From owner-bio-matrix@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.bio-matrix Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 15 Apr 1996 02:00:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604150900.CAA06031@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ---------------------------------------------------------------------- From owner-bio-matrix@net.bio.net Tue Apr 23 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: "KARL KLEINE " Newsgroups: bionet.molbio.bio-matrix Subject: Complete DNA sequence of the Yeast genome available NOW!!! Date: 24 Apr 1996 15:41:25 +0100 Lines: 152 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4lleil$lo2@mserv1.dl.ac.uk> Original-To: biomatrx@dl.ac.uk ====================================================================== The Complete DNA Sequence of S. cerevisiae ====================================================================== The complete sequence of the yeast Saccharomyces cerevisiae strain S288C has been determined in an international collaboration of more than 100 laboratories. By April 24th, the sequence data can be copied from the following ftp sites: Europe ftp.mips.embnet.org (directory /yeast) ftp.ebi.ac.uk America ftp-genome.stanford.edu Japan Riken institute (soon) The contributing consortia are: complete chromosomes partial chromosomes EU (Goffeau) II, III, VII, X, XI IV, XII, XVI XIV,XV St. Louis (Johnston) VIII IV, XVI Sanger (Barrell) IX, XIII IV, XVI McGill (Bussey) I XVI Stanford (Davis) V IV Riken (Murakami) VI CHROMOSOME DNA Coordinator Length Release I H. Bussey, Montreal 230,195 1995 (modif. 4-1996) II H. Feldmann, Munich 813,137 8-1994 (modif. 4-1996) III S. Oliver, Manchester 315,344 12-1991 (modif. 4-1996) IV (I) C. Jacq, Paris IV (II) B. Barrell, Cambridge IV (III) M. Johnston, St. Louis IV (IV) R. Davis, Stanford 1,522,191 4-1996 V R. Davis, Stanford 574,860 1995 (modif. 4-1996) VI Y. Murakami, Tokyo 270,148 1995 VII H. Tettelin, Louvain 1,090,936 4-1996 VIII M. Johnston, St. Louis 562,638 8-1994 IX B. Barell, Cambridge 439,885 1995 X F. Gallibert, Rouen 745,443 10-1995 (modif. 4-1996) XI B. Dujon, Paris 666,448 4-1994 XII (left) J. Hoheisel, Heidelberg XII (right) M. Johnston, St. Louis 1,078,171 4-1996 XIII B. Barell, Cambridge 924,430 1995 XIV P. Philippsen, Basel 784,328 4-1996 XV B. Dujon, Paris 1,091,282 4-1996 XVI (I) A. Goffeau, Louvain XVI (II) H. Bussey, Montreal XVI (IIa) R. Davis, Stanford XVI (III) B. Barrell, Cambridge XVI (IV) M. Johnston, St. Louis 948,061 4-1996 mitochondrial genome (as compiled by de Zamaroczy M. and Bernardi G.) Length: 78,520 nt __________________________________________ Total: 12,136,020 nt 12,057,500 nt (without mitochondrial genome) The yeast genome contains several regions with extensive repeated sequences. These repeats have not been sequenced in their entirety but at least one or two copies have been included in the final sequences. Missing repeated sequences: ~ 100 copies of rDNA repeat(chrXII) each ~9,137 nt = 913,700 nt 2 copies of the ENA2 (chrIV) repeat ~3,885 nt = 7,770 nt ~ 10 copies of the CUP1 repeat (chrVIII) ~ 1,998 nt = 19,980 nt ~ 3-5 copies of Y' elements each ~6,700 nt (chrIV telR 2-3 copies; chrXII telR 1-2 copies) = 26,800 nt ~ 750 nt of telomeric sequence of chrVI = 750 nt ___________________________________________________________________ Total of missing repeated sequences: 969,000 nt The total genome of S.c. S288C therefore contains: 12,136,020 nt + 969,000 nt _______________ 13,105,020 nt NOTE: The strain S288C lacks some of the gene families found in brewery and other industrial strains such as the MEL, MAL and SUC gene families and maybe others. Sequence data released before April 1996 are annotated and the systematic nomenclature has been assigned. Due to the priority of the rapid release of the data to the scientific community, the assignment of the systematic nomenclature for open reading frames has not yet been completed for all 16 chromosomes. In collaboration with the consortia involved in this project these nomenclature will subsequently be added to the information on the WWW pages (see below) and finally included in tables on the FTP sites. (Please do NOT start doing your own nomenclature to avoid unnecessary confusion!) Detailed information on open reading frames, genetic elements, and the graphical display by the GSG (Genome Sequence Graph) are available on the WWW: http://www.mips.biochem.mpg.de Reference information is linked to the S. cerevisiae page for each chromosome. Information on the web includes homology listings and graphical display of the chromosomes. A detailed classification of open reading frames is in progress. H.W. Mewes & K. Kleine Max-Planck-Inst. f. Biochemie MIPS 82152 Martinsried, Germany Tel.: +49 89 8578 2657 FAX : +49 89 8578 2655 email: mewes@mips.embnet.org kleine@mips.embnet.org ========================================================================= The data were assembled (EU part) and edited by MIPS (Max-Planck-Inst. f. Biochemie, Martinsried, Germany). We are greatful for comments, corrections of sequence data, and any contribution to the annotation of the data (to be submitted to : zollner@mips.embnet.org ). Acknowledgement: The ftp-directories contain the proper reference for each chromosome. The following MIPS staff members have contributed to the data evaluation: Yeast sequence processing: K. Kleine, K. Albermann, J. Hani, H. Tettelin (Louvain), A. Zollner Informatics: A. Gleissner, C. Harris (WWW), K. Heumann (HPT/GSG), S. Liebl (XChromo), H.W. Mewes (coordinator), A. Maierl, P. Zaccharia Protein Sequence Databank (annotation): G. Fobo, F. Pfeiffer MIPS is supported by the Max-Planck-Gesellschaft, the Forschungszentrum f. Umwelt u. Gesundheit (GSF), the European Commission, and the BMBF =========================================================================