few other standard (or not) libraries... If I have to pay 5% for each of these, I may end paying more royalties than the cost of the final product. Quite senseful, isn't it? More yet since I'm not american, and royalties could be greater, and I'd had to add import/export royalties... Fine, what kind of programs can I write? >Fifth, for the next three (3) years, all commercial services which >certify a signature's authenticity for a fee may be operated >royalty free. Thereafter, all providers of such commercial >certification services shall pay a royalty to PKP of $1.00 per >certificate for each year the certificate is valid. Wow! I work in the academic world, but this sounds to me as if a car factory using injection engines from other company were granted a three-year use license. And each additional year *I* used my car they had to pay an additional amount. This gets curiouser... >Sixth, provided the foregoing royalties are paid on such products >or services, all other practice of the DSA shall be royalty free. While the company doesn't decide to change politics... >... more stuff deleted. -------------- Well, I can't say much for myself. If my country didn't invest in developing these algorithms I agree I must pay. It is my duty to enforce my politicians to fund research or else to restrict certain patent application policies. But, the same holds for all of us. IMHO the solution NOW is either to support additional research and develop a new algorithm that could replace that standard being public, or either to try to stop certain kinds of patent application which may derive in worst use of public funds. IMHO, a gov. resource should be exploited by the gov. or only by a company that is it or its policies directly controlled by the gov. I agree that govs. have right to develop their own anythings and to exploit them. But I can't see any excuse for any public-dependent (i.e. non fascist) goverment to give away -in full, in part or temporarily- all the rights of public goodies to a private party, hence leaving the public -which is the real owner of the good- at the hands of a private and self-interested party. J. R. Valverde Biomedical Research Insitute Madrid - SPAIN Disclaimed: the opinions depicted above are my own and only my own. They do not necessary reflect the opinion of anyone else. From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: JRAMON@mvax.fmed.uam.es Newsgroups: bionet.software Subject: Fwd: Digital Signature Standard Message-ID: <1993Jul2.085004.11189@gserv1.dl.ac.uk> Date: 2 Jul 93 10:51:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 270 X-Organization: Universidad Autonoma de Madrid (UAM) X-Envelope-To: bio-software@daresbury.ac.uk Original-To: bio-software@uk.ac.daresbury X-Vms-To: IN"bio-software@daresbury.ac.uk" Comments: Pasarela de correo electronico local Internet<->DECnet de la UAM From: CCUAM2::IN%"info-gnu-request@prep.ai.mit.edu" 2-JUL-1993 06:11:38.65 To: IN%"info-gnu@prep.ai.mit.edu" CC: Subj: Digital Signature Scandal Return-path: Received: from life.ai.mit.edu by ccuam2 (PMDF #12458) id <01H0221C8DK091VW2R@ccuam2>; Fri, 2 Jul 1993 06:11 GMT Received: from pop-tarts (pop-tarts.ai.mit.edu) by life.ai.mit.edu (4.1/AI-4.10) for JRAMON@uamed.uam.es id AA11905; Thu, 1 Jul 93 22:44:19 EDT Received: by pop-tarts (4.1/AI-4.10) id AA05259; Thu, 1 Jul 93 22:44:17 EDT Resent-date: Tue, 29 Jun 93 16:30:21 edt Date: Tue, 29 Jun 93 16:30:21 edt Resent-from: info-gnu-request@prep.ai.mit.edu From: friedman@gnu.ai.mit.edu (Noah Friedman) Subject: Digital Signature Scandal Sender: gnulists@ai.mit.edu To: info-gnu@prep.ai.mit.edu Resent-message-id: <9307020244.AA05259@pop-tarts> Message-id: <9306292030.AA01764@nutrimat.gnu.ai.mit.edu> X-Envelope-to: JRAMON@uamed [The following is an official announcement from the League for Programming Freedom. Please redistribute this as widely as possible.] Digital Signature Scandal Digital signature is a technique whereby one person (call her J. R. Gensym) can produce a specially encrypted number which anyone can verify could only have been produced by her. (Typically a particular signature number encodes additional information such as a date and time or a legal document being signed.) Anyone can decrypt the number because that can be done with information that is published; but producing such a number uses a "key" (a password) that J. R. Gensym does not tell to anyone else. Several years ago, Congress directed the NIST (National Institute of Standards and Technology, formerly the National Bureau of Standards) to choose a single digital signature algorithm as a standard for the US. In 1992, two algorithms were under consideration. One had been developed by NIST with advice from the NSA (National Security Agency), which engages in electronic spying and decoding. There was widespread suspicion that this algorithm had been designed to facilitate some sort of trickery. The fact that NIST had applied for a patent on this algorithm engendered additional suspicion; despite their assurances that this would not be used to interfere with use of the technique, people could imagine no harmless motive for patenting it. The other algorithm was proposed by a company called PKP, Inc., which not coincidentally has patents covering its use. This alternative had a disadvantage that was not just speculation: if this algorithm were adopted as the standard, everyone using the standard would have to pay PKP. (The same patents cover the broader field of public key cryptography, a technique whose use in the US has been mostly inhibited for a decade by PKP's assiduous enforcement of these patents. The patents were licensed exclusively to PKP by the Massachusetts Institute of Technology and Stanford University, and derive from taxpayer-funded research.) PKP, Inc. made much of the suspect nature of the NIST algorithm and portrayed itself as warning the public about this. On June 8, NIST published a new plan which combines the worst of both worlds: to adopt the suspect NIST algorithm, and give PKP, Inc. an *exclusive* license to the patent for it. This plan places digital signature use under the control of PKP through the year 2010. By agreeing to this arrangement, PKP, Inc. shows that its concern to protect the public from possible trickery was a sham. Its real desire was, as one might have guessed, to own an official national standard. Meanwhile, NIST has justified past suspicion about its patent application by proposing to give that patent (in effect) to a private entity. Instead of making a gift to PKP, Inc., of the work all of us have paid for, NIST and Congress ought to protect our access to it--by pursuing all possible means, judicial and legislative, to invalidate or annull the PKP patents. If that fails, even taking them by eminent domain is better (and cheaper in the long run!) than the current plan. You can write to NIST to object to this giveaway. Write to: Michael R. Rubin Active Chief Counsel for Technology Room A-1111, Administration Building, National Institute of Standards and Technology Gaithersburg, Maryland 20899 (301) 975-2803. The deadline for arrival of letters is around August 4. Please send a copy of your letter to: League for Programming Freedom 1 Kendall Square #143 P.O.Box 9171 Cambridge, Massachusetts 02139 (The League for Programming Freedom is an organization which defends the freedom to write software, and opposes monopolies such as patented algorithms and copyrighted languages. It advocates returning to the former legal system under which if you write the program, you are free to use it. Please write to the League if you want more information.) Sending copies to the League will enable us to show them to elected officials if that is useful. This text was transcribed from a fax and may have transcription errors. We believe the text to be correct but some of the numbers may be incorrect or incomplete. --------------------------------------------------------------------- ** The following notice was published in the Federal Register, Vol. 58, No. 108, dated June 8, 1993 under Notices ** National Institute of Standards and Technology Notice of Proposal for Grant of Exclusive Patent License This is to notify the public that the National Institute of Standards and Technology (NIST) intends to grant an exclusive world-wide license to Public Key Partners of Sunnyvale, California to practice the Invention embodied in U.S. Patent Application No. 07/738.431 and entitled "Digital Signature Algorithm." A PCT application has been filed. The rights in the invention have been assigned to the United States of America. The prospective license is a cross-license which would resolve a patent dispute with Public Key Partners and includes the right to sublicense. Notice of availability of this invention for licensing was waived because it was determined that expeditious granting of such license will best serve the interest of the Federal Government and the public. Public Key Partners has provided NIST with the materials contained in Appendix A as part of their proposal to NIST. Inquiries, comments, and other materials relating to the prospec- tive license shall be submitted to Michael R. Rubin, Active Chief Counsel for Technology, Room A-1111, Administration Building, National Institute of Standards and Technology, Gaithersburg, Maryland 20899. His telephone number is (301) 975-2803. Applica- tions for a license filed in response to this notice will be treated as objections to the grant of the prospective license. Only written comments and/or applications for a license which are received by NIST within sixty (60) days for the publication of this notice will be considered. The prospective license will be granted unless, within sixty (60) days of this notice, NIST receives written evidence and argument which established that the grant of the license would not be consistent with the requirements of 35 U.S.C. 209 and 37 CFR 404.7. Dated: June 2, 1993. Raymond G. Kammer Acting Director, National Institute Standards and Technology. Appendix "A" The National Institute for Standards and Technology ("NIST") has announced its intention to grant Public Key Partners ("PKP") sublicensing rights to NIST's pending patent application on the Digital Signature Algorithm ("DSA"). Subject to NIST's grant of this license, PKP is pleased to declare its support for the proposed Federal Information Processing Standard for Digital Signatures (the "DSS") and the pending availability of licenses to practice the DSA. In addition to the DSA, licenses to practice digital signatures will be offered by PKP under the following patents: Cryptographic Apparatus and Method ("Diffie-Hellman") No. 4,200,770 Public Key Cryptographic Apparatus and Method ("Hellman-Merkle") No. 4,315,552 Exponential Cryptographic Apparatus and Method ("Hellman-Pohlig") No. 4,434,414 Method For Identifying Subscribers And For Generating And Verifying Electronic Signatures In A Data Exchange System ("Schnorr") No. 4,995,082 It is PKP's intent to make practice of the DSA royalty free for personal, noncommercial and U.S. Federal, state and local government use. As explained below, only those parties who enjoy commercial benefit from making or selling products, or certifying digital signatures, will be required to pay royalties to practice the DSA. PKP will also grant a license to practice key management, at no additional fee, for the integrated circuits which will implement both the DSA and the anticipated Federal Information Processing Standard for the "key escrow" system announced by President Clinton on April 16, 1993. Having stated these intentions, PKP now takes this opportunity to publish its guidelines for granting uniform licenses to all parties having a commercial interest in practicing this technology: First, no party will be denied a license for any reason other that the following: (i) Failure to meet its payment obligations, (ii) Outstanding claims of infringement, or (iii) Previous termination due to material breach. Second, licenses will be granted for any embodiment sold by the licensee or made for its use, whether for final products software, or compfinal products software, or components such as integrated circuits and boards, and regard- less of the licensee's channel of distribution. Provided the requisite royalties have been paid by the seller on the enabling component(s), no further royalties will be owned by the buyer for making or selling the final product which incorporates such components. Third, the practice of digital signatures in accordance with the DSS may be licensed separately from any other technical art covered by PKP's patents. Fourth, PKP's royalty rates for the right to make or sell products, subject to uniform minimum fees, will be no more than 2 1/2% for hardware p From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!apldbio.com From: james@apldbio.com (James Candlin) Newsgroups: bionet.announce,bionet.biology.computational,bionet.software Subject: Call for Computer Demonstrations Message-ID: <514@biosys.apldbio.COM> Date: 2 Jul 93 01:22:20 GMT Sender: kristoff@net.bio.net Reply-To: james@apldbio.com Followup-To: bionet.announce Organization: Applied Biosystems, Inc. Lines: 231 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:603 bionet.biology.computational:475 bionet.software:5378 Macromolecules, Genes, and Computers: Chapter Three International Symposium and Workshop August 17-22, 1993 Waterville Valley Resort and Conference Center Waterville Valley, New Hampshire Sponsored By: o The BMERC of the College of Engineering, Boston University o Applied Biosystems Additional Sponsors: Digital Equipment Corporation DNA*, Inc. Genetics Computer Group Hitachi Software Engineering America, Ltd. IntelliGenetics, Inc. Molecular Simulations, Inc. Sun Microsystems, Inc. Sybase, Inc. There are a few openings remaining in the "Computational Biology Tools" computer demonstration workshop scheduled as part of this meeting. If you wish to participate, please fill in and return the attached application form to Dawn Madden at Applied Biosystems (dawn@apldbio.com). Symposium Philosophy This international symposium and workshop has been designed to facilitate the exchange of information in the interdisciplinary domain overlapping computer science, mathematics, genetics, medicine, and molecular biology. The agenda has been planned to optimize this exchange through formal and informal formats in an enjoyable mountain resort environment. The session topics have been chosen to direct discussions toward the fundamental properties of biological systems; the enabling technologies; and the anticipated computational challenges within this interdisciplinary domain. Meeting Program Summary Keynote Speaker: Stuart Kauffman, Santa Fe Institute Computer Demonstration Workshops: Participants wishing to demonstrate software must submit abstract, system requirements, and whether they will supply their own equipment for demonstrations during workshops. I. Computational Biology Resources Represented resources and academic centers will provide "hands on" demonstrations of their computer software and databases. Emphasis will be on applications to the problems within the interdisciplinary domain of the symposium. II. Computational Biology Tools Contributors will present "hands on" demonstrations of specialized software and hardware during this "electronic poster session". Associated poster will describe current and future applications. Tutorial Workshops: I. Use of NCBI's Tools and Services Organizer: Jim Ostell II. Molecular Biology Overview for the Non-Molecular Biologist Organizer: Bob Gross III. An Overview of Computational Tools Useful to Molecular Biologists Organizer: Dawn Madden Discussion Workshops: I. Converging on a sequence database format different packages could share Organizer: Leslie Taylor II. Linking Analytical Tools through Interprocess Communication Organizers: Chris Sander and Pat Gillevet Sessions: Session 1 - Genome and Biotechnology Challenges Organizers: Charles Cantor and Patrick Gillevet Speakers: Chris Sander, B. Dujon, Sydney Brenner, Ben Koop, Michael Waterman, Nat Goodman Session 2 - Molecular Docking and Recognition: New Approaches and Remaining Challenges Organizers: Steve Bryant and A. Keith Dunker Speakers: L. Mario Amzel, Edward Dratz, Stephen Fodor, Terry Lybrand, Scott Dixon, Wayne Anderson Session 3 - Aspects of RNA Structures and Their Analyses Organizers: Michael Zuker and Jude Shavlik Speakers: Robert Cedergren, David Bartel, Gary J. Olsen Session 4 - Protein Structure Analyses and Prediction Organizers: Jean Garnier and Timothy Havel Speakers: J. Greer, Gordon Crippen, Robert Swendsen, Mark Rance Nobuhiro Go, Jorge Navaza, Robert Bruccoleri, Chris Sander, Jan Hermans Session 5 - Gene Regulation: Representation, Modeling, and Generalization Organizers: David Farb and John Reinitz Speakers: Carl Parker, Nadia Rosenthal, David Sharp, Denis Thieffry, Alan P. Wolffe Session 6 - New Artificial Intelligence and Computational Methods Organizers: Richard Lathrop and Jude Shavlik Speakers: David Haussler, Larry Hunter, David Searls Session 7 - Biological Databases: Design and Function Organizer: David Landsman Speakers: Jim Ostell, Amos Bairoch, Bill Gelbart ------------------------------------------------------------------------------- Meeting and Computer Workshop Application Form Please return by July 9, 1993 to: Dawn Madden Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 FAX: 415-572-2743 Phone: 415-570-6667x8803 E-mail: dawn@apldbio.com Registration Information Name: [ ] Title:[ ] Sex: [ ] M [ ] F Institutional Affiliation: [ ] Address: [ ] [ ] [ ] Phone: [( ) ] FAX: [( ) ] E-mail: [ ] Are you applying for travel support? [ ] Yes [ ] No Housing and Meal Options Please check your preference: [ ] Conference fee-double occupancy $485 per person (Includes conference registration fee, housing, meals and banquet) Indicate desired roommate, if known: [ ] [ ] Conference fee-single occupancy $600 per person (Includes conference registration fee, housing, meals and banquet) [ ] Housing only-for guests not attending conference $300 per person (Includes double occupancy housing only. All meals must be paid for separately.) Please check banquet meal preference: [ ] Filet Mignon [ ] Broiled Swordfish [ ] Vegetarian Do you have any special housing or dietary needs? If so, please indicate their nature. [ ] Please mail a 10% deposit with hard copy of this form in addition to submitting the filled in form by electronic mail. (Make check payable to Applied Biosystems) Signature [ ] Date: [ ] Equipment and Telecommunications Requirements for Computer Demonstration: Computer Equipment You Will Provide: Abstract Type a brief abstract of your anticipated poster session, computer application workshop presentation, or current research activities in the space below. All participants are expected to contribute to either a poster session or computer workshop. Title: Author(s): Abstract: --- James Candlin ------------------------------------------------------------------------ email: james@apldbio.com Applied Biosystems, Inc phone: +1 415 570 6667 x8742 850 Lincoln Centre Drive fax: +1 415 572 2743 Foster City CA 94404, USA ------------------------------------------------------------------------ From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!UVMVAX.UVM.EDU!D_CAMPBELL From: D_CAMPBELL@UVMVAX.UVM.EDU Newsgroups: bionet.software Subject: Ordination software Message-ID: <01H01HKWHE7O000AUD@uvmvax.uvm.edu> Date: 2 Jul 93 01:26:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 I am looking for a current copy of ECOSURVEY, programes for the analysis of ecological data, produced by T.J. Carleton (U. of Toronto). or copies of ordination - classifaction software (decorana/twinspan) that is IBM compatable. David L. Campbell (802) 655-6232 or 656-2930 University of Vermont From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!NCCCOT7.AGR.CA!EM609MBCPHL From: EM609MBCPHL@NCCCOT7.AGR.CA Newsgroups: bionet.software Subject: DNASIS Message-ID: <01H02KGT56WY005SNU@GW.AGR.CA> Date: 2 Jul 93 20:05:38 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 I am interested in comments on the Sequence analysis packages DNASIS and PROSIS, particularly as they compare to PC/GENE. Please reply by email or to "methods-and-reagents". I apologize for a questions which may have already been discussed. I did try a waismail search for DNASIS which seemed to give a large volume of irrelevant material. Thanks, Pat Covello Central Plant Health Lab Agriculture Canada From owner-software@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!USAV01.GLAXO.COM!MJA12046%USA.decnet From: MJA12046%USA.decnet@USAV01.GLAXO.COM ("USA::MJA12046") Newsgroups: bionet.software Subject: Gopher Hole for GBASE??? Message-ID: <9307021851.AA15181@net.bio.net> Date: 2 Jul 93 19:35:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 Hi, Does anyone know of a way to access the GBASE (mouse genetic map data) through Gopher? thanks! Mike Agostino Glaxo, Inc. mja12046@usav01.glaxo.com From owner-software@net.bio.net Sun Jul 04 23:00:00 1993 Path: biosci!uwm.edu!wupost!uunet!mcsun!news.funet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software,vmsnet.networks.tcp-ip.multinet,vmsnet.sources.d Subject: Re: Looking for xmosaic for VMS Message-ID: <1993Jul5.144457.11025@nic.funet.fi> Date: 5 Jul 93 14:44:57 GMT References: <1993Jul5.092319.7229@mcclb0.med.nyu.edu> Sender: usenet@nic.funet.fi Organization: Finnish Academic and Research Network Project - FUNET Lines: 21 Xref: biosci bionet.software:5388 Nntp-Posting-Host: convex.csc.fi In <1993Jul5.092319.7229@mcclb0.med.nyu.edu> smith@mcclb0.med.nyu.edu writes: >SO. If anyone knows where that port is, please re-post the FTP site address. >Thanks! You can get xmosaic in various flovours from nic.funet.fi via anonymous ftp. lrwxrwxrwx 1 root funstaff 19 Jul 4 18:18 xmosaic-alpha.Z lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 xmosaic-dec.Z lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 xmosaic-ibm.Z lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 xmosaic-sgi.Z lrwxrwxrwx 1 root funstaff 25 Jul 4 18:18 xmosaic-sun-lresolv.Z lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 xmosaic-sun.Z RGDS -=ROB=- -- Rob Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-software@net.bio.net Sun Jul 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!cs.utexas.edu!rutgers!mcclb0.med.nyu.edu!smith From: smith@mcclb0.med.nyu.edu Newsgroups: bionet.software,vmsnet.networks.tcp-ip.multinet,vmsnet.sources.d Subject: Looking for xmosaic for VMS Message-ID: <1993Jul5.092319.7229@mcclb0.med.nyu.edu> Date: 5 Jul 93 14:23:19 GMT Organization: NYU Medical Center, New York, NY 10016, USA Lines: 15 Xref: biosci bionet.software:5387 No more than 3 weeks ago someone posted an announcement of a port of 'xmosaic' to VMS. I immediately grabbed it and put it on my machine. It works quite nicely. However, the individual who did the port never put a signature anywhere (that I can find) in the documentation. Consequently, I can not find the site where it came from. (I know, I know, it pretty stupid, but ...) SO. If anyone knows where that port is, please re-post the FTP site address. Thanks! +----------------------------------------------------------------------------+ |Ross Smith, Research Computing Resource, Department of Cell Biology, NYU-MC| |E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| +----------------------------------------------------------------------------+ From owner-software@net.bio.net Mon Jul 05 23:00:00 1993 Path: biosci!parc!decwrl!ames!haven.umd.edu!uunet!pipex!uknet!nessie!v4.cgu.mcc.ac.uk!mzagsaa From: mzagsaa@v4.cgu.mcc.ac.uk (Tony Arnold) Newsgroups: bionet.software,vmsnet.networks.tcp-ip.multinet,vmsnet.sources.d Subject: Re: Looking for xmosaic for VMS Message-ID: <1993Jul6.091203.21639@nessie.mcc.ac.uk> Date: 6 Jul 93 09:12:03 GMT References: <1993Jul5.092319.7229@mcclb0.med.nyu.edu> <1993Jul5.144457.11025@nic.funet.fi> Sender: mzagsaa@umrcc.cgu.mcc.ac.uk (Tony Arnold) Reply-To: A.C.Arnold@mcc.ac.uk Organization: Manchester Computing Centre Lines: 45 Xref: biosci bionet.software:5390 In article <1993Jul5.144457.11025@nic.funet.fi>, harper@convex.csc.FI (Rob Harper) writes: |>Newsgroups: |>bionet.software,vmsnet.networks.tcp-ip.multinet,vmsnet.sources.d |>From: harper@convex.csc.FI (Rob Harper) |>Subject: Re: Looking for xmosaic for VMS |>Date: Mon, 5 Jul 93 14:44:57 GMT |> |>In <1993Jul5.092319.7229@mcclb0.med.nyu.edu> |>smith@mcclb0.med.nyu.edu writes: |> |>>SO. If anyone knows where that port is, please re-post the FTP |>site address. |>>Thanks! Yes please! |> |>You can get xmosaic in various flovours from nic.funet.fi via |>anonymous ftp. |> |> |>lrwxrwxrwx 1 root funstaff 19 Jul 4 18:18 |>xmosaic-alpha.Z |>lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 |>xmosaic-dec.Z |>lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 |>xmosaic-ibm.Z |>lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 |>xmosaic-sgi.Z |>lrwxrwxrwx 1 root funstaff 25 Jul 4 18:18 |>xmosaic-sun-lresolv.Z |>lrwxrwxrwx 1 root funstaff 17 Jul 4 18:18 |>xmosaic-sun.Z These look like the files that NCSA distribute. To my understanding, they are all Unix flavour implementation. NCSA does not have a VMS port, but if someone has one, please let me know as I am keen to run this stuff on our aging VAXs. Tony Arnold, OpenVMS Systems Manager, University of Manchester, UK. From owner-software@net.bio.net Mon Jul 05 23:00:00 1993 Path: biosci!UCRVM2.BITNET!SMELGAR From: SMELGAR@UCRVM2.BITNET Newsgroups: bionet.software Subject: components of variance question Message-ID: <9307060028.AA26398@net.bio.net> Date: 6 Jul 93 00:28:22 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Could anybody please tell me which statistical package can I use to obtain comp onents of variance of a hierarchical analysis of variance with one covariable? The main problem is that the analysis is unbalanced, therefore it is very difficult to obtain the estimates of components of variance by hand. I will appreciate any help. My e-mail address is SMELGAR@UCRVM2 Thank you, Sergio Melgar Escuela de Biologia Universidad de Costa Rica From owner-software@net.bio.net Mon Jul 05 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!lhc!laputa!altschul From: altschul@laputa.nlm.nih.gov (Stephen Altschul) Newsgroups: bionet.software Subject: Sequence Analysis Workshop Message-ID: <1993Jul6.202230.9826@nlm.nih.gov> Date: 6 Jul 93 20:22:30 GMT Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 95 X-Newsreader: Tin 1.1 PL4 ******************************************************************************** WORKSHOP ON MOLECULAR SEQUENCE ANALYSIS Hartley Conference Center Mitchell School of Earth Sciences Stanford University, Stanford, CA August 5 - 6, 1993 THURSDAY: AUGUST 5, 1993 Session I. Protein Structure (12:30 - 3:00) Chairman: F. Cohen T. Smith A Protein Core Structure Library and Its Use in Nonhomologous Extension Modeling S. Bryant A Residue Contact Potential for Threading Protein Sequence Through Folding Motif T. Lybrand Generation of Three-Dimensional Protein Models Using Computational Methods and Experimental Data C. Ring Application of Homology-Built Structures J. Blaney Conformationally Flexible Docking and Evolution of Molecules to Fit a Binding Site of Known Structure. Break - 45 minutes Session II. Sequence Alignment (3:45 - 7:15) Chairman: M. Waterman C. Lawrence Gibbs Free Energy and the Gibbs Sampler Converge to Align Multiple Biopolymer Sequences D. Sankoff Genomic Distances G. Stormo Identifying Domains in RNA Composed of Sequence and Structure Break - 30 minutes G. Gonnet (tentative) The IMD Sequence Alignment Algorithm: Theory and Practice S. Henikoff Amino Acid Substitution Matrices without Extrapolation V. Brendel Score Statistics for Molecular Sequence Analysis FRIDAY: AUGUST 6, 1993 Session III. Repeating Structures and Sequence Inhomogeneity (9:00 - 12:30) Chairman: S. Karlin M. Calos Evolution of Repeats and Transposable Elements from Bacteria to Humans J. Jurka Identification and Analysis of Human Interspersed Repetitive Elements P. Green Analysis of C. Elegans Genomic Sequence Break - 30 minutes P. Pevzner Genome Inhomogeneity and Overlapping Words Paradox G. Schachtel Assessing Inhomogeneities in Long DNA Sequences D. States TBA Session IV. Informal Presentations and Discussion (2:30 - 6:00) Chairman: S. Altschul Break - 4:30 There is no registration fee. However, for those who need lodging, dormitory rooms are available on the Stanford campus at $42.50 single and $35.00 shared. Those planning to attend and requiring a room are advised to make a reservation as soon as possible by contacting Samuel Karlin. Attendees with a reservation may pick up room keys at Elliot Program Center. Telephone FAX email -------------- -------------- ---------------------------- Samuel Karlin (415) 723-2204 (415) 725-2040 fd.zgg@forsythe.stanford.edu Fred Cohen (415) 426-8519 (415) 476-6515 cohen@cgl.ucsf.edu Michael Waterman (213) 740-2408 (213) 740-2437 msw@hto.usc.edu Stephen Altschul (301) 496-2475 (301) 480-9241 altschul@nlm.nih.gov From owner-software@net.bio.net Mon Jul 05 23:00:00 1993 Path: biosci!crunch.unm.edu From: stanly@crunch.unm.edu (Stanly Steinberg) Newsgroups: bionet.announce,bionet.software,comp.edu,sci.aeronautics,sci.bio,sci.bio.technology,sci.chem,sci.edu,sci.electronics,sci.energy Subject: Symbolic Computing Short Course -- Advertisement Summary: 3 day short course emphasizing Mathematica Keywords: Computer Algebra, Symbol Manipulation, Mathematica Message-ID: <21am70INNq4b@lynx.unm.edu> Date: 6 Jul 93 01:57:52 GMT Sender: kristoff@net.bio.net Organization: Professional Engineering Lines: 22 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:606 bionet.software:5392 comp.edu:1462 sci.aeronautics:1478 sci.bio:4037 sci.bio.technology:468 sci.chem:5667 sci.edu:1318 sci.electronics:19801 sci.energy:6532 The University of New Mexico College of Engineering will offer a three-day workshop on Computer Algebra Systems emphasizing Mathematica. The workshop will take place August 2-4, 1993. The course will be taught by three experts in computer algebra systems, Professors Eric Nuttall and Stanly Steinberg of UNM, and Dr. Michael Wester, of Cotopaxi. The course begins with an overview of the various major computer algebra systems (CASs) and an introduction to what kinds of problems can and cannot be solved with them. This will be followed by an in-depth discussion of the CAS Mathematica with live demonstrations of Mathematica's key functions and operations, Practical experience in solving engineering problems will be provided along with actual student hands-on training and tutorials. The course is intended for professionals who are required to perform a wide range of numerical, symbolic, and graphical analyses, and is suitable for both beginners and advanced users of Mathematica. For more registration information, contact the Professional Engineering Development workshop office at (800) 453-3940 or through e-mail; at pedws@bootes.unm.edu. From owner-software@net.bio.net Mon Jul 05 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!indyvax.iupui.edu!imhw400 From: imhw400@indyvax.iupui.edu Newsgroups: bionet.software,vmsnet.networks.tcp-ip.multinet,vmsnet.sources.d Subject: Re: Looking for xmosaic for VMS Message-ID: <1993Jul6.090643.1363@indyvax.iupui.edu> Date: 6 Jul 93 14:06:43 GMT References: <1993Jul5.092319.7229@mcclb0.med.nyu.edu> <1993Jul5.144457.11025@nic.funet.fi> <1993Jul6.091203.21639@nessie.mcc.ac.uk> Lines: 19 Xref: biosci bionet.software:5391 In article <1993Jul6.091203.21639@nessie.mcc.ac.uk>, mzagsaa@v4.cgu.mcc.ac.uk (Tony Arnold) writes: [Deletia] > These look like the files that NCSA distribute. To my understanding, they > are all Unix flavour implementation. NCSA does not have a VMS port, but > if someone has one, please let me know as I am keen to run this > stuff on our > aging VAXs. I got a 1.0 port from BCHM2ACLCB.PURDUE.EDU. I've also heard of one done by Martin Gelbaum . The Purdue port needed some minor work but looks good. The amount of code added for VMS is truly amazingly small -- the NCSA team did a really good job of making Xmosaic portable w.r.t. VMS, whether they knew it or not. Join the fun over on comp.infosystems.www if you're interested in Xmosaic. -- Mark H. Wood, Lead Systems Programmer +1 317 274 0749 [@disclaimer@] Internet: IMHW400@INDYVAX.IUPUI.EDU BITNET: IMHW400@INDYVAX Celebrate freedom: read a banned newsgroup. From owner-software@net.bio.net Tue Jul 06 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!pipex!uknet!pavo.csi.cam.ac.uk!mrc-lmb.cam.ac.uk!rs From: rs@mrc-lmb.cam.ac.uk (Staden R.) Newsgroups: bionet.molbio.embldatabank,bionet.software Subject: Re: Use of sequence library indexes Message-ID: <1993Jul7.135349.4203@infodev.cam.ac.uk> Date: 7 Jul 93 13:53:49 GMT References: <1993Jul1.234108.1@molbiol.ox.ac.uk> <1993Jul2.055206.7673@comp.bioz.unibas.ch> Sender: news@infodev.cam.ac.uk (USENET news) Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 39 Xref: biosci bionet.molbio.embldatabank:204 bionet.software:5395 Nntp-Posting-Host: al.mrc-lmb.cam.ac.uk There have been several articles about the use of indexes for extracting entries from the sequence libraries and the problems that gcg has when an accession number occurs in more than one entry. Mention was made of a package (SRS) that does not have this problem. Readers may be interested to know of our own method of dealing with sequence library indexes (and which also does not suffer from the accession number problem). We decided to use the indexing system that is included on the EMBL cdrom, and using it we can extract entries based on accession number and entry name. In addition we can perform instantaneous author and text searches (the text indexes include every non-trivial word throughout an entry - not just the keywords - so we find it very useful). So this allows us to use EMBL and SWISSPROT from the cdrom (or copied to disk for extra speed), but we also wanted to be able to use EMBL updates and PIR and GenBank. To make this possible we wrote software to create EMBL cdrom style indexes for all libraries ie we create entryname, accession number, author and freetext indexes for all library formats. It is important to realise that we do not change the libraries, but leave them as distributed. Not having to reformat or change the libraries obviously saves a great deal of time and temporary disk space. An article dexcribing the initial work on this subject was buried in Staden,R and Dear,S "Indexing the sequence libraries: software providing a common indexing system for all the standard sequence libraries. DNA Sequence 3, 99-105 (1992). Rodger Staden -- Rodger Staden, Medical Research Council Laboratory Of Molecular Biology, Hills Road, Cambridge, CB2 2QH, ENGLAND Telephone: 0223 402389 Internet: rs@UK.AC.Cam.MRC-LMB Facsimile: 0223 412282 From owner-software@net.bio.net Tue Jul 06 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!math.ohio-state.edu!wupost!waikato.ac.nz!canterbury.ac.nz!chmeds.ac.nz!mkennedy From: mkennedy@chmeds.ac.nz (Martin Kennedy) Newsgroups: bionet.software Subject: Re: Gopher Hole for GBASE??? Message-ID: <1993Jul7.132002.273@chmeds.ac.nz> Date: 7 Jul 93 01:20:02 GMT References: <9307021851.AA15181@net.bio.net> Distribution: bionet Lines: 32 In article <9307021851.AA15181@net.bio.net>, MJA12046%USA.decnet@USAV01.GLAXO.COM ("USA::MJA12046") writes: > Hi, > Does anyone know of a way to access the GBASE (mouse genetic map data) > through Gopher? > thanks! > > Mike Agostino > Glaxo, Inc. > mja12046@usav01.glaxo.com Mike, Gopher to merlot.welch.jhu.edu, then select: -->13 Search databases at Hopkins... -->8 Mouse databases -->1 Encyclopaedia of the mouse genome I haven't played with it, but it seems to be up and running. Good luck, Martin NNNN NN Martin A Kennedy (E-mail = mkennedy@chmeds.ac.nz) ZZZZZZZ NN NN NN Cytogenetic and Molecular Oncology Unit ZZZ NN NN NN Christchurch School of Medicine ZZZ NN NNNN Christchurch, New Zealand ZZZZZZZ Phone (64-3)364-0880 Fax (64-3)364-750 From owner-software@net.bio.net Tue Jul 06 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!caen!batcomputer!munnari.oz.au!sol.deakin.OZ.AU!ausom!klb From: klb@ausom.oz.au (Kevin Blaze) Newsgroups: bionet.software Subject: Wanted - Software advice - Biological classification/identification Message-ID: <1993Jul7.200347.7244@ausom.oz.au> Date: 7 Jul 93 20:03:47 GMT Organization: AUSOM - The Apple Users Society of Melbourne Lines: 14 I need a program that will help me to produce a biological key (for identificatio n). Presumably, it will produce a dendrogram. Presumably, I will be able to enter data that is coded either a) as presence or absence, or b) as numeric. I would prefer it to run on the Mac. Please reply to klb@ausom.oz.au Kevin L. Blaze VCAH (Burnley) Burnley Gardens Swan St Richmond AUSTRALIA 3121 From owner-software@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!agate!spool.mu.edu!nigel.msen.com!yale.edu!news.yale.edu!news From: STONE@biomed.med.yale.edu (Lynna Stone-Infeld) Newsgroups: bionet.software Subject: HP7475 -> postscript translator Message-ID: <1993Jul8.201006.1651@news.yale.edu> Date: 8 Jul 93 20:10:06 GMT Sender: news@news.yale.edu (USENET News System) Organization: Yale University Lines: 26 Nntp-Posting-Host: biomed.med.yale.edu X-News-Reader: VMS NEWS 1.20 I seem to remember a Mac application that would convert HP7475 output to postscript. I have looked on several FTP servers and don't see it. Does anyone know if such a thing exists and where I could get it. Thanks. - Lynna ======================================================================= - Lynna Stone-Infeld, Manager, User Services AND Manager, Molecular Biology Computing Resources Internet: STONE@BIOMED.MED.YALE.EDU Bitnet: STONE@YALEMED Biomedical Computing Unit, Yale University, School of Medicine P.O. Box 3333, New Haven, CT, 06510 ======================================================================= ======================================================================= - Lynna Stone-Infeld, Manager, User Services AND Manager, Molecular Biology Computing Resources Internet: STONE@BIOMED.MED.YALE.EDU Bitnet: STONE@YALEMED Biomedical Computing Unit, Yale University, School of Medicine P.O. Box 3333, New Haven, CT, 06510 ======================================================================= From owner-software@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.software Subject: MacPattern 3.0 available Message-ID: Date: 8 Jul 93 10:32:37 GMT Followup-To: bionet.software Organization: EMBL Data Library Lines: 21 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de The new version 3.0 of the MacPattern sequence analysis program is now available. MacPattern assists in finding putative functions for new protein sequences by supporting pattern searches using the PROSITE database, block searches using the BLOCKS database, and statistical analyses (maximal segment score analysis). Major changes in v3.0 are vastly improved pattern searches (search a 900 aa protein against all of PROSITE in 6 seconds on a Mac IIcx), a new, faster approximate block search method, and translations of nucleotide sequences in three or six reading frames. MacPattern runs on any Macintosh with at least 750 kb of free RAM and System version 6.0.5 or greater. Copies can be obtained by anonymous ftp from ftp.embl-heidelberg.de (/pub/software/mac/macpattern.hqx) or by email from Netserv@EMBL-Heidelberg.DE (get mac_software:macpattern.hqx). Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-software@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!pitt.edu!shannon From: shannon@belenos.pci.upmc.edu (bill shannon) Newsgroups: sci.math.num-analysis,bionet.software Subject: Numerical Recipes in C Message-ID: <16115@blue.cis.pitt.edu> Date: 8 Jul 93 16:24:12 GMT Sender: news+@pitt.edu Followup-To: sci.math.num-analysis Organization: Biostatistics Center, Pittsburgh Cancer Institute Lines: 17 Xref: biosci sci.math.num-analysis:3492 bionet.software:5398 Originator: shannon@belenos Hi, Are the programs from Willaim Press' book "Numerical Recipes in C, 2nd Ed." available somewhere on the net? And if so, where? I need to do some sorting and would prefer not to type in all the source code from the book. All help is appreciated. Thanks Bill Shannon Pittsburgh Cancer Institute e-mail: shannon@atonal.pci.upmc.edu From owner-software@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!uwm.edu!post.its.mcw.edu!not-for-mail From: halligan@post.its.mcw.edu (Brian Halligan) Newsgroups: bionet.software Subject: Re: HP7475 -> postscript translator Message-ID: <21i7gl$nsb@post.its.mcw.edu> Date: 8 Jul 93 22:36:05 GMT References: <1993Jul8.201006.1651@news.yale.edu> Organization: Medical College of Wisconsin; Milwaukee Wisconsin Lines: 32 NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.1 PL7] Lynna Stone-Infeld (STONE@biomed.med.yale.edu) wrote: : : : : I seem to remember a Mac application that would convert HP7475 output to : postscript. I have looked on several FTP servers and don't see it. Does anyone : know if such a thing exists and where I could get it. Thanks. : : - Lynna : ======================================================================= : - Lynna Stone-Infeld, Manager, User Services : AND Manager, Molecular Biology Computing Resources : Internet: STONE@BIOMED.MED.YALE.EDU : Bitnet: STONE@YALEMED : Biomedical Computing Unit, Yale University, School of Medicine : P.O. Box 3333, New Haven, CT, 06510 : ======================================================================= : : : ======================================================================= : - Lynna Stone-Infeld, Manager, User Services : AND Manager, Molecular Biology Computing Resources : Internet: STONE@BIOMED.MED.YALE.EDU : Bitnet: STONE@YALEMED : Biomedical Computing Unit, Yale University, School of Medicine : P.O. Box 3333, New Haven, CT, 06510 : ======================================================================= -- Brian D. Halligan halligan@post.its.mcw.edu Assistant Professor 414-257-8413 (voice) Department of Microbiology 414-257-8427 (FAX) Medical College of Wisconsin From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!bloom-beacon.mit.edu!genome.wi.mit.edu!lstein From: lstein@genome.wi.mit.edu (Lincoln Stein) Newsgroups: bionet.molbio.gene-linkage,bionet.genome.chromosomes,bionet.software Subject: ANNOUNCING RELEASE 3 OF WI/MIT CGR MOUSE GENETIC MAP Keywords: SSLP genetic map linkage genome center mouse mus Message-ID: <21k03u$i6h@harpo.wi.mit.edu> Date: 9 Jul 93 14:42:06 GMT Expires: 1 Aug 1993 00:00:01 GMT Organization: Whitehead Institute for Biomedical Research Lines: 65 Xref: biosci bionet.molbio.gene-linkage:195 bionet.genome.chromosomes:53 bionet.software:5405 NNTP-Posting-Host: loco.wi.mit.edu ANNOUNCING THE THIRD RELEASE OF THE WHITEHEAD INSTITUTE/MIT GENOME CENTER GENETIC MAP OF THE MOUSE Release Three of the Whitehead Institute/MIT Genome Center Genetic Map of the Mouse is now available. This map consists of randomly-chosen simple sequence length polymorphisms (microsatellites) that can be analyzed using the polymerase chain reaction, as described in Dietrich, W., et al., Genetics 131:423-447 (1992). Currently the released map contains 1524 markers. The markers fall into 20 linkage groups spanning approximately 1400 cM with an average spacing of less than 1 cM. This data can be obtained in two different ways. 1. Via anonymous ftp to genome.wi.mit.edu. Log in as "anonymous" and use your e-mail address as password. The release can be found in the directory /distribution/mouse_sslp_release/july93/. The file "README" describes the file format and gives other information about the map. 2. Via internet e-mail using a database e-mail server. Using this service you can obtain locus and assay names of mapped SSLPs, the forward and reverse primer sequences, the genotypes of the loci on the mapping cross, the sizes of the PCR products on selected standard inbred strains, and other useful information. The database can be queried for markers meeting a number of different criteria. For example, you can ask for markers by name, by chromosome, or by position on the map. You can even request a list of markers that are polymorphic between two mouse strains. To obtain copies of the most current query forms, send a message to "genome_database@genome.wi.mit.edu" with either a subject line or body text of "help". You will receive instructions and a query form by return mail. Just fill out the form, send it to "genome_database@genome.wi.mit.edu", and the answer to your query will be mailed back automatically. This project is an ongoing one. As new markers are added to the map they will be released on a quarterly basis on approximately the following schedule: 1 October 1993 1 January 1994 1 April 1994 1 July 1994 &c. Please address questions and comments to me at the address below. Lincoln Stein ======================================================================== Lincoln Stein, M.D.,Ph.D. lstein@genome.wi.mit.edu MIT Genome Center (617) 252-1916 Whitehead Institute for Biomedical Research (617) 252-1902 FAX 9 Cambridge Center Cambridge, MA 02142 ======================================================================== -- ======================================================================== Lincoln D. Stein lstein@genome.wi.mit.edu Whitehead Institute, Cambridge, MA ======================================================================== From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!parc!decwrl!pa.dec.com!hydrox.enet.dec.com!mek From: mek@hydrox.enet.dec.com (Mark Klamerus) Newsgroups: bionet.software Subject: Request for Info on Force Field assisted Particle Recognition Message-ID: <9307091747.AA28403@enet-gw.pa.dec.com> Date: 9 Jul 93 17:47:39 GMT Lines: 33 X-Received: by usenet.pa.dec.com; id AA26852; Fri, 9 Jul 93 10:47:40 -0700 X-Received: by enet-gw.pa.dec.com; id AA28403; Fri, 9 Jul 93 10:47:39 -0700 X-Received: from hydrox.enet; by decwrl.enet; Fri, 9 Jul 93 10:47:39 PDT X-To: bionet.software.usenet X-Apparently-To: bionet.software.usenet Hi, I'm currently in the graduate biocomputing program at Wayne State Univ in Detroit. I'm particuarly focusing in on the computational aspects of proteins (and associated molecules like enzymes, RNA, etc.). I was looking to do my paper/thesis on the information processing aspects of pattern/particle recognition of molecules (real or otherwise) assisted by force fields (the way protein recognize each other and form mosaics). Can anyone point to any works done in this area or provide any suggestions/recommendations. In particular, I've read many articles on Brownian Dynamics, but interested to pointers to articles on molecular liquids, force fields, diffusion, etc. which relate to the above area. I'm not especially interested in the thermodynamics/statistical side of things. At least, not too much on the statistical side. I'm especially interested in abstracting the concepts/theories away from the physical side of things (for now), but will take anything in this area I can get. I'm also open for any opinions on whether this seems to be worthy of study, any direction to focus this research, discouragement (if appropriate), and info on whether this has been done already. thanks very much, Mark Klamerus mek@hydrox.det.dec.com ------- End of Forwarded Message From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: embnet.net-dev,bionet.software Subject: AXP POSIX Message-ID: <1993Jul9.113838.29554@comp.bioz.unibas.ch> Date: 9 Jul 93 11:38:38 GMT Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 19 Xref: biosci bionet.software:5403 Nntp-Posting-Host: biox.embnet.unibas.ch I would like to know who would be interested to discuss POSIX on VMS - with respect to program usage and maintenance. I need experience reports on stability and versatility for biologists, etc. Would it make sense to make a software distribution in POSIX also, i.e. is it used well enough in biologist's machines to try the effort? Thanks Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!mcsun!news.funet.fi!ousrvr.oulu.fi!mac36157.oulu.fi!vaisanen From: vaisanen@lbiok-1.oulu.fi (Timo Visnen) Newsgroups: bionet.software Subject: Computer simulated electrophoresis Message-ID: Date: 9 Jul 93 12:06:56 GMT Sender: news@ousrvr.oulu.fi Organization: Oulun yliopisto Lines: 8 I would like to find out if there are programs that can simulate DNA electrophoresis in agarose/acrylamide gels. If this kind of programs exist, are they available from any FTP site ? My PC has MS-DOS/Windows operating system. If you have some information about these programs, please mail the information to me. Timo Vaisanen timo.vaisanen@oulu.fi From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.software Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9307090900.AA19054@net.bio.net> Date: 9 Jul 93 09:00:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!indyvax.iupui.edu!imhw400 From: imhw400@indyvax.iupui.edu Newsgroups: bionet.software,vmsnet.networks.tcp-ip.multinet,vmsnet.sources.d Subject: Re: Looking for xmosaic for VMS Message-ID: <1993Jul9.153705.1397@indyvax.iupui.edu> Date: 9 Jul 93 20:37:05 GMT References: <1993Jul5.092319.7229@mcclb0.med.nyu.edu> <1993Jul5.144457.11025@nic.funet.fi> <1993Jul6.091203.21639@nessie.mcc.ac.uk> <1993Jul6.090643.1363@indyvax.iupui.edu> Lines: 9 Xref: biosci bionet.software:5409 In article <1993Jul6.090643.1363@indyvax.iupui.edu>, imhw400@indyvax.iupui.edu writes: > I got a 1.0 port from BCHM2ACLCB.PURDUE.EDU. I've also heard of one done by Oops! That should be BCHM2.ACLCB.PURDUE.EDU. (Note the additional period.) Thanks to David Woodruff at MIT for pointing out the error. Sorry about that. -- Mark H. Wood, Lead Systems Programmer +1 317 274 0749 [@disclaimer@] Internet: IMHW400@INDYVAX.IUPUI.EDU BITNET: IMHW400@INDYVAX Celebrate freedom: read a banned newsgroup. From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!JHUHYG.BITNET!NWALKER From: NWALKER@JHUHYG.BITNET (Nigel Walker) Newsgroups: bionet.software Subject: Quantitative scanning eqpmnt Message-ID: <9307092154.AA21572@net.bio.net> Date: 9 Jul 93 21:23:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 Hi all Ive read recently that several groups have been using Macs,scanners, Photoshop and Image to do quantitation of Northen blot autoradiograms. How does this package compare with the PDI Quantity One software (for unix) and the Biorad quantitation systems that cost 12-15K. Does the type of scanner significantly affect the quantitation or do the $1-2K scanners at 600dpi do as good a job? What software do others out there use for Northern quantitation and how fast is it? Time is our problem at the moment with single autorads taking sev. hours to complete analyses that can be done in minutes on other systems. Thanks in advance Nigel Walker Johns Hopkins University Batimore USA From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!harpo.wi.mit.edu From: lstein@harpo.wi.mit.edu (Lincoln Stein) Newsgroups: bionet.announce,bionet.genome.chromosomes,bionet.software,bionet.molbio.gene-linkage Subject: ANNOUNCING RELEASE 3 OF WI/MIT CGR MOUSE GENETIC MAP Keywords: SSLP genetic map linkage genome center mouse mus Message-ID: <21jv8f$hlt@harpo.wi.mit.edu> Date: 9 Jul 93 14:27:27 GMT Sender: kristoff@net.bio.net Followup-To: lstein@genome.wi.mit.edu Organization: Whitehead Institute for Biomedical Research Lines: 66 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:617 bionet.genome.chromosomes:54 bionet.software:5407 bionet.molbio.gene-linkage:196 ANNOUNCING THE THIRD RELEASE OF THE WHITEHEAD INSTITUTE/MIT GENOME CENTER GENETIC MAP OF THE MOUSE Release Three of the Whitehead Institute/MIT Genome Center Genetic Map of the Mouse is now available. This map consists of randomly-chosen simple sequence length polymorphisms (microsatellites) that can be analyzed using the polymerase chain reaction, as described in Dietrich, W., et al., Genetics 131:423-447 (1992). Currently the released map contains 1524 markers. The markers fall into 20 linkage groups spanning approximately 1400 cM with an average spacing of less than 1 cM. This data can be obtained in two different ways. 1. Via anonymous ftp to genome.wi.mit.edu. Log in as "anonymous" and use your e-mail address as password. The release can be found in the directory /distribution/mouse_sslp_release/july93/. The file "README" describes the file format and gives other information about the map. 2. Via internet e-mail using a database e-mail server. Using this service you can obtain locus and assay names of mapped SSLPs, the forward and reverse primer sequences, the genotypes of the loci on the mapping cross, the sizes of the PCR products on selected standard inbred strains, and other useful information. The database can be queried for markers meeting a number of different criteria. For example, you can ask for markers by name, by chromosome, or by position on the map. You can even request a list of markers that are polymorphic between two mouse strains. To obtain copies of the most current query forms, send a message to "genome_database@genome.wi.mit.edu" with either a subject line or body text of "help". You will receive instructions and a query form by return mail. Just fill out the form, send it to "genome_database@genome.wi.mit.edu", and the answer to your query will be mailed back automatically. This project is an ongoing one. As new markers are added to the map they will be released on a quarterly basis on approximately the following schedule: 1 October 1993 1 January 1994 1 April 1994 1 July 1994 &c. Please address questions and comments to me at the address below. Lincoln Stein ======================================================================== Lincoln Stein, M.D.,Ph.D. lstein@genome.wi.mit.edu MIT Genome Center (617) 252-1916 Whitehead Institute for Biomedical Research (617) 252-1902 FAX 9 Cambridge Center Cambridge, MA 02142 ======================================================================== -- ======================================================================== Lincoln D. Stein lstein@genome.wi.mit.edu Whitehead Institute, Cambridge, MA ======================================================================== From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!elroy.jpl.nasa.gov!news.claremont.edu!nntp-server.caltech.edu!seqvax.caltech.edu!mathog From: mathog@seqvax.caltech.edu (David Mathog) Newsgroups: bionet.software Subject: Cheapest color hardcopy for protein structures? Message-ID: <8JUL199316592422@seqvax.caltech.edu> Date: 9 Jul 93 00:59:00 GMT Organization: Division of Biolgy, CALTECH Lines: 23 NNTP-Posting-Host: seqvax.bio.caltech.edu News-Software: VAX/VMS VNEWS 1.41 We need color hardcopy for a protein structure class where students will be generating images on SGI workstations. We can already get screen dumps to a slidemaker, but that works out to around $1.00/picture. We'd like to get the cost below 20 cents per image. Speed is also a concern - images should print in no more than a minute or two. Around 90% of the images don't need shading and consist only of lines and points. It would be a big help if we could at least get these printed cheaply. Are color inkjet printers a good place to start looking? Anybody have experience with these in this application? Other suggestions? Thanks, David Mathog mathog@seqvax.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!Corp.Sun.COM!Alexandre.Valais From: Alexandre.Valais@Corp.Sun.COM (Alexandre Valais) Newsgroups: bionet.software Subject: GCG ... Message-ID: <9307091940.AA09196@frenchy.Corp.Sun.COM> Date: 9 Jul 93 19:40:31 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 Need a contact name , phone and fax number for GCG . Thanks a lot . _______________________________________________________________________________ Alexandre V. Valais phone# : 415-336-0771 Medical & Biotech MSMgr fax# : 415-336-0643 E&R Market Dev. Group TIMDG / Sun Microsystems email : Alexandre.Valais@Corp.Sun.COM _______________________________________________________________________________ From owner-software@net.bio.net Fri Jul 09 23:00:00 1993 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU Newsgroups: bionet.software Subject: mapmaker3 for NeXTStep? Message-ID: <9307100432.AA03184@nature.berkeley.edu.cnr-net> Date: 10 Jul 93 04:32:33 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 To the group, Has anyone compiled mapmaker3 on a NeXT? And could they tell me how they did it? According to the documentation this could be straightforward, but I believe they mean for those who are educated in these matters. The simplest attempts like 'cc' -> 'cc -bsd' aren't sufficent. I will certainly summarize back to the group. Thank you for your attention to these matters, ------------------------------------------------------------ Brian Osborne Plant Gene Expression Center bosborne@nature.berkeley.edu Albany CA USA ------------------------------------------------------------ From owner-software@net.bio.net Fri Jul 09 23:00:00 1993 Path: biosci!NET.BIO.NET!web!ceniai.cu!ingen.cu!carmas From: web!ceniai.cu!ingen.cu!carmas@NET.BIO.NET (Carlos Israel Armas) Newsgroups: bionet.software Subject: POPmail and NUPOP source code? Message-ID: Date: 9 Jul 93 23:31:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 Hi netters! anyone knows where to ftp for the source code of POPmail or NUPOP? both run on IBM PC MSDOS. I don't have access to archie or ftp. it's clients for POP services. (RFCs 1081, 1082) thanks a lot in advance, warm regards, carlos -- carlos armas carmas%ingen@web.apc.org network manager automation division center of genetic engineering & biotechnology pobox 6162 havana, cuba voice: 537 218200 fax: 537 218070 From owner-software@net.bio.net Fri Jul 09 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!usenet.ins.cwru.edu!axa12-slip.DIALIN.CWRU.Edu!ashok From: ashok@biochemistry.cwru.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: POPmail and NUPOP source code? Message-ID: Date: 10 Jul 93 15:45:25 GMT References: Distribution: bionet Organization: Department of Biochemistry, Case Western Reserve University Lines: 19 NNTP-Posting-Host: axa12-slip.dialin.cwru.edu In article web!ceniai.cu!ingen.cu!carmas@NET.BIO.NET (Carlos Israel Armas) writes: >Hi netters! >anyone knows where to ftp for the source code of POPmail or NUPOP? >both run on IBM PC MSDOS. I don't have access to archie or ftp. >it's clients for POP services. (RFCs 1081, 1082) To the best of my knowledge, source code for either is not available. If you are interested in looking at POP2 or POP3 client code, I would recommend taking a look at the source for the KA9Q clients. Off course these are not GUI clients .... Ashok -- Ashok Aiyar Mail: ashok@biochemistry.cwru.edu Department of Biochemistry Tel: (216) 368-3300 CWRU School of Medicine, Cleveland, Ohio Fax: (216) 368-4544 MIME Enclosures OK From owner-software@net.bio.net Sat Jul 10 23:00:00 1993 Path: biosci!uwm.edu!wupost!uunet!news.claremont.edu!pomona.claremont.edu!GREG From: greg@pomona.claremont.edu (Tigger) Newsgroups: bionet.software,vmsnet.sources.d,vmsnet.mail.pmdf Subject: Re: Need source-code for BinHex Message-ID: <0096F57F.221357E4@pomona.claremont.edu> Date: 11 Jul 93 21:21:28 GMT References: <1993Jul11.112112.7233@mcclb0.med.nyu.edu> Sender: news@news.claremont.edu (The News System) Reply-To: greg@pomona.claremont.edu Organization: Pomona College Lines: 10 Xref: biosci bionet.software:5415 In article <1993Jul11.112112.7233@mcclb0.med.nyu.edu>, smith@mcclb0.med.nyu.edu writes: > >Does anyone know where I could find a copy of the source for BinHex. I don't know about source, but there is a document called binhex-40-specs.txt available via anonymous ftp from the Info-Mac archives at sumex-aim.stanford.edu (36.44.0.6), in /info-mac/dev/info. That should probably tell you everything you need to know to write your own code. Greg From owner-software@net.bio.net Sat Jul 10 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!uwm.edu!rutgers!mcclb0.med.nyu.edu!smith From: smith@mcclb0.med.nyu.edu Newsgroups: bionet.software,vmsnet.sources.d,vmsnet.mail.pmdf Subject: Need source-code for BinHex Message-ID: <1993Jul11.112112.7233@mcclb0.med.nyu.edu> Date: 11 Jul 93 16:21:12 GMT Organization: NYU Medical Center, New York, NY 10016, USA Lines: 15 Xref: biosci bionet.software:5414 Does anyone know where I could find a copy of the source for BinHex. My goal is to get a version that will run on a VAX (or under UNIX for that matter). We want it so as to be able to process BinHex stuff from a Mac without having to play silly file-server games and unBinHex it on a Mac. This is to deal with BinHexed mail attachments that come from people with Macs using Eudora. I seem to remember that there is a MS-DOS version somwewhere. Maybe this would be a good place to start, if someone has not already done the job... +----------------------------------------------------------------------------+ |Ross Smith, Research Computing Resource, Department of Cell Biology, NYU-MC| |E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| +----------------------------------------------------------------------------+ From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: CHRIS@wwg3.uovs.ac.za Newsgroups: bionet.software Subject: Re: Need source-code for BinHex Message-ID: <1993Jul12.080738.15629@gserv1.dl.ac.uk> Date: 12 Jul 93 10:08:11 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Organization: Computer Sience, UOFS, Bfn, RSA Lines: 33 Original-To: bio-software@uk.ac.daresbury Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Return-Receipt-To: CHRIS@wwg3.uovs.ac.za Does anyone know where I could find a copy of the source for BinHex. My goal is to get a version that will run on a VAX (or under UNIX for that matter). We want it so as to be able to process BinHex stuff from a Mac without having to play silly file-server games and unBinHex it on a Mac. This is to deal with BinHexed mail attachments that come from people with Macs using Eudora. I seem to remember that there is a MS-DOS version somwewhere. Maybe this would be a good place to start, if someone has not already done the job... +----------------------------------------------------------------------------+ |Ross Smith, Research Computing Resource, Department of Cell Biology, NYU-MC| |E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| +----------------------------------------------------------------------------+ Dear Ross Smith, I have found a BinHex program for MS-DOS. I have searched in vain for a MS-DOS version of DeBinHex. Kind regards Chris ___________________________________________________________________ |Chris Viljoen | Dept. of Microbiology & | |Internet: chris@wwg3.uovs.ac.za | Biochemistry | |Telephone: (051) 401-2875 | Univ. of the Orange Freestate | |Telefax: 27/51/482004 | P.O. Box 339, Bloemfontein, 9300| | | South Africa | ------------------------------------------------------------------- From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!ARTHUR.CITI2.FR!CHASSE From: CHASSE@ARTHUR.CITI2.FR Newsgroups: bionet.software Subject: Looking for an aligment sw for PC Message-ID: <930712120600.2020cc8e@ARTHUR.CITI2.FR> Date: 12 Jul 93 10:06:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 I am looking for a DOS or WINDOWS program for IBM-PC which is doing a aligment with two sequences ( a program as KANEHISA on VMS ). J.F.CHASSE CHASSE@arthur.citi2.fr From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!agate!library.ucla.edu!psgrain!ee.und.ac.za!ford.ee.up.ac.za!zeno.up.ac.za!bio1 From: bio1@navi.up.ac.za (Fourie Joubert) Newsgroups: bionet.software Subject: NIH Image question Message-ID: Date: 12 Jul 93 12:55:23 GMT Organization: University of Pretoria Lines: 16 NNTP-Posting-Host: zeno.up.ac.za I'm thinking of putting together a Mac system for gel analysis using NIH Image. Can NIH Image read TIFF or similar files created on a PC scanner? If not, is there a relatively cheap card available for connecting a Mac to our lab video camera? Please mail, thanks a lot!! __________________________________________________________________________ _/_/_/_/ _/_/_/_/_/ Fourie Joubert _/ _/ Department of Biochemistry _/ _/ University of Pretoria _/_/_/_/ _/ South Africa _/ _/ bio1@navi.up.ac.za _/ _/_/_/_/ Disclaimer: "Fourie who?" __________________________________________________________________________ From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!gatech!willis1.cis.uab.edu!ramermac.nrc.uab.edu!user From: ramer@nrc-iris.nrc.uab.edu (Kevin W. Ramer) Newsgroups: bionet.software Subject: Re: Need source-code for BinHex Message-ID: Date: 12 Jul 93 14:51:50 GMT References: <1993Jul11.112112.7233@mcclb0.med.nyu.edu> <0096F57F.221357E4@pomona.claremont.edu> Sender: root@cis.uab.edu (Operator) Followup-To: bionet.software,vmsnet.sources.d,vmsnet.mail.pmdf Organization: UAB - Neurobiology Research Center Lines: 19 In article <0096F57F.221357E4@pomona.claremont.edu>, greg@pomona.claremont.edu (Tigger) wrote: > > In article <1993Jul11.112112.7233@mcclb0.med.nyu.edu>, smith@mcclb0.med.nyu.edu writes: > > > >Does anyone know where I could find a copy of the source for BinHex. > > I don't know about source, but there is a document called binhex-40-specs.txt > available via anonymous ftp from the Info-Mac archives at > sumex-aim.stanford.edu (36.44.0.6), in /info-mac/dev/info. That should > probably tell you everything you need to know to write your own code. That being said: There are various unix utilities located at sumex-aim.stanford.edu. Among them are xbin, mcvert, macbinary, unsit. These will convert various formats for transfer to your mac. -- Kevin From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!cs.utexas.edu!uunet!nih-csl!pico.nimh.nih.gov!user From: wayne@helix.nih.gov (Wayne Rasband) Newsgroups: bionet.software Subject: Re: NIH Image question Message-ID: Date: 12 Jul 93 15:26:52 GMT References: Sender: postman@alw.nih.gov (AMDS Postmaster) Followup-To: bionet.software Organization: NIH Lines: 23 In article , bio1@navi.up.ac.za (Fourie Joubert) wrote: > > I'm thinking of putting together a Mac system for gel analysis using NIH > Image. Can NIH Image read TIFF or similar files created on a PC scanner? NIH Image can read 8-bit uncompressed TIFF files created on little-endian DOS/Windows machines. Image 1.50(now in beta) adds the ability to import 16-bit TIFF files. > If not, is there a relatively cheap card available for connecting a Mac to > our lab video camera? The least expensive frame grabber directly supported by NIH Image is the Scion LG-3, which has a list price of $895. Scion's phone number is 301-695-7870. The Image 1.50 beta can acquire images from any Mac frame grabber or scanner that has a Photoshop plug-in. The current version of NIH Image(1.49), as well as the 1.50 beta, are available by anonymous FTP from zippy.nimh.nih.gov[128.231.98.32], in the /pub/image directory. --wayne From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!uwm.edu!post.its.mcw.edu!pixel.cellbio.mcw.edu!ttrusk From: ttrusk@its.mcw.edu (Thomas Trusk, PhD) Newsgroups: bionet.software Subject: Re: NIH Image question Message-ID: Date: 12 Jul 93 16:24:10 GMT References: Organization: Medical College of Wisconsin Lines: 19 NNTP-Posting-Host: pixel.cellbio.mcw.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #7] In article bio1@navi.up.ac.za (Fourie Joubert) writes: >I'm thinking of putting together a Mac system for gel analysis using NIH >Image. Can NIH Image read TIFF or similar files created on a PC scanner? >If not, is there a relatively cheap card available for connecting a Mac to >our lab video camera? We've had NO trouble getting ANY computer image data, no matter what the source, into NIH Image. Just know the format! *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*==**=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*==* *Thomas Trusk, PhD * * *Dept. of Cellular Biology & Anatomy * I'm a peripheral visionary. * *Medical College of Wisconsin * I can see into the future... * *Milwaukee, WI 53226 * Just way off to the side. * *MaBellNet: (414) 257-8504 * * *INTERNET: ttrusk@its.mcw.edu * Steven Wright * *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*==**=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*==* From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!UVVM.UVIC.CA!JCOWARD From: JCOWARD@UVVM.UVIC.CA Newsgroups: bionet.software Subject: CALL FOR PAPERS - ITCH'94 Message-ID: <9307121700.AA21979@net.bio.net> Date: 12 Jul 93 16:58:10 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 76 ITCH 1994 INFORMATION TECHNOLOGY IN COMMUNITY HEALTH OCTOBER 30 - NOVEMBER 2, 1994 VICTORIA, B.C. CANADA A CONFERENCE ADDRESSING INFORMATION TECHNOLOGY ISSUES IN COMMUNITY HEALTH 2nd: CALL FOR PAPERS This conference provides a forum for academics, health professionals and computer system professionals to present and exchange of ideas and research results in the general area of information technology for community health. Prospective contributors to the ITCH '94 Conference are encouraged to address topics in the following list. Technology * Community health data networks * Health data communication protocols * Appropriate technology * Telehealth Policy * Community health system assessment * Community health system planning * Program evaluation * Cost/benefit analysis * Technology assessment Applications * Community health information systems * Community health information resources * Diagnostic and clinical expert systems * Client and care giver education * Community health databases * Rehabilitation * Software user interfaces * User interfaces for the disabled * Systems for developing countries Papers should be limited to 20 minutes in length. Abstracts of 250 words will be accepted up to February 15 1994; authors will be notified by March 15 1994 and completed papers will be due August 15 1994. Please submit your abstract to: Dr. Kenneth Thornton, Chairman ITCH '94 - Scientific Program Committee School of Health Information Science University of Victoria P.O. Box 3050, Victoria B.C. V8W 3P5 SUBMISSIONS MAY BE SENT BY E-MAIL TO: KTHORNTO@HSD.UVIC.CA or by fax to (604) 721-1457 To obtain more information about the conference, please contact: Dr. Paul Fisher, Chairman - ITCH '94 School of Health Information Science University of Victoria P.O. Box 3050, Victoria B.C. V8W 3P5 INQUIRIES MAY BE SENT BY E-MAIL TO:PFISHER@HSD.UVIC.CA or by phone at (604) 721-8575 or by fax to (604) 721-1457 Paul Fisher, Ph.D. School of Health Information Science The University of Victoria Box 3050 Victoria B.C., Canada Phone: (604) 721-8578 FAX: (604) 721-1457 From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!cs.utexas.edu!uunet!mcsun!sunic!trane.uninett.no!nntp.uio.no!NewsWatcher!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.software Subject: Re: NIH Image question Message-ID: Date: 12 Jul 93 15:22:59 GMT References: Followup-To: bionet.software Organization: Inst for Cancer Research, Oslo Lines: 16 NNTP-Posting-Host: pcdnr05.uio.no In article , bio1@navi.up.ac.za (Fourie Joubert) wrote: > > I'm thinking of putting together a Mac system for gel analysis using NIH > Image. Can NIH Image read TIFF or similar files created on a PC scanner? > Yes, you can import the files if you know their header size, length and width. Ola Myklebost Email ola.myklebost@dnr.uio.no Dept of Tumor Biology Inst for Cancer Research The Norwegian Radium Hospital N-0310 OSLO, Norway Tel +47-22-50-60-50, xtn 9830, Fax +47-22-52-24-21 From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!usenet.ins.cwru.edu!axa12-slip.cwru.edu!ashok From: ashok@biochemistry.cwru.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Where to find Binhex/HexBin for DOS (was Re: Need source-code for BinHex) Message-ID: Date: 13 Jul 93 01:55:32 GMT References: <1993Jul12.080738.15629@gserv1.dl.ac.uk> Distribution: bionet Organization: Department of Biochemistry, Case Western Reserve University Lines: 35 NNTP-Posting-Host: axa12-slip.dialin.cwru.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #7] In article <1993Jul12.080738.15629@gserv1.dl.ac.uk> CHRIS@wwg3.uovs.ac.za writes: >Newsgroups: bionet.software >Does anyone know where I could find a copy of the source for BinHex. >My goal is to get a version that will run on a VAX (or under UNIX for that >matter). We want it so as to be able to process BinHex stuff from a Mac >without having to play silly file-server games and unBinHex it on a Mac. >This is to deal with BinHexed mail attachments that come from people with Macs >using Eudora. >I seem to remember that there is a MS-DOS version somwewhere. Maybe this >would be a good place to start, if someone has not already done the job... >+----------------------------------------------------------------------------+ >|Ross Smith, Research Computing Resource, Department of Cell Biology, NYU-MC| >|E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| >+----------------------------------------------------------------------------+ >Dear Ross Smith, >I have found a BinHex program for MS-DOS. I have searched in vain >for a MS-DOS version of DeBinHex. Check boombox.micro.umn.edu in /pub/pc/binhex .... works both ways. I also archive a copy at biochemistry.bioc.cwru.edu in /pub/dos Ashok -- Ashok Aiyar Mail: ashok@biochemistry.cwru.edu Department of Biochemistry Tel: (216) 368-3300 CWRU School of Medicine, Cleveland, Ohio Fax: (216) 368-4544 MIME Enclosures OK From owner-software@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!cricket.bio.indiana.edu!user From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: NIH Image question Message-ID: Date: 12 Jul 93 14:37:29 GMT References: Sender: news@usenet.ucs.indiana.edu (USENET News System) Followup-To: bionet.software Organization: Biology - Indiana University Lines: 23 Nntp-Posting-Host: cricket.bio.indiana.edu In article , bio1@navi.up.ac.za (Fourie Joubert) wrote: > > I'm thinking of putting together a Mac system for gel analysis using NIH > Image. Can NIH Image read TIFF or similar files created on a PC scanner? Yes. Many other common Mac graphics applications can read TIFF also, including Canvas and Photoshop. > If not, is there a relatively cheap card available for connecting a Mac to > our lab video camera? Video Spigot is such a card that is inexpensive ($400 for nubus mac, other models for LC and SI) and links to many kinds of video input -- VCR, camcorder, TV. I haven't used one. I'm looking at the blurb for it in MacWarehouse mail order catalog. Phones: 800.622.6222, Fax: 203.855.1386, paper mail: MacWareHouse, 47 Water St., Norwalk, CT 06854. Other Mac mail-order companies will also sell this. _________________ Don Gilbert, Biocomputing Office, Biology, Indiana Univ., Bloomington, IN 47405 From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!cs.utexas.edu!uunet!news!demon!genesys.demon.co.uk!Duncan From: Duncan@genesys.demon.co.uk ("Dr. Duncan Clark") Newsgroups: bionet.software Subject: DNA Gel Image capture Message-ID: <742503147snz@genesys.demon.co.uk> Date: 12 Jul 93 18:52:27 GMT Sender: usenet@demon.co.uk Reply-To: Duncan@genesys.demon.co.uk Organization: GeneSys Ltd. Lines: 20 X-Newsreader: Simple NEWS 1.90 (ka9q DIS 1.21) Hi Netters, In the most recent Biotechniques, June pp902-905, an inexpensive image capture system was described complete with equipment sources/cat. no.'s and prices. The authors gave a price for a Sony UP860 thermal printer as $1000. Here in the UK that will equate to 1000+ UK pounds regardless of exchange rates etc. I asked a friend in the US to check the price and then buy one for me and ship it over etc. The best price he has been quoted is $1550. Anyone know of a better source/price. Failing that has anyone a FAX or Email address for the authors, Stephan Winans or Michael Rooks at Section of Microbiology, National Nanofabrication Facility, Cornell University, Ithaca, NY. Many thanks. Duncan Clark -- ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys@demon.co.uk GeneSys Ltd. | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!swrinde!gatech!usenet.ins.cwru.edu!axa12-slip.cwru.edu!ashok From: ashok@biochemistry.cwru.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Restriction enzyme database in DBF format .... Message-ID: Date: 13 Jul 93 07:29:17 GMT Organization: Department of Biochemistry, Case Western Reserve University Lines: 11 NNTP-Posting-Host: axa12-slip.dialin.cwru.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #7] If someone can provide me with the REBASE database in DBF format, I would *greatly* appreciate it! Thanks, Ashok -- Ashok Aiyar Mail: ashok@biochemistry.cwru.edu Department of Biochemistry Tel: (216) 368-3300 CWRU School of Medicine, Cleveland, Ohio Fax: (216) 368-4544 MIME Enclosures OK From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!CSC.FI!Rob.Harper From: Rob.Harper@CSC.FI (Rob Harper) Newsgroups: bionet.software Subject: Prospero... Message-ID: <199307130834.AA07782@csc.fi> Date: 13 Jul 93 08:34:28 GMT Sender: daemon@net.bio.net Lines: 121 >Path: funic!news.funet.fi!sunic!pipex!bnr.co.uk!bnrgate!nott!torn!utnut!cs.utexas.edu!usc!news.isi.edu!venera.isi.edu!swa >From: swa@ISI.EDU (Steven Seger Augart) >Newsgroups: comp.infosystems.www >Subject: Prospero Alpha 5.2 available; relevant to WWW folks >Date: 7 Jul 93 02:04:36 >Organization: USC-ISI >Lines: 109 >Distribution: comp >Message-ID: >NNTP-Posting-Host: zephyr.isi.edu We posted the following announcement today to comp.infosystems.gopher. I am posting it here to let you all know that we are working on a similar integration of WWW and Prospero. An Alpha release of version 5.2 of the Prospero file system is now available by anonymous FTP from PROSPERO.ISI.EDU in the file pub/prospero/prospero-alpha.5.2.tar.Z. It can also be obtained through Prospero itself from /releases/prospero/prospero-alpha.5.2.tar.Z. The name prospero.tar.Z in those directories still points to the stable Beta 5.1 release; this has been done for the sake of the archie server maintainers and other information providers who depend upon Prospero. Some important changes since the last Prospero release should be of interest to the readers of comp.infosystems.gopher: (a) A menu-based browser client, similar to the Gopher client (b) A gateway server which makes all of Gopherspace available through Prospero queries. (c) A menu-based browser API interface library to Prospero, which allows one to easily write new browsers that use Prospero to make their underlying calls. The menu-based browser supports all of the basic Gopher types: searches, text files, data files, and portals (what Gopher calls telnet sessions). It does not yet support sophisticated display of binary image files, reading Postscript or MIME documents, playing sounds, or automatic decoding of uuencoded, compressed, or tarred files. These enhancements will be added shortly; the protocol definitions for them have already been made. We support authenticated remote modifications to menus, though not presently from within the browser itself. For now you will have to learn how to use a few Prospero commands to add new menus or items and set descriptions. We plan to eventually support remote update within the browser itself. Prospero, and thus menus available to the menu browser (as a Prospero client), supports fine grained access control based on client identity. Authentication is provided using 4 alternative authentication mechanisms, depending on your specific needs: (a) Kerberos (version 5); (b) per user passwords; (c) trusted port and trusted host assertion (like the Berkeley R commands); and (d) a check of the host from which a request originated and the asserted user identity of the client. Prospero provides full access control list mechanisms for those who wish to put fine-grained permissions on particular objects or directories. For instance, one can easily set some directories so that anybody at your company or university can read data in them, only a particular group of people can insert data into them, and only the system administrator or the author of a particular piece of information is allowed to modify and delete it. Of course, anyone who does not need these security mechanisms can export data using the default permissions defined on a per server basis. An elegant new Prospero feature we're rather proud of is the search interface. We support a variety of search methods, including direct queries to Prospero-speaking database servers, such as Archie servers and all Gopher servers via a Prospero-Gopher gateway. The search servers are self defining, exporting attributes that tell the client what to prompt for, help messages to display if requested by the user, and how to package the search when it is sent to the server. Client implementors need not worry about the generality of this mechanism since they can make perfectly functional clients that use only a small subset of the available data. The menu browser has a subset of this search interface built into it. The philosophy behind this work, or why we are doing this: One of Gopher's greatest strengths is its clear, straightforward user interface. However, the gopher protocol itself has a number of limitations which keep it from being suitable as a universal Internet information infrastructure, such as the fact that all updates to data must be made through means outside the protocol (i.e., editing files on the server) and its lack of security mechanism. Most current Internet information services, such as Gopher, World Wide Web, and WAIS, have their own specialized clients, servers, and network protocols. This makes it difficult for these services to interoperate smoothly. People attempt to address these issues with inefficient ad-hoc gateways, such as the Gopher servers that make Archie queries on behalf of Gopher clients, or even our own Prospero-Gopher gateway. These are not very good solutions. Prospero provides a framework for integrating information from diverse sources. Client writers can work on interesting clients, and service providers can publish their data, without needing to work on issues of little interest to them. We explore these ideas in greater depth in the paper 'Prospero: A Base for Building Information Infrastructure', to be presented at the INET '93 conference in August, and available via anonymous FTP from PROSPERO.ISI.EDU as /pub/papers/prospero/prospero-bii.ps.Z. We encourage others to build clients that make their queries through Prospero and to publish their data through Prospero. We provide an application library (much better documented in this release than in previous ones) and a simple application interface designed specifically for the authors of read-only menu browsers. It is also not difficult to publish your data through Prospero, and we are eager to work with those who wish to do so. -- Steven Seger Augart Research Staff, USC Information Sciences Institute -- B. Clifford Neuman Scientist, USC Information Sciences Institute email: info-prospero@isi.edu From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: daj@nhm.ic.ac.uk ((David Johnston) daj) Newsgroups: bionet.software Subject: Re: POPmail and NUPOP source code? Message-ID: <1993Jul13.083026.2029@gserv1.dl.ac.uk> Date: 13 Jul 93 08:10:17 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 28 Original-To: bio-software@uk.ac.daresbury X-Popmail-Charset: British Original-Cc: daj@uk.ac.ic.nhm On 9 Jul 93 23:31:44 GMT, Carlos Israel Armas writes: >Hi netters! >anyone knows where to ftp for the source code of POPmail or NUPOP? >both run on IBM PC MSDOS. I don't have access to archie or ftp. >it's clients for POP services. (RFCs 1081, 1082) >thanks a lot in advance, >warm regards, >carlos >-- >carlos armas carmas%ingen@web.apc.org >network manager automation division >center of genetic engineering & biotechnology >pobox 6162 havana, cuba >voice: 537 218200 fax: 537 218070 For POPMAIL, try to Email: popmail@boombox.micro.umn.edu or write to: POPmail project University of Minisota Room 125 Shepherd Labs Minneapolis, MN55455 USA From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: GRGGTA@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK Newsgroups: bionet.software Subject: SLIDES/POSTER DRAWING SOFTWARE Message-ID: <1993Jul13.112631.5240@gserv1.dl.ac.uk> Date: 13 Jul 93 12:14:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 34 Original-To: BIO-SOFTWARE@UK.AC.DARESBURY From: CBS%UK.AC.DARESBURY.DLGM::PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK::GRGGTA 13-JUL-1993 11:11:41.42 To: grggta CC: Subj: Slides/poster drawing software Via: UK.AC.DARESBURY.DLGM; Tue, 13 Jul 93 11:11 GMT Received: by gserv1 (4.1/DL-V2.3) id AA03617 ( for dl_sun_server); Tue, 13 Jul 93 10:42:25 BST Resent-From: Date: Tue, 13 Jul 1993 09:19:00 GMT Resent-Date: Tue, 13 Jul 93 10:42:24 UT To: "bionet.molbio.methds-reagnts mail newsgroup" Message-Id: <93713104224.MIN-LBBAa03049.bionet-news@uk.ac.daresbury> Resent-Message-Id: <1993Jul13.085252.2724@gserv1.dl.ac.uk> From: GRGGTA@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK Reply-To: GRGGTA@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK Sender: "bionet.molbio.methds-reagnts mail newsgroup" Subject: Slides/poster drawing software X-Article-Number: bionet.molbio.methds-reagnts Msg # 4575 Comments: List problems/queries to Comments: To mail both the group and netnews send to (methods@daresbury.ac.uk) Dear All, We are about to update our ancient 'GEM' graphics drawing software (circa 1987) for something better. We use this software for molecular biology- oriented slides, posters, thesis illustrations etc. It includes graph presentation and drawing applications. I have arrived at three alternatives Coreldraw v3 or v4 at 3x the price, harvard graphics or Micrographix Graphics Works. Our reqiurements are that it should be easy to use and offer as much control over the image as possible, without requiring 'professional graphics designer levels of complexity. Our budget extends to 300 sterling and 40MB (plus DOS v6 file compression ie approx 70MB in total? Any suggestions or comments? Graham Atherton From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: GRGGTA@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK Newsgroups: bionet.software Subject: slides/poster drawing software Message-ID: <1993Jul13.121109.6612@gserv1.dl.ac.uk> Date: 13 Jul 93 13:11:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 34 Original-To: BIO-SOFTWARE@UK.AC.DARESBURY From: CBS%UK.AC.DARESBURY.DLGM::PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK::GRGGTA 13-JUL-1993 11:11:41.42 To: grggta CC: Subj: Slides/poster drawing software Via: UK.AC.DARESBURY.DLGM; Tue, 13 Jul 93 11:11 GMT Received: by gserv1 (4.1/DL-V2.3) id AA03617 ( for dl_sun_server); Tue, 13 Jul 93 10:42:25 BST Resent-From: Date: Tue, 13 Jul 1993 09:19:00 GMT Resent-Date: Tue, 13 Jul 93 10:42:24 UT To: "bionet.molbio.methds-reagnts mail newsgroup" Message-Id: <93713104224.MIN-LBBAa03049.bionet-news@uk.ac.daresbury> Resent-Message-Id: <1993Jul13.085252.2724@gserv1.dl.ac.uk> From: GRGGTA@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK Reply-To: GRGGTA@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK Sender: "bionet.molbio.methds-reagnts mail newsgroup" Subject: Slides/poster drawing software X-Article-Number: bionet.molbio.methds-reagnts Msg # 4575 Comments: List problems/queries to Comments: To mail both the group and netnews send to (methods@daresbury.ac.uk) Dear All, We are about to update our ancient 'GEM' graphics drawing software (circa 1987) for something better. We use this software for molecular biology- oriented slides, posters, thesis illustrations etc. It includes graph presentation and drawing applications. I have arrived at three alternatives Coreldraw v3 or v4 at 3x the price, harvard graphics or Micrographix Graphics Works. Our reqiurements are that it should be easy to use and offer as much control over the image as possible, without requiring 'professional graphics designer levels of complexity. Our budget extends to 300 sterling and 40MB (plus DOS v6 file compression ie approx 70MB in total? Any suggestions or comments? Graham Atherton From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!mcsun!dkuug!uts!biobase!pamaga From: pamaga@biobase.aau.dk (Paulo Magalhaes) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: AutoR software - new thoughts Message-ID: Date: 13 Jul 93 09:02:36 GMT Organization: The Danish BioBase Lines: 25 Xref: biosci bionet.molbio.methds-reagnts:6433 bionet.software:5431 A while back I posted a request for "quantification/analysis" of scanned images of autoradiograms. Thanks for the contributions. Here's a brief review and some more questions :) * Image Master, from Pharmacia - it sounds pretty good, but the price is ridiculously high... * PhotoShop for Windows - does this program do exactly the same thing as the Mac version? Who commercializes it? * QuantiScan, from BioSoft - does this program do the same as Image 1.44 (for the Mac)? Does anyone have any experience with it? It seems as if it is a good alternative, but we'd like to know a little more about it before we take the plunge. Price, anyone? * AND AGAIN: we're still looking for a PC program that provides the same features as Image 1.44 - amongst other things, we need to quantify and print autoRs... Your suggestions will be much appreciated. That's all for the time being :) All the best from Copenhagen, Paulo From owner-software@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: Lynx 2.0.10 Message-ID: <1993Jul13.083541.2195@gserv1.dl.ac.uk> Date: 13 Jul 93 08:36:41 GMT Sender: harper@fi.csc Distribution: bionet Lines: 103 Original-To: bio-soft@uk.ac.daresbury >Path: funic!vttux1!news.funet.fi!sunic!uunet!news.cnri.reston.va.us!newsserver.jvnc.net!howland.reston.ans.net!math.ohio-state.edu!caen!kuhub.cc.ukans.edu!stat1.cc.ukans.edu!local >Newsgroups: comp.infosystems.www >Subject: Lynx 2.0.10 Now Available >Message-ID: <1993Jul12.181600.51671@kuhub.cc.ukans.edu> >From: local@stat1.cc.ukans.edu (Lou Montulli) >Date: 12 Jul 93 18:15:59 CST >Keywords: Hypertext, browser, Lynx, Version 2.0.10 >Summary: Lynx 2.0.10, a WWW browser, is now available. >Nntp-Posting-Host: stat1.cc.ukans.edu >X-Newsreader: TIN [version 1.1 PL9] >Lines: 90 Lynx Ver. 2.0.10 is now available for anonymous ftp from FTP2.cc.ukans.edu as /pub/lynx/lynx2-0-10.tar.Z ( ftp://ftp2.cc.ukans.edu/pub/lynx/lynx2-0-10.tar.Z ) *NOTE: This is a new ftp site. The old ftp site (acs220) is no longer valid. Ftp2.cc.ukans.edu will be the new PERMANENT ftp site! Acs220 will carry a README file explaining the new site information for a period of at least two to three weeks. Lynx is a distributed hypertext browser with full World Wide Web capibilities. For an explanation of features and a demo, telnet to "kufacts.cc.ukans.edu" and login as "www". This release of Lynx has been compiled by me on the following platforms: o IBM (AIX 3.2) o DEC (Ultrix, VMS) o Sun 3 and 4 o NeXT (Mine is an older version of NeXTStep, but it should work with newer ones too.) Binaries for the following platforms are available: o IBM (AIX 3.2, will work with 3.1 as well) o Ultrix o Sun 4 o VMS (for multinet) A new listserv list has been created for the distribution of Lynx related information and updates. o Lynx-Dev@ukanaix.cc.ukans.edu Send a subscribe request to listserv@ukanaix.cc.ukans.edu to be added to the list. All new releases will be anounced on this list. The following new features have been added: o IMG tags are recognized and the word [IMAGE] appears in its place. (not in VMS) o "mailto:" URL's are now supported. o Document owners can now be defined using the "link" tag. will define me as the creator of the document. When the comment feature, the 'C' command in Lynx, is used, Lynx will use the "href" value as the destination of the comment. (not in VMS) o Now uses the 2.9 version of the WWW Common Code Library. (not in VMS) o Uses the full HTTP/1.0 protocol. o The environment variable WWW_HOME is now recognized. o Updated search routines. o WAIS support. (not in VMS, except gateway functions) o Optional Emacs-style key definitions. o Gopher Directory format has been changed to show verbose information by default, and the screen format has changed. o 'V' is now used to "View" the bookmark file. o 'G' is now used to "Go" to a random user specified URL.