From owner-www@net.bio.net Thu Feb 02 22:00:00 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: Barry Barker Subject: [Q] WISDOM Database Message-ID: <1995Feb3.181747.12488@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 1 Feb 1995 12:25:46 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 5 Is there such a database for Biomed information, if so where?Can you help? Thank you for your time and trouble. i Sent by: the WWW suggestion program @EMBnet Switzerland (info@ch.embnet.org) Signed: Barry Barker Date: Feb 1 1995 at 12:25:46 GMT. From owner-www@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: 5015920@mcimail.com Subject: WWW Job Opening for Nature Message-ID: <1995Feb3.175544.11817@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 1 Feb 1995 06:36:09 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 21 [note from the moderator: We imply non-profit means non-commercial] Attention! The Nature Conservancy, a non-profit conservation group dedicated to preserving the world's dwindling biological diversity with offices across the U.S. and partner organizations in Canada and Latin America seeks a "Webmaster" for an immediate opening. The position will initially build a Web server with pages for 60 biodiversity monitoring programs -- known as the Natural Heritage Network. Ultimately, this Web server will be the top level of a series of "hot-linked" Natural Heritage Network Web servers that will be distributed across the Western Hemisphere. Sound interesting? I also have an immediate opening for a Unix-TCP/IP specialist as well to help these distributed programs with overall connectivity. Put your skills to work preserving Nature. Dave Meyer The Nature Conservancy 5015920@mcimail.com From owner-www@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Jeff Matthews Subject: New Radiation Biology Web Site Message-ID: <1995Feb3.173454.11488@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 2 Feb 1995 22:29:40 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 9 There's a new WWW site dedicated to Radiation Biology. Point your web browser to http://www.science.ubc.ca/departments/physics/radbio/HomePage.html THere's current journal contents, a job board, conference listings and monthly editorials. There's also a list of e-mail adresses of other radiation biologists. Come in, take a look around, sign the guest book and let us know what you think! From owner-www@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Mike Cherry Subject: Saccharomyces Genome Database Message-ID: <1995Feb3.180646.12222@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 1 Feb 1995 06:34:34 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 34 Saccharomyces Genomic Information Resource http://genome-www.stanford.edu/ This WWW server provides access to the yeast database called SacchDB built using the ACEDB software (Durbin, Sanger Centre and Thierry-Mieg, CNRS Montpellier). The ACEDB/WWW gateway (Decoux, Moulon) is used to provide the WWW access. The results of the international effort to sequence the S. cerevisiae genome, edition 12 of the Mortimer genetic maps, the Olson physical map, links to other yeast information, documentation on using ACEDB databases, index of the BioSci Yeast conference and more is available from the above URL. SacchDB for Macintosh (680X0 and PPC) and several flavors of UNIX is available from either: ftp://genome-ftp.stanford.edu/pub/yeast/SacchDB ftp://ncbi.nlm.nih.gov/repository/SacchDB A WAIS index of the information contained in SacchDB, index of BioSci Yeast conference, as well as images and tables derived from the database, and more, are available from: gopher://genome-gopher.stanford.edu/11/Saccharomyces These yeast resources are provided by the Saccharomyces Genome Database project at Stanford University through a grant from the National Center for Human Genome Research, National Institutes of Health, USA. J. Michael Cherry Internet: cherry@genome.stanford.edu Stanford DNA Sequence & Tech. Center Saccharomyces Genome Database Stanford University School of Medicine Stanford, California 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 From owner-www@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Adam Bernstein Subject: FAQ Transparent/Interlaced GIF seekers READ ME Message-ID: <1995Feb3.183415.13139@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 2 Feb 1995 08:16:33 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 66 [ Article crossposted from comp.infosystems.www.announce ] [ Posted on 30 Jan 1995 16:43:16 -0800 ] [NOTE: This document is also available on the World-Wide Web at .] Before you ask about transparentizing and interlacing GIF's, please point yourself at the WWW FAQ, which covers these topics in Section 5.7.7. The URL is: Come to think of it, I'm guessing that info is also contained in FAQs for the graphics newsgroups, but this one I know for sure. The advantage to this one is that it has hyperlinks to all the relevant pages and tools for the various platforms. Where, you may ask, could you get any other FAQs, if you so desired? You could try FTP to: which contain archives by newsgroup of every FAQ there is (I think). Pretty impressive, no? For heaven's sake, don't overload them. The WWW FAQ leaves out one worthy item: In Windows, the program LviewPro 1A can save GIFs as interlaced and as GIF89a format with the background color transparent (and it's a full-featured graphics manipulation program). Check it out at your favorite SIMTEL mirror FTP site: Also for Windows (or DOS), I highly recommend Alchemy Mindworks' Graphics Workshop, though I can't recall if it does transparent/interlaced stuff or not. They have a new program called GIF Construction Set for Windows, which does do transparent (though the docs don't mention interlaced, so I don't know about that). Their URL is: And finally, you all might want to check out the Graphics Archive Web site, which is muy bueno for all kinds of graphics stuff: I'm going to post this regularly for a while, unless screaming hordes of enraged net surfers bombard my mailbox with "Stop posting that transparent/ interlaced GIF crap, you dweeb" messages, and then only if the number of said messages exceeds the number of people posting to request info on transparent and interlaced GIFs. The only reason I'm doing this is because the regular postings of the FAQ don't seem to be frequent enough to cut down on this AMFAQ (Apparently Most FAQ). Thank you, and good night. Adam Bernstein Jet Propulsion Lab Avionic Equipment Section, MS 198-235 Optical Tracking Group 4800 Oak Grove Dr. http://dragon.jpl.nasa.gov/~adam/ Pasadena, CA 91109 adam@dragon.jpl.nasa.gov Phone: 818 354-9784 or adam.c.bernstein@jpl.nasa.gov FAX: 818 393-6105 From owner-www@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Lincoln Stein Subject: MIT CGR HUMAN PHYSICAL MAPPING DATA RELEASE 4 Message-ID: <1995Feb3.183503.13208@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 1 Feb 1995 16:35:36 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 80 [ Article crossposted from bionet.genome.chromosomes,bionet.announce ] [ Posted on 31 Jan 1995 15:13:37 -0800 ] ANNOUNCING: WHITEHEAD INSTITUTE/MIT CENTER FOR GENOME RESEARCH HUMAN GENOMIC MAPPING PROJECT DATA RELEASE 4 (JANUARY 1995) The fourth release of data from the Human Physical Mapping Project at the Whitehead Institute/MIT Genome Center, covering data generated through the end of January, 1995, is now available. This data release contains YAC screening data for 5525 sequence tagged sites (STSs) screened on the CEPH mega-YAC library. For each STS, we report addresses for the YACs found to contain the STS. From the data obtained so far, there are over 900 contigs assembled using double linkage between STSs. The data is available electronically in two ways. ANONYMOUS FTP: The entire data release is available as a set of Microsoft Excel files and tab-delimited ascii files on our ftp server. Using an ftp client (such as "Fetch" on the Macintosh), connect to "ftp-genome.wi.mit.edu". Use "anonymous" as your user name, and give your e-mail address as your password. The data files are present in the directory /distribution/human_STS_releases/july94. The contents are as follows: 01-95.INTRO.mswd - Description of the data release, Macintosh format. 01-95.INTRO.txt - The same as ascii text 01-95.STS.YAC.sea.hqx - STS & YAC screening data, in MS-Excel format. 01-95.STS.YAC.txt - The same as tab-delimited text. 01-95.sequence - Full sequences of previously unpublished STSs. THE WORLD-WIDE WEB: You will need a World Wide Web client such as Mosaic (Unix, MS-Windows and Macintosh) or MacWeb (Macintosh). Instruct your client to connect to "http://www-genome.wi.mit.edu/". >From there, follow the "Human Physical Mapping Project" link. You will be able to browse and download the raw data set as well as to view doubly-linked contigs. A subset of the STSs (those for which we have chromosomal assignments) are also available through the Genome Database (GDB). QUESTIONS AND PROBLEMS. If users have any questions or problems, please contact us at human_STS_help@genome.wi.mit.edu We invite suggestions about how to make these data release most useful. DATA RELEASE POLICY AND CITATION. Data releases are scheduled every 90 days. At the end of each calendar quarter, all genomic mapping data are reviewed and prepared for distribution via CGR's electronic databases. Data releases typically occur within two weeks of the close of the quarter (i.e., in mid-January, mid-April, mid-July and mid-October). Releases are announced by electronic messages posted to the following two newsgroups: "bionet.genome.chromosomes" and "bionet.announce". CGR's data release policy aims to ensure that scientific colleagues have immediate access to information that may assist them in the search for genes. Data releases do not constitute scientific publication of CGR's work, but rather provide scientists with a regular look into our lab notebooks. For projects aimed at the analysis of particular genes or subchromosomal regions, permission is hereby granted to use our data without the need for a formal collaboration, subject only to appropriate acknowledgment. For projects aimed at large-scale mapping of entire chromosomes or entire genomes, use of the data and markers should be on a collaborative basis. The information for the human genome mapping project should be cited as: Whitehead Institute/MIT Center for Genome Research, Human Physical Mapping Project, Data Release 4 (January 1995). -- ======================================================================== Lincoln D. Stein Whitehead Institute/MIT Genome Center lstein@genome.wi.mit.edu Cambridge, MA 02142 ======================================================================== From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: "M. Kelly" Subject: MBx on the World Wide Web Message-ID: <1995Feb13.082246.17171@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 7 Feb 1995 00:22:51 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 38 MBx on the World Wide Web The European Collaborative Interspecific Backcross (EUCIB) provides the resources for the high resolution genetic mapping of the mouse genome. One of the primary aims is to construct a high resolution microsatellite map of all available simple sequence length polymorphisms across the entire mouse genome. The MBx database supports the mapping effort. The database was constructed using distributed client/server database - Sybase, Sybase application development tools (APT), the C and XView programming languages. MBx stores all locus, probe and SSLP data. Allele data at each locus is presented as a scrollable matrix on screen. MBx can compute genetic linkage between loci and in addition, can automatically perform the necessary haplotype analysis by minimising the number of observed recombinants across any chromosome region in order to derive genetic order of loci. Furthermore MBx can abstract all mice carrying recombinants in any chromosome region. Such information when downloaded to robots is imported for the automated and error free selection of correct DNA's for subsequent high resolution microsatellite mapping in a particular chromosome region. To date the latest EUCIB maps and mapping data, including ACeDB type Multimaps have been available via the UK HGMP Resource Centre Computing Menu. MBx is accessed from the HGMP menu by typing 'mbx' at the menu prompt. EUCIB genetic maps in "Encylopedia of the Mouse Genetic Map" format, and MBx-ACeDB Multimaps which compare MBx and MIT genetic data are available. In addition MBx is now available on the World Wide Web. http://www.hgmp.mrc.ac.uk/local-data/mbx/Mbx_Homepage.html The following items are available via World Wide Web: -pedigree information from the EUCIB backcross, -probe and locus information, -haplotype panels, -genetic maps EotM format, -information on accessing the EUCIB User Service. From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: Keith Robison Subject: Attention Web Masters: The Top of the Web has moved Message-ID: <1995Feb13.071743.16166@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 8 Feb 1995 00:19:40 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 29 Just to publicize something which hasn't been publicized much. CERN is handing over the World Wide Web project to the W3 organization, which will continue to develop the project. As such, most hyperlinks that reference CERN should switch over to referencing W3 So, change all your references to http://info.cern.ch/... to http://www.w3.org/... (of course, it wouldn't hurt to check the new addresses :-) At the current time, automatic redirects are actually moving you to www.w3.org whenever you try to reach info.cern.ch, but some time later this year info.cern.ch will quit doing this. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: WebSub Subject: WebSub: New DNA Sequence Submission Method Message-ID: <1995Feb13.065713.15659@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Sat, 4 Feb 1995 04:15:56 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 58 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=- The Genome Sequence Data Base at the -=-=-=-=- =-=-=-=- National Center for Genome Resources Announces -=-=-=-=- =-=-=-=- WebSub: A New DNA Sequence Submission Method -=-=-=-=- -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- The Genome Sequence Data Base is pleased to announce the beta version of WebSub -- a new means of submission for your nucleotide sequence data. In response to many requests, GSDB has developed a World Wide Web (WWW) submission form. The convenience of the traditional submission form is now available on-line for use with your Macintosh, PC or Sun. Much like the ASCII text form, this is a simple fill-in-the-blank form which is submitted with the click of a button. This form eliminates the need for the use of additional applications such as email, text editors or Authorin(tm). WebSub produces automatically-processable submissions like those created by Authorin, and thus they should be usable by all of the nucleotide sequence databases. However, during the beta test phase, all submissions prepared with WebSub will be processed by GSDB and the results will be immediately forwarded on to the other databases (DDBJ, EMBL, and NCBI) for inclusion in their data collections. The URL to directly access WebSub on the World Wide Web (WWW) is: http://www.ncgr.org/gsdb/WebSub.html If you do not currently have access to a Web browser that supports forms, please do not hesitate to contact us. We will be happy to direct you to ftp sites from which you may download these applications. Please note that the following browsers have been found to be compatible with this tool and are therefore recommended. Sun Users -- Mosaic & Netscape Mac Users -- Netscape IBM/compatible Users -- Netscape At this time, WebSub is known not to work with Mosaic on either the Mac or IBM PC; but WebSub does work with Netscape on these platforms. In addition, should you already have access to the World Wide Web, the GSDB server (http://www.ncgr.org/gsdb) offers a wide range of services, such as data retrieval, tailored query capability, submission status information, software and documentation, as well as on-line updates (http://www.ncgr.org/gsdb/update.html). Due to restrictions in current WWW browsers there are some limitations on the amount of data that can be submitted with WebSub (e.g., 31k basepairs of sequence and ten features). However, these limitations will not present a problem for the majority of submissions. For more information see the submission overview page on our WWW server. We thank you for your time and we look forward to receiving your data and your comments through WebSub. If you have not received an acknowledgment of your submission within one working day or need any other assistance, please contact us at WebSub@gsdb.ncgr.org or 505/982-7840. From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!bloom-beacon.mit.edu!usc!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: Keith Robison Subject: WWW VL Biosciences Update Message-ID: <1995Feb13.072549.16285@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 8 Feb 1995 17:53:35 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 44 Recent additions to the WWW Virtual Library Biosciences: Developmental Biology http://golgi.harvard.edu/biopages/develop.html Immunology http://golgi.harvard.edu/biopages/immuno.html Mycology http://muse.bio.cornell.edu/taxonomy/fungi.html Kathy Hodge KH11@cornell.edu Caenorhabditis elegans http://eatworms.swmed.edu/VLhome.html Leon Avery leon@eatworms.swmed.edu Drosophila http://www-leland.stanford.edu/~ger/drosophila.html Gerard Manning ger@leland.stanford.edu Pharmacy (Medicine) http://www.cpb.uokhsc.edu/pharmacy/pharmint.html David Bourne david-bourne@uokhsc.edu Yeasts http://genome-www.stanford.edu/VL-yeast.html Mike Cherry cherry@genome.stanford.edu Also, the WWW VL Genetics has moved Genetics http://www-bprc.mps.ohio-state.edu/cgi-bin/hpp?genetics.html Ray Grimalia mcb42@unicorn.bwco.com Keith R. Biosciences Coordinator From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Shun'ichi Kuroda Subject: [repost] [Q] Promoter Sequence Analysis Message-ID: <1995Feb13.160849.25030@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 9 Feb 1995 07:08:35 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 30 Dear Sirs: I am an assistant professor of Kobe university. Before the severve earthquake on Jan 17, I posted same question to this NG. But the RESs for my question could not be arrived at our server, since the server was broken by the earthquake. So I repost the same question. (Question) I have a novel promoter sequence from human genome, of which length is about 2kbp and has enough transcriptional activity. However, it has been still unclear whether the promoter sequence contains known promoter motifs or not. If the database of the known promoter motifs is available, it will be helpful for us to construct the deletion mutants and understand the essential transcriptional region of the promoter sequence. Therefore, I want to know the services for analyzing the promoter sequence, which are on internet or distributed as commercial softwares. Any comments will be appreciated. Many thanks, -- SHUN'ICHI KURODA BIOSIGNAL RES CENTER KOBE UNIVERSITY NADA, KOBE, 657 JAPAN E-mail: skuroda@inherit.biosig.kobe-u.ac.jp URL:http://inherit.biosig.kobe-u.ac.jp/biosighome.html Tel +81-78-803-1255 Fax +81-78-803-0994 From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Victor V. Solovyev" Subject: Exon-exon junctions in cDNA by BCM Gene-finder Message-ID: <1995Feb13.154533.24483@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 10 Feb 1995 19:45:32 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 38 New program: ************************************************************************* 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 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. From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Wilfried Janning Subject: FlyView - A Drosophila Image Database Message-ID: <1995Feb13.163508.25593@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 13 Feb 1995 16:07:58 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 21 [ Article crossposted from bionet.drosophila ] [ Posted on 9 Feb 1995 17:05:03 GMT ] Dear Drosophilists, we are starting to construct an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes). Our aim is to establish the possibilty to compare images on the computer screen or to search for special patterns at different developmental stages. Therefore, all images are accompanied by text descriptions that can be used to search with keywords. You may be interested to try the experimental version of FlyView. It is available on World Wide Web, URL is http://pbio07.uni-muenster.de/ Please send any comments, suggestions or problems to janning@vnwz00.uni-muenster.de Best regards, Wilfried Janning From owner-www@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Michael A. Chipperfield Subject: Genome Project Message-ID: <1995Feb13.164453.25759@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 13 Feb 1995 16:15:18 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 34 [ Article crossposted from bionet.molbio.genome-program ] [ Posted on Sat, 4 Feb 1995 22:27:25 GMT ] [Answer to a question 'what is the Human Genome Project' ? ] Jon, There is an excellent WWW site maintained by the Department of Energy, which outlines the goals for the Human Genome Program, and provides as well a primer on the basic science of the project. The URL for this site is: http://www.er.doe.gov/production/oher/hug_top.html Hope this helps! Sincerely, Michael A. Chipperfield DNA Data Coordinator Genome Data Base In article <3grkcq$80l@maze.dpo.uab.edu>, Mpsy0l3@uabdpo.uab.edu (Flames) wrote: > Could Someone PLEASE TELL ME EXACTLY WHAT THIS PROGRAM IS?!?!!?!? > Thank You very much. I have to write a paper on it, so anything you could > give me would be VERY appreciated. > > THANKS!!! > > Jon, University of Alabama. From owner-www@net.bio.net Thu Feb 16 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Keith Robison Subject: NCSA HTTPD 1.3 Security Problem Message-ID: <1995Feb17.180837.16558@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 16 Feb 1995 14:39:28 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 89 For those webmasters who haven't seen it yet, there is a security hole in NCSA HTTPD 1.3 which can apparently be exploited by an automated script. NCSA has not yet provided fixed source or binaries, but the CIAC folks recommend a simple fix in the source. I have recompiled NCSA httpd 1.3 for SunOS 4.x using gcc, and this binary is available via anonymous FTP ftp://golgi.harvard.edu/pub/robison/httpd Replace your existing httpd binary with this one and restart the server. CIAC advisory attached. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu > _____________________________________________________ > The U.S. Department of Energy > Computer Incident Advisory Capability > ___ __ __ _ ___ > / | /_\ / > \___ __|__ / \ \___ > _____________________________________________________ > ADVISORY NOTICE > Unix NCSA httpd Vulnerability > February 14, 1995 1030 PST Number F-11 > _____________________________________________________________________________ > PROBLEM: A vulnerability has been discovered in the NCSA WWW server > software (httpd). > PLATFORMS: Unix systems running NCSA httpd version 1.3. > DAMAGE: Remote users may gain unauthorized access. > SOLUTION: Implement workaround as described below. > _____________________________________________________________________________ > VULNERABILITY This vulnerability, along with an automated exploitation > ASSESSMENT: script, has been announced in public forums on the Internet. > CIAC recommends that sites install the workaround on affected > systems as soon as possible. > _____________________________________________________________________________ > Critical Information about the NCSA httpd Vulnerability > CIAC has learned of a serious vulnerability in the NCSA WWW server software, > httpd. By sending a carefully constructed request to the WWW server, an > intruder can cause an internal buffer overflow and push arbitrary > instructions onto the program stack. These new instructions may allow the > intruder unauthorized access to the WWW server. > Until official patches are available from NCSA, CIAC recommends the following > temporary fix be installed. In the file httpd.h, change the string length > definitions from: > /* The default string lengths */ > #define MAX_STRING_LEN 256 > #define HUGE_STRING_LEN 8192 > to: > /* The default string lengths */ > #define HUGE_STRING_LEN 8192 > #define MAX_STRING_LEN HUGE_STRING_LEN > Then rebuild, install, and restart the new httpd server. > It is likely that these attacks will generate unusual server log entries. > The httpd access_log file should be examined for unusual requests, especially > those containing control characters. > Note that while this workaround addresses the vulnerability currently being > exploited, there are likely to be other similar vulnerabilities present in > this and other WWW server software. To lessen the chance of compromise, it > is strongly recommended that WWW servers run as unprivileged users (e.g. > user "nobody") and that they be locked into a restricted filesystem via the > chroot() system call. For more information, please see CIAC Document 2308, > "Securing Internet Information Servers," which is available via anonymous > FTP from ciac.llnl.gov in the directory /pub/ciac/ciacdocs/. From owner-www@net.bio.net Thu Feb 16 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Georg Fuellen Subject: [Q] WWW / Internet Resources for Multiple Alignment !? Message-ID: <1995Feb17.174928.16087@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 16 Feb 1995 18:02:02 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 65 Dear All, I'd like to complete the following list of Internet Resources for Multiple Alignment. It will be used for a Biocomputing Course offered for free, as described at the end of this message. I will post a summary if I'm pointed to other resources. PLEASE REPORT ANY USEFUL RESOURCES THAT ARE NOT ON THIS LIST !!!!! PLEASE REPORT ANY USEFUL RESOURCES THAT ARE NOT ON THIS LIST !!!!! (sorry for shouting, but I'd really like to get a few responses :-) http://geoff.biop.ox.ac.uk/servers/amas_server.html AMAS - Analyse Multiply Aligned Sequences http://ibc.wustl.edu/msa.html MSA, Calcutating Multiple Alignments. http://cbrg.inf.ethz.ch/subsection3_1_1.html#SECTION0001100000000000000 AllAll: Calculate Phylogenetic Trees, Alignments and a lot more http://geoff.biop.ox.ac.uk/papers/rev93_1/rev93_1.html Protein Sequence Alignment and Database Scanning, by Geoffrey Barton gopher://s-crim1.dl.ac.uk/00/EMBnet%20Bioinformation%20Resource%20UK/Data%20%26% 20Software/databases/3d_ali/3d_ali.doc 3D-Ali Information File http://www.embl-heidelberg.de/srs/srsc?-info||ALI 3D-ALI Database Interface http://www.embl-heidelberg.de/predictprotein/predictprotein.html The PredictProtein server, utilizing MaxHom Alignments (Are MaxHom Alignments offered anywhere ??) http://www.blocks.fhcrc.org/ Detection and verification of protein sequence homology : BLOCKS WWW Server Thanks a lot for any hints ! *************************************************************************** Also, I'd like to ask whether the following resources are available somewhere on the net: 1. The ATLAS interface to sequence data, by which you can retrieve a sequence using a suitable subsequence of only a few amino acids. 2. McClure's Multiple Alignment Data (they are supposed to be at ftp.embl-heidelberg.de, according to the EMBL File Server News, Number 11, but I could not find them). 3. Kececioglu's maximum weight trace data, Reference: J. D. Kececioglu, The maximum weight trace problem in multiple sequence alignment. In Proc. of the 4th Symp. on Comb. Pattern Matching, LNCS 684, pp. 106-119 (1993) *************************************************************************** best wishes, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@MIT.EDU http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html For info about a free online Biocomputing Course, to be offered in Summer 1995 under the auspices of GNA-VSNS, please point your WWW/hypertext browser to http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/BCDhome.html Please visit this page before inquiring about the course ! From owner-www@net.bio.net Thu Feb 16 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Jason Brinck Subject: [Q] Pseudomonas information Message-ID: <1995Feb17.172304.15244@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 16 Feb 1995 17:48:36 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 8 Does anyone know of any Pseudomonas WWW pages / databases out there? Anything on P.putida would be even better! Thanks in advance, Jason Brinck, School of Biochemistry, University of Birmingham, UK From owner-www@net.bio.net Thu Feb 16 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!moderate From: Pedro M Coutinho Subject: Re: [repost] [Q] Promoter Sequence Analysis Message-ID: <1995Feb17.140924.9687@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 16 Feb 1995 20:52:15 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 51 Hi! In article <1995Feb13.160849.25030@comp.bioz.unibas.ch>, Shun'ichi Kuroda writes: |> Dear Sirs: |> |> I have a novel promoter sequence from human genome, of which |> length is about 2kbp and has enough transcriptional activity. |> However, it has been still unclear whether the promoter sequence |> contains known promoter motifs or not. |> If the database of the known promoter motifs is available, it will |> be helpful for us to construct the deletion mutants and understand |> the essential transcriptional region of the promoter sequence. |> Therefore, I want to know the services for analyzing the promoter |> sequence, which are on internet or distributed as commercial |> softwares. |> Any comments will be appreciated. |> Many thanks, |> |> -- |> SHUN'ICHI KURODA |> BIOSIGNAL RES CENTER |> KOBE UNIVERSITY |> NADA, KOBE, 657 JAPAN |> E-mail: skuroda@inherit.biosig.kobe-u.ac.jp |> URL:http://inherit.biosig.kobe-u.ac.jp/biosighome.html |> Tel +81-78-803-1255 Fax +81-78-803-0994 You might find something useful in the following URLs, especially in PSORT. EPD - Eucaryotic Promoter Database at EMBL-Heidelberg http://www.embl-heidelberg.de/srs/srsc?-id||781260221_129.186.4.14||-info||EPD PSORT - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan http://psort.nibb.ac.jp/ Good Luck! Pedro Coutinho --------------------------------- H2N-CH-CO-NH-CH-CO-...-NH-CH-COOH -- Pedro M. Coutinho - Graduate Student \ \ \ IOWA STATE UNIVERSITY R1 R2 Rn Department of Chemical Engineering Phone: 1-515-294-9370 2114 Sweeney Hall Fax: 1-515-294-2689 Ames, IA 50011-2230 E-mail: pedro@iastate.edu U.S.A. URL: http://www.public.iastate.edu/~pedro/ ---------------------------------------------------------------------- -- Pedro M Coutinho pedro@iastate.edu From owner-www@net.bio.net Thu Feb 16 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Ole Matzura Subject: Introducing RNAdraw! Message-ID: <1995Feb17.174312.15789@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 17 Feb 1995 13:17:02 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 18 [The following text is in the "iso-8859-1" character set] [Your display is set for the "US-ASCII" character set] [Some characters may be displayed incorrectly] Hello Everybody! A new RNA structure program for Windows (3.1/NT/95) has seen the light! Please take a look at: http://broccoli.mfn.ki.se/rnadraw/rnadraw.html Thank you, have a nice weekend! Ole Matzura (ole@mango.mef.ki.se) From owner-www@net.bio.net Sun Feb 19 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: "Martin D. Leach" Subject: Re: [Q] WWW / Internet Resources for Multiple Alignment !? Message-ID: <1995Feb20.162149.9444@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 17 Feb 1995 21:12:41 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 36 check out http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html BCM Search Launcher The purpose of BCM Search Launcher is to organize molecular biology-related search and analysis services available on the WWW by function, and to provide a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters). Please send suggestions for additions to these pages to: www@mbcr.bcm.tmc.edu good luck ciao Martin -- ..... Martin Leach Email:leach@bu.edu _|____ Dept. of Pharmacology Phone: (617) 638-5323 / o / Boston Univ. School of Med. Fax: (617) 638-4329 _/ |-/__==/ 80 E. Concord St. (L603) (BULLDOZER) \_ Boston MA 02118 "Not the old underpants USA on your head.....WIBBLE" My homepage: http://155.41.115.114/Leach.html Biotech company listing: http://155.41.115.114/jumper/biolcomm.html p.s. try BioMOO -virtual biology on the internet.. telnet bioinfo.weizmann.ac.il 8888 From owner-www@net.bio.net Sun Feb 19 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Marc Colet Subject: WWW2GCG beta testers please... Message-ID: <1995Feb20.160544.9201@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 17 Feb 1995 17:12:38 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 31 Announcing beta test phase for WWW2GCG This is to announce the beta release of WWW2CGC, a set of software elements to run the WWW interface to access the GCG sequence analysis software package. We are looking for voluntary GCG managers who would be willing to install the software, and come up with recommendations/criticisms for further improvements. Initial installation was on an OSF/1 DEC AXP machine. A successful port to a Dec MIPS ULTRIX (5000/200) workstation could be done with minor efforts. Several conditions must be met in order to install the software : - a UNIX computer on which GCG version 8 is installed and running - the right to recompile the GCG package, after some minor change (In our hands, the slight adaptation to the GCG software had no detectable effect whatsoever on the way GCG itself is running...) - the right of super-user for some of the installation operations - some disc space to install the whole bunch of files, including an httpd server. This must be an independent server from any other eventually already running on the same computer. A total of about 10 megabyte seems adequate. Please send a email to rwww@dbmdec5.ulb.ac.be to receive the informations about how/where to get hold of a copy of the package. Marc Colet (mcolet@ulb.ac.be) From owner-www@net.bio.net Thu Feb 23 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Roy Goodacre Subject: Announcing a WWW neural networks in (micro)biology page Message-ID: <1995Feb24.065702.6903@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Wed, 22 Feb 1995 07:04:07 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 30 Dear All, This is to announce that a new WWW site (or at least a very large update) about our applications of neural networks within microbiology and biology can be found at the following addresses: A CHEMOMETRICS HOME PAGE http://gepasi.dbs.aber.ac.uk/roy/chemom.htm PYROLYSIS MASS SPECTROMETRY HOME PAGE http://gepasi.dbs.aber.ac.uk/roy/pymshome.htm MY CV WHICH GIVES LINKS TO ABOVE http://gepasi.dbs.aber.ac.uk/roy/rgcv.htm The sort of things found here deal with: 1. The use of supervised and unsupervised learning. 2. What pyrolysis mass spectrometry is. 3. The identification and classification of bacteria. 4. The quantification of biological systems (eg fermentor broths). 5. The adulteration of food stuffs. Any sensible comments would be gratefully received. Dr Roy Goodacre E-mail: rrg@aber.ac.uk FTP: 144.124.112.36 Voice: +44 970 623111 ext 4187 (work) Fax: +44 970 622354 +44 974 241236 (home) URL: http://gepasi.dbs.aber.ac.uk/roy/rgcv.htm Snail: Inst Biol Sci, University of Wales, Aberystwyth, Dyfed, UK From owner-www@net.bio.net Thu Feb 23 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: yichena@ifi.uio.no Subject: [Q] Read data from client site Message-ID: <1995Feb24.075945.8726@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 23 Feb 1995 10:49:21 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 13 Hi, How is it implemented or has this been implemented if a WWW server simply reads in long sequence data then does some computation on it and send the results back to the clients? I know one way is to use FORM/POST with input type of TEXTAREA. and you may expect your clients to understand copy-paste. However, is it possible to open the file on client sites and read in ? Any reply will be appreciated, and please E-mail me! Yicheng From owner-www@net.bio.net Sun Feb 26 22:00:00 1995 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: Jean Thioulouse Subject: WWW online multivariate analysis service Message-ID: <1995Feb27.071705.24825@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 24 Feb 1995 17:10:29 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 12 NetMul is an online multivariate analysis WWW service. You can use it to perform multivariate analyses (Principal Components Analysis, Correspondence Analysis and Multiple Correspondence analysis) on your data sets. http://biomserv.univ-lyon1.fr/base.html -- Jean Thioulouse - Laboratoire de Biometrie - Universite Lyon 1 69622 Villeurbanne CEDEX - France Fax: (33) 78 89 27 19 Try NetMul, a WWW online multivariate analysis system: http://biomserv.univ-lyon1.fr/base.html