From owner-www@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Randall Smith Subject: ANNOUNCE: New WWW protein and DNA analysis services Message-ID: <1995Apr4.174232.25567@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 30 Mar 1995 14:25:30 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 60 The Human Genome Center, Baylor College of Medicine, is pleased to announce two new WWW services which speed the analysis of DNA and protein sequences. These services are now available via the "BCM Search Launcher" Web page: http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html (The BCM Search Launcher organizes and simplifies molecular biology-related search and analysis services available on the WWW. It provides a single point-of-entry for related services, for example, a single page for launching sequence searches using standard parameters). 1) Multiple Sequence Alignment Server CLUSTAL-W (Thompson, Higgins, and Gibson, 1994), MAP (Huang, 1994), and PIMA (Smith and Smith, 1992) multiple sequence alignments can now be run remotely on our server via the Search Launcher. The server uses Don Gilbert's readseq program to input sequences in any one of a variety of formats (e.g., FASTA, GCG, NBRF, EMBL). Both DNA and protein multiple alignments can be performed. 2) BEAUTY searches of a new Annotated Protein Sequence Database The Annotated Sequences database consists of all Entrez protein sequences containing at least one domain or site (see below). BEAUTY performs a standard BLAST search of this database and generates a graphic for each database hit showing the locations of all annotated domains and sites with respect to the locations of the hits within each matched sequence. SRS links to the appropriate record in the Entrez, PROSITE, BLOCKS, and PRINTS databases are also provided. These enhancements make it much easier to detect functionally significant matches in BLAST database searches. A database of annotated domains/sites was created by 1) scanning the NCBI's Entrez database for protein sequence records containing annotations of domains and sites, and storing the location of all such regions, 2) matching each Entrez protein sequence against the sequence motifs in the PROSITE pattern database, and storing the location of each hit, 3) extracting the locations of the conserved blocks within the sequences represented in the BLOCKS database, and 4) extracting the locations of all domains identified in the sequences in the PRINTS protein fingerprint database. The Annotated Sequences database currently contains 55,566 sequences. A more detailed program description, is available at: http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/beauty.html ------------------------------------------------------------------------ Kim Worley, Brent Wiese, and Randall Smith Human Genome Center, Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine, Houston, TX 77030 USA kworley@bcm.tmc.edu, brent@bcm.tmc.edu, rsmith@bcm.tmc.edu ------------------------------------------------------------------------ From owner-www@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: Purdue Neuroscience Subject: Purdue Neuro WWW Server URL Update Message-ID: <1995Apr4.080759.14096@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 31 Mar 1995 05:58:47 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 16 Purdue University Neuroscience Purdue Neuroscience WWW Server The Purdue Neuroscience WWW server has been upgraded to a faster system. The new uniform resource locator (URL) is: http://bieber.bio.purdue.edu Stephen Hall Purdue University Neuroscience Program Purdue University West Lafayette, IN 47907-1392 Voice: 317-494-9001 FAX: 317-494-0876 From owner-www@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Victor V. Solovyev" Subject: Prediction Bacterial coding regions New server Message-ID: <1995Apr4.170805.25015@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 29 Mar 1995 17:58:10 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 97 ************************************************************************* CDSB - Prediction of Protein coding regions in Bacterial sequences (Version 1. 3.21.95) Department of Cell Biology, Baylor College of Medicine ========================================================================= Analysis of uncharacterized human sequences is available through University of Houston and Weizmann Institute of Science servers: with the name of the program in the subject line Examples: mail -s cdsb service@theory.bchs.uh.edu < test.seq mail -s cdsb services@bioinformatics.weizmann.ac.il < test.seq where test.seq a file with your sequence. Method description: ********************** The method is based on the discriminant analysis of open reading frames flanked ATG(GTG) and STOP codon pairs. Prediction is performed by linear discriminant function combining characteristics describing 5'- and 3'-mRNA regions and also coding region for each open reading frame. The program parameters were calculated based on E.coli annotated gene sequences. Accuracy: ******************************** The accuracy is about 94% recognition of coding nucleotides within a sequence up to 400000 bp long. The program predict nonoverlapping protein coding regions in a given sequence. Submitting sequences via email: *********************************** For email submission the sequences must have the following format: Nane of your sequence ccatctctgtcttgcaggacaatgccgtcttctgtctcgtggggcatcctcctgctggca ggcctgtgctgcctggtccctgtctccctggctgaggatccccagggagatgctgcccag aagacagatacatcccaccatgatcaggatcacccaaccttcaacaagatcacccccaac ctggctgagttcgccttcagcctataccgccagctggcacaccagtccaacagcaccaat atcttcttctccccagtgagcatcg............... (Restrict the line length to 80 characters or less). Hexon output: ****************** 1st line - name of the program 2nd line - name of your sequence 3nd line - length of your sequence, thereshold (will be optional), number of potential CDS 4th line and next - positions and scores of predicted exons and amino acid sequences of predicted CDS For example: CDSB search for protein coding regions in E.coli sequences ECAPTS 3708 bp DNA BCT Length: 3708 Threshold: 0.0, # of potential CDS: 3 152 - 886 w= 0.94 1612 - 2277 w= 0.26 2572 - 3300 w= 0.72 CDS- 1 Amino acid sequence - 245aa MKKVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANNQIVGFDVVDLAQALCKEID ATCTFSNQAFDSLIPSLKFRRVEAVMGGMDITPEREKQVLFTTPYYDNSALFVGQQGKYT SVDQLKGKKVRSVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLENGRIDGVFGDTAVV HEWLKDNPKLVVVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYN KWFQK CDS- 2 Amino acid sequence - 222aa MFEYLPELMKGLHTSLTLTVASLIVALILALIFTIILTLKTPVLVWLVRGYITLFTGTPL LVRIFLIYYGPGQFPTLQEYPALWHLLSEPWLCALIALSVNSAAYTTQLFYGAIRAIPEG QWQSCSALGMSKKDTLAILLPYAFKRSLSSYSNEVVLVFKSTSLAYTITLMEVMGYSQLL YGRTYDVMVFGAAGIIYLVVNGLLTLMMRLIERKAVAFERRN CDS- 3 Amino acid sequence - 243aa MKKLVLAALLASFTFGASAAEKINFGVSATYPPFESIGANNEIVGFDIDLAKALCKQMQA ECTFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENSAVVIAKKDTYKT FADLKGKCIGMENGTTHQKYIQDQHPEVKTVSYDSYQNAFIDLKNGRIDGVFGDTAVVNE WLKTNPQLGVATEKVTDPQYFGTGLGIAVRPDNKALLEKLNNALAAIKADGTYQKISDQW FPQ Reference about the methods: The method is described in detail in: Solovyev V.V.,Salamov A.A., Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. (Nucl.Acids Res.,1994, 22,24, 5156-5163). Solovyev V.V., Salamov A.A. , Lawrence C.B. The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. in: The Second International conference on Intelligent systems for Molecular Biology (eds. Altman R., Brutlag D., Karp R., Latrop R. and Searls D.), AAAI Press, Menlo Park, CA 1994, 354-362. Problems, comments, and suggestion: can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-www@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: "Victor V. Solovyev" Subject: New server for exon-exon junctions prediction Message-ID: <1995Apr4.085121.15018@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 29 Mar 1995 17:57:43 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 89 ************************************************************************* RNASPL - Prediction of exon-exon junction positions in cDNA sequences Department of Cell Biology, Baylor College of Medicine ========================================================================= Analysis of human cDNA sequences is available through University of Houston and Weizmann Institute of Science servers: with the name of the program in the subject line Example: mail -s rnaspl service@theory.bchs.uh.edu < test.seq mail -s rnaspl services@bioinformatics.weizmann.ac.il < test.seq where test.seq a file with the sequence. And you can run the program by WWW BCM Human Genome Center and Search launcher Home page URL:http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html for accsess to Gene-finder prediction Help files and programs. -> BCM Gene Finder Description: ********************** Recognition of exon-exon junctions in cDNA may be very useful for gene sequencing when starting with a sequence of cDNA clone. In a given cDNA sequence we need to select sites for PCR primers that (hopefully) lie in adjacent exons. Prediction is performed by linear discriminant function combining characteristics describing tipical sequences around exon-exon junctions. The method is described in Solovyev V.V.,Salamov A.A., Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. (Nucl.Acids Res.,1994, 22,24, 5156-5163). Accuracy: ******************************** We can not predict exon-exon junction position with very high accuracy, because some information was lost after splicing. We predict positions marked by '*', where 75% of potential exon-exon junctions are localized. Additionally, we mark '-' positions where exon-exon junctions absent with probability about 90%. We recommend to select primer sequences in continuous '-' regions, that do not cross '*' or ' ' positions. Submitting sequences via email: *********************************** For email submission the sequences must have the following format: Nane of your sequence ccatctctgtcttgcaggacaatgccgtcttctgtctcgtggggcatcctcctgctggca ggcctgtgctgcctggtccctgtctccctggctgaggatccccagggagatgctgcccag aagacagatacatcccaccatgatcaggatcacccaaccttcaacaagatcacccccaac ctggctgagttcgccttcagcctataccgccagctggcacaccagtccaacagcaccaat atcttcttctccccagtgagcatcg............... (Restrict the line length to 80 characters or less). RNASPL output: ****************** 1st line - name of your sequence 2nd line - your sequence 3d line: '*' shows potential exon-exon junction position (Pr > 0.75) '-' shows position where exon-exon junction absent (Pr > 0.90) 'n' is nonanalyzed flanking position ................................ For example: HSACHG7 690 bp DNA PRI 18-DEC-1990 10 20 30 40 50 60 ATGGCGGCGACGGCGAGTGCCGGGGCCGGCGGGATGGACGGGAAGCCCCGTACCTCCCCT nnnnnnnnnnnnnnnnnnnn-------- ---------*---- ----*---------- 70 80 90 100 110 120 AAGTCCGTCAAGTTCCTGTTTGGGGGCCTGGCCGGGATGGGAGCTACAGTTTTTGTCCAG ----- *----*--------- -- --------*------- --------------- - 130 140 150 160 170 180 CCCCTGGACCTGGTGAAGAACCGGATGCAGTTGAGCGGGGAAGGGGCCAAGACTCGAGAG -----------*-*--- ---- ------ --*----- -----------*------ -- 190 200 210 220 230 240 TACAAAACCAGCTTCCATGCCCTCACCAGTATCCTGAAGGCAGAAGGCCTGAGGGGCATT ------ ---------- ---------------- ------------------------ 250 260 270 280 290 300 TACACTGGGCTGTCGGCTGGCCTGCTGCGTCAGGCCACCTACACCACTACCCGCCTTGGC ----- -- ------------------------------------------------ -- Problems, comments, and suggestion: can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-www@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: "Charles E. Weaver" Subject: RE: [Q] ATCC www site and 800 number??? Message-ID: <1995Apr4.183115.26236@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Sat, 1 Apr 1995 13:13:14 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 36 [ Article crossposted from bionet.general ] [ Posted on 30 Mar 1995 14:46:35 GMT ] In article <3lcg31$749@vixen.cso.uiuc.edu>, bl-chen@uxa.cso.uiuc.edu (chen bi-liang) wrote: > Can someone help me with ATCC's www site and their 1-800 phone? > Thanks in advanced. > Martin leach provides a very extensive list of biotech companies their email address/www address/phone numbers etc... ATCC is one of these Martin Leaches Biotech Company listing is at: http://155.41.115.114/jumper/wfgo.html ATCC's www site is http://www.atcc.org/ || || || || __ __ __ __ __ ____ __ ______ || || \ \ | | | | \ | \\^// | | | |_ | |__ /__ \ | \\^// / | | \ | \\^// / / | | |__/ \ | \\^// / / | | | \| \\^// Charles E.Weaver \\^// Boston University School of Medicine Phone (617)638-5323 | Department of Pharmacology L-603 Fax (617)638-4329 | 80 East Concord Street Boston MA 02118 cweaver@acs.bu.edu \________/\___/\___/\______________DoD#_1441_____81_CB750c____~o&o ~ \_/ \_/ `-:>~ From owner-www@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Eric H. Mercer" Subject: [ANNOUNCEMENT] new mouse and rat home page and mail list Message-ID: <1995Apr4.180720.25935@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 31 Mar 1995 22:48:45 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 46 I am pleased to announce the establishment of the Mouse and Rat Research Home Page on the World Wide Web. This site centralizes the numerous internet resources directly relevant to biomedical researchers using mice or rats in their work. You may reach it at: http://www.cco.caltech.edu/~mercer/htmls/rodent_page.html or by selecting the link at the bottom of this message if you are using a web-aware mail browser. ________________________________________________ In conjunction with this page, the "rodent-research" e-mail list has been established. The following is quoted from the "info" file for the mail list: This list is for announcements, questions, and discussion related to the use of rodents in biomedical research. You can expect messages on topics as diverse as husbandry, surgical anesthesia methods, embryonic stem cell culture, or NIH animal use guidelines. Announcements of particular interest to researchers using rodents are also appropriate to this list, although commercial advertisers are encouraged to use restraint both with respect to length and frequency of posts. This list exists primarily as a means for biomedical researchers to discuss common problems and develop conclusions drawn from a broad base of experience. You can join rodent-research by sending an e-mail message to: majordomo@cco.caltech.edu with a single line of message text: subscribe rodent-research All researchers using mice or rats are welcome to use these new services. Eric Mercer California Institute of Technology Mouse and Rat Research Home Page -- Eric H. Mercer California Institute of Technology Division of BIology; 216-76 Pasadena, CA 91125 (818) 356-6822 mercer@seqvax.caltech.edu From owner-www@net.bio.net Tue Apr 04 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: "J. Coire Angus" Subject: New Natural History Web Site Message-ID: <1995Apr5.062853.7906@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 4 Apr 1995 22:14:32 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 26 The Natural History Museum of Los Angeles County invites you to visit its new WWW site. The site features information about the museum, virtual exhibitions and links to hundreds of other museums around the world. Be sure to visit the newly opened virtual gallery "Schreber's Fantastic Beasts". In 1774 Johann Christian Dan Schreber authored a multivolume set of books entitled 'Die Saugthiere in Abbildungen nach der Natur mit Beschreibungen'. Focusing on mammals of the world, these books were lavishly illustrated with 755 hand-colored plates. There was a slight problem though: in most instances the artists had never seen the animals they were rendering onto paper. Explorers would return from their travels and describe the animals in question to the artists. The end result was that some of the drawings, though representing real animals, looked more like they had come from someone's nightmares. The Natural History Museum of Los Angeles County http://cwis.usc.edu/lacmnh/default.html Jim Angus-web manager -- Jim Angus Natural History Museum of Los Angeles County Molecular Systematics Laboratory From owner-www@net.bio.net Tue Apr 04 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Goodwin Institute Subject: WWW Page for Anti-Viral Antibodies and Cancer Research Message-ID: <1995Apr5.070310.8582@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 5 Apr 1995 04:46:05 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 7 [ Article crossposted from bionet.announce ] [ Posted on 4 Apr 1995 15:13:48 -0700 ] The Goodwin Institute for Cancer Research is located at: http://www.gate.net/~goodwin From owner-www@net.bio.net Wed Apr 05 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: DENNIS CHURCHILL Subject: Frog Clipart Message-ID: <1995Apr6.181301.1745@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 28 Mar 1995 17:18:28 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 4 Does anyone know of clipart of frogs and tadpoles - especially of tadpole stages - available on the net? Thanks in advance. Dennis From owner-www@net.bio.net Wed Apr 05 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Howard Flack Subject: XPLOR Message-ID: <1995Apr6.072334.17105@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 5 Apr 1995 10:31:09 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 12 [ Article crossposted from bionet.xtallography ] [ Posted on Wed, 5 Apr 1995 07:27:25 GMT ] X-ray software: the X-PLOR www home page is now online at: http://xplor.csb.yale.edu From owner-www@net.bio.net Thu Apr 06 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Dick Keefe Subject: Re:[Q] Frog Clipart Message-ID: <1995Apr7.082226.18835@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 6 Apr 1995 23:57:00 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 11 Used to be's (I haven't checked them recently!!): The "Froggy Page" at http://www.cs.yale.edu/HTML/YALE/CS/HyPlans/loosemore-sandra/froggy.html and the Xenopus laevis Pages at http://timpwrmac.clh.icnet.uk/xenopusintro.html for starters. From owner-www@net.bio.net Thu Apr 06 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: chengs1@jaguar.uofs.edu Subject: [Q] Software...bacteria management...dataBase.. Message-ID: <1995Apr7.083311.19656@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 3 Apr 1995 23:24:10 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 10 Does anyone know where I can obtain a software (PC or Mac version) for bacteria strains management? We have many clinical isolates. We need a special database for our expanding bacteria collections. Thanx. S.C. Chengs1@jaguar.uofs.edu From owner-www@net.bio.net Sun Apr 09 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Ann Cooper Subject: EMBL JOB VACANCIES: 95/11. Message-ID: <1995Apr10.062020.178@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 7 Apr 1995 15:59:46 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 14 Please check the EMBL WWW page for current vacancies. http://www.embl-heidelberg.de/ExternalInfo/jobs/ There is a new one posted today for Staff Scientists ! Regards, Ann Cooper Personnel Officer EMBL Heidelberg From owner-www@net.bio.net Tue Apr 11 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: Randall Smith Subject: [ANNOUNCEMENT] BLAST- & FASTA-based Pattern Searches Message-ID: <1995Apr12.105251.15635@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 12 Apr 1995 02:36:02 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 46 BLASTPAT and FASTPAT Pattern Database Search Tools for Fast and Sensitive Gene Function Identification BLASTPAT and FASTPAT are tools designed to identify protein sequences whose functions are not identified by standard BLAST or FASTA database searches. These modified versions of BLAST and FASTA perform rapid and sensitive searches of our Pattern Induced Multiple Alignment (PIMA) Pattern Database. The PIMA Pattern Database contains 22,422 patterns generated from multiple sequence alignments of 12,669 protein families we have identified in the NCBI's Entrez protein sequence database. Both FASTPAT and BLASTPAT searches can be performed using the BCM Search Launcher WWW pages, provided by the Human Genome Center, Baylor College of Medicine (Houston, Texas): http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html Patterns in the PIMA database are encoded by a maximized information content alphabet. This extended alphabet includes the standard 20 letter IUPAC amino acid codes plus 61 other characters (lowercase characters, digits, other symbols) representing those combinations of residues which contribute the highest information as observed across all aligned positions in our protein family alignments. Pattern database searches are performed using new log-odds scoring matrices that we have developed for use with this new extended alphabet. In contrast to standard scoring matrices like PAM or BLOSUM, these new pattern-based matrices distinguish between conserved and variable positions, increasing search sensitivity and selectivity. A more detailed description of these program is available on our WWW pages: http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/blastpat.html http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/fastpat.html ___________________________________________________________________ Istvan Ladunga, Brent Wiese, and Randall F. Smith Human Genome Center, Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine, Houston, TX 77030, USA {istvanl,brent,rsmith}@bcm.tmc.edu; 713-798-8089, FAX: 713-798-5386 ___________________________________________________________________ From owner-www@net.bio.net Mon Apr 17 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: Paolo Romano Subject: [ANNOUNCEMENT] HyperCLDB new release (Apr 95) Message-ID: <1995Apr18.071632.13163@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Sat, 15 Apr 1995 00:54:17 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 30 Dear bionetters, this is to announce availability of the new release of HyperCLDB, the hypertextual version of the Cell Line Data Base, by the CBA-IST joint WWW server (URL: http://www.ist.unige.it). Current release is version April 1995 and includes detailed descriptions of ca. 3000 cell lines from European culture collections (ca. 26 Mbytes of data, with a 7% increment). Recent updates include insertion of the cell culture collection (TUMORBANK) of the German Cancer Research Center (Deutsches Krebsforschungszentrum) located in Heidelberg. Data refer to 231 tumoral human and animal (man, mouse, rat and hamster) cell lines, more than 130 of which were not previously included in HyperCLDB. You are warmly invited to navigate HyperCLDB starting at http://www.ist.unige.it/cldb/indexes.html and send your comments to paolo@risc1.ist.unige.it. Paolo Romano (http://www.ist.unige.it/staff/PR.html) -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Paolo Romano is a Research Assistant at the Biotechnology Department of the National Institute for Cancer Research of Genoa, located in Viale Benedetto XV 10, 16132 Genova, Italy. You can phone (+39-10-5737288/297), fax (+39-10-5737295) or email (paolo@risc1.ist.unige.it) him. He will kindly answer. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-www@net.bio.net Mon Apr 17 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: EMBnet Switzerland Subject: [FEEDBACK WELCOME] JAM Version 2.0 BETA-3 Message-ID: <1995Apr18.075540.14004@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 18 Apr 1995 05:26:06 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 48 [ Article crossposted from bionet.announce ] [ Posted on 17 Apr 1995 19:07:14 -0700 ] We have developed the tool 'JAM' (Just Another Metaformat). A new version (Version 2.0) has been put into beta status (stage 3) as of today. Availability: ------------- The location bioftp.unibas.ch has this version in the directory programs/bioftp-sw/jam2.0 - directories contain source code and description. What does JAM ? --------------- The program 'jam' (ASCII interface) or 'jamgui' (Graphical User Interface, made possible by using J.Kahn's VIBRANT toolkit) takes a sufficiently formatted text in 'JAM' format and produces wither HTML, LaTEX, or RTF format. Jam has been used to create a preliminary version of the 'biocomputing survival guide', which will be released later this year in its final version (Preview and sources are available from the URL http://www.ch.embnet.org). Documentation: -------------- ftp://bioftp.unibas.ch/programs/bioftp-sw/jam2.0/examples/JAMINX.HTML HYPERTEXT ftp://bioftp.unibas.ch/programs/bioftp-sw/jam2.0/examples/JAM.RTF RTF version ftp://bioftp.unibas.ch/programs/bioftp-sw/jam2.0/examples/*.TEX LaTEX version The purpose of this release of beta stage software is to collect productive feedback on the enhancements and possible requirements for a final release. Comments are welcome. Regards Reinhard Doelz EMBnet Switzerland ================== -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-www@net.bio.net Mon Apr 17 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: "Daniel M. Cabirac" Subject: Agricultural Biotech WWW/Gopher Site Message-ID: <1995Apr18.073239.13695@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 18 Apr 1995 02:07:33 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 43 *************************************************************** THE BIOTECHNOLOGY INFORMATION CENTER OF THE NATIONAL AGRICULTURAL LIBRARY (USDA) Provides AG BIOTECHNOLOGY INFORMATION via WWW and Gopher *************************************************************** WWW access: http://www.inform.umd.edu/EdRes/Topic/AgrEnv/Biotech Instructions for our gopher are given below. **BIOTECH EDUCATIONAL RESOURCES** **BIOTECH SOFTWARE** **LEGISLATION AND REGULATION** **SELECT FULL TEXT AG BIOTECH PATENTS** **TRANSGENIC TOMATO** **BST-BOVINE GROWTH HORMONE** **BIOTECHNOLOGY OF ALGAE** **BIOTECH VIDEO LIST** **FULL TEXT BIOTECH NEWSLETTERS** AND many more files, as well as links to other Agricultural Biotechnology WWW sites and Gophers. Use our WWW site listed above or our gopher: gopher gopher.nalusda.gov -Information Centers -Biotechnology Information Center Please send us your questions and comments. +---------------------------------------------------------------------------+ | Biotechnology Information Center (BIC) voice1: (301)-504-5947 | | National Agricultural Library - USDA voice2: (301)-504-5340 | | 10301 Baltimore Blvd. fax: (301)-504-7098 | | Beltsville, MD 20705-2351 USA e-mail:biotech@nalusda.gov | +---------------------------------------------------------------------------+ | Daniel Cabirac biotech@nalusda.gov | | Ray Dobert rdobert@nalusda.gov | +---------------------------------------------------------------------------+ From owner-www@net.bio.net Mon Apr 17 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: "Dr. Alex Reisner" Subject: Australian National Genomic Information Service WWW Server Message-ID: <1995Apr18.081650.14502@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Sun, 16 Apr 1995 21:24:48 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 8 The Australian National Genomic Information Service (ANGIS) has implemented a World Wide Web server to publicize its existence to browsers on the Web as well as to make available some useful information. The URL is http://morgan.angis.su.oz.au/ Alex Reisner From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: "Ian Kluft" ikluft@amdahl.com Subject: [DISCUSSION] RESULT: comp.infosystems.www reorganization passes Message-ID: <1995Apr21.115614.1167@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 21 Apr 1995 05:57:21 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 704 [ Article crossposted from news.announce.newgroups,news.groups,comp.infosystems.www.misc,comp.infosystems.www.providers,comp.infosystems.www.users ] [ Posted on 20 Apr 1995 15:28:59 -0400 ] RESULT comp.infosystems.www reorganization Voting for the comp.infosystems.www reorganization vote ended 23:59:59 GMT, 19 April 1995. This vote was conducted by a neutral third party. For questions about voting procedures only contact Ian Kluft (the votetaker). For questions about the newsgroups contact Thomas Boutell and M. L. Grant (the proponents). There were 419 valid votes submitted during the voting period. Each proposed newsgroup, in order to pass, must have at least 2/3 YES votes and at least 100 more YES than NO votes. The results are as follows: comp.infosystems.www reorg results - 419 valid votes Yes No : 2/3? >100? : Pass? : Group ---- ---- : ---- ----- : ----- : ------------------------------------------- 339 45 : Yes Yes : Yes : comp.infosystems.www.advocacy 342 37 : Yes Yes : Yes : comp.infosystems.www.browsers.mac 385 22 : Yes Yes : Yes : comp.infosystems.www.browsers.misc 352 39 : Yes Yes : Yes : comp.infosystems.www.browsers.ms-windows 354 34 : Yes Yes : Yes : comp.infosystems.www.browsers.x 335 45 : Yes Yes : Yes : comp.infosystems.www.servers.ms-windows 362 29 : Yes Yes : Yes : comp.infosystems.www.servers.unix 330 44 : Yes Yes : Yes : comp.infosystems.www.servers.mac 379 19 : Yes Yes : Yes : comp.infosystems.www.servers.misc 390 18 : Yes Yes : Yes : comp.infosystems.www.authoring.html 373 24 : Yes Yes : Yes : comp.infosystems.www.authoring.cgi 349 48 : Yes Yes : Yes : comp.infosystems.www.authoring.images 387 19 : Yes Yes : Yes : comp.infosystems.www.authoring.misc 9 invalid votes All parts of the proposal passed. There is a five day discussion period after these results are posted. If no serious and significant allegations of voting irregularities are raised, the moderator of news.announce.newgroups will create the newsgroups shortly thereafter. The following newsgroups will be removed on 26 July 1995: comp.infosystems.www.users (replaced by comp.infosystems.www.browsers.misc) comp.infosystems.www.providers (replaced by comp.infosystems.www.authoring.misc) The remainder of the results contains Newsgroups Lines Charters Final Voting Acknowledgements Voting Analysis NEWSGROUPS LINES comp.infosystems.www.advocacy Comments and arguments over the best and worst. comp.infosystems.www.browsers.mac Web browsers for the Macintosh platform. comp.infosystems.www.browsers.misc Web browsers for other platforms. comp.infosystems.www.browsers.ms-windows Web browsers for MS Windows. comp.infosystems.www.browsers.x Web browsers for the X-Window system. comp.infosystems.www.servers.ms-windows Web servers for MS Windows and NT. comp.infosystems.www.servers.unix Web servers for UNIX platforms. comp.infosystems.www.servers.mac Web servers for the Macintosh platform. comp.infosystems.www.servers.misc Web servers for other platforms. comp.infosystems.www.authoring.html Writing HTML for the Web. comp.infosystems.www.authoring.cgi Writing CGI scripts for the Web. comp.infosystems.www.authoring.images Using images, imagemaps on the Web. comp.infosystems.www.authoring.misc Miscellaneous Web authoring issues. CHARTERS These are the newsgroup charters as submitted by the proponent. The following newsgroups are to be created. The existing newsgroups comp.infosystems.www.providers and comp.infosystems.www.users will be removed, by renaming comp.infosystems.www.providers to comp.infosystems.www.authoring.misc and comp.infosystems.www.users to comp.infosystems.www.browsers.misc. The existing newsgroups comp.infosystems.www.announce and comp.infosystems.www.misc will not be affected. Detailed explanation follows the list; please read the entire post before responding. comp.infosystems.www.advocacy comp.infosystems.www.browsers.mac comp.infosystems.www.browsers.misc comp.infosystems.www.browsers.ms-windows comp.infosystems.www.browsers.x comp.infosystems.www.servers.ms-windows comp.infosystems.www.servers.unix comp.infosystems.www.servers.mac comp.infosystems.www.servers.misc comp.infosystems.www.authoring.html comp.infosystems.www.authoring.cgi comp.infosystems.www.authoring.images comp.infosystems.www.authoring.misc [Note that comp.infosystems.www.announce and comp.infosystems.www.misc already exist and are not affected by the reorganization.] comp.infosystems.www.advocacy This newsgroup is for comments, arguments, debates, and discussions about which Web browsers, servers, external viewer programs, and other software is better or worse than any other. Posts should not be crossposted to this group and to any other Web group. However, this group is a good place to direct follow-ups if a thread in another Web group begins to take on a "this program is better than that one" flavor. Possible subjects include: "The web is better than print"; "Netscape is better than anything else"; "CERN httpd kicks butt"; etc. comp.infosystems.www.authoring.html This newsgroup covers discussion of HyperText Markup Language (HTML) as it relates to web page authoring. Possible subjects include HTML editors, formatting tricks, and current and proposed HTML standards. comp.infosystems.www.authoring.cgi This newsgroup covers discussion of the development of Common Gateway Interface (CGI) scripts as they relate to Web page authoring. Possible subjects include discussion how to handle the results of forms, how to generate images on the fly, and how to put together other interactive Web offerings. comp.infosystems.www.authoring.images This newsgroup covers discussion of the creation and editing of images as they relate to web page authoring. Possible subjects include how best to leverage the image-display capabilities of the web and common questions and solutions for putting up imagemaps. comp.infosystems.www.authoring.misc This newsgroup covers miscellaneous World-Wide Web authoring issues not covered by the other c.i.w.authoring.* groups. Possible subjects include the use of audio and video, etc. comp.infosystems.www.browsers.mac This newsgroup covers discussion of World-Wide Web browsers for the Macintosh platform. Possible subjects include configuration questions/solutions, external viewers (helper applications), and bug reports. comp.infosystems.www.browsers.ms-windows This newsgroup covers discussion of World-Wide Web browsers for the MS Windows and NT platforms. Possible subjects include configuration questions/solutions, external viewers (helper applications), and bug reports. comp.infosystems.www.browsers.x This newsgroup covers discussion of World-Wide Web browsers for the X-Window system. Possible subjects include configuration questions/solutions, external viewers (helper applications), and bug reports. comp.infosystems.www.browsers.misc This newsgroup covers discussion of World-Wide Web browsers for all other platforms. Possible subjects include configuration questions/solutions, external viewers (helper applications), and bug reports. Platforms included are Amiga, DOS (*not* Windows), VMS, and Unix text-mode. comp.infosystems.www.servers.mac This newsgroup covers discussion of World-Wide Web servers for the Macintosh (MacOS) platform. Possible subjects include configuration questions/solutions, security issues, directory structure, and bug reports. comp.infosystems.www.servers.ms-windows This newsgroup covers discussion of World-Wide Web servers for the MS Windows and NT platforms. Possible subjects include configuration questions/solutions, security issues, directory structure, and bug reports. comp.infosystems.www.servers.unix This newsgroup covers discussion of World-Wide Web servers for Unix platforms. Possible subjects include configuration questions/solutions, security issues, directory structure, and bug reports. comp.infosystems.www.servers.misc This newsgroup covers discussion of World-Wide Web servers for other platforms, such as Amiga, VMS, and others. Possible subjects include configuration questions/solutions, security issues, directory structure, and bug reports. comp.infosystems.www.misc Miscellaneous World-Wide Web discussion which does not fit into the above categories. This group already exits and will not change. comp.infosystems.www.announce Announcements of new and updated Web resources. This group already exists and will not change. FINAL VOTING ACKNOWLEDGEMENTS comp.infosystems.www.authoring.misc ---------------+ comp.infosystems.www.authoring.images --------------+| comp.infosystems.www.authoring.cgi -------------+|| comp.infosystems.www.authoring.html ------------+||| comp.infosystems.www.servers.misc -----------+|||| comp.infosystems.www.servers.mac ----------+||||| comp.infosystems.www.servers.unix ---------+|||||| comp.infosystems.www.servers.ms-windows --------+||||||| comp.infosystems.www.browsers.x -------+|||||||| comp.infosystems.www.browsers.ms-windows ------+||||||||| comp.infosystems.www.browsers.misc -----+|||||||||| comp.infosystems.www.browsers.mac ----+||||||||||| comp.infosystems.www.advocacy ---+|||||||||||| ||||||||||||| A.H.Henry@bath.ac.uk --YYY-Y-YYYYY aadrrd1@peabody.sct.ucarb.com Alan Ronemus YYYYYYYYYYYYY aahz@netcom.com Aahz YYYYYYYYYYYYY aaronrp@best.com Aaron Priven YYYYYYYYYYYYY abm@digital.net Al Meador -NYNNNNNYNNNY ache@astral.msk.su Andrey A. Chernov YYYYYYYYYYYYY acp@pruxp.att.com Alex Podlecki YYYYYYYYYYYYY actor@telerama.lm.com Philip R. Spagnolli YYYYYYYYYYYYY adair@bigpine.csee.usf.edu Jonathan Adair -YYYYYYYYYYYY aelman@cs.stanford.edu Adam Elman YYYYYYYYYYYYY afrinl@honc.mhs.musc.edu Lawrence B. Afrin, M.D. YYYYYYYYYYYYY ahmlhs@baram.kaist.ac.kr Lee, "AHMLHS" Ho-sun YYYYYYYYYYYYY alanc@ocf.Berkeley.EDU Alan Coopersmith -YY-Y-YYYYYYY alex@mips.complang.tuwien.ac.at Alexander Forst YYYYYYYYYYYYY Alexander.Jung@bln.sel.alcatel.de Alexander Jung YYYYYYYYYYYYY Alexander_Spohr@multiversum.com Alexander Spohr YYYNYNYYYYYYY and@mgulvt.mgul.ac.ru Andrey A Perminov YYYYYYYYYYYYY andrews@hal.fmhi.usf.edu Vicki Andrews Y-YY-YY--Y-YY april@ils.nwu.edu David April YYYYYYYYYYYNY archer@frmug.fr.net Vincent Archer NNNNNNNNNNNNN ARNE@ko.hhs.dk Arne Vajhoej YYYYYYYYYYYYY ault@cs.albany.edu Jim Ault YYYYYYYYYYYYY ayoung@wimsey.com Adrian Young YYYYYYY--Y--Y babafou@ensta.fr Marc Baudoin YYYYYYYYYYYYY bailey@hagar.ph.utexas.edu Ed Bailey NNYNYNYNYYNNY barr@math.psu.edu Dave Barr YYYYYYYYYYYYY barryn@netcom.com Barry Nathan YYYYYYYYYYYYY bdboyle@maverick1.erenj.com Bryan D. Boyle YYYYYYYYYYYYY bdealy@c3i.saic.com Brian Dealy YYYYYYYYYYYYY beccat@magicats.org Becca Thomas YYYYYYYYYYYYY ben@speedy.zool.lsu.edu Ben Curtis YYYYYYYYYYYYY bengtl@maths.lth.se Bengt Larsson YYYYYYYYYYYYY bex@ncsu.edu Brian Exelbierd YYYYYYYYYYYYY bgingery@Wyoming.COM Bruce Gingery YYYYNYYYYYYYY bill@netagw.com Bill Aten YYYYYYYYYYYYY billbusen@aol.com Bill Busen YYYYYYYYYYYYY billy@utdallas.edu Billy Barron NNNNNYYYYYYYY bjv@herbison.com B.J. Herbison YYYYYY--YYY-Y Bob.Gibbons@dseg.ti.com bob gibbons YYYYYYYYYYYYY bob.ray@tstation.mn.org BOB RAY NNYNNNNNYNNNY boba@wwa.com Bob Allison YYYYYYYYYYYYY bobg@uic.edu Bob Goldstein 996-6664 YYYYYYYYYYYYY bobs@access.digex.net Bob Smith YYYYYYYYYYYYY bonelli@ifctr.mi.cnr.it Giuseppe Bonelli YYYYYYYYYYYYY booda@us1.msrcnavo.navy.mil Martin H. Booda NNNNNNNNNNNNN boutell@netcom.com Thomas Boutell YYYYYYYYYYYYY bouvin@daimi.aau.dk Niels Olof Bouvin YYYYYYYYYYYYY bparker@interaccess.com Ben Parker YYYYYYYYYYYYY braynor@jupiter.kcc.com William J. Raynor, Jr. YYYYYYYYYYYYY brianh@fast.net Brian Hillegass YYYYYYYYYYYYY bruceab@teleport.com Bruce Baugh YYYYYYYYYYYYY brunner@isa.informatik.th-darmstadt.de Michael Brunner YYYYYYYYYYYYY Bruno.Beaufils@lifl.fr Bruno Beaufils YNYNNNNNYYYYY bryan@Novell.COM Bryan Cardoza YYYYYYYYYYYYY Bryce_Jasmer@NeXT.COM Bryce Jasmer YYYYYYYYYYYYY Bryek@MAIL.STATE.WI.US Kent Brye NYYYYYYYYYYYY BSCHLESINGER@NSSDCA.GSFC.NASA.GOV Barry M. Schlesinger YYY---Y-YY-YY bucata@cs.hope.edu Jason Bucata YYYYYYYYYYYYY C.R.Ritson@newcastle.ac.uk Chris Ritson YYYYYYYYYYYYY C96@vm.urz.Uni-Heidelberg.de Alexander Eichener N-N-Y-YYYY-YN ca@informatik.uni-kiel.de Claus Assmann Y-Y-Y-Y-YYYYY cac@mtmis1.mis.semi.harris.com Clint Chamberlin YYYYYYYYYYYYY CARPENTERV@VMS.CSD.MU.EDU Vinit Carpenter YYNYYYYYYYYYN cbstone@phoenix.Princeton.EDU Chris Stone NYYYNYYYYYYYY ccardoso@ax.apc.org Cesar de Andrade Cardoso YYYYYYYYYYYYY chris@loncps.demon.co.uk Chris Salter YYYYYYYYYYYYY chris@tali.hsc.colorado.edu Chris Yoder YYYYYYYYYYYYY Chris_Marble@hmc.edu Chris Marble NNYNYNNNYYNNY chuck@sage.cgd.ucar.EDU Charles D'Ambra YYYYYYYYYYYYY chughes@cwk000.webo.dg.com Christopher J. Hughes YYYYYYYYYYYYY churchh@uts.cc.utexas.edu Henry Churchyard YYYYYYYYYYYYY ckd@loiosh.kei.com Christopher Davis YYYYYYYYYYYYY cks@hawkwind.utcs.toronto.edu Chris Siebenmann YYYYYYYYYYYYY cline@cs.scarolina.edu Ernest Cline N-Y-----Y--NY clstampe@mailbox.syr.edu Chris Stamper YYYYYYYYYYYYY cmullins@cwa.com Charlie Mullins YYYYYYYYYYYYY compulov@raven.cybercom.com Leigh Koven YYYYYYYYYYYYY cookie@venus.etri.re.kr Song, Woo Geel YNYYYNYNYYYNY crouchkp@flidh103.delcoelect.com K. P. CROUCH ------------- crow@coos.dartmouth.edu Preston F. Crow YYYYYYYYYYYYY crow@dev.tivoli.com David L. Crow YYYYYYYYYYYYY crutch@sartre.minerva.bah.com Steven M. Crutchfield YYYYYYYYYYYYY cvarela@ncsa.uiuc.edu Carlos Varela NYYYYYYYYYYYY cverver@u.washington.edu Craig Verver YYYYYYYYYYYYY cward@Think.COM Christopher Ward NNYNNNNNYNNNY D.L.Sutton@open.ac.uk Dianne Sutton ---Y--------- d3c572@shaq.pnl.gov Darren Curtis YYYYYYYYYYYYY dan@cthulhu.control.com Dan L. Pierson YYYYYYYYYYYYY datah@pinn.net Douglas Heimburger YYYYYYYYYYYYY dave.barberi@Bentley.COM Dave Barberi [Bentley] YYYYYYYYYYYYY dave@ZEL.ETF.HR Drazen Kacar (Cihlar) YYYYYYYYYYYYY david@iris.claremont.edu David Hoekman YYYYYYYYYYYYY David@masthead.demon.co.uk dAVID bRAZENDALE NYYYYYYYYYYYY dbacon@medio.net Dan Bacon YYYYYYYYYYYYY dbigwood@locus.nalusda.gov Doug Bigwood YYYYYYYYYYYYY ddkilzer@iastate.edu David D. Kilzer YYYYYYYYYYYYY derek@pipex.net Derek Harding YYYYYYYYYYYYY derville@lannion.cnet.fr Frank Derville YYYYYYYYYYYYY dhartung@mcs.com Daniel A. Hartung YYYYYYYYYYYYY dijon@netcom.com Douglas Krause YYYYYYYYYYYYY dlewine@cheshirecat.webo.dg.com Donald Lewine YYYYYYYYYYYYY dmosher@nyx10.cs.du.edu David Mosher YYNYYYYYNYYYY dms1070@hertz.njit.edu David Shaw YYYYYYYYYYYYY doctorkb@vortex.netbistro.com Kris Benson YYYYYYYYYYYYY dongil@ecn.purdue.edu Dongil Shin YYYYYYYYYYYYY dpc@ipp-garching.mpg.de David Coster TOK YYYYYYYYYYYYY drosenba@panix.com Daniel Rosenbaum YYYYYYYYYYYYY dr_legge@postoffice.utas.edu.au David Robert Legge YYYYYYYYYYYYY dube@NIEHS.NIH.GOV Jed Dube YYYYYYYYYYYYY dusan.pirc@snet.fer.uni-lj.si Dussan Pirc Y-Y-Y-Y-YYYYY dweeo@ffg05.navy.gov.au LEUT Mark Purcell YYYYYYYYYYYYY dxh0844@teche.cacs.usl.edu Duke Hillard YYYYYYYYYYYYY ehillman@access.digex.net Edward Lloyd Hillman YYYYYYYYYYYYY eijkhout@math.ucla.edu Victor Eijkhout YYYYYYYYYYYYY emma@sled.gsfc.nasa.gov Emma Kolstad YYYYYYYYYYYYY erez@cac.washington.edu Sheryl Erez YYYYYYYYYYYYY escharff@SunLab.CIT.Cornell.EDU Eric Scharff YYYYYNYYYYYNY esrlj@csv.warwick.ac.uk Mark Coleman YYYNYNYYYYYYY ewl@panix.com Emery Lapinski YNYNYNYNYYYNY ex@uiah.fi Samu Mielonen YYYYYYYYYYYYY fche@db.toronto.edu Frank Ch. Eigler NYYYYYYYYYYNY fduross@moose.uvm.edu Frank B. DuRoss Jr. YYYYYYYYYYYYY fgriffin@teleport.com Fred Griffin YYYYYYYYYYYYY fpaterek@uceng.uc.EDU F. Harald Paterek YYYYYYYYYYYYY fuy1@gl.umbc.edu Francis Uy --Y-----YY--Y gabe@angus.mystery.com Gabe Helou YYYYYYYYYYYYY gaillard@panix.com Edward Gaillard YYYYYYYYYYYYY Gareth.Rees@cl.cam.ac.uk Gareth Rees ---------YYYY geoff@eecs.wsu.edu Geoff Allen -YY-Y-YYYYYYY gerald@cs.ualberta.ca Gerald Oskoboiny YYYYYYYYYYYYY gert@aztec.co.za Gert Blij Y-YY-YY-YYYYY ghsst6+@pitt.edu Geoff Spear YYYNYNNNYYYNY gibbins@cpd.ntc.nokia.com Nick Gibbins YYYYYYYYYYYYY gil@cc.gatech.edu Gil Neiger -NYNNNNNY---- gildas@crih.fdn.org NOEL Gildas YYYYYYYYYYYYY gjb@gba.oz.au Greg Black YYYYYYYYYYYYY gmager@teleport.com Gary R. Mager YYYYYYYYYYYYY gnb@bby.com.au Gregory Bond YYYYYYYYYYYYY gnma76@udcf.gla.ac.uk Donald J. Ballance YYYYYYYYYYYYY godfrey2@coventry.ac.uk Bill Godfrey YNNNNNNNYYYYY grant@halcyon.com M. L. Grant YYYYYYYYYYYYY gregm@WPI.EDU Gregory Marr YYYYYYYYYYYYY grendel@netaxs.com Michael Handler YYYYYYYYYYYYY groo@netcom.com Kiran Wagle YYYYYYYYYYYYY gt0670e@prism.gatech.edu Brennan T. Price YYYYYYYYYYYYY Hans.Arents@mtm.kuleuven.ac.be Hans C. Arents YYYYYYYYYYYYY harlan@cs.wisc.edu Harlan Harris YYYYYNNNNYYYY hayden@krypton.mankato.msus.edu Robert A. Hayden YYYYYYYYYYYYY heatwole@clark.net Tony Heatwole YYYYYYYYYYYYY heidenre@oasys.dt.navy.mil Todd R. Heidenreich YYYYYYYYYYYYY heiko@chemie.fu-berlin.de Heiko Schlichting YYYYYNYNYYYYY Helmut.Geyer@IWR.Uni-Heidelberg.De Helmut Geyer YYYYYYYYYYYYY hmm@heeg.de Hans-Martin Mosner YYYYYYYYYYYYY hmueller@pcnet.com Harry Mueller YYYYYYYYYYYYY hskarkka@snakemail.hut.fi Samuli K=E4rkk=E4inen YYYYYYYYYYYYY hustvedt@cream.putney.com Eric Hustvedt YYYYYYYYYYYYY i6211209@ws.rz.tu-bs.de Ralf G. Doeblitz YYYYYYYYYYYYY i9130989@unicorn.it.wsu.edu Ronald E Kinion ---------Y--- icottrel@emr.ca Ian Cottrell YYYYYYYYYYYYY ilana@niwot.scd.ucar.EDU Ilana Stern NNYNNYYYYYYNY ir000697@interramp.com Marc Hedlund YYYYYYYYYYYYY irilyth@infersys.com Josh Smith YYYYYYYYYYYYY ivler@crl.com J.M. Ivler YYYYYYYYYYYYY J.E.Wheeler@newcastle.ac.uk Janet Wheeler -YY-Y-YYYYYYY Jaap.Romers@cs.ruu.nl Jaap Romers YYYYYYYYYYYYY jake@netins.net Robert R. Jakoubek YYYYYYYYYYYYY jay@gordian.com Jay Laefer NYYYYYYYYYYYY jbc@cyberverse.com John Callender YYYYYYYYYYYYY jbs30@eng.amdahl.com Joel Storm YYYYYYYYYYYYY jcmurphy@smurfland.cit.buffalo.edu Jeff Murphy NNNNNNNNNNNNN jcohen@dri.cornell.edu Jeffrey David Cohen YYYYYYYYYYYYY jda@cyberscience.com Jon Abbott YYYYYYYYYYYYY jdalmand@news.doas.state.ga.us James D. Almand NNNNNNNNNNNNN mwm@contessa.phone.net Mike Meyer YNNNNNNNNYYYY MWOOD@INDYVAX.IUPUI.EDU Mark H. Wood YYYYYYYYYYYYY n9146070@janice.cc.wwu.edu Jacob C Kesinger -NNNNNNNNNNNN nancy_vandermey@qmlink.ple.af.mil Cat House NNNNNNNNNNNNN nick@inferno.fc.hp.com Nick Ingegneri YNYNNNNNYYNNN Nicolas.Graner@lri.fr -YYYYYYYYYYYY noele@msu.edu Noel Estabrook NYYYNYYYYYYYY norman@astro.gla.ac.uk Norman Gray YYYYYYYYYYYYY novak@pt4427.pto.ford.com Louis M. Novak YYYYYYYYYYYYY nrp@chernikeeff.co.uk Neil Padgen -YYYYNNNYYYYY nuesken@lie.mathe.uni-konstanz.de Michael Nuesken YYYYYYYYYYYYY oace@nature.Berkeley.EDU Susan M. Oace NYYYYNNNNYYYY ohrenber@x4u2.desy.de Kars Ohrenberg YYYYYYYYYYYYY orc@gehenna.apple.com david parsons --N---------N orioli@impa.br Sergio Orioli Parreiras YNNNNNYNYYYYY otto@vaxb.acs.unt.edu M. "web potato" Otto ------------- ove@yoyo.neu.sgi.com Ove Hansen YYYYYYYYYYYYY overlord@access.digex.net David Coe YYYYYYYYYYYYY P.C.Sutton@bradford.ac.uk Paul Sutton YYYYYYYYYYYYY parker@dorite.iquest.net Scott Parker YYYYYYYYYYYYY patl@catfish.LCS.MIT.EDU Patrick J. LoPresti NNNNNNNNNNNNN paul.russell@DaytonOH.ATTGIS.COM Paul G. Russell YYYYYYYYYYYYY paul@cs.washington.edu ---------YY-- paula@ora.com Paula Ferguson YYYYYYYYYYYYY paulr@cmysys.po.my Paul Russell YYYYYYYYYYYYY pbrooks@micromind.com Peter Brooks NYYYY-------- petera@hpopd.pwd.hp.com Peter R. Auber Y-YY-----Y--Y peterson@csc.ti.com Bob Peterson YYYYYYYYYYYYY philip@storcomp.demon.co.uk Philip Hunt YYYYYYY-YY--Y philippe@pablo.physics.lsa.umich.edu Philippe P. Brieu YYYYYYYYYYYYY Pierre-Marie.Aubertel@grif.grif.fr Pierre-Marie Aubertel YYYYYYYYYYYYY pkwong@singnet.com.sg Peng Kin WONG --YYYY---Y--Y plutchak@porter.geo.brown.edu Joel Plutchak -NYNNNNNYNNNY POLING@Eisner.DECUS.Org JIM POLING Y-YY-YY-YYYYY pp002327@interramp.com Manuel D. Garcia YYYYYYYYYYYYY pringle@cs.monash.edu.au GLen Pringle YYYYYYYYYYYYY pshuang@MIT.EDU Ping Huang YYYYYYYYYYYYY ptbast@owl.WPI.EDU Pete Bastien YYYYYYYYYYYYY pw@cacs.usl.edu Pirawat Watanapongse YYYYYYYYYYYYY pwiseman@mindspring.com Patrick Wiseman YYYYYYYYYYYYY pww@gwis2.circ.gwu.edu Philip W. Wirtz YYYYYYYYYYYYY PYLD@grove.iup.edu Matt Schnierle --Y-----YYNN- r1938c@ismuc.sps.mot.com Christian Murphy YYYYYYYYYYYNY rabenou@c4.fdn.fr Jerome Rabenou YYYYYYYYYYYYY ralenr@ix.netcom.com Allen Rice YYYYYYYYYYYYY ramesh@scr.siemens.com Ramesh Viswanathan YYYYYYYYYYYYY ramsey.saar.de!torstenb@tmpuhf.saar.de Torsten Blum YYYYYYYYYYYYY randerso@carbon.cudenver.edu Richard H. Anderson YYYYYYYYYYYYY Raphael.Quinet@aachen.eed.ericsson.se Raphael Quinet NNYN-NYNYYYNY ratzloff@ix.netcom.com Janet Ratzloff Y-YY-Y--YYYYY rcsiebel@vub.ac.be Roland Siebelink YYYYYYYYYYYYY rdieringer@pol.com Rick Dieringer YYYYYYYYYYYYY rew@Nuance.Com Ryan Waldron NNNNNNNNNNNNN rhaar@albert.cs.gmr.com Robert L. Haar YYYYYYYYYYYNY rick@bcm.tmc.edu Richard Miller YYYYYNNNYYYYY rjhaskel@pwinet.upj.com Roy Haskell NYYYYYYYYYYNY rjl@dow.com Robert Lindesmith YYYYYYYYYYYYY rkleitma@neumann.uwaterloo.ca Rob Leitman YYYYYYYYYYYYY robsmith@u.washington.edu Robert P. Smith --N-----N---N roderick@ibcinc.com Roderick Schertler YYYYYYYYYYYYY roger@larry.westfalen.de Roger Schwentker YYYYYYYYYNNNY Roshne@faerun.sojourn.com Rod Shelton YYYYYYYYYYYYY roth@sunny.mpimf-heidelberg.mpg.de Arnd Roth YYYNYNYYYYYYY roy-wright@ti.com Roy Wright YYYYYYYYYYYYY rsebek@vt.edu Robert Sebek YYYYYYYYYYYYY rshough@fandago.Read.TASC.COM Rick Hough YYYYYYYYYYYYY rveitch@atc.gov.au Ross Veitch YYYYYYYYYYYY- sbd@itd.dsto.gov.au Scott Davis -YYYY-YYYYYYY sburr@PrimeNet.Com Steven J. Burr YYYYYYYYYYYYY scimitar@gulf.net Ken Gaillot NYYYYYYYYYYYY scytale+@CMU.EDU Daniel Martinez YYYYYYYYYYYYY segerge@ss2.sews.wpafb.af.mil Gaylord E. Seger -Y--Y-YY-YY-Y sherman@trln.lib.unc.edu Dennis R. Sherman YYYYYYYYYYYYY sherwood@zeta.is.tcu.edu Frank Sherwood YYYYYYYYYYYYY shields@tembel.org Michael Shields YNYNNYYYYYYYY shrdlu@earthlink.net Lynda L. True YYYYYYYYYYYYY sidewin@ot.com Daniel A. Dewey -NYYNNYNYYYYY signell@cpcug.org Karl Signell YYYYYYYYYYYYY simon@darkmere.midland.co.nz Simon Lyall YYYYYYYYYYYYY sjohnson@strfleet.gsfc.nasa.gov steve johnson -YYYYYYY-YYNY sjwalter@winternet.com Scott J. Walter YYYY-YY-YYYYY skip@automatrix.com Skip Montanaro YYYYYYYYYYYYY smd@PrimeNet.Com Stephen Diamond YYYYYYYYYYYYY snabb@niksula.hut.fi Janne Snabb YYYYYYYYYYYYY snevel@crl.com Simeon ben Nevel YYYYYYYYYYYYY sparre@phyast.pitt.edu Jacob Sparre Andersen YYYYYYYYYYYYY SPB@tntv5.ntrs.com Steve Bonine YYYYYYYYYYYYY spcoltri@exmidway.ecn.uoknor.edu Steve Coltrin YYYYYYYYYYYYY spon@macadam.mpce.mq.edu.au Tom McDermott YYYYYYYYYYYYY sr1@irz.inf.tu-dresden.de Sven Rudolph YYYYYYYYYYYYY ssd@tad.eds.com Sean Dowd YYYYYNYNYYYNY st@stardiv.de Stefan Taxhet YYYYY-YYYYYYY stainles@bga.com Dwight Brown NNNNNNNNNNNNN starling@cpdee.ufmg.br Luiz Carlos Portugal Starling YYYYYYYYYYYYY steintr@intac.com Russell Steinthal YYYYYYYYYYYYY Stephane.Laveau@sophia.inria.fr Stephane Laveau YYYYYYYYYYYYY steve@omniplus.com Steve Mitchell YYYYYYYYYYYYY steve@vigra.com Steve Haehnichen NYYYYYYYYYYYY steveg@pa.dec.com YYYYYYYYYYYYY stevejg@wni.com Steve Green YYYYYYYYYYYYY stewa@etek.chalmers.se Stefan Waborg YYYYYYYYYYYYY stone001@nelle.mc.duke.edu Alan Stone YYYYYYYYYYYYY stricherz@masig.fsu.edu James Stricherz (stricherz@coaps.fsu. YYYYYYYYYYYYY stuart.antcliff@bt-sys.bt.co.uk Stuart Antcliff YYY----YYYY-- stullr@css583.GORDON.ARMY.MIL Robert S. Stull YYYYYYYYYYYYY styx@amanda.dorsai.org William Hao YYYYYYYYYYYYY sumrn@crd.GE.COM Robert Sum YYYYYYYYYYYYY SUPERVISOR@ipe.et.uni-magdeburg.de Martin Wollschlaeger YYYYYYYYYYYYY sverker.forsberg@radek.slu.se Sverker Forsberg YYYYYYYYYYYYY swhatle@Starbase.NeoSoft.COM Steven Whatley YYYYYYYYYYYYY sxs@psu.edu Steven A. Schrader YYYYYYYYYYYYY taavi@vs.ee Taavi Talvik YYYYYYYYYYYYY taft@cs.unc.edu Todd D. Taft YYYYYYYYYYYYY takata@umich.edu Azumi Ann Takata YYYYYYYYYYYYY taob@gate.sinica.edu.tw Brian Tao YYYYYYYYYYYYY tbas@sybase.com Tony Basoglu YYYYYYYYYYYYY techint@winternet.com Technical Intelligence-MN-USA YYYYYYYYYYYYY ted.smith@cdmg.uucp.netcom.com TED SMITH Y-YY-YY-Y--YY terra@PrimeNet.Com Terra NY-YYYYY-YYY- tes@zombie.ncsc.mil Terry Suitor YYYYYYYYYYYYY Tim.Bunce@ig.co.uk Tim Bunce YYYYYYYYYYYYY TIMMI@UMWELT.ecolink.org YYYYYYYYYYYYY tina@tezcat.com Discord (Tina Sikorski) --YY-YY-YYY-Y tobin.anthony@gsfc.nasa.gov Tobin C. Anthony YYYYYYYYYYYYY tonyd@dvcorp.com Anthony DeStefanis -NYNNYYYYYYYY treber@telenet.de Christian Treber YYYYYYYYYYYYY trondare@hsr.no Y-YYYYYNYYYYY tuusital@butler.cc.tut.fi Teuvo Uusitalo YYYYYYYYYYYYY twpierce@midway.uchicago.edu Tim Pierce YYYYYYYYYYYYY tyketto@cwis.unomaha.edu Brad Littlejohn YYYYYYYYYYYYY untulis@netcom.com Jason Untulis YYY-Y--YYYYNY UZ33105@vm1.ulg.ac.be Van de Paar YYYYYYYYYYYYY vampyr@acs.bu.edu Eamon Daly YYYYYYYYYYYNY vit0202@comune.bologna.it Aldo Brucale -YYYYYYYYYYNN vparada@inf.utfsm.cl Victor Parada YYYYYYYYYYYYY walterg@YorkU.CA Walter W. Giesbrecht YYYYYYYYYYYYY warkentyne@di.epfl.ch Ken Warkentyne --Y-Y-Y-YYYYY Warren.Jones@per.dmp.csiro.au Warren Jones YYYYYYYYYYYYY wbd@pmafire.inel.gov W. Brad DeBow YYYYYYYYYYYYY widmeyer@umich.edu George Widmeyer YYYYYYYYYYYYY WILLIAMSCA@HIRAM.EDU Curtis Williams NYYYYYYYYYYYY winter@vision.rs.ch Martin Winter YYYYYYYYYYYYY wstearns@cybermalls.com William Stearns YYYYYYYYYYYYY wtb10@juts.ccc.amdahl.com Wilton Byrum YYYYYYYYYYYYY yuval.kfir@Indigo.co.il Yuval Kfir NYYYYYYYYYYYY zamorski@execpc.com Richard J. Zamorski YYYYYYYYYYYYY zeus@jhu.edu Jeffrey M. Odom NYYYYYYYYYYYY Votes in error ------------------------------------------------------------------------------ bruce.white@dse.mpx.com.au Bruce White ! No ballot dmon@ipac.net Julie Meloni ! No ballot hyer@tigger.jvnc.net Warren "Clint" Hyer ! No ballot jsnell@macuser.ziff.com Jason Snell ! No ballot leobueno@netpoint.net Leo Bueno ! No ballot marie-christine.mahe@yale.edu Marie-Christine Mahe ! No ballot mgm@xmission.com michael moncur ! No ballot Post_Office@tyrellco.com Post Office ! No ballot sfarmer@sabre.goldsword.com Susan B. Farmer ! No vote statement in message VOTING ANALYSIS All dates and times in this section are in US Pacific Time, standard or daylight time as appropriate. (Pacific Daylight Time began April 2 at 2AM.) The first vote arrived at Wed Mar 29 15:35:59 1995. comp.infosystems.www.advocacy passed on Sat Apr 1 13:06:54 1995 comp.infosystems.www.browsers.mac passed on Fri Mar 31 10:33:55 1995 comp.infosystems.www.browsers.misc passed on Fri Mar 31 00:15:57 1995 comp.infosystems.www.browsers.ms-windows passed on Fri Mar 31 10:53:40 1995 comp.infosystems.www.browsers.x passed on Fri Mar 31 08:23:47 1995 comp.infosystems.www.servers.ms-windows passed on Sat Apr 1 05:33:12 1995 comp.infosystems.www.servers.unix passed on Fri Mar 31 11:53:48 1995 comp.infosystems.www.servers.mac passed on Sat Apr 1 04:57:15 1995 comp.infosystems.www.servers.misc passed on Fri Mar 31 01:12:55 1995 comp.infosystems.www.authoring.html passed on Fri Mar 31 00:50:47 1995 comp.infosystems.www.authoring.cgi passed on Fri Mar 31 02:53:28 1995 comp.infosystems.www.authoring.images passed on Fri Mar 31 12:33:03 1995 comp.infosystems.www.authoring.misc passed on Thu Mar 30 23:54:40 1995 Supplemental graphs of vote totals, arrival rates, ratios, and differences have been made available by the votetaker at the following URL on the World-Wide Web: http://www.amdahl.com/~ikluft/c.i.www/ From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: "Y. W. Chen" ywchen@laue.biochem.ubc.ca Subject: [DISCUSSION] CABIOS WWW page? Message-ID: <1995Apr21.111225.28789@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 20 Apr 1995 01:32:07 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 12 Dear All, Does any one know if there is a WWW page for CABIOS (computer applications for biological sciences)? -- =================================================================== Yu Wai CHEN Department of Biochemistry ................................. & Molecular Biology Faculty of Medicine tel: (604)-822 5007 2146 Health Sciences Mall fax: (604)-822 5227 University of British Columbia email: ywchen@laue.biochem.ubc.ca Vancouver BC V6T 1Z3 CANADA =================================================================== From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: Stuart Green Subject: [DESCRIPTION] Journal of Computer-Aided Molecular Design Message-ID: <1995Apr21.104452.28283@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 19 Apr 1995 08:06:36 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 25 [ Article crossposted from bionet.molec-model ] [ Posted on 18 Apr 1995 08:34:38 -0700 ] ESCOM Publishers B.V. in collaboration with the Center for Molecular Design present an experimental Web based version of the The Journal of Computer-Aided Molecular Design. http://wucmd.wustl.edu/jcamd/jcamd.html This server carries complete articles (equations, text and figures all included) from Volume 9 Number 1 (February 1995), Number 2 coming soon. We welcome your feedback regarding the presentation of such media on WWW. Any thoughts or comments please email jcamd@wucmd.wustl.edu --- Stuart M. Green stuart@wucmd.wustl.edu Center for Molecular Design Campus Box 1099 Washington University Tel 314-935-4671 St. Louis, MO 63130-4899 Fax 314-935-4979 From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: "Reinhard Doelz, Biocomputing Basel" Subject: [DISCUSSION] Re: [FEEDBACK WELCOME] JAM Version 2.0 BETA-3 Message-ID: <1995Apr21.080910.25680@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 19 Apr 1995 07:18:25 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 26 On Tue, 18 Apr 1995, Lar Kaufman wrote: > What does JAM do for you that you can't do with SGML? (1) SGML tools are only emerging and are demanding in memory, display (GUI) and associated tools (W3 browser or similar). JAM is capable to run on a DOS system and available for nearly a year now. (2) SGML tools cannot flexibly expand links into reflector/receptor links. (3) The overhead of -Writing- SGML is considerable, as is writing RTF, TEX or other descriptive language. JAM is simple. (4) JAM does site-specific includes and branches accordingly with a C-preprocessor like #ifdef construct. This allows to describe two or more setups in a single document. Hope this helps Regards Reinhard R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: Reece Hart Subject: [DESCRIPTION] WWW SITE: Washington University in St. Louis Message-ID: <1995Apr21.074715.25467@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 17 Apr 1995 03:27:46 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 17 There is a new WWW Site for the Department of Biochemistry and Molecular Biophysics at Washington University School of Medicine in St. Louis. The URL is http://bmb.wustl.edu/ The site includes documents regarding the the department's members and their research interests, the graduate program, and research facilities. A variety of other documents pertaining to the program are planned for the near future. -- Reece Kimball Hart | Internet: reece@dasher.wustl.edu Biophysics & Biochemistry, Box 8231 | WWW URL: http://dasher.wustl.edu/~reece Washington Univ. School of Medicine | Phone: (314) 362-4198 (lab) 660 South Euclid | -7183 (fax) St. Louis, Missouri 63110 (USA) | PGP public key available by finger & WWW From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: Joe Felsenstein joe@genetics.washington.edu Subject: [DESCRIPTION] World Wide Web site for the PHYLIP Phylogeny Inference Package Message-ID: <1995Apr24.110007.24376@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 24 Apr 1995 09:05:54 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 18 [ Article crossposted from bionet.molbio.evolution,bionet.population-bio,bionet.software ] [ Posted on 22 Apr 1995 05:20:29 GMT ] We have set up a World Wide Web (WWW) site for the PHYLIP Phylogeny Inference Package. It describes various aspects of the package and its distribution, and allows the user to download the latest distributions and register as a user. Its URL is: http://evolution.genetics.washington.edu/phylip.html Graphical net-browsers such as Netscape and Mosaic should be able to take full advantage of its features, but character-oriented browsers such as Lynx may not be able to. ----- Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: "Nicole Redaschi" redaschi@biox.embnet.unibas.ch Subject: [TEACHING] Installation of SRSWWW under CERN httpd 3.0 - Part 1 Message-ID: <1995Apr24.114002.25846@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 24 Apr 1995 09:21:17 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 388 ******************************************************************************** Installation of SRSWWW under CERN httpd 3.0 Part 1: Installation of CERN WWW Server ******************************************************************************** This documentation is a "cookbook recipe" for the installation of CERN httpd 3.0 on UNIX platforms using precompiled binaries. It contains step-by-step instructions for the basic (!) setup of the CERN http server. For more detailed informations read the CERN Server Guide (see below). 1. Getting Informations and the Program --------------------------------------- Go to the directory where you want to install the http server (in this example called "WWW"). % cd WWW The CERN server distribution is available from the "ftp.w3.org" anonymous ftp account. At the date of this writing, informations about the CERN http deamon are located in the directory "pub/www/doc": look for the files "cern-httpd-guide.ps.Z" and "cern-httpd-docs.tar.Z" and 'get' them. The first is a PostScript version of the CERN Server User Guide, the second is a directory comprising a set of HTML documents for the WWW version of the Guide. In this example, the WWW version of the Guide will be used to test the successful installation of the server. To get the httpd binaries you have to go to the directory "pub/www/bin". From there, go to the subdirectory corresponding to your machine architecture (eg. "osf1" if you have an osf1 machine), 'get' the files "cern_httpd_3.0.tar.Z" and "cern_httpd_utils_3.0.tar.Z" and 'quit'. % ftp ftp.w3.org Name: anonymous Password: ftp> cd pub/www/doc ftp> ls -lsa ftp> get cern-httpd-guide.ps.Z ftp> get cern-httpd-docs.tar.Z ftp> cd ../bin ftp> ls -lsa ftp> cd osf1 ftp> ls -lsa ftp> get cern_httpd_3.0.tar.Z ftp> get cern_httpd_utils_3.0.tar.Z ftp> quit Uncompress all files and untar the tar files. "cern-httpd-docs.tar.Z" will form the directory "httpd_docs"; "cern_httpd_3.0.tar.Z" together with "cern_httpd_utils_3.0.tar.Z" will form the common directory tree "cern_httpd_3.0". % uncompress cern-httpd-guide.ps.Z % uncompress cern-httpd-docs.tar.Z % uncompress cern_httpd_3.0.tar.Z % uncompress cern_httpd_utils_3.0.tar.Z % tar xvf cern-httpd-docs.tar % tar xvf cern_httpd_3.0.tar % tar xvf cern_httpd_utils_3.0.tar 2. Customizing the http Configuration File ------------------------------------------ In the subdirectory "config" of your new directory "cern_httpd_3.0" you will find example configuration files. Keep the originals and work on a copy! The "httpd.conf" file is for a regular http server, the "caching.conf" file is for a proxy server and has the advantage that it allows caching. Below are examples of customized versions of the "httpd.conf" and "caching.conf" configuration files. The edited parts are given between pairs of wavy lines (#~~~~~~). Follow these examples to customize your configuration file. EXAMPLE ------------------------------ "httpd.conf"-begin ------------------------------ # # Sample configuration file for cern_httpd for running it # as a normal HTTP server. # # See: # # # for more information. # # Written by: # Ari Luotonen April 1994 # # # Set this to point to the directory where you unpacked this # distribution, or wherever you want httpd to have its "home" # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # ServerRoot /where/ever/server_root ServerRoot /AbsolutePath.../WWW/httpd_docs #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # The default port for HTTP is 80; if you are not root you have # to use a port above 1024; good defaults are 8000, 8001, 8080 # Port 80 # # General setup; on some systems, like HP, nobody is defined so # that setuid() fails; in those cases use a different user id. # UserId nobody GroupId nogroup # # Logging; if you want logging uncomment these lines and specify # locations for your access and error logs # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # AccessLog /where/ever/httpd-log AccessLog /AbsolutePath.../WWW/log/httpd-access # ErrorLog /where/ever/httpd-errors ErrorLog /AbsolutePath.../WWW/log/httpd-error #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LogFormat Common LogTime LocalTime # # User-supported directories under ~/public_html # UserDir public_html #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # The Map-directive maps a virtual URL into a physical path in your file # system. In this example, URLs starting with /httpd-internal-icons/* will # be mapped to the path /cern_icons/*. This address will be passed to the # Exec- and Pass-directives that follow. # Map /httpd-internal-icons/* /cern_icons/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Scripts; URLs starting with /cgi-bin/ will be understood as # script calls in the directory /your/script/directory # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Exec /cgi-bin/* /your/script/directory/* Exec /cgi-bin/* /AbsolutePath.../WWW/cern_httpd_3.0/cgi-bin/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # URL translation rules; If your documents are under /local/Web # then this single rule does the job: # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Pass /* /local/Web/* Pass /* /AbsolutePath.../WWW/httpd_docs/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ "httpd.conf"-end -------------------------------- EXAMPLE ---------------------------- "caching.conf"-begin ------------------------------ # # Sample configuration file for cern_httpd for running it # as a proxy server WITH caching. # # See: # # # for more information. # # Written by: # Ari Luotonen April 1994 # # # Set this to point to the directory where you unpacked this # distribution, or wherever you want httpd to have its "home" # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # ServerRoot /where/ever/server_root ServerRoot /AbsolutePath.../WWW/httpd_docs #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Set the port for proxy to listen to # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Port 8080 Port 80 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # General setup; on some systems, like HP, nobody is defined so # that setuid() fails; in those cases use a different user id. # UserId nobody GroupId nogroup # # Logging; if you want logging uncomment these lines and specify # locations for your access and error logs # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # AccessLog /where/ever/httpd-log AccessLog /AbsolutePath.../WWW/log/httpd-access ProxyAccessLog /AbsolutePath.../WWW/log/proxy-access CacheAccessLog /AbsolutePath.../WWW/log/proxy-cache # ErrorLog /where/ever/httpd-errors ErrorLog /AbsolutePath.../WWW/log/proxy-error #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LogFormat Common LogTime LocalTime # # Proxy protections; if you want only certain domains to use # your proxy, uncomment these lines and specify the Mask # with hostname templates or IP number templates: # # Protection PROXY-PROT { # ServerId YourProxyName # Mask @(*.cern.ch, 128.141.*.*, *.ncsa.uiuc.edu) # } # Protect * PROXY-PROT # # Pass the URLs that this proxy is willing to forward. # Pass http:* Pass ftp:* Pass gopher:* Pass wais:* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # If you want to run a regular http server at the same time, add the # following rules (see the above example for the "http.conf" file) # Map /httpd-internal-icons/* /cern_icons/* Exec /cgi-bin/* /AbsolutePath.../WWW/cern_httpd_3.0/cgi-bin/* Pass /* /AbsolutePath.../WWW/httpd_docs/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Enable caching, specify cache root directory, and cache size # in megabytes # Caching On #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # CacheRoot /your/cache/root/dir CacheRoot /AbsolutePath.../WWW/cache_root #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CacheSize 5 # # Specify absolute maximum for caching time # CacheClean * 2 months # # Specify the maximum time to be unused # CacheUnused http:* 2 weeks CacheUnused ftp:* 1 week CacheUnused gopher:* 1 week # # Specify default expiry times for ftp and gopher; # NEVER specify it for HTTP, otherwise documents generated by # scripts get cached which is usually a bad thing. # CacheDefaultExpiry ftp:* 10 days CacheDefaultExpiry gopher:* 2 days # # Garbage collection controls; daily garbage collection at 3am; # Gc On GcDailyGc 3:00 ---------------------------- "caching.conf"-end -------------------------------- 3. Creating Directories and Symbolic Links ----------------------------------------- If you are not interested in logging information, just leave the corresponding part as it is in the original configuration files. If you copied one of the customized example files above, go to your directory "WWW" and create the subdirectory "log": % cd WWW % mkdir log If you want to run a proxy server with caching, you also had to indicate the "CacheRoot" directory, which is "/AbsolutePath.../WWW/cache_root" in the given example. Create the corresponding directory: % mkdir cache-root In the customized configuration files, the Pass-directive for the regular http server will map all URLs to the directory "/AbsolutePath.../WWW/httpd_docs" (which is the "ServerRoot" directory). If certain URLs have to be mapped to a different directory, you have to do two things: 1. go to your "ServerRoot" directory and add a symbolic link pointing to the respective directory 2. to your httpd configuration file, add a Map-directive which maps all URLs that start with a certain path to that symbolic link Eg. the Map-directive "Map /httpd-internal-icons/* /cern_icons/*" maps all URLs starting with "/httpd-internal-icons/*" to the symbolic link "cern_icons", which shall point to the directory "/AbsolutePath.../WWW/cern_httpd_3.0/icons/". For this to work, you have to add the symbolic link "cern_icons", pointing to the directory "/AbsolutePath.../WWW/cern_httpd_3.0/icons/", to the "ServerRoot" directory. % cd WWW/httpd_docs % ln -s /AbsolutePath.../WWW/cern_httpd_3.0/icons cern_icons 4. Trying It Out in Verbose Mode -------------------------------- In order to check whether everything has been set correctly, start the http server by hand in verbose mode and look what happens when you make a request with your browser. You have to indicate the path of your http configuration file with the command line option "-r". Test servers are typically run on a non- priviledged port above 1024, often 8001, 8080, or such (the official http port is 80). The server port is defined in the configuration file by the Port- directive, but you can override it with the command line option "-p" while testing it. % cd WWW/cern_httpd_3.0/bin % httpd -v -r /AbsolutePath.../WWW/cern_httpd_3.0/config/httpd.conf -p 8080 or: % httpd -v -r /AbsolutePath.../WWW/cern_httpd_3.0/config/caching.conf -p 8080 Now, start your browser and open the URL http://your_server:8080. If everything works fine you should get the CERN "index.html" (-> "Guide.html") page as a Welcome page. There you can read more details about CERN httpd 3.0. 5. Stand-Alone Installation --------------------------- If you are done with testing, stop the test run. Before starting the http server in stand-alone mode, change the protection of the two directories "log" and "cache_root" to allow access by "nobody". % chmod -R 777 log % chmod -R 777 cache_root For the actual installation of httpd in stand-alone mode, you need to create a new startup file. Go to the directory where you keep your system startup files and set up a new file "S_httpd" as described below. ----------------------------- "S_httpd"-begin ---------------------------------- #!/sbin/sh if [ -f /AbsolutePath.../WWW/cern_httpd_3.0/bin/httpd ] ; then if [ -f /AbsolutePath.../WWW/cern_httpd_3.0/config/httpd.conf ] ; then echo "Starting httpd" (/AbsolutePath.../WWW/cern_httpd_3.0/bin/httpd -r /AbsolutePath.../WWW/cern_ httpd_3.0/config/httpd.conf) &> /dev/console else echo "Problem with configuration file: no httpd started" fi else echo "Problem with httpd image: no httpd started" fi ----------------------------- "S_httpd"-end ------------------------------------ Change the protection of the new startup file, then start it. # chmod 744 S_httpd # S_httpd If you did everything correctly, you will get the message "Starting httpd". Have fun! Nicole Redaschi -------------------------------------------------------------------------------- Nicole Redaschi Biocomputing-Biozentrum der Universitaet Basel-Klingelbergstr.70-CH 4056 Basel -------------------------------------------------------------------------------- From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!bioftp.unibas.ch!moderate Newsgroups: bionet.software.www Subject: [DESCRIPTION] biotech catalogs online Message-ID: <1995Apr25.062632.15845@comp.bioz.unibas.ch> From: "Paula Burch" pburch@roc.mbcr.bcm.tmc.edu Date: Mon, 24 Apr 1995 16:28:39 GMT Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Approved: bio-www@comp.bioz.unibas.ch Lines: 33 [Note from the moderator: It has been confirmed that this is a non-profit organisation posting this as service in a non-commercial environment] I've been keeping a listing of biotechnology companies' catalogs at http://condor.bcm.tmc.edu/buying.html, with the kind help of some individuals who've sent in links that they know about, but it's still pretty short. Surely more laboratory suppliers have a web presence by now. If your laboratory supply company has an on-line catalog, or if you know of a company that does, please let me know. I'm interested only in those companies supplying laboratory equipment and reagents of interest to biologists, biochemists, and molecular biologists. Locations that make some provision for on-line ordering are to be preferred, but anything that can substitute for a paper catalog will do. What I have so far: ATCC, Beckman Instruments, Cambridge Scientific, Cold Spring Harbor, Fisher Scientific, Gelman Sciences, GibcoBRL, Invitrogen, LabTools, Inc, Millipore, Molecular Dynamics, New England Biolabs, Novagen, Promega, Research Genetics, and Wallac. (I also have some outdated info for dialing up to Sigma.) Thanks in advance for any suggestions. Instead of posting a summary of what I learn, I'll update the http://condor.bcm.tmc.edu/buying.html page. ________________________________________________________________________ Paula E. Burch, Ph.D. Molecular Biology Computational Resource Baylor College of Medicine phone: (713)798-6023 fax: (713)798-4279 Houston, Texas 77030 internet: pburch@bcm.tmc.edu http://condor.bcm.tmc.edu/pburch.html www@mbcr.bcm.tmc.edu From owner-www@net.bio.net Tue Apr 25 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!moderate From: "Nicole Redaschi" redaschi@biox.embnet.unibas.ch Subject: [TEACHING] Installation of SRSWWW under CERN httpd 3.0 - Part 2 Message-ID: <1995Apr24.120656.27103@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 24 Apr 1995 09:23:05 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 290 ******************************************************************************** Installation of SRSWWW under CERN httpd 3.0 Part 2: Installation of SRS ******************************************************************************** This documentation contains step-by-step instructions, for the basic (!) installation of the SRS software package on UNIX platforms. For details, see the SRS manual at the URL http://www.embl-heidelberg.de/srs/srsman.html. 1. Getting the Program ---------------------- Go to the directory where you want to install SRS (in this example called "SRS"). % cd SRS The SRS package is available from the "ftp.embl-heidelberg.de" anonymous ftp account. At the date of this writing, the most recent version of SRS ("srs4_04.tar.gz") is located in the directory "pub/software/unix/srs". (If you do not find the SRS package there, 'get' the INDEX first and search for the keyword "srs".) 'ftp' to "ftp.embl-heidelberg.de" and go to the directory "pub/software/unix/srs", 'get' the file "srs4_04.tar.gz" and 'quit'. Uncompress ('gunzip' requires modification of the filename extension!) and untar the file. You will get the directory "srs4_04". % ftp ftp.embl-heidelberg.de Name: anonymous Password: ftp> cd pub/software/unix/srs ftp> ls -lsa ftp> bin ftp> get srs4_04.tar.gz ftp> quit % mv srs4_04.tar.gz srs4_04.tar.z % gunzip srs4_04.tar % tar xvf srs4_04.tar 2. Customizing the ODD-Files (".sdl") ------------------------------------- All ".sdl" files are located in the directory "srs4_04/odd". Before you can start to compile the programs, you have to edit the file "srsdb.sdl": 1. Customize the object "#environment" with the name "unix". 2. Remove or outcomment ("!") all "#libenv" definitions of databanks you do not have at your site. 3. For each databank that you would like to index with SRS, modify the given "#libenv" definition if necessary: each databank must be associated with the name of the directory that contains the flatfiles. For databanks not listed in the default "srsdb.sdl" file, add a new "#libenv" definition to the object "#environment" and a new "#libid" definition to the object "#srsdb" (set "n" to a number between 1 and 255 that has not been used yet.) EXAMPLE -------------------------------- "srsdb.sdl" ----------------------------------- ... #environment /name=unix { #libenv /lib=@SWISSPROT_DB /dir="/data/swissprot/" #libenv /lib=@PIR_DB /dir="/data/pir/" ! #libenv /lib=@PIRALN_DB /dir="/data/pir/" #libenv /lib=@EMBL_DB /dir="/data/embl_dna/" #libenv /lib=@EMNEW_DB /dir="/data/emnew/" #libenv /lib=@XEMBL_DB /dir="/data/emnew/" #libenv /lib=@XXEMBL_DB /dir="/data/emnew/" ... #srsdb { #libid /n=1 /library=@SWISSPROT_DB #libid /n=2 /library=@PIR_DB #libid /n=3 /library=@EMBL_DB #libid /n=4 /library=@EMNEW_DB #libid /n=10 /library=@XEMBL_DB #libid /n=11 /library=@XXEMBL_DB ... -------------------------------- "srsdb.sdl" ----------------------------------- Some sequence databanks have a special format when used under GCG (EMBL, Genbank, Swissprot). For each of these you need to edit the respective ".sdl" file ("embl.sdl","genbank.sdl", "swissprot.sdl"). 1. Change the file name(s) that are defined in the "#file" objects. (Eg. the EMBL file "est" is usually called "em_est" in the GCG format) 2. Modify the "#libformat" definition: change the attribute "file_type" so that it points to "GCGREF_FILE" and "GCGSEQ_FILE". All you need to do is to move the outcomment character ("!"). EXAMPLE -------------------------------- "embl.sdl" ------------------------------------ ... #library /id=%EMBL_DB /group=@SEQUENCE_LIBS /name=EMBL /logicname=EM, EMBL /format=@EMBL_FORMAT /cachesize=2048 /maxIndexSizeKb=3200 /oddfile="embl.sdl" !{ ! #file /name=est ! #file /name=patent ... ! #file /name=sts !} !names of the files in GCG format { #file /name=em_est /logicname=EM_EST #file /name=patent /logicname=EM_PAT ... #file /name=em_sts /logicname=EM_STS } ... #libformat /id=%EMBL_FORMAT /parser=@EMBL_PARSER ! /file_type=@EMBLREF_FILE, @EMBLSEQ_FILE !GCG format /file_type=@GCGREF_FILE, @GCGSEQ_FILE /featureExpression=@EMBL_FEATURE_EXPRESSION { ... -------------------------------- "embl.sdl" ------------------------------------ If you have added new databanks to the file "srsdb.sdl", you need to provide corresponding ".sdl" files for the new databanks! Do not start from scratch, look first what you can use from the existing ".sdl" files. Whenever possible copy and paste from what is there and modify where required. If your new databank has the same format as one of those for which you already have an ".sdl" file" you may simply add the following things to this file: 1. a "#library" definition for the new databank 2. a "#libformat" definition for the new databank 3. "#link" definitions if desired As an example, see the file "embl.sdl" which contains data for both EMBL and EMBLNEW. 3. Compilation -------------- Now, you can start with the compilation of the programs. Go to the SRS root directory ("srs4_04") and invoke 'srsinstall'. This script will ask you first for the 'make' and 'cc' commands, then it will compile all programs and create a new binary file with all the data defined by the ".sdl" files. (If you get an ERROR message, you have to edit the appropriate file and recompile the programs.) To build the indices, 'source' the file "etc/prep_srs" and issue the command 'srscheck'. (If you get an ERROR message, you have to edit the appropriate file and then run 'srssection' to recompile the ".sdl" files.) If all worked fine, issue the command 'srsupdate' to start the indexing. % cd srs4_04 % srsinstall all ... [make] (press return) ... [cc] (press return) (% srsinstall all) % source etc/prep_srs % srscheck (% srssection) (% srscheck) % srsupdate To keep the indices up to date automatically, you can create a crontab file with the three commands 'source /AbsolutePath.../etc/prep_srs', 'srscheck' and 'srsupdate'. 4. Installation of SRSWWW under CERN httpd 3.0 ---------------------------------------------- (See Part 1 for the installation of CERN WWW server) On the WWW side: ---------------- Go to your httpd "ServerRoot" directory (in this example "WWW/httpd_docs") and add two symbolic links (srs, srs_map) which point to the SRS home directory "srs4_04/www": % cd WWW/httpd_docs % ln -s /AbsolutePath.../srs4_04/www srs % ln -s /AbsolutePath.../srs4_04/www srs_map Now, you have to edit your httpd configuration file (eg. "httpd.conf" or "caching.conf"). Add the following Map- and Exec-directives: EXAMPLE ---------------------- "httpd.conf"-/"caching.conf"-begin ---------------------- ... Map /srs/ /srs_map/index.html Map /srs/*.html /srs_map/*.html Map /srs/*.gif /srs_map/*.gif Map /cgi-bin/imagemap/srs/* /cgi-bin/htimage/srs_map/* ... Exec /srs/* /AbsolutePath.../srs4_04/www/* ... ---------------------- "httpd.conf"-/"caching.conf"-end ------------------------ Finally, you have to change the format of the image configuration file "srswww.map" (in directory "srs4_04/www") to fit the CERN style: EXAMPLE ----------------------------- "srswww.map"-begin ------------------------------- rect (287,168) (382,195) /srs/srsc?-info%20swissprot rect (80,127) (137,153) /srs/srsc?-info%20embl rect (376,222) (440,253) /srs/srsc?-info%20hssp ... circle (57,100) 5 /srs/srsc?-linfo%20ecd%20embl circle (75,107) 5 /srs/srsc?-linfo%20epd%20embl circle (57,169) 5 /srs/srsc?-linfo%20mimmap%20embl ... default /srs/net.html ----------------------------- "srswww.map"-end --------------------------------- On the SRS side: ---------------- Go to the directory "srs4_04/www" and edit the script "srsc": replace "./wgetz" by the full path name "/AbsolutePath.../srs4_04/www/wgetz". EXAMPLE ------------------------------ "srsc"-begin ------------------------------------ #!/bin/csh set noglob # turn off file name expansion...[]! if (${#argv} == 0) then /AbsolutePath.../srs4_04/www/wgetz -top else /AbsolutePath.../srs4_04/www/wgetz $* endif ------------------------------ "srsc"-end - ------------------------------------ SRSWWW inserts many hypertext links into the entries before display. The configurations of the hypertext links are defined in the file "hyperlink.sdl". You need to edit this file if one or more of the databanks addressed are missing at your site. Eg. if you do not have MEDLINE installed, use the URL given in the example below. In other cases you may address SRSWWW servers installed on other nodes (Eg. replace "/srs/srsc" by "www.embl-heidelberg.de/srs/srsc".) EXAMPLE ------------------------- "hyperlink.sdl"-begin -------------------------------- ... #linkcall /id=%FETCH_MEDLINE /call="%s" ... #linkcall /id=%FETCH_FNUCACCNO /call="%s" ... ------------------------- "hyperlink.sdl"-end-- -------------------------------- After the changes you must run the command "srssection" to recompile the ODD- files! Now, go to the SRS root directory ("srs4_04") and invoke 'srsinstall' with the commandline option "www": % srsinstall www You can now access SRSWWW with the URL "http://your_server/srs/srsc". Have fun! Nicole Redaschi -------------------------------------------------------------------------------- Nicole Redaschi Biocomputing-Biozentrum der Universitaet Basel-Klingelbergstr.70-CH 4056 Basel -------------------------------------------------------------------------------- From owner-www@net.bio.net Wed Apr 26 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Herve de VILLEMEUR" Herve.de-Villemeur@univ-rennes1.fr Subject: [DISCUSSION] Re: CABIOS WWW page? Message-ID: <1995Apr27.085336.17533@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 27 Apr 1995 08:14:34 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 26 [ Article crossposted from bionet.journals.note ] [ Posted on 26 Apr 1995 08:46:50 GMT ] In article <3n4dg5$np8@nntp.ucs.ubc.ca>, ywchen@laue.biochem.ubc.ca says... > >Dear all, > >Does any one know if there is a WWW page for CABIOS "Computer >Applications in Biological Science"? No CABIOS WWW page but a page of Oxford University Press : http://www.oup.co.uk/ ________________________________________________________________ Herve de VILLEMEUR Universite de Rennes 1 CNRS URA 256 : Biologie Cellulaire et Reproduction Bibliotheque Campus de Beaulieu, 35042 Rennes cedex, France Tel : (33) 99 28 61 23 poste 51 22, Fax : (33) 99 28 67 94 Herve.de-Villemeur@univ-rennes1.fr ________________________________________________________________ From owner-www@net.bio.net Wed Apr 26 23:00:00 1995 Path: biosci!biosci!not-for-mail From: pommert@uke.uni-hamburg.de (Andreas Pommert) Newsgroups: bionet.software.www Subject: IMDM WWW pages Date: 27 Apr 1995 16:51:54 -0700 Organization: University Hospital Eppendorf, Hamburg, Germany Lines: 24 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <3npamq$fg9@net.bio.net> Reply-To: pommert@uke.uni-hamburg.de NNTP-Posting-Host: net.bio.net Dear Colleagues, the Institute of Mathematics and Computer Science in Medicine (IMDM) is happy to announce its first pages on the world wide web, available under http://www.uni-hamburg.de/~medizin/imdm The presented information includes - a short overview of our research in 3D medical imaging - MANY images created with VOXEL-MAN (3D anatomical views of various regions such as skull, brain and abdomen) - lists of papers, faculty members, addresses, etc. See and enjoy! Andreas ------------------------------------------------------------------------ Andreas Pommert Inst. of Math. and Computer Science in Medicine (IMDM) University Hospital Eppendorf, Martinistr. 52, 20246 Hamburg, Germany pommert@uke.uni-hamburg.de tel ++49(40) 4717-2300 fax ++49(40) 4717-4882 ------------------------------------------------------------------------ From owner-www@net.bio.net Wed Apr 26 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Victor V. Solovyev" Subject: [SERVER] New Gene-finder program to test E. coli contamination Message-ID: <1995Apr27.173408.929@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 27 Apr 1995 16:05:18 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 88 ************************************************************************* HBR - Recognition of Human and E.coli sequences to test a library for E. coli contamination Department of Cell Biology, Baylor College of Medicine ========================================================================= Analysis of sequences is available through Weizmann Institute of Science server with the name of the program in the subject line Example: mail -s hbr services@bioinformatics.weizmann.ac.il < test.set Soon HBR will be installed in the University of Houston server: mail -s hbr service@theory.bchs.uh.edu < test.set where test.set a file with one or some sequences. And you can run the program by WWW BCM Human Genome Center and Search launcher Home page URL:http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html for accsess to Gene-finder prediction Help files and programs. -> BCM Gene Finder Description: ********************** Recognition of human and bacterial sequences (HBR) to test a library for E. coli contamination by sequencing example clones. The program calculates the probability to be a human sequence (P) or E.coli sequence (1-P) for each sequence of your set and the total percentage human and bacterial sequences in the set. The method is based on linear discriminant functions Solovyev V.V.,Salamov A.A., Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. (Nucl.Acids Res.,1994, 22,24, 5156-5163). Accuracy: ******************************** The accuracy of recognition is about 99%. But you have better to present long sequences and enough representative set of them. We recommend to analyse 400 bp and longer sequences and do not take into account the sequences with 0.4 < P < 0.6 which can not be reliable assigned to human or E.coli group. Submitting sequences via email: *********************************** For email submission the sequences must have the following format: Name of 1st sequence ccatctctgtcttgcaggacaatgccgtcttctgtctcgtggggcatcctcctgctggca ggcctgtgctgcctggtccctgtctccctggctgaggatccccagggagatgctgcccag aagacagatacatcccaccatgatcaggatcacccaaccttcaacaagatcacccccaac ctggctgagttcgccttcagcctataccgccagctggcacaccagtccaacagcaccaat Name of 2nd sequence ccatctctgtcttgcaggacaatgccgtcttctgtctcgtggggcatcctcctgctggca ggcctgtgctgcctggtccctgtctccctggctgaggatccccagggagatgctgcccag atcttcttctccccagtgagcatcg............... ...... (Restrict the line length to less than 80 characters; The line with the sequence name must have at least one 'Space' symbol in the first position). HBR output: ****************** 1st line - total number and % of human and E.coli sequences the next groups of 3 lines: 1st line - numbers of your sequences 2nd line - length of them 3d line - Probability to be Human sequence (P) or bacterial (1-P) For example: Number of sequences- 12 % human= 50 % bacterial= 50 1 2 3 4 5 6 7 8 9 10 900 960 1501 360 360 1020 330 480 240 541 1.00 1.00 0.83 1.00 1.00 0.00 0.01 0.01 0.00 0.01 11 12 720 540 0.57 0.01 Problems, comments, and suggestion: can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-www@net.bio.net Thu Apr 27 23:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Francisco M. De La Vega" fvega@lambda.gene.cinvestav.mx Subject: [DESCRIPTION] New Spanish-English list on Bioinformatics Message-ID: <1995Apr28.073930.16721@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 27 Apr 1995 21:09:45 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 140 Dear all, Following is the information sheets of a newly created E-Mail disscusion list on the topic of Bioinformatics mainly directed to latin-american and spanish speaking scientists (altough you can use both english and spanish in the messages). You will find both english and spanish versions of the info. PLEASE repost and distribute freely to groups or people you think might be interested. Thank you. Francisco M. De La Vega Assistant Professor ------------------------------------------------------------------------- INFORMACION SOBRE LA LISTA DE DISCUSION ELECTRONICA SOBRE BIOINFORMATICA ------------------------------------------------------------------------- NOMBRE DE LA LISTA: BIOINFORMATICA LENGUAJE A USAR: BILINGUE ESPANOL/INGLES MODERADOR: Francisco M. De La Vega Coordinador de la Unidad de Analisis de Biosecuencias y Estructuras del Depto. de Genetica y Biologia Molecular del CINVESTAV-IPN E-MAIL MODERADOR: fvega@gene.cinvestav.mx E-MAIL LISTA: bioinfo@gene.cinvestav.mx Espejo en WWW: URL http://www.gene.cinvestav.mx/listas.html TOPICOS PRINCIPALES: Bioinformatica, biologia teorica, analisis de secuencias de DNA y proteinas, inteligencia artifical en biologia molecular, bases de datos de secuencias, evolucion molecular. OBJETIVOS: La finalidad de esta lista es que sea un puente de comunicacion que facilite la colaboracion entre los investigadores de habla hispana trabajando en esta area en Mexico y latino america principalmente, investigadores hispanos trabajando en otros paises, o investigadores con afinidades con los paises hispanos.Discusion sobre temas relacionados con la bio-informatica, bases de datos de biologia molecular, evolucion molecular, aspectos teoricos de la biologia molecular, sofware y algoritmos aplicables a la investigacion biologica (e.g. estadistica, inteleigencia artificial, metodos graficos, linguisticos, etc.). Anuncios de conferencias locales e internacionales relacionadas con el tema. Anuncios e informacion sobre recusros de bio-computacion accesibles a investigadores latino-americanos o de todo el mundo. ANFITRION: Departamento de Genetica y Biologia Molecular CINVESTAV-IPN, Ciudad de Mexico. ---------------------------------------------------------------------------- Para subscribirse enviar un mensaje de correo electronico a la direccion majordomo@gene.cinvestav.mx con el siguiente comando incluido en el cuerpo del mensaje: subscribe bioinfo [e-mail] Nota: envie este mensaje desde la cuenta a la que quiera recibir su subscripcion pues el servidor tomara esta direccion de correo electronico por defecto. Para solicitar ayuda sobre los servicios del servidor de correo envie un mensaje con el comando HELP en el cuerpo del mensaje a la direccion: majordomo@gene.cinvestav.mx Tambien puede accesar el URL http://www.gene.cinvestav.mx/listas.html para realizar cualquier operacion con el servidor de listas a traves de una interface WWW/E-Mail. ----*****---- ------------------------------------------------------------------------------ INFORMATION OF THE BSAU BIOINFORMATICS DISCUSSION LIST ------------------------------------------------------------------------------ LIST NAME: BIOINFO LENGUAGE: Bilingual Spanish/English, but mainly Spanish LIST-OWNER: Francisco M. De La Vega Head of the Biosequence Analisis Unit of the Dept. of Genetics and Molecular Biology CINVESTAV-IPN, Mexico City E-Mail-OWNER: FVega@Gene.CINVESTAV.Mx E-Mail-LIST: bioinfo@gene.cinvestav.mx WWW-Mirror URL: http://www.gene.cinvestav.mx/listas.html MAIN TOPICS: Bioinformatics, theoretical biology, biosequence analisis techniques and algoritms, AI ,graphical and statistical methods for pattern recognition, biosequence databanks, molecular evolution. GOLAS: The main goal of this list is to provide a communication means to hispanic researchers working in some topic of bioinformatics and working in Mexico, Latin America, spanish speaking countries or abroad. Contri- butions from non-spanish speaking scientists with affinity to our countries are also wellcome. Discussions on any facet of bio-informatics are encouraged. As examples: sequence databank implementation and interoperability, molecular evolution, theorethical biology, software, algorithms, AI, statistical approaches, linguistic methods, graphical methods, etc. Announcements on new services (e.g. Web servers) and resources available for latin-american scientists or globaly, meetings, courses, conferences, etc., are also of interest. HOST: Department of Genetics and Molecular Biology, Centro de Investigacion y Estudios Avanzados del I.P.N. Mexico City, Mexico ----------------------------------------------------------------------------------- To subscribe send a message to majordomo@gene.cinvestav.mx including in the body of the message the words: subscribe bioinfo [e-mail] Note: Subject line is not proccesed. If you send the message from the e-mail address you wish to use for the list, the [e-mail] argument is not neccesary. You can also subsribe directly using Mosaic or other WWW clients that support forms using the majordomo-WWW interface located at the URL: http://www.gene.cinvestav.mx/listas.html In that page you can also read previous postings to the lists managed by us. ------------------------------------------------------------------------------------ Management of BSAU Administracion de la UABE Depto. de Genetica y Biol. Molec. CINVESTAV-IPN, Ciudad de Mexico http://www.gene.cinvestav.mx/uabe.html