From owner-bio-matrix@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!biosci!not-for-mail From: toms@fcs260c2.ncifcrf.gov (Tom Schneider) Newsgroups: bionet.announce,bionet.molbio.bio-matrix,bionet.molbio.genbank Subject: Philosophy Paper Date: 2 Jun 1994 20:35:34 -0700 Organization: Frederick Cancer Research and Development Center Lines: 21 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1186 bionet.molbio.bio-matrix:485 bionet.molbio.genbank:1641 My paper on the philosophy of genetic sequence databases is almost finished. People who would like to read and comment on the current version can find a current copy in my archive: ftp ftp.ncifcrf.gov anonymous (your email address) cd pub/delila binary prompt mget philgen* I will greatly appreciate your comments. Please mention the version number. (The current version is 1.69) Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-bio-matrix@net.bio.net Fri Jun 03 23:00:00 1994 Newsgroups: bionet.molbio.bio-matrix,bionet.molbio.genbank Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!fcsparc6!toms From: toms@fcsparc6.ncifcrf.gov (Tom Schneider) Subject: Philosophy Paper Message-ID: Sender: usenet@ncifcrf.gov (C News) Nntp-Posting-Host: fcsparc6.ncifcrf.gov Organization: Frederick Cancer Research and Development Center Date: Sat, 4 Jun 1994 02:36:40 GMT Lines: 24 Xref: biosci bionet.molbio.bio-matrix:486 bionet.molbio.genbank:1642 My paper on the philosophy of genetic sequence databases is almost finished. People who would like to read and comment on the current version can find a current copy in my archive: ftp ftp.ncifcrf.gov anonymous (your email address) cd pub/delila binary prompt mget philgen* I will greatly appreciate your comments. Please mention the version number. (The current version is 1.70, only references changed from version 1.69, and the ascii version is cleaner.) The paper describes what's fundamentally wrong with the current databases and proposes how to fix them. Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-bio-matrix@net.bio.net Fri Jun 03 23:00:00 1994 Path: biosci!SPEEDY.COACADE.UV.MX!evargas From: evargas@SPEEDY.COACADE.UV.MX (Enrique Vargas) Newsgroups: bionet.molbio.bio-matrix Subject: Ig-germline directory Date: 4 Jun 1994 12:49:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406041957.AA17860@speedy.speedy.coacade.uv.mx> NNTP-Posting-Host: net.bio.net Hi! I am interested to obtain updated versions of directories of germline genes and pseudogenes of Ig-Vh and Ig-Vl for human and mouse (translated to aminoacids) like that published for Ig-Vh by Tomlinson et al. in J. Mol. Biol. (1992) 227,776-798. Does somebody could provide to me some or all of these directories? Thanks in advance, ******************************************************************************* * Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * * * optional: salazar@redvax1.dgsca.unam.mx * ******************************************************************************* * Laboratorio de Biologia Molecular * Phone number: (28)125757 * * e Inmunologia Teorica. * FAX number: (28)125757 * ******************************************************************************* * Instituto de Investigaciones Biologicas * Universidad Veracruzana * * * Xalapa, Veracruz; Mexico. * ******************************************************************************* * POSTAL ADRESS: * * Juan de la Barrera 54, * * Col. Electricistas, C.P. 91000 * * Xalapa, Veracruz; Mexico. * *************************************** From owner-bio-matrix@net.bio.net Tue Jun 07 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 8 Jun 1994 02:00:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 319 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406080900.CAA10560@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-bio-matrix@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!world!news.bu.edu!waffle From: waffle@bu.edu (Adrian Zai) Newsgroups: bionet.molbio.bio-matrix Subject: BioTechNet Date: 10 Jun 1994 05:43:33 GMT Organization: Boston University Lines: 7 Message-ID: <2t8ui5$o10@news.bu.edu> NNTP-Posting-Host: acs2.bu.edu X-Newsreader: TIN [version 1.2 PL0] I was told that I can access BioTechNet through Internet. Can someone tell me how? I heard you can do it through gopher. Thanks, Adrian Zai Whitaker Cardiovascular Institute From owner-bio-matrix@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!BIOTECHNET.COM!JEMERTON From: JEMERTON@BIOTECHNET.COM Newsgroups: bionet.molbio.bio-matrix Subject: Re: BioTechNet Access Via Internet Date: 10 Jun 1994 05:37:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HDDD1LT3D891WVVW@delphi.com> NNTP-Posting-Host: net.bio.net Good Morning: Regarding the inquiry about accessing BioTechnet via Internet, pleae (that's please) telnet to: BIOTECHNET.COM (192.80.63.1) Of course, you'll need an account to use the service, but a free demo online is available by entering username BIOTECH and password INFOCTR Jim Emerton Network Manager BioTechNet From owner-bio-matrix@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!ARGUS.MBL.EDU!mriley From: mriley@ARGUS.MBL.EDU (Monica Riley) Newsgroups: bionet.molbio.bio-matrix Subject: genome meeting Date: 10 Jun 1994 11:25:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406101836.AA01130@argus.mbl.edu> NNTP-Posting-Host: net.bio.net Meeting Announcement The Third International E. coli Genome Meeting will be held November 4-8, 1994 in Woods Hole, MA, USA. Topics to be covered include Large-scale Sequencing, Sequence Analysis, Databases, Sequence Divergence, Repeated Sequences and Regulatory Motifs, Mutations, Rearrangements and Stress Responses, and Origin of Genes. Speakers will include A. Campbell, F. Blattner, R. Doolittle, C. Kurland, J. Miller, S. Letovsky, J. Roth, K. Rudd. There will be a Database Workshop for demos and hands-on opportunities. For more information and registration materials, send request to confserv@hoh.mbl.edu From owner-bio-matrix@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.molbio.bio-matrix Subject: URGENT QUESTION Date: 13 Jun 1994 10:13:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406131713.AA17612@morpheus> NNTP-Posting-Host: net.bio.net Question: I am interested in any help from anyone out there on the following subject. We have become an information gathering society. One of the areas of interest is the gathering of large databases of information. I was wondering if anyone out there might know of databases of biomedical information and how to access them. For example, GenBank, census data, databases of medical images, databases of population statistics, environmental toxicity data, dental data, etc. If you know of such data, would you please send me the following information: Name of Database: Is the database public or private: How to contact database or database owner. I will summarize the responses for the list. This is a rather urgent request so, rapid answers would be appreciated. Do not worry about duplicating others. Feel free to cross post this note to any other lists that might be appropriate. Thanks, Matthew Witten, Ph.D. Head, Department of Applications Research and Development Associate Director UT System Center For High Performance Computing Balcones Research Center, 1.154 CMS 10100 Burnet Road, Austin, TX 78758-4497 USA Phone: (512) 471-2472 FAX: (512) 471-2445 E-MAIL MWITTEN@CHPC.UTEXAS.EDU From owner-bio-matrix@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.molbio.bio-matrix Subject: URGENT QUESTION Date: 13 Jun 1994 10:15:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406131713.AA17632@morpheus> NNTP-Posting-Host: net.bio.net Question: I am interested in any help from anyone out there on the following subject. We have become an information gathering society. One of the areas of interest is the gathering of large databases of information. I was wondering if anyone out there might know of databases of biomedical information and how to access them. For example, GenBank, census data, databases of medical images, databases of population statistics, environmental toxicity data, dental data, etc. If you know of such data, would you please send me the following information: Name of Database: Is the database public or private: How to contact database or database owner. I will summarize the responses for the list. This is a rather urgent request so, rapid answers would be appreciated. Do not worry about duplicating others. Feel free to cross post this note to any other lists that might be appropriate. Thanks, Matthew Witten, Ph.D. Head, Department of Applications Research and Development Associate Director UT System Center For High Performance Computing Balcones Research Center, 1.154 CMS 10100 Burnet Road, Austin, TX 78758-4497 USA Phone: (512) 471-2472 FAX: (512) 471-2445 E-MAIL MWITTEN@CHPC.UTEXAS.EDU From owner-bio-matrix@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!sal.cs.uiuc.edu!knight From: knight@sal.cs.uiuc.edu (Marion Knight) Newsgroups: bionet.molbio.bio-matrix Subject: database for param & topol files ? Date: 13 Jun 94 21:26:50 GMT Organization: University of Illinois at Urbana Lines: 9 Message-ID: NNTP-Posting-Host: sal.cs.uiuc.edu Summary: Does anyone know of a database for param and/or top files ? Keywords: parameter topology I'm trying to find out if there is a computerized database for X PLOR compatible parameter and/or topology files (containing bond information, etc) similar to the the Protein Data Bank's database for coordinate files. Any information would be greately appreciated. Thanks in advance, Marion Knight From owner-bio-matrix@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!biosci!not-for-mail From: brutlag@cmgm.stanford.edu (Doug Brutlag) Newsgroups: bionet.announce,bionet.biology.computational,bionet.software,bionet.molbio.bio-matrix,news.announce.conferences,sci.bio,sci.engr.biomed,sci.med Subject: ISMB Special Open Poster Session Date: 14 Jun 1994 10:18:21 -0700 Organization: Stanford University Lines: 41 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: bionet Message-ID: Reply-To: ismb@camis.stanford.edu NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1213 bionet.biology.computational:564 bionet.software:8509 bionet.molbio.bio-matrix:495 news.announce.conferences:3479 sci.bio:9568 sci.engr.biomed:1556 sci.med:40726 Intelligent Systems for Molecular Biology SPECIAL OPEN POSTER SESSION August 16, 1994 7:30 PM - 9:30 PM Fairchild Auditorium Stanford University Stanford, CA ISMB-94 will host a special open poster session for informal presentations of promising and early research in the area of complex software systems for molecular biology applications. Appropriate posters for this session would highlight creative approaches, novel problem formulations, and interesting recent results; and should present material that will be new to most of the audience. The primary goal of the ISMB Conference is the high quality of its formal presentations and published Proceedings. However, another major goal is to foster productive professional interactions. This special poster session is intended to bring researchers into informal contact with each other and with the latest work in their area of interest. The special poster session is unreviewed and open to all, but participants must register in advance to ensure that space will be available. Registration will be taken on a first-come first-served basis, and will continue until all available slots are filled. Space is limited, and early registration is encouraged. To register for this special poster session, send email giving name, contact information and an abstract to ISMB@camis.stanford.edu. Conference registration material can be obtained by sending a request to ismb@camis.stanford.edu or by fax (415) 725-7944 or phone (415) 723-6979. It can also be found in WWW page: file://camis.stanford.edu/pub/altman/www/ismb.html Doug Brutlag (415) 723-6593 Department of Biochemistry (415) 328-7837 FAX Beckman Center, B400 brutlag@cmgm.stanford.edu Stanford University School of Medicine Stanford, California 94305-5307 From owner-bio-matrix@net.bio.net Mon Jun 13 23:00:00 1994 Newsgroups: bionet.molbio.bio-matrix Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: Re: URGENT QUESTION Message-ID: <1994Jun14.174519.4632@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility X-Newsreader: TIN [version 1.2 PL1] References: <9406131713.AA17612@morpheus> Date: Tue, 14 Jun 1994 17:45:19 GMT Lines: 43 mwitten@CHPC.UTEXAS.EDU wrote: : Question: : I was wondering if : anyone out there might know of databases of biomedical : information and how to access them. This section is from the document '/Genome/hgnews/old/1993/march-93-hgn.data'. From Dan's-Gopher Fri Jun 17 00:00:00 1993 Author : HGMIS staff Source : Human Genome News, March 1993;4(6):12 Subject: Informatics Resource Version 3.0 of the Listing of Molecular Biology Databases (LiMB), a tool for locating and accessing data sets and designing and linking pertinent databases, has been released. LiMB contains (1) a brief database list, (2) a data dictionary describing the meanings of fields in a LiMB entry, (3) a full database list, and (4) a cross index of databases and data types. LiMB data are gathered from questionnaires, journals, and the BIOSCI electronic bulletin board. This preliminary release, to be confirmed by a full questionnaire cycle, offers over 100 databases (25 more entries than release 2.0). To acquire LiMB, send the message text (limb- data) to (bioserve@life.lanl.gov). For information only, send the message text (limb-info) to the same address. Additional copies of LiMB in hardcopy or floppy disk are available on request. [Contact: Christian Burks; LiMB; Theoretical Biology and Biophysics Group, T-10, K710; Los Alamos National Laboratory; Los Alamos, NM 87545 (505/667-7510, Internet: limb@life.lanl.gov.] -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * ******************************************************************** From owner-bio-matrix@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!CYCLONE.CS.MISSOURI.EDU!murali From: murali@CYCLONE.CS.MISSOURI.EDU (Muralidhar G B) Newsgroups: bionet.molbio.bio-matrix Subject: HELP !!!! Date: 16 Jun 1994 09:55:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi Bio-Comp folks, Does anyone out there know of anything about three-dimensional scoring schemes for finding n-best sequence alignments in case of protein or DNA sequences. I am trying to find information specific to the Dynamic programming algorithm that is to be enhanced for 3-dimensional scoring to calculate frameshifts among sequence patterns. Thanks for your time. If any of u know of any reference material please let me know asap. Thanks /murali =========================================================================== Muralidhar G B | E-Mail: murali@cyclone.cs.missouri.edu | gauribid@condor.cs.missouri.edu System & Network Administrator | Molecular Biology Program Network | Voice (W): (314)882-5759 Univ. of Missouri, Columbia. | (H): (314)875-0658 =========================================================================== From owner-bio-matrix@net.bio.net Thu Jun 16 23:00:00 1994 Path: biosci!CYCLONE.CS.MISSOURI.EDU!murali From: murali@CYCLONE.CS.MISSOURI.EDU (Muralidhar G B) Newsgroups: bionet.molbio.bio-matrix Subject: Online version of a paper Date: 17 Jun 1994 11:53:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406171853.AA09647@cyclone.cs.missouri.edu> NNTP-Posting-Host: net.bio.net Hi folks Does anyone out there have an online copy of the following paper. I am not able to get access to the journal here in my school. The paper is: COmput. Appl. Biosci, Vol 9 , 1993 - Pg 587-591 Thanks for your time. Please let me know asap. Thanks /murali From owner-bio-matrix@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!UV4.INVEST.UV.MX!evargas From: evargas@UV4.INVEST.UV.MX (Enrique Vargas Madrazo) Newsgroups: bionet.molbio.bio-matrix Subject: Database Search Date: 21 Jun 1994 17:33:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406220029.AA01462@uv4.invest.uv.mx> NNTP-Posting-Host: net.bio.net ---------- X-Sun-Data-Type: default X-Sun-Data-Name: server.wp X-Sun-Content-Lines: 31 X-Sun-Charset: us-ascii Dear colleagues: We have been working on the obtaining of Ig sequences; our interest is the building of an immunoglobulin gene sequence database. There is impossible to access extensively any specific database (Germline genes, Pseudogenes, Rearranged genes, etc.) using a server. This is because there are not consistent rules in the assigned keywords to sequences of the same type. For example, there are not one keyword that can be found in all the pseudogenes of the Ig heavy variable domain in GenBank (either in definition or keyword fields). In many other databases like PIR and Kabat, the problems are similar. That is, THERE ARE MANY INCONSISTENCES IN THE CODIFICATION PROCEDURES OF THE INFORMATION THAT SPECIFIES THE CHARACTERISTICS OF THE SEQUENCES. We think that in the context of the tremendous growth rate of the databases, this deficiency constitutes a very hard problem for the management, organization and rational analysis of the sequences. It is important to catch the eye of the database manager about this problematic situation. ****************************************************************************** * * evargas@uv4.invest.uv.mx * * Dr. Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * * * optional: salazar@redvax1.dgsca.unam.mx * ****************************************************************************** * Laboratorio de Biologia Molecular * Phone number: (28)125757 * * e Inmunologia Teorica. * FAX number: (28)125757 * ****************************************************************************** * Instituto de Investigaciones Biologicas * Universidad Veracruzana * * * Xalapa, Veracruz; Mexico. * ****************************************************************************** * POSTAL ADRESS: * * Juan de la Barrera 54, * * Col. Electricistas, C.P. 91000 * * Xalapa, Veracruz; Mexico * ************************************** From owner-bio-matrix@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!UV4.INVEST.UV.MX!evargas From: evargas@UV4.INVEST.UV.MX (Enrique Vargas Madrazo) Newsgroups: bionet.molbio.bio-matrix Subject: Database Search Date: 21 Jun 1994 18:07:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406220103.AA01519@uv4.invest.uv.mx> NNTP-Posting-Host: net.bio.net ---------- X-Sun-Data-Type: default X-Sun-Data-Name: carta11 X-Sun-Charset: us-ascii X-Sun-Content-Lines: 31 Dear colleagues: We have been working on the obtaining of Ig sequences; our interest is the building of an immunoglobulin gene sequence database. There is impossible to access extensively any specific database (Germline genes, Pseudogenes, Rearranged genes, etc.) using a server. This is because there are not consistent rules in the assigned keywords to sequences of the same type. For example, there are not one keyword that can be found in all the pseudogenes of the Ig heavy variable domain in GenBank (either in definition or keyword fields). In many other databases like PIR and Kabat, the problems are similar. That is, THERE ARE MANY INCONSISTENCES IN THE CODIFICATION PROCEDURES OF THE INFORMATION THAT SPECIFIES THE CHARACTERISTICS OF THE SEQUENCES. We think that in the context of the tremendous growth rate of the databases, this deficiency constitutes a very hard problem for the management, organization and rational analysis of the sequences. It is important to catch the eye of the database manager about this problematic situation. ****************************************************************************** * * evargas@uv4.invest.uv.mx * * Dr. Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * * * optional: salazar@redvax1.dgsca.unam.mx * ****************************************************************************** * Laboratorio de Biologia Molecular * Phone number: (28)125757 * * e Inmunologia Teorica. * FAX number: (28)125757 * ****************************************************************************** * Instituto de Investigaciones Biologicas * Universidad Veracruzana * * * Xalapa, Veracruz; Mexico. * ****************************************************************************** * POSTAL ADRESS: * * Juan de la Barrera 54, * * Col. Electricistas, C.P. 91000 * * Xalapa, Veracruz; Mexico * ************************************** From owner-bio-matrix@net.bio.net Fri Jun 24 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!csulb.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!not-for-mail From: dgh6592@u.cc.utah.edu (Dinesh Haryadi) Newsgroups: bionet.molbio.bio-matrix Subject: PAPAIN Date: 25 Jun 1994 09:01:21 -0600 Organization: University Of Utah Computer Center Lines: 26 Message-ID: <2uhgs1$3hj@u.cc.utah.edu> NNTP-Posting-Host: u.cc.utah.edu X-Newsreader: TIN [version 1.2 PL0] Does anyone know where I can obtain information concerning "PAPAIN" , its production, refinement , etc. (2 x Recrystallized papain is used as a chemical reagent and medicine) It is the dried latex of green papaya. Your suggestions and pointers are appreciated in advance. -Dinesh Haryadi Dinesh.Haryadi@m.cc.utah.edu ********************************************************************** //// email : Dinesh.Haryadi@m.cc.utah.edu //// | .. voice : (801)585-5444 (Work) | .. C ^ (801)531-7086 (Home) C ^ \ ~/ fax : (801)581-4367 \ ~/ <><> mail : Bioengineering, 3C444 <><> Dept of Anesthesia, Medical Ctr Univ of Utah, SLC 84132 ********************************************************************** Confused minds are the source of all inventions **********************************************************************