From owner-srs@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Mac port is available Date: 5 May 1995 04:12:41 GMT Organization: Biology, Indiana University - Bloomington Lines: 16 Message-ID: <3oc8jp$hvi@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu I've modified Thure Etzold's SRS, version 4.02, to work on macintoshes. It is available at IUBio Archive, ftp://iubio.bio.indiana.edu/molbio/browse/srs-on-mac/ Included here is every thing you need to use it w/o compiling it, in 68K and PPC versions, some sample data, as well as the modified source files and files of differences from the original, and project files for compiling it with CodeWarrior. Note: SRSwgetz doesn't interface w/ Mac HTTPD servers because I haven't rewritten the Unix "getenv()" format to use Apple Events for inter-application communications. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Sun May 07 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Mac port is available Date: 8 May 1995 12:55:22 GMT Organization: EMBL Heidelberg Lines: 27 Distribution: world Message-ID: <3ol4bq$gu0@comet.EMBL-Heidelberg.DE> References: <3oc8jp$hvi@usenet.ucs.indiana.edu> NNTP-Posting-Host: phenix.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b3 (X11; I; IRIX64 6.0.1 IP21) X-URL: news:3oc8jp$hvi@usenet.ucs.indiana.edu gilbertd@sunflower.bio.indiana.edu (Don Gilbert) wrote: >I've modified Thure Etzold's SRS, version 4.02, to work on macintoshes. >It is available at IUBio Archive, > ftp://iubio.bio.indiana.edu/molbio/browse/srs-on-mac/ > I will try to incorporate these changes as soon as possible - they will probably be in the release 4.06 ...so the overnext release >Note: SRSwgetz doesn't interface w/ Mac HTTPD servers because I haven't >rewritten the Unix "getenv()" format to use Apple Events for >inter-application communications. that function as soon as it becomes available should be easy to incorporate ..there is a function void FilSetTranslate (char *(*translate)(char *, INT4)); (futil.c)x that sets a new function for translating environment variables to real path names regards Thure =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Tue May 23 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: ListA4 Message-ID: <1995May24.115033.18943@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Distribution: bionet Date: Wed, 24 May 1995 11:50:33 GMT Lines: 168 The SDL files for LISTA are available at the sources mentioned below. Regards Reinhard [ Article crossposted from bionet.molbio.yeast ] [ Author was patrick linder ] [ Posted on 24 May 1995 10:09:23 +0100 ] Dear Netters, We are happy to announce the release of ListA4.1. The document which follows has been extracted (and shortened) from lista.doc describing the database. Please refer to the original document for full documentation. For comments, informations and suggestions, please contact: Patrick Linder, Dept. of med. Biochemistry, CMU, 1, rue Michel Servet, 1211 Geneva, Switzerland Tel +41 22 - 702 54 84 FAX +41 22 - 702 55 02 Email: linder@cmu.unige.ch ======================================================================= LISTA, Release 4.1, March 1995 A comprehensive compilation of nucleotide sequences encoding proteins from the yeast Saccharomyces Doelz, R., Mosse, M. O., Slonimski, P. P., Bairoch, A. and Linder, P. (1994). LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces. Nucleic Acids Res. 22, 3459-3461. 3.2.1 NEW DATA FIELDS IN RELEASE 4 The CL field (chromosomal localization) was added in order to indicate where the gene has been localized. The AC field (accession number) was added, one for each entry. Note that the accession numbers start with SC (for Saccharomyces Cerevisiae). Access ion numbers introduced in the interim release 3.1 were dropped, to account for the principle of one accession number per gene rather than one per quoted reading frame. The DT field has been added to facilitate maintenance. . 3.2.2 CROSS-REFERENCESTO THE SWISS-PROT DATABASE Since release 4.1 an effort has been made to include all the entries in SWISS-PROT and to introduce a DR field for crossreference with Swissprot. This supplements the functionality as already present earlier as via the SWSS-PROT database is immediately linked to the corresponding MEDLINE reference quotation via the SRS system (see below). 3.4 GROWTH LISTA 4.1 contains data from 1909 sequences,corresponding to 1420 genes and 376 synonyms. The exact growth curve is shown below: LISTA 1 400 genes and synonyms LISTA 2 811 genes, 125 synonyms, 1001 sequences LISTA 3 1127 genes, 176 synonyms, 1400 sequences LISTA 4.1 1420 genes, 376 synonyms, 1909 sequences 4 NOMENCLATURE Genetic nomenclature relies on the glossary compiled by [6] and was used whereever possible. In many cases, however,no or incorrect gene designations have been given to published sequences.Moreover,the same name was given to different sequences or differen t names have been given to the same sequence. To sort out this problem of nomenclature a priority rule for naming genes in the present database [2] was established. According to this rule the name of the first pub- lished sequence (date of acceptance of th e publication) is used in the list, provided it is in accordance with the standard genetic nomenclature.Other names are included as synonyms. In some cases four letter designations (ARGR1,MRPL20) or gene names followed by a letter (RPL4A, TIF51A) have als o been used. In the case of historically well established gene designations such as HO,it was self- evident that they should be retained. Although these rules are straight and easy to handle, in some cases this leads to the use of names which are no longer in use. In such cases the currently used name is given and the "historical" name is given as synonym. 6 STATUS OF THE DATABASE 6.1. AVAILABILITY The LISTA database is available either by anonymous FTP from bioftp.unibas.ch [131.152.8.1] in the archive_data/lista directory or its mirror ftp.switch.ch [130.59.1.40] in the mirror/embnet-ch/archive_data/lista directory on the internet. New sequences a nd comments on the existing database may be sent to P. Linder (linder@cmu.unige.ch). LISTA is distributed by the EMBL data library and the associated services (CD-ROM, FTP, EMAIL servers). ListA can also be queried using the SRSWWW system on one of the corresponding servers, e.g. http://www.ch.embnet.org/srs/srsc. 6.2. FUTURE (INCREMENTAL) RELEASES Further releases are still open for feed-back and suggestions, and it is suggested to contact linder@cmu.unige.ch for comments and desired enhancements. An effort will be made to add new entries to the existing list without any announcement. The new entries will be available in Lista4_new. 6.3. ADDITIONS: HOMOLOGY CALCULATIONS The LISTA database does not currently contain any sequence data from entries available in the EMBL data library. Experimental versions of an EMBL-formatted file which includes sequence data are available as LISTA-HON (the homologies on the Nucleotide leve l) and LISTA-HOP (the homologies on the Protein level). The release of ODD files describing the LISTA , LISTA-HON and LISTA-HOP format for parsing into the SRS system [7] is experimental at this point of time and suggestions are most welcome to doelz@ch.e mbnet.org (Reinhard Doelz, address see above). 6.4. FILES FOR USE IN THE SRS SYSTEM The SDL files to be modified are srsdb.sdl, hyperlink.sdl and lista.sdl. The latter is provided as part of the distribution. For proper integration, do the following additions similar to the example: (lines without : are wrapped for ease of reading) 7 ACKNOWLEDGEMENTS We are very grateful to all those, who have provided input in solving nomenclature problems and giving informations on inconsistencies. We would also like to thank Thure Etzold for assistance in building the LISTA.SDL file.This work was supported by grants from the Ministere de la Recherche et de l'Espace (program GREG; P.S.), from the Swiss National Science Foundation (R.D. and A.B), the University of Basel (R.D. and P.L) and the University of Geneva (P.L. and A.B.). We are very grateful to S. Brouillet, J.L. Risler and the Rechenzentrum of the University of Basel for help. -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-srs@net.bio.net Tue May 23 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!gatech!EU.net!ieunet!maths.tcd.ie!news.tcd.ie!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Method to do indexing @production server Message-ID: <1995May24.170405.29434@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 24 May 1995 17:04:05 GMT Lines: 102 Colleagues, we need to index data while the server is expected to answer replies. As the normal procedure of srscheck/srsupdate will invalidate indices during the process of srsbuild, we came up with the following solution. Maybe you have found a better way of doing it, we'd like to hear from you! Note: The following still assumes that the data are not needed, only the indices. This is OK as long as searches or SRS operations need only the indices. This assumption is only true as a rough approximation. Procedures could be developed which handle this, too. Principle: 1. Buy disks. 2. Make a scratch dir and symlink each entry in SRSINX. 3. Parse output from srscheck and delete all symlinks to files which are to be rebuilt. 4. reassign SRSINX and rebuild indices. 5. Delete all symlinks in the scratch directory. 6. copy all newly created indices into production SRSINX. The following shell does this, exemplarically. In order to map logical names to file names, the following awk script is needed (must be modified, too). ============================> map.awk <===================================== { if ($1 == "XEMBL") { print "xembl" } if ($1 == "XXEMBL") { print "xxembl" } if ($1 == "EMNEW") { print "emnew" } if ($1 == "GBNEW") { print "gbnew" } if ($1 == "GBNEW_EXCL"){ print "gbnew_excl" } if ($1 == "TREMBLNEW") { print "tremblnew" } } =============================> end of map.awk <============================== =========================> update.csh <=================================== #!/bin/csh unlimit # common SRS practice setenv SCRATCHBIN /bioz1/software/www/SRSUPDATE # location of map.awk setenv SCRATCHINX /biox4/srs # scratch directory source /bioz1/software/www/SRS/etc/prep_srs # srs prep # #----------------------------------- create linkages # cd $SRSINX foreach i (*) ln -s $SRSINX/$i $SCRATCHINX/$i end cd $SCRATCHINX # #------------------------------------ see, is there something to be done? srscheck >& log cat log | grep must | nawk '{n = split ($0,field,"\""); print field[2]}' | nawk -f $SCRATCHBIN/map.awk | sort -u > log2 # #----------------------------------- delete all links which have these # unalias ls foreach i ( `cat log2`) rm $SCRATCHINX/$i''* end # #---------------------------------- establish working index # setenv SRSSAV $SRSINX setenv SRSINX $SCRATCHINX # #---------------------------------- redo the srscheck and do srsupdate # (dont reassign SRSINX in prep_srs) srscheck cat `which srsupdate` | grep -v prep_srs > $SCRATCHBIN/pilot.csh source $SCRATCHBIN/pilot.csh # #---------------------------------- remove all files which are symlinks # cd $SCRATCHINX find . -type l -exec rm '{}' # #---------------------------------- copy newly survived index files # foreach i (*) cp $i $SRSSAV end =========================> end of update.csh <=============================== I forgot to mention that this works only on UNIX. Regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-srs@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!prairienet.org!sword From: sword@prairienet.org (Andrew D. Seale) Newsgroups: bionet.software.srs Subject: 486 motherboard Date: 26 May 1995 23:08:26 GMT Organization: Prairienet, the East-Central Illinois Free-Net Lines: 9 Message-ID: <3q5n1a$bp1@vixen.cso.uiuc.edu> NNTP-Posting-Host: firefly.prairienet.org X-Newsreader: TIN [version 1.2 PL2] Looking for a 486 mother board. Right now just wanna see whats out on the market. -- =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= | Andy Seale | Go to my homepage!!! | | sword@prairienet.org | http://www.prairienet.org/~sword/ | =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= From owner-srs@net.bio.net Mon May 29 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: srs4.05 is ready Date: 30 May 1995 14:43:32 GMT Organization: EMBL Heidelberg Lines: 110 Distribution: world Message-ID: <3qfauk$6h7@comet.EMBL-Heidelberg.DE> NNTP-Posting-Host: phenix.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b3 (X11; I; IRIX64 6.0.1 IP21) X-URL: news:bionet.software.srs dear all, release 4.05 of SRS is available now. Get the file pub/software/unix/srs/srs4_05.tar.gz via anonymous ftp from felix.embl-heidelberg.de There were some problems installing SRS with the new httpd from NCSA as reported by Jack Leunissen and Steve Taylor which should be fixed now. The cgi's and the document files are declared to reside now in two different directories (see the installation procedure in the README of the distribution or http://www/srs/srsman_install.html. Please tell me if it works or if there are still problems with it. I added Tom Boutell's 'gd' library for creating GIF images and a new program 'srspict' that creates a picture with the databank network and a link diagram. for the network it needs a file with the coordinates of all databanks which you can create with a tcl/tk script (primitive graph editor) ...instructions in README. The last important change is the complete replacement of the algorithm for finding the shortest path in the library network ...which was about to crack on large systems. The new algorithm is much faster and should work even with several hundred databanks;-). Here is the complete list of changes since srs4.04: 1995/04/05 if a flat file is not accessible, eg, the file est.dat from embl then this will be mentioned only once ...eg during listing a list of embl entries together with selected fields ...still the names for these entries can be displayed 1995/05/05 Added function LibIsDataType which tells whether a databank contains "protein" or "dna" sequences ...function can be easily extended for other data types 1995/05/05 GCG formatted list file for features does not list "Strand" for protein sequences 1995/05/05 enhanced srscheck to look at all single indices if they need rebuilding or compression 1995/05/05 fixed problem with retrieving integer ranges ...integers are no longer treated as floats 1995/05/05 prep_srs puts the srs directories at the begin of the PATH variable 1995/05/05 the '?' for begin and end positions in swissprot are now understood 1995/05/09 a number of blast files can now be indexed - each entry witll receive a name composed of filename, number within that file, and the sequence found (eg, swissprot name). The file names are stored in the IDX file 1995/05/09 added new attribute isSystem for #field - all fields marked with that should be ignored by user interfaces - use LibIsField (field, "system") to find out. 1995/05/10 Replaced the algorithm for finding the shortest path in the library network ...now there is NO limit left to hinder its growth 1995/05/17 Added buffer function for matching regular expressions 1995/05/17 Changed script module so that it understands variables in labels and in the text 1995/05/19 the script module provides now a utility to check number and type of arguments when printing from a label with print arguments 1995/05/26 executables and document files can now be in different directories 1995/05/26 stdout for SRSWWW is no longer buffered. This fixes a problem with the httpd on OSF1 ..have fun regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Tue May 30 23:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!news.hgmp.mrc.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: srs4.05 is ready Date: 31 May 1995 15:37:01 GMT Organization: MRC Human Genome Resource Centre Lines: 23 Distribution: world Message-ID: References: <3qfauk$6h7@comet.EMBL-Heidelberg.DE> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Thure Etzold's message of 30 May 1995 14:43:32 GMT CC: pmr In article <3qfauk$6h7@comet.EMBL-Heidelberg.DE> Thure Etzold writes: >release 4.05 of SRS is available now. Get the file >pub/software/unix/srs/srs4_05.tar.gz via anonymous ftp from >felix.embl-heidelberg.de > >I added Tom Boutell's 'gd' library for creating GIF images and a new program >'srspict' that creates a picture with the databank network and a link diagram. >for the network it needs a file with the coordinates of all databanks which you >can create with a tcl/tk script (primitive graph editor) ...instructions in README. I now have the new database GIFS (tcl/tk script and srspict program) working and running with the CERN web server (the image map format is different). If anyone is interested, I can provide more details of the changes. I have passed them on to Thure for inclusion in a future release. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England