From owner-bio-matrix@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!HOH.MBL.EDU!mriley From: mriley@HOH.MBL.EDU ("Monica Riley") Newsgroups: bionet.molbio.bio-matrix Subject: E. coli Genome meeting Date: 5 Sep 1994 17:15:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: <30030.mriley@hoh.mbl.edu> NNTP-Posting-Host: net.bio.net Second Announcement: Third International E. coli Genome Meeting The Third International E. coli Genome Meeting will be held November 4-8, 1994, at the Marine Biological Laboratory in Woods Hole, Massachusetts. This Meeting will include invited talks, poster sessions, and workshops analyzing the E. coli genome at the genetic, sequence, and structural levels with the goal being to facilitate a coordinated structure/function analysis of the genome. Specific topics will include: status reports on large-scale sequence efforts; genome mapping technologies; applications of sequence analysis; genome organization, rearrangements; interrelationships and demonstrations of databases; global regulatory mechanisms; repeated sequences; evolutionary origin of genes. Speakers will be: A. Bairoch, M. Berlyn, F. Blattner, A. Campbell, G. Church, A. Danchin, B. Demple, R. Doolittle, B. Hall, M. Hofnung, K. Isono, P. Karp, E. Kofoid, C. Kurland, S. Letovsky, R. Milkman, J. Miller, M. O'Neill, J. Ostell, G. Perriere, M. Riley, R. Robbins, S. Rosenberg, J. Roth, K. Rudd, R. Schleif, T. Schneider, P. Sharp, R. Van Bogelen, B. Wanner, G. Weinstock, T. Whittam. There will be two concurrent sessions of posters and database/software demonstrations. Poster abstracts or short descriptions of the database/software you wish to demonstrate should be submitted by September 26, 1994. Advance registration is requested; deadline is September 26, 1994. For registration materials please send your name and address to: Conference Services, P.O. Box 477, Woods Hole, MA 02543-0477, phone 508-540-6055, fax 508-540-0155, e-mail confserv@mbl.edu Meeting Organizers: M. Riley (Woods Hole), J. Miller (UCLA), P. Sharp (Nottingham), P. Karp (SRI), and M. Berlyn (Yale). Monica Riley, Senior Scientist Email:mriley@hoh.mbl.edu Marine Biological Laboratory Fax: (508) 540-6902 Woods Hole, MA 0543 Phone: (508) 548-3705 ext 612 From owner-bio-matrix@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!csus.edu!netcom.com!ix.netcom.com!netnews From: heel@ix.netcom.com (Robert Williams) Newsgroups: bionet.molbio.bio-matrix Subject: food web Date: 6 Sep 1994 06:44:38 GMT Organization: Netcom Lines: 1 Distribution: world Message-ID: <34h34m$hse@ixnews1.ix.netcom.com> NNTP-Posting-Host: ix-nwk4-11.ix.netcom.com From owner-bio-matrix@net.bio.net Tue Sep 06 23:00:00 1994 Newsgroups: bionet.molbio.bio-matrix Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!anapat From: anapat@reks.uia.ac.be (*Anatomo Pathologie) Subject: Collagen Message-ID: <1994Sep7.103602.24752@reks.uia.ac.be> Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 Date: Wed, 7 Sep 1994 10:36:02 GMT Lines: 19 Hi, I'm asking this question for a friend in industry without e-mail connection. They are looking for an expert on the use and problems relating the use of collagen in foodindustry. They are of course willing to pay for the service. If you know someone with this knowledge or who has a sound understanding of collagens, please mail me back. Thanks again for your time. JP Bogers, MD anapat@uia.ac.be jpbogers@uia.ac.be -- -------------------------------------------------------------------- Universitaire Instelling Antwerpen (UIA) Lab Pathology 2610 Wilrijk From owner-bio-matrix@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!SCRI.FSU.EDU!STRELETS From: STRELETS@SCRI.FSU.EDU ("VICTOR B. STRELETS") Newsgroups: bionet.molbio.bio-matrix Subject: Sagittarius PIR-41 availability announcement Date: 13 Sep 1994 06:06:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 344 Sender: daemon@net.bio.net Distribution: world Message-ID: <940913090613.204044d5@scri.fsu.edu> NNTP-Posting-Host: net.bio.net SAGITTARIUS PIR-41 (30 June 1994) variant ***************************************** SAGITTARIUS PIR is a highly compact databank variant of original PIR database designed to assist individual researchers and software developers in utilization of sequence database information without huge storage space requests. It contains custom compressed PIR information and C-written interface which allow fast direct access to the stored information without total decompressing of corresponding files. Starting from this PIR-41 version, one and the same databank files as well as interface C-file can be used on both PC-compatibles and UNIX V computers (with forthcoming Mac interface version), without any modifications. Interface supports all standard PIR Request Network queries (i.e. get databank SEQ number by entry; for the defined databank SEQ number, get specified information like: name, organism(s), keyword(s), sequence, sequence features with coordinates etc.). In difference with PIR Request Network, SAGITTARIUS PIR allows you to call PIR-contained information directly from your C program, even on the personal computer separated from any network. In addition, all numerical information like introns placement and concrete feature coordinates are aquired by calling program in the form of constants instead of text strings what simplifies (sub)sequence manipulations. For even larger storage compactness and flexibility, SAGITTARIUS PIR was realized in the form of separate file sets, where each file set contains database information of independent type (i.e. sequences, entry indexes, organisms etc.). On the particular computer, available configuration of the PIR information could be easily changed as needed by the user itself without any damage for retrievals of other types of stored information. For example, a file set which contains protein sequences itself and their PIR entry indexes (including reverse indexation arrays) takes less than 12Mb of disk space. For PC-compatibles (with fortcoming version for UNIXV/Xwindow), a dialog shell is available which supports all standard PIR Request Network queries plus homology searches, alignments etc. SAGITTARIUS PIR is distributed freely (all databank file sets, interface C-file, test/example program C-file, PC-shell executable) via anonymous FTP. File sets and interface can be used/included in any commercially distributed package without any restrictions. Consultations and advanced interface variants (currently used to support fast effective database manipulations in other SAGITTARIUS family packages) are available from the developers upon request. For now, SAGITTARIUS PIR compressed databank stores in custom compressed form following original informational types (fields) of PIR database: - database entry index - accession number(s) - other (non-PIR) database crossreference(s) - protein name - organism name(s) - alternative protein name(s) - keyword(s) - superfamily name(s) - gene name(s) - map position(s) - unusual start codon(s) - intron(s) placement - literature reference(s), including for each: -journal or citation -author(s) -title -free-format comment - sequence feature(s) - free-format comment - protein sequence itself For PIR-41, all bank files takes 33+ Mb on hard disk (20+ Mb in ZIP-compressed form). Each original database informational field (i.e. sequences, organisms, names, keywords etc.) is stored in separate file set what allows the user to configure reduced bank variants by simply excluding unnecessary information files from unpacking. For example, deletion of literature references reduces the bank to only 23 Mb. Core (minimal configuration supported by available PC-shell) variant of databank files includes only indexes and sequences. All more complete configurations could be produced by simply adding (depacking from distributive) of corresponding file sets. List of distributive files with decompressed files description ************************************************************** ------------------------------------------------------------------------------- ZipFile ZipSize Content Description ------------------------------------------------------\/ Core config part \/ CORE 11,105,308 Entry indexes + sequences itself ------------------------------------------------------\/ User-variable part \/ NAME 991,927 Sequence names ORGANISM 488,638 Organisms KEYWORD 270,868 Keywords S_FAMILY 156,485 Superfamily classifications CROSSREF 284,114 Other database crossreferences FEATURE 850,677 Sequence features GENE_MAP 25,803 Genetic map positions ALT_NAME 174,754 Sequence alternative names GENE 163,812 Genes CODON 7,543 Unusual start codons ACC_CODE 1,394,839 PIR accession codes COMMENT 256,560 Sequence comments INTRON 30,991 Intron(s) placement REF_JOU 897,568 References core : references itself REF_AUTH 1,593,198 Ref. extention : reference authors REF_TITL 1,840,525 Ref. extention : reference titles REF_COMM 92,982 Ref. extention : reference comments ------------------------------------------------------\/ Dialog shell for PC \/ PC_SHELL 146,967 PC-executable + two MAP-files (to \PIR) ------------------------------------------------------\/ Interface \/ INTERFAC 15,383 Interface and test program, C-files, PRJ file ------------------------------------------------------------------------------- SAGITTARIUS PIR Data Bank Shell ******************************* SAGITTARIUS PIR Automated Sequence Bank is a dialog shell for manipulation of the compressed sequence database information with orientation on MS DOS/Windows PC-compartibles, with installed hard disk optimizers (like Smartdrive, Hyperdisk, Ncache etc.). 386 or 486 are recommended, 86 and 286 will be significantly slower but still are OK. Recommended minimal size of memory allocation by disk optimizer is 512 Kb, but shell will be still usable (but significantly slower) even without any optimizer. The dialog data shell supports the following main operations: - selection of sequences to bank buffer by - dictionary-defined record for specified informational field (name, source, keyword, feature etc.) - user-defined context in specified informational field (name, source, keyword, feature etc.) - set of dictionary-defined records for different informational fields (source, keyword, superfamily etc.) - SEQ (non)perfect homology with user-defined short sequence - store and retrieve buffer content (SEQ bank numbers and indexes) between sessions - output user-specified (buffer) SEQ data to disk files - fast SEQ homology searches (for user-defined SEQ of length not more than 50-100 positions, only 1 hour with full PIR bank on 486/33) - fast subregion-sensitive pairwaise alignments (user-defined sequence with buffer SEQ's or full bank) - easy data access from user programs (C) as a support for applications development SAGITTARIUS data bank files are usually filled out by current available PIR database information only by distributors (2 to 4 times in a year). Distributive variant includes ready-for-use informational files, interface and executables - all in compressed form. ----------------------------------------------------------------------------- SAGITTARIUS PIR is available by anonymous FTP from: FTP.SCRI.FSU.EDU, directory /pub/genetics/pir/ SAGITTARIUS PIR is also available by anonymous FTP from some of the well-known bio-servers (IUBIO etc.). ---------------------------------------------------------------------------- Installation on UNIX V system ***************************** All decompressed SAGITTARIUS databank files must be placed in one and the same directory which name should be correctly specified in the interface C-file (first strings). Placement of the 'X' symbol in the first position of the corresponding text string (instead of '/') will force interface to carry out formal check for databank files presence. Installation on PC ****************** If you plan to use PC-shell, all decompressed SAGITTARIUS databank files must be placed in the directory \PIR on any (but one and the same) logical drive. Otherwise all decompressed SAGITTARIUS databank files must be placed in one and the same directory which name should be correctly specified in the interface C-file (first strings). Placement of the 'X' symbol in the first position of the corresponding text string (instead of some drive letter) will force interface to carry out 1) search of corresponding directory on all available logical drives and 2) formal check for databank files presence. Bank executable BANK.EXE may be placed in any directory on any logical drive. Important: .MAP-files contained in the same PC-shell compressed file should be moved into the directory \PIR where other databank files are placed. It is highly reccomended to run BANK.EXE from directory (and/or logical drive) other than data location to avoid random bank files structure damage. Bank is oriented on file-server data accession and can find \PIR directory (and test them for correct data configuration) on any logical drive. ---------------------------------------------------------------------------- SAGITTARIUS PIR is a FREE DOMAIN software. This package (with compressed data files) can be redistributed freely without any limitations but only free of charge and for non-commercial usage. No changes in data files and/or executables are allowed. You may include compressed SAGITTARIUS datafiles in your application packages freely even in the case of any commercial usage. -------------------------------------------------------------- For HELPFUL comments and discussions please contact Dr. Victor B. Strelets (strelets@scri.fsu.edu) Computational Genetics and Biophysics, Supercomputer Computations Research Institute, FSU B-186, Tallahassee, FL 32306-4052, USA --------------------------------------------------------------- For control purposes you may use the following info about SAGITTARIUS PIR distributive files (with information about containing compressed files): CORE ZIP 11,105,308 SEQ0 BAN 299,040 SEQ BAN 9,613,474 DIC BAN 330,888 DIC2 BAN 106,496 IND0 BAN 299,040 IND2 BAN 301,056 IND BAN 598,080 0IND REV 299,040 1IND REV 299,040 NAME ZIP 991,927 NAM0 BAN 299,040 NAM2 BAN 180,224 NAM BAN 929,160 0NAM REV 179,196 1NAM REV 299,040 ORGANISM ZIP 488,638 SOU0 BAN 299,040 SOU1 BAN 78,468 SOU2 BAN 24,576 SOU BAN 105,816 0SOU REV 23,972 1SOU REV 461,716 KEYWORD ZIP 270,868 KW0 BAN 298,936 KW1 BAN 98,916 KW2 BAN 6,144 KW BAN 20,536 0KW REV 5,560 1KW REV 270,868 GENE ZIP 163,812 GENE0 BAN 286,272 GENE1 BAN 37,176 GENE2 BAN 30,720 GENE BAN 75,168 0GENE REV 29,748 1GENE REV 50,200 ALT_NAME ZIP 174,754 ANAM0 BAN 298,892 ANAM1 BAN 35,376 ANAM2 BAN 28,672 ANAM BAN 116,104 0ANAM REV 28,560 1ANAM REV 48,004 S_FAMILY ZIP 156,485 SFAM0 BAN 293,424 SFAM1 BAN 26,116 SFAM2 BAN 14,336 SFAM BAN 58,840 0SFAM REV 13,520 1SFAM REV 123,060 ACC_CODE ZIP 1,394,839 AC0 BAN 299,040 AC1 BAN 334,516 AC2 BAN 333,824 AC BAN 665,760 0AC REV 332,880 1AC REV 332,880 CODON ZIP 7,543 CDN BAN 192 CDN0 BAN 216,476 CDN1 BAN 148 CDN2 BAN 2,048 0CDN REV 96 1CDN REV 3,352 FEATURE ZIP 850,677 FT0 BAN 298,672 FT1 BAN 222,132 FT2 BAN 47,104 FT BAN 259,144 FTN0 BAN 298,672 FTN1 BAN 222,132 FTN BAN 904,984 0FT REV 46,272 1FT REV 214,004 GENE_MAP ZIP 25,803 MAP0 BAN 277,236 MAP BAN 29,480 COMMENT ZIP 256,560 CC0 BAN 283,604 CC BAN 468,496 CROSSREF ZIP 284,114 CR0 BAN 299,040 CR BAN 362,176 INTRON ZIP 30,991 INTR0 BAN 207,764 INTR1 BAN 39,084 REF_JOU ZIP 897,568 REF0 BAN 299,040 REF1 BAN 403,020 REF BAN 1,109,376 REF_AUTH ZIP 1,593,198 AUT0 BAN 299,040 AUT1 BAN 403,020 AUT BAN 2,419,248 REF_TITL ZIP 1,840,525 TITLE0 BAN 299,040 TITLE1 BAN 365,264 TITLE BAN 2,978,768 REF_COMM ZIP 92,982 REFCOM0 BAN 299,020 REFCOM1 BAN 49,324 REFCOM BAN 105,032 PC_SHELL ZIP 146,967 BANK EXE 468,640 BANK1 MAP 151,200 BANK2 MAP 151,200 ----------------------------------------------------------------- Standard disclaimer: Author(s) will in no way be held liable for any loss of profit or any other commercial damage including but not limited to special, incidental, consequential or other damages from use of this package. You may use them only with the understanding that you use it at your own risk and that your use of the software and datafiles is your agreement to this disclaimer.  From owner-bio-matrix@net.bio.net Thu Sep 15 23:00:00 1994 Newsgroups: bionet.molbio.bio-matrix Path: biosci!bcm!news.msfc.nasa.gov!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!news.bu.edu!gw1.att.com!fnnews.fnal.gov!overload.lbl.gov!dog.ee.lbl.gov!news.cs.utah.edu!emba-news.uvm.edu!moose.uvm.edu!wschaeff From: "Warren I. Schaeffer" Subject: New Journal Message-ID: <1994Sep16.193627.5326@emba.uvm.edu> Originator: wschaeff@moose.uvm.edu Sender: news@emba.uvm.edu Organization: EMBA Computer Facility, University of Vermont Date: Fri, 16 Sep 1994 19:36:27 GMT Lines: 116 Greetings! I hesitated to use the newsgroup to disseminate the following information but, on reflection, knew that I would want to know about a new journal with direct relevance to my research. However, if this posting offends anyone, I would appreciate their responding directly to me rather than by cluttering the newsgroup. Therefore, I would like to call your attention to a new journal "METHODS IN CELL SCIENCE"which is to be published by Kluwer Academic Publishers of Dordrecht, The Netherlands. I have recently accepted the position of Editor-in-Chief. Below are the Aims & Scope of the journal for your perusal. In addition, I am including the initial Area Descriptors which will be the areas under which prospective authors will submit their manuscripts. I am currently in the process of assembling the Editorial Board and hope to have it appointed within the next two months. ************************ AREA DESCRIPTORS: Biotechnology; Cellular and Molecular Toxicology; Cell Biology; Developmental Biology; Growth, Differentiation or Senescence; Genetics; Immunology; Infectious Diseases/Cellular Pathology; Neurobiology; Plant Biology and Virology. ************************ AIMS AND SCOPE: The aim of METHODS IN CELL SCIENCE is to provide _the_ forum for publishing the most up-to-date, cutting edge, methods developed during the course of cell science research involving vertebrates, inverte- brates, plants or single-celled prokaryotic or eukaryotic organisms. The research relevant to this publication is ordinarily conducted using in vitro systems rather than the whole animal or plant, an exception being research in which the animal or plant itself must be viewed microscopically. Manuscripts will also be accepted which describe the design or construction of equipment, media, or quality control procedures that are ancillary to cellular research. Descriptions of the subheadings used in the Table of Contents of METHODS IN CELL SCIENCE (found in the "Instructions for Authors") provide prospective authors with additional information about the subsections of the journal that would be most appropriate for their manuscripts. Manuscripts will be peer reviewed and will only be published in METHODS IN CELL SCIENCE if they provide sufficient detail to enable a researcher to successfully duplicate the method using only the protocol described in the manuscript. In contrast, methods published in most scientific journals, whose emphasis is different than that of METHODS IN CELL SCIENCE, often lack the details required for readers to do so without prior experience with the method or by consulting the author(s). All manuscripts submitted will describe methods original to the author's laboratory which either have never before been published or which were originally published as part of a research paper submitted to another journal. To be acceptable for publication in METHODS IN CELL SCIENCE, rewritten methods must now contain the original citation and all of the detail which could not be included in the original manuscript. A rewritten method, published in METHODS IN CELL SCIENCE, will provide an opportunity for the author to reach a wider audience. SPECIAL ISSUES will devote an entire issue to methodology involved in a specialized area of cellular research. Such specialized areas might, for example, include: Methods in Invertebrate Cell Clulture Research; Methods in Oral Streptococci Research; Research Techniques Involving Caenorhabditis elegans; Methods in Plant Molecular Biology; Molecular Genetic Techniques Using Zebra Danio or Drosophila or, etc. Editors of special issues will solicit, compile and review the necessary manuscripts to complete such an issue. Editors of special issues will often be invited to participate but authors interested in compiling such an issue should contact the Editor-in-Chief. REVIEW ARTICLES: Both mini reviews and full-length reviews, covering various aspects of developments in methodological approaches, equipment, media or quality control procedures related to cellular research will be accepted. Usually they will be invited, but authors interested in contributing such a paper should contact the Editor-in-Chief, describing the proposed review, before submitting a manuscript. A mini review will ordinarily span no more than four to five printed pages whereas full reviews may be ten or more printed pages. *********************** I do hope that you are sufficiently interested in the raison d'etre of the journal that you will join me in this enterprise by submitting manuscripts to it. I believe that this will not be just another journal (we probably have too many now) but will serve a definite purpose. The methods presented will be as complete as it is possible to write them. One should, by reading the paper, be "transported" to the lab bench in the author's laboratory and be following along as the protocol is demonstrated. I firmly believe that there is a place for this kind of presentation. One plan for the journal includes publishing in a "three-hole punched" format so that either the entire issue, or one or more of the methods can be placed right into the laboratory's methods notebook. This may be a possibility. Initially, the journal will appear quarterly, but I hope that with rising interest, it can ultimately appear bimonthly or even monthly. Please contact me at the address below if you wish to obtain an initial copy of the "Information for Authors" or if you are interested in a subscription to the journal. You may also direct your institution to do the same if they are interested in a subscription for the library. If your library currently subscribes to the "Journal of Tissue Culture Methods", they will automatically be contacted by the publishers as that journal will be replaced by METHODS IN CELL SCIENCE. Many of you have wanted to see a journal such as this one available and now I believe this has come to fruition. With the usual few delays in getting something new underway, METHODS IN CELL SCIENCE should be available at the beginning of the new year. I would appreciate receiving any comments you may have regarding this new enterprise (however, please respond directly to me rather than through the newsgroup) and, especially, your manuscripts and suggestions for Special Issues. ___________________________________________________________________________ Warren I. Schaeffer, University of Vermont, Markey Center for Molec. Genet., Microbiol. & Molec. Genetics Dep't., 117 Stafford Bldg. Burlington, Vt.05405 Phone: (802)656-2290 * Fax:(802)656-8749 * e-mail: wschaeff@moose.uvm.edu ____________________________________________________________________________ -- ___________________________________________________________________________ Warren I. Schaeffer "Never, for the sake of peace and quiet Microbiology & Molec. Genetics deny your own experience or convic- 117 Stafford Building tions" Dag Hammarskjold