Date: Thu, 16 Mar 1995 19:06:06 GMT
Organization: European Bioinformatics Institute
X-Newsreader: TIN [version 1.2 PL2]
Lines: 210
Xref: biosci bionet.software.srs:25 bionet.molbio.embldatabank:479
I sent this out a week ago, but due to local distribution problems, most of
the world never saw it.
For the people that did see the previous announcement,
an important new feature is added, so do read on.
Also people looking for non WWW access to the databases could be interested
Included is a short manual on the use of an FTP to SRS gateway, developed
in the EMBL Outstation - EBI. It can be used right now, but I do not
garantee yet, that the service will be officially supported.
Please try it, and if you find any problems, or have any suggestions, let
me know (jecop@ebi.ac.uk)
The idea is that it can be used in automated checking/retrieving new
sequences of interest.
Jeroen
-
USING SRS (Sequence Retrieval System [1]) from Anonymous FTP
------------------------------------------------------------
(Jeroen Coppieters, 17-Mar-1995, srsftp version 1.1beta)
This document describes SRSFTP as it is maintained at
EMBL Outstation, the European Bioinformatics Institute
further referenced as "the EBI"
The Anonymous FTP server of the EBI has a gateway to SRS,
developped by Jeroen Coppieters and RJ White.
This allows the retrieval of sequences from Swissprot and EMBL (as well as
all other databases that are maintained in SRS at the EBI [2]), using
the power of SRS.
A query can be executed from any directory, after connecting to the
anonymous ftp server.
All results of the query will be stored in the file you name.
The sequences are stored in flat-file EMBL format by default
In any query, the * wildcard can be used
three formats of queries are available:
- simple sequence retrieval
- simple srs query
- full srs query
1) SIMPLE SEQUENCE RETRIEVAL
---------------------------
FORMAT:
get DB:INDEX:QUERYSTRING FILENAME
DB is one of the following:
embl, emblnew, emblall, nuc
swissprot, swissnew, swissall, pep
if any of the xxall databases is specified, both the release and the
updates are searched. If a sequence has been updated since the last
release, both the old and new entry will be returned.
INDEX DATABASE SEARCHFIELD QUERYSTRING
acc accession number accession nr (e.g. X07888)
id identifier identifier (e.g. ATP6_YEAST)
dat date date (e.g. 20-NOV-1994)
fts feature feature name (e.g. intron)
ref reference Journal reference
(e.g. Plant Mol. Biol. 10:91-104(1987))
sl sequence length number (e.g. 2400)
or range (e.g. 2300:5000)
def definition string
aut author string
cc comment string
org organism string
tit reference title string
all all text fields string
EXAMPLES:
get emblall:acc:x07888 x07888.seq
retrieve sequence from embl/emnew with accession number x07888
store in the file x07888.seq
get swissprot:all:nitrate* nitrate.pep
get all swissprot entries that have a word starting with nitrate
in any of the text fields.
Store in the file nitrate.pep
2) SIMPLE SRS QUERY
------------------
FORMAT:
get srs:QUERYSTRING
This allows linking of several databases
For more information on SRS queries, have a look at the SRS manual
This however does not allow the complete functionality of SRS.
Restrictions are: - NO SPACES are allowed in the query.
- no command line parameters can be included
EXAMPLES
get srs:[embl-fts:intron]>parent&[embl-org:arabidopsis*] arain.seq
retrieve all sequences from Arabidopsis spec. that contain an intron.
get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot kinase.pep
retrieve all proteins, that contain a tyrosine kinase motif (PROSITE)
get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot>pdb kinase.pdb
retrieve 3D structures (if known) from the above proteins
3) FULL SRS QUERY
-----------------
If you want to have access to command line options (e.g. to change the
output format), a full blown getz command is available.
FORMAT:
From UNIX, VMS+Multinet, MSDOS+NCSA ftp:
get getz+commandline+options+querystring filename
VMS+UCX:
get "getz+commandline+options+querystring" filename
- All spaces in the query should be replaced by plus (+)
- If you want to include a + in a query, use a double plus (++)
- do not put quotes round the querystring
- if you want to escape a character with a backslash (\), duplicate
the backslash (\\)
- contrary to forms 1 and 2, there is no colon in the command
- the getz program has a new command line option -pipe "string"
where string can be "/bin/compress" or "/bin/gzip"
this will compress the results before transmitting the data,
thus minimizing network traffic
Do not forget to use BINARY TRANSFER if you use this option
- On UNIX systems, whenever ftp expects a filename,
this can be replaced by - (dash)
the retrieved file will be printed on stdout
EXAMPLES
get getz+-help file
retrieve help on the usage of getz
get getz+-libs libs.lst
get a list of all available databases
get getz+-d+-sf+fasta+-pipe+"/bin/gzip"+[emnew-org:drosophila*] dro.seq.gz
retrieve all Drosophila sp. sequences from emnew in fasta format. Gzip
before transmitting
get getz+-l+swissprot+-l+swissnew+[sq-id:*_ecoli] ecoli.lst
generate a list of all ecoli proteins in swissprot and swissnew
============================================================
NOTES:
-----
[1] More information on SRS is available from the author: Thure Etzold
Via WWW: http://www.embl-heidelberg.de/srs/srsman.html
Refererences:
Thure Etzold and Patrick Argos, SRS an indexing and retrieval tool for flat
file data libraries. Comput. Appl. Biosci. 9:49-57, 1993
Thure Etzold and Patrick Argos, Transforming a set of biological flat file
libraries to a fast access network. Appl. Biosci. 9:59-64, 1993
[2] on March 14th 1995, these database were:
Library Group Entries Index Date
-------------------------------------------------------------------
SWISSPROT Sequence 40292 2/28/95
SWISSNEW Sequence 9036 3/8/95
PIR Sequence 71995 2/28/95
EMBL Sequence 234501 2/28/95
EMNEW Sequence 102576 3/14/95
NRL3D Sequence 4153 3/1/95
NRSUB Sequence 248 3/1/95
PDB ProteinStruct 3391 3/1/95
HSSP ProteinStruct 3070 3/4/95
DSSP ProteinStruct 2968 3/2/95
ALI ProteinStruct 84 3/1/95
FSSP ProteinStruct 436 3/4/95
PROSITE SeqRelated 1029 3/1/95
PROSITEDOC SeqRelated 786 3/1/95
BLOCKS SeqRelated 770 3/1/95
EPD SeqRelated 1251 3/1/95
ECDC SeqRelated 3571 3/1/95
ENZYME SeqRelated 3546 3/1/95
REBASE SeqRelated 2454 3/1/95
PRODOM SeqRelated 23105 3/1/95
FLYGENE SeqRelated 7126 3/10/95
SWISSDOM SeqRelated 28224 3/1/95
PIRALN SeqRelated 1183 3/1/95
SEQANALREF Literature 2579 3/1/95
MEDLINE Literature 179262 3/1/95
LIMB Others 120 3/1/95
TFSITE TransFac 4042 3/14/95
TFFACTOR TransFac 1412 3/14/95
DBEST TaggedSites 3264 3/8/95
--
======================================================================
. O . Jeroen Coppieters
. O O o O . Software Support
O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk
O O O O( *o )O O (or jecop@ebi.ac.uk)
)O O O O o* O O( ++44 1223 494422
O O O O( o* )O O
)O O O O *o O O( EMBL Outstation EBI
O O O O( *o )O O (European Bioinformatics Institute)
)O @ O O o* O O( Hinxton Hall
O O O( o* )O(' Hinxton
` O( *o O ' Cambridge CB10 1RQ
` O ' UK
http://www.ebi.ac.uk
======================================================================
From owner-srs@net.bio.net Thu Mar 16 22:00:00 1995
Newsgroups: bionet.software.srs
Path: biosci!daresbury!bioftp.unibas.ch!doelz
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Subject: [POSITION AVAILABLE] SRS team at Basel, CH
Message-ID: <1995Mar17.092945.3832@comp.bioz.unibas.ch>
Organization: EMBnet Switzerland [Basel]
X-Newsreader: TIN [version 1.2 PL2]
Date: Fri, 17 Mar 1995 09:29:45 GMT
Lines: 86
Our software development team working on the SRS package seeks a
Assistant Programmer
to help coding the required interprocess communication and network
modules. Our current work deals with issues of server-server coupling
to be achieved with a dedicated version of the HASSLE protocol. This
project includes tight collaboration with the team of Thure Etzold
(author of SRS), at EMBL Heidelberg, coordinated by Pat Argos.
Duties: Network programming, in particular
- to develop pipe, queue and special protocol features
- to help maintain and expand the current SRS package, including
local, WWW and development versions in a heterogeneous network
- to implement the approaches and algorithms defined by the project
and developed at BioComputing Basel as well in the international
team
Qualifications: Programming Skills, in particular
***Essential
- fluent knowledge of the programming language "C"
- ability to integrate code in a multi-platform development environment
based on UNIX and other operating systems
- willingness to learn quickly about SRS and HASSLE tools and code
structure, in particular the scope and limitations
- ability to perform administrative tasks reliably and to work on
mission-critical tasks in a team
- good knowledge of written and spoken English
***Desirable
- work experience in an international environment
- previous exposure to the Internet
- basic experience with networked information retrieval in Biology
Suitable for both biologists and informatics areas:
The position is suitable both for those with computational skills willing
to learn about the application in Biology and to recent graduates in
Biology with Internet and C programming experience willing to do a
sophisticated project in the programming area. Female applicants are
explicitly encouraged.
Benefits: Working at a Leading Site
BioComputing Basel is a recognized site in the area. Working in a non-
smoking team office on modern Workstations in a open-minded, friendly
environment. The position is funded by the Bundesamt for Bildung
und Wissenschaften (BBW) in a EU-funded BIOMED I framework project "SRS".
The position is open immediately and currently limited to June 1, 1996.
Extension is, depending on qualification and funding continuation,
possible. Salary is in the 4600 SFr/month range. Swiss citizenship
preferred, Working permit (or equivalent B or C permit) required, can
be arranged as temporary working permit if required. The ideal candidate
is based in proximity of Basel (Switzerland, Germany or France).
The successful applicant reports to the Scientific Responsible officer
and the Programme Coordinator with respect to long-term goal accomplish-
ment.
Application to:
Reinhard Doelz
BioComputing Basel
EMBnet Switzerland
Biozentrum der Universitaet Basel
CH 4056 Basel
SWITZERLAND
Applications, including previous work description, a CV and at least two
references should be submitted in confidence to the address above and
should be received no later than 31st of March, 1994. Electronic Mail and
FAX applications will not be considered.
References:
[1] EMBnet Switzerland
[2a] SRS, by Thure Etzold
[2b] SRS, status page
[3] Environment
--
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 Sun Mar 19 22:00:00 1995
Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr
From: pmr@unst.sanger.ac.uk (Peter Rice)
Newsgroups: bionet.software.srs
Subject: SRS Database Descriptions
Date: 20 Mar 1995 12:18:37 GMT
Organization: University of Cambridge, England
Lines: 28
Message-ID:
NNTP-Posting-Host: unst.sanger.ac.uk
OK, so you can get a status report of the databases out there.
Now, suppose you are intesrested in one of the databases. What do
you do next? How do you find out what it is? Can you install it
locally to get all those new cross-references working?
Well, at the Sanger Centre I have updated the descriptions of all our
databases in the wgetz_text.script file so that, for each database,
there is a decription of the database, access to the SDL file, and a
pointer to where to get the data files.
Just clicking on the "?!" for a database at the Sanger Centre will
give you our full description.
I have put the text up on our FTP server:
URL: ftp://ftp.sanger.ac.uk/pub/pmr/srs/wgetz_text.script
--
------------------------------------------------------------------------
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
From owner-srs@net.bio.net Sun Mar 19 22:00:00 1995
Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr
From: pmr@unst.sanger.ac.uk (Peter Rice)
Newsgroups: bionet.software.srs
Subject: SRS Database Updates
Date: 20 Mar 1995 12:13:57 GMT
Organization: University of Cambridge, England
Lines: 40
Message-ID:
NNTP-Posting-Host: unst.sanger.ac.uk
As the SRS network grows, it seems increasingly complicated to keep up
with the new sites and the database updates.
At the Sanger Centre, I now have 14 SRSWWW sites included in the daily
status report, and 74 databases (although a few of these are alternative
names for the same data) spread around these sites.
The status report URL is:
http://www.sanger.ac.uk/srs/status.html
and other SRSWWW sites should have a similar status report although as
discussed on this group earlier a few sites may lose lines if they
have an old copy of the script that writes the report.
You can easily check the status report to see which sites have old releases
of databases.
I considered writing a script to check for other sites with more entries
in a database, but in a few cases (EMNEW, SWISSNEW, ECDCONTIG) the number
of entries can legitimately go down with an update.
An increasing number of sites are also, I see, putting the release numbers
on their SRS indices.
If you don't know what the databases are, you can simply click on the
"?!" at the end of the status report line to get a report, directly from
that site, describing the database and providing access to the SDL file
they used.
More of that in the next posting.
--
------------------------------------------------------------------------
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
From owner-srs@net.bio.net Sun Mar 19 22:00:00 1995
Path: biosci!agate!news.duke.edu!convex!cs.utexas.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr
From: pmr@unst.sanger.ac.uk (Peter Rice)
Newsgroups: bionet.software.srs
Subject: SRS Tutorial
Date: 20 Mar 1995 12:22:39 GMT
Organization: University of Cambridge, England
Lines: 24
Message-ID:
NNTP-Posting-Host: unst.sanger.ac.uk
A few other sites have discovered the strange new icon on the
Sanger Centre's SRSWWW server.
The SRS world icon with a black hat (in England that is a teacher's hat :-)
takes you to the Sanger Centre SRS Tutorial.
The URL is:
http://www.sanger.ac.uk/srstutor-main.html
Please try it, and if you can think of some useful examples (either how to
do something useful, or simply asking about a task that seems impossible
at present with SRSWWW), please mail me (pmr@sanger.ac.uk) and I will try
to write a new tutorial example. So far we have examples for the sequence
databases and OMIM.
--
------------------------------------------------------------------------
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
From owner-srs@net.bio.net Tue Mar 21 22:00:00 1995
Path: biosci!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!clpd-newsserver!news.nysernet.net!news.sprintlink.net!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news
Newsgroups: bionet.software.srs
Subject: Re: vt100 interface still necessary
Message-ID: <1995Mar18.182512.175@immunbio.mpg.de>
From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann)
Date: 18 Mar 95 18:25:12 +0100
References: <3k487m$o7f@rc1.vub.ac.be>
Distribution: world
Organization: Max-Planck-Institut fuer Immunbiologie
Nntp-Posting-Host: mpi1.immunbio.mpg.de
X-News-Reader: VMS NEWS 1.24In-Reply-To: gbottu@ben.vub.ac.be's message of 14 Mar 1995 14:12:06 GMTLines: 37
Lines: 37
In <3k487m$o7f@rc1.vub.ac.be> gbottu@ben.vub.ac.be writes:
> Recently, there has been a discussion whether the vt100 interface for
> SRS should not be abandonned. An important issue in this debate is that,
> at the present, there are a number of things that you cannot do with the
> WWW interface :
> - save all the entries of a set in separate files with one
> command (with vt100 you use CopySet)
> - obtain a sequence range defined relative to a feature
> (e.g. the 10 bases upstream and downstream of
> an intron-exon boundary).
>
> That is why at the BEN site we have a computer with SRS 4 with WWW
> interface under OSF/1 and another computer with SRS 3 with vt100
> interface under SunOS. This is an unpleasant intermediary situation,
> the more that the indexation of SRS 3 often crashes.
> Therefore, it would be a good thing if the vt100 interface for
> SRS 4 were ready, or if the WWW interface could be rendered as
> flexible as the vt100 interface.
>
> Has somebody a comment about that ?
Of course ;-) I agree completely. Our users prefer the VT100 interface and
me as well. In addition if there existed a VT100 interface for V4 besides the
WWW interface one wouln't be forced to set up a WWW server or rely on more
or less stable links.
Regards,
Christoph Gartmann
+----------------------------------------------------------------------------+
| Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 |
| Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN |
| Postfach 1169 Internet: gartmann@immunbio.mpg.de |
| D-79011 Freiburg, FRG |
+----------- Do you know MENUE, the user environment for OpenVMS? -----------+
From owner-srs@net.bio.net Tue Mar 21 22:00:00 1995
Newsgroups: bionet.software.srs
Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop
From: jecop@ebi.ac.uk (Jeroen Coppieters)
Subject: query display in QueryManager
Sender: news@ebi.ac.uk (Mr news)
Message-ID:
Date: Wed, 22 Mar 1995 16:29:26 GMT
Organization: European Bioinformatics Institute
X-Newsreader: TIN [version 1.2 PL2]
Lines: 54
I got a request to change the SRS Query manager form, from one of our users,
and I think I have the solution. To make sure, that I did not overlook
anything important, here's the description. If you see a problem that I did
not see, or a better solution, let me know.
Jeroen
Problem:
WWW interface to SRS 4.02, Query manager form.
Previous queries are displayed as following example:
Q1 (retrieval) := "[Sequence-AllText:kinase*]&[Sequence-AllText:tyrosin*]"
found 183 entries
The "..." query string does not contain blanks. WWW clients cannot wrap
strings without blanks. So long queries run out of view and the form
cannot be properly printed to paper.
Solution: add blanks in the query-string or add blanks to on-screen
representation of query-string
I had a look at the code and the most obvious place to add these blanks
is in WwwStringEncode (srswww.c)
The 4 lines marked with /* JC */ were added
char *WwwStringEncode (char *s)
{
SmSwapS (s, "&", " & "); /* JC */
SmSwapS (s, "|", " | "); /* JC */
/* Add blanks before and after > and < signs
this is the original
SmSwapS (s, "<", "<");
SmSwapS (s, ">", ">");
following is the changed version */
SmSwapS (s, "<", " < ");
SmSwapS (s, ">", " > "); /* JC*/
return s;
}
--
======================================================================
. O . Jeroen Coppieters
. O O o O . Software Support
O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk
O O O O( *o )O O (or jecop@ebi.ac.uk)
)O O O O o* O O( ++44 1223 494422
O O O O( o* )O O
)O O O O *o O O( EMBL Outstation EBI
O O O O( *o )O O (European Bioinformatics Institute)
)O @ O O o* O O( Hinxton Hall
O O O( o* )O(' Hinxton
` O( *o O ' Cambridge CB10 1RQ
` O ' UK
http://www.ebi.ac.uk
======================================================================
From owner-srs@net.bio.net Wed Mar 22 22:00:00 1995
Newsgroups: bionet.software.srs
Path: biosci!daresbury!bioftp.unibas.ch!doelz
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Subject: SRS Tutorial
Message-ID: <1995Mar23.062302.19810@comp.bioz.unibas.ch>
Organization: EMBnet Switzerland [Basel]
X-Newsreader: TIN [version 1.2 PL2]
Date: Thu, 23 Mar 1995 06:23:02 GMT
Lines: 37
[Just to complete the srs group as there still seem to be logistics problems
on the Hinxton areal. Peter Rice posted this but it never showed up.]
[ Article crossposted from bionet.software ]
[ Author was Peter Rice ]
[ Posted on 21 Mar 1995 20:37:07 GMT ]
A few other sites have discovered the strange new icon on the
Sanger Centre's SRSWWW server.
The SRS world icon with a black hat (in England that is a teacher's hat :-)
takes you to the Sanger Centre SRS Tutorial.
The URL is:
http://www.sanger.ac.uk/srstutor-main.html
Please try it, and if you can think of some useful examples (either how to
do something useful, or simply asking about a task that seems impossible
at present with SRSWWW), please mail me (pmr@sanger.ac.uk) and I will try
to write a new tutorial example. So far we have examples for the sequence
databases and OMIM.
--
------------------------------------------------------------------------
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
--
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 Wed Mar 22 22:00:00 1995
Newsgroups: bionet.software.srs
Path: biosci!daresbury!bioftp.unibas.ch!doelz
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Subject: SRS Database Descriptions
Message-ID: <1995Mar23.062317.19875@comp.bioz.unibas.ch>
Organization: EMBnet Switzerland [Basel]
X-Newsreader: TIN [version 1.2 PL2]
Date: Thu, 23 Mar 1995 06:23:17 GMT
Lines: 34
[ Article crossposted from bionet.software ]
[ Author was Peter Rice ]
[ Posted on 21 Mar 1995 20:35:54 GMT ]
OK, so you can get a status report of the databases out there.
Now, suppose you are intesrested in one of the databases. What do
you do next? How do you find out what it is? Can you install it
locally to get all those new cross-references working?
Well, at the Sanger Centre I have updated the descriptions of all our
databases in the wgetz_text.script file so that, for each database,
there is a decription of the database, access to the SDL file, and a
pointer to where to get the data files.
Just clicking on the "?!" for a database at the Sanger Centre will
give you our full description.
I have put the text up on our FTP server:
URL: ftp://ftp.sanger.ac.uk/pub/pmr/srs/wgetz_text.script
--
------------------------------------------------------------------------
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
--
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 Wed Mar 22 22:00:00 1995
Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet
From: Thure Etzold
Newsgroups: bionet.software.srs
Subject: Re: query display in QueryManager
Date: 23 Mar 1995 09:32:35 GMT
Organization: EMBL Heidelberg
Lines: 14
Distribution: world
Message-ID: <3krf7j$qhm@comet.EMBL-Heidelberg.DE>
References:
NNTP-Posting-Host: phenix.embl-heidelberg.de
jecop@ebi.ac.uk (Jeroen Coppieters) wrote:
>
> I got a request to change the SRS Query manager form, from one of our users,
> and I think I have the solution. To make sure, that I did not overlook
> anything important, here's the description. If you see a problem that I did
> not see, or a better solution, let me know.
>
solution looks good to me ...will put that into the next release.
thure
From owner-srs@net.bio.net Wed Mar 22 22:00:00 1995
Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet
From: Thure Etzold
Newsgroups: bionet.software.srs
Subject: Re: vt100 interface still necessary
Date: 22 Mar 1995 10:46:22 GMT
Organization: EMBL Heidelberg
Lines: 29
Distribution: world
Message-ID: <3kov5u$cs8@comet.EMBL-Heidelberg.DE>
References: <3k487m$o7f@rc1.vub.ac.be>
NNTP-Posting-Host: phenix.embl-heidelberg.de
gbottu@ben.vub.ac.be (Guy Bottu) wrote:
>
> Recently, there has been a discussion whether the vt100 interface for
> SRS should not be abandonned. An important issue in this debate is that,
> at the present, there are a number of things that you cannot do with the
> WWW interface :
> - save all the entries of a set in separate files with one
> command (with vt100 you use CopySet)
> - obtain a sequence range defined relative to a feature
> (e.g. the 10 bases upstream and downstream of
> an intron-exon boundary).
I am glad to announce that a proposal to the EMBnet to support
the development of a vt100 interface for srs4 was approved.
Gijs Schaftenaar at the CAOS/CAMM center in Nijmegen volunteered to
do the work and will use a combination of curses and tcl for the
implementation. He is confident that both are supported on all
platforms (unix, vms) where srs3.1 is currently installed.
We expect to see a first version in about 2 months and the goal is
to keep it very similar to the version 3.1 but I would like to encourage
people to send their thoughts about improving the vt100
interface.
regards
thure etzold
From owner-srs@net.bio.net Wed Mar 22 22:00:00 1995
Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!xyplex14.uio.no!rodrigol
From: rodrigol@ulrik.uio.no (Rodrigo Lopez)
Newsgroups: bionet.software.srs
Subject: SRS 4.x and EMBL 42
Date: Thu, 23 Mar 1995 09:52:50
Organization: The Norwegian EMBnet node
Lines: 40
Message-ID:
NNTP-Posting-Host: xyplex14.uio.no
X-Newsreader: Trumpet for Windows [Version 1.0 Rev A]
Hi!
Taking the liberty of posting this message on behalf of the SRS support team
to all SRS 4.x administrators.
In case you haven't noticed, there is a small problem with the features index
creation with release 42 of EMBL. The fix is:
1. edit $SRSROOT/src/ids.c
2. search for the line that reads:
#define IDSxTMPSETSIZE 300000
3. change that line to read:
#define IDSxTMPSETSIZE 600000
4. remove all objects from your bin directory
5. recompile
6. remove all EMBL 42 indices from your index directory
7. rebuild
On behalf of the SRS support team.
R:)
----------------------------------------------------------------
Rodrigo Lopez The
Norwegian
rodrigo.lopez@biotek.uio.no EMBnet
tel: xx-47-22724757 node
fax: xx-47-22694130
gopher: gopher.no.embnet.org WWW: www.no.embnet.org
----------------------------------------------------------------
From owner-srs@net.bio.net Wed Mar 22 22:00:00 1995
Newsgroups: bionet.software.srs
Path: biosci!daresbury!bioftp.unibas.ch!doelz
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Subject: SRS Database Updates
Message-ID: <1995Mar23.062354.19940@comp.bioz.unibas.ch>
Organization: EMBnet Switzerland [Basel]
X-Newsreader: TIN [version 1.2 PL2]
Date: Thu, 23 Mar 1995 06:23:54 GMT
Lines: 50
[ Article crossposted from bionet.software ]
[ Author was Peter Rice ]
[ Posted on 21 Mar 1995 20:34:37 GMT ]
As the SRS network grows, it seems increasingly complicated to keep up
with the new sites and the database updates.
At the Sanger Centre, I now have 14 SRSWWW sites included in the daily
status report, and 74 databases (although a few of these are alternative
names for the same data) spread around these sites.
The status report URL is:
http://www.sanger.ac.uk/srs/status.html
and other SRSWWW sites should have a similar status report although as
discussed on this group earlier a few sites may lose lines if they
have an old copy of the script that writes the report.
You can easily check the status report to see which sites have old releases
of databases.
I considered writing a script to check for other sites with more entries
in a database, but in a few cases (EMNEW, SWISSNEW, ECDCONTIG) the number
of entries can legitimately go down with an update.
An increasing number of sites are also, I see, putting the release numbers
on their SRS indices.
If you don't know what the databases are, you can simply click on the
"?!" at the end of the status report line to get a report, directly from
that site, describing the database and providing access to the SDL file
they used.
More of that in the next posting.
--
------------------------------------------------------------------------
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
--
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 Mon Mar 27 23:00:00 1995
Path: biosci!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!clpd-newsserver!news.sprintlink.net!EU.net!Germany.EU.net!zib-berlin.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news
Newsgroups: bionet.software.srs
Subject: Re: vt100 interface still necessary
Message-ID: <1995Mar25.161939.180@immunbio.mpg.de>
From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann)
Date: 25 Mar 95 16:19:38 +0100
References: <3k487m$o7f@rc1.vub.ac.be> <3kov5u$cs8@comet.EMBL-Heidelberg.DE>
Distribution: world
Organization: Max-Planck-Institut fuer Immunbiologie
Nntp-Posting-Host: mpi1.immunbio.mpg.de
X-News-Reader: VMS NEWS 1.24In-Reply-To: Thure's message of 22 Mar 1995 10:46:22 GMTLines: 37
Lines: 37
In <3kov5u$cs8@comet.EMBL-Heidelberg.DE> Thure writes:
> I am glad to announce that a proposal to the EMBnet to support
> the development of a vt100 interface for srs4 was approved.
>
> Gijs Schaftenaar at the CAOS/CAMM center in Nijmegen volunteered to
> do the work and will use a combination of curses and tcl for the
> implementation. He is confident that both are supported on all
> platforms (unix, vms) where srs3.1 is currently installed.
>
> We expect to see a first version in about 2 months and the goal is
> to keep it very similar to the version 3.1 but I would like to encourage
> people to send their thoughts about improving the vt100
> interface.
Nice to hear. And here are some suggestions:
- in V 3.1 there is a differnce between "forms" and "buffers" in that you
use a function key or control key to leave the former but you have to
press "q" to leave the latter. I would like to have the function/control
keys for both (preferably F10 [I am on VMS ;-) ] ).
- selecting a database during a query: in V3.1 you find a "@" in a field.
Our users find this a bit cryptic. Why not just highlight the text
"select database to query" and put the cursor just onto this text and
press Return to display the databases. Or just display the databases
before the actual query map. This will ensure that the user is aware
of the databases currently selected.
Regards,
Christoph Gartmann
+----------------------------------------------------------------------------+
| Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 |
| Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN |
| Postfach 1169 Internet: gartmann@immunbio.mpg.de |
| D-79011 Freiburg, FRG |
+----------- Do you know MENUE, the user environment for OpenVMS? -----------+
From owner-srs@net.bio.net Wed Mar 29 23:00:00 1995
Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet
From: Thure Etzold
Newsgroups: bionet.software.srs
Subject: Re: on my SunOS4 w/ gcc 2.6.2,
Date: 30 Mar 1995 10:57:20 GMT
Organization: EMBL Heidelberg
Lines: 30
Distribution: world
Message-ID: <3le2qg$685@comet.EMBL-Heidelberg.DE>
References: <3lcjfm$di1@usenet.ucs.indiana.edu>
NNTP-Posting-Host: phenix.embl-heidelberg.de
gilbertd@sunflower.bio.indiana.edu (Don Gilbert) wrote:
>
> Has anyone seen this kind of failure using SRS?
>
> sunflower% getz '[prosite-def:tubulin] > prositedoc'
> Bus error
>
>
> This bus error happens whenever I try a ">" query that should work.
> getz w/o a ">" works. This happens on two Sun Sparcs with SunOS 4.1.3,
> using gcc compiler v2.6.2. It does not happen on a Sun Sparc
> with Solaris 2 using Sun's CC compiler. I've tried this with
> clean releases of srs_4.0, 4.02 and 4.03, with links between
> swissprot & prosite, with links b/n prosite & prositedoc, &
> with rebase, and links with genbank, etc. All give the same problem.
>
we have sunos 4.1.3 and gcc 2.5.8 ...and the above query works
with srs4.03
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
URL: http://www.embl-heidelberg.de/srs/srsc |
From owner-srs@net.bio.net Wed Mar 29 23:00:00 1995
Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!cs.utexas.edu!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: on my SunOS4 w/ gcc 2.6.2, "query > newlib" gives bus error
Date: 29 Mar 1995 21:29:26 GMT
Organization: Biology, Indiana University - Bloomington
Lines: 24
Message-ID: <3lcjfm$di1@usenet.ucs.indiana.edu>
NNTP-Posting-Host: sunflower.bio.indiana.edu
Has anyone seen this kind of failure using SRS?
sunflower% getz '[prosite-def:tubulin] > prositedoc'
Bus error
This bus error happens whenever I try a ">" query that should work.
getz w/o a ">" works. This happens on two Sun Sparcs with SunOS 4.1.3,
using gcc compiler v2.6.2. It does not happen on a Sun Sparc
with Solaris 2 using Sun's CC compiler. I've tried this with
clean releases of srs_4.0, 4.02 and 4.03, with links between
swissprot & prosite, with links b/n prosite & prositedoc, &
with rebase, and links with genbank, etc. All give the same problem.
If someone has this working on a Sun Sparc/Sunos4.1.3 with some
version of gcc, I might suspect the version of gcc I have installed.
Thanks, Don
PS. After some quick modifications last weekend I have SRS working
on Macintoshes.
--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu
From owner-srs@net.bio.net Wed Mar 29 23:00:00 1995
Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!news1.channel1.com!news.channel1.com!channel1!chuck.frieser
Distribution: world
Newsgroups: bionet.software.srs
Subject: Attention Shareware Autho
From: chuck.frieser@channel1.com (Chuck Frieser)
Message-ID: <40.3.3179@channel1.com>
Date: Mon, 27 Mar 1995 22:38:00 -0500
Organization: Channel 1(R) 617-864-0100 Info
Lines: 76
Second Annual Ziff-Davis Shareware Awards
*** DEADLINE: APRIL 1, 1995 ***
Attention all shareware authors! Ziff-Davis Interactive (ZDI),
PC Magazine, Computer Life and Computer Gaming World are
sponsoring the second annual Ziff-Davis Shareware Awards,
honoring the best PC-based shareware written or significantly
upgraded between June 1, 1994 and April 1, 1995.
The awards will be presented at a banquet during this year's
Summer Shareware Seminar. Judges for the awards will include
editors from the sponsoring magazines and Ziff-Davis Interactive.
Ziff-Davis Shareware Award winning programs will be featured in
special editorial coverage by the sponsoring magazine. The
winning programs will also be posted in highly visible sections
of the software libraries on ZiffNet and Interchange Computing.
Authors who want to submit their shareware for the awards can
enter by posting their programs in a special section of the
Ziff-Davis Interactive Author Upload Center or by mailing
the submissions on disk. Submissions will be accepted beginning
on February 1, 1995. The submission deadline is April 1, 1995.
Finalists will be announced on April 15, 1995.
INSTRUCTIONS FOR SUBMITTING YOUR PROGRAMS
A special section of Ziff-Davis Interactive's Author
Upload Center has been established to allow authors
to submit their programs electronically. To send your
programs, just dial:
1-800-426-3425
8 lines/2400-28.8k baud/24 hour access
Follow the instructions on-screen to upload your program.
The deadline for all submissions is midnight April 1, 1995.
International callers can send their products for entry
by calling the Author Upload Center BBS (617) 252-5510
or sending disk-based material to:
ZDI Shareware Awards
25 First St.
Cambridge, Ma. 02141
Submission Criteria:
- All entries must be shareware programs first released
or significantly upgraded between June 1, 1994 and
April 1, 1995.
- All programs must be compressed using PKZip v2.04g.
- All entries must be in a single package: please do
not upload multi-part ZIPs (such as FILEA.ZIP, FILEB.ZIP,
FILEC.ZIP, etc.).
- Please submit the unregistered evaluation version
of your program.
Problems? Questions?
If you are having difficulty uploading your submission,
or have questions about the Ziff-Davis Shareware Awards,
please call our Shareware Author Hotline at (617) 252-5527.
Mail-In Submissions
For directions on submitting your programs by mail, please
call our Shareware Author Hotline at (617) 252-5527.
From owner-srs@net.bio.net Wed Mar 29 23:00:00 1995
Path: biosci!daresbury!trane.uninett.no!nac.no!nntp.uio.no!xyplex13
From: rodrigol@biotek.uio.no (Rodrigo Lopez)
Newsgroups: bionet.software.srs
Subject: SRS on Mac and PC
Date: 30 Mar 1995 19:29:11 GMT
Organization: Norwegian EMBnet node
Lines: 10
Message-ID: <3lf0q7$j6v@hermod.uio.no>
NNTP-Posting-Host: xyplex13.uio.no
X-Newsreader: News Xpress Version 1.0 Beta #3
Having read Don's short message stating he's got SRS working on Mac I would
like to inquire further about it. Would Don be so kind as to provide the
readership with some background/details about his SRS on the Mac. Perhaps,
Thure could let us know about on-going work to get SRS to work on PC's too?
These are very exciting improvements!
R:)
From owner-srs@net.bio.net Thu Mar 30 23:00:00 1995
Path: biosci!daresbury!bioftp.unibas.ch!ubaclu.unibas.ch!doelz
From: doelz@ubaclu.unibas.ch (R.Doelz,Biocomputing Basel;+41 61 267 22 47)
Newsgroups: bionet.software.srs
Subject: Re: SRS on Mac and PC
Message-ID: <1995Mar31.214143.44651@yogi.urz.unibas.ch>
Date: 31 Mar 95 21:41:43 MET
References: <3lf0q7$j6v@hermod.uio.no> <3lfgbr$lbs@usenet.ucs.indiana.edu>
Organization: University of Basel, Switzerland
Lines: 8
In article <3lfgbr$lbs@usenet.ucs.indiana.edu>, gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes:
> I have all of Thure's SRS software running on a mac.
Don,
which configuration/compiler was used? I'd be interested in Think C.
Regards
Reinhard
From owner-srs@net.bio.net Thu Mar 30 23:00:00 1995
Path: biosci!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!clpd-newsserver!news.sprintlink.net!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Newsgroups: bionet.software.srs
Subject: Re: SRS on Mac and PC
Date: 30 Mar 1995 23:54:35 GMT
Organization: Biology, Indiana University - Bloomington
Lines: 43
Message-ID: <3lfgbr$lbs@usenet.ucs.indiana.edu>
References: <3lf0q7$j6v@hermod.uio.no>
NNTP-Posting-Host: sunflower.bio.indiana.edu
I have all of Thure's SRS software running on a mac.
Most of the changes for this were minor. In fact, it didn't
have the query bug that my Sun system did.
I did a quick hack to get this working which involved compiling
in fixed paths to data. To make this system usable on some one
else's mac w/o recompiling or renaming hard disks, I'll put something
else in. With a bit more effort, it will be possible to have
"getz" working well enough that one could use a Mac file server
w/ all of the biology databanks that SRS supports, and a set of
indexes, and have all the functionality of "getz".
The "odd" and "srsbuild" functions both work properly -- one
can build a full set of srs indices on a mac. But one can also
transfer indices from another system and have them work right (as
I did from Sun to Mac). "wgetz" does properly spit out HTML versions
of the data.
I don't yet see a good way of having "wgetz" functionalilty running t
his on a Mac -- that would involve rewriting an HTML browser to
work with "wgetz". As far as I know there isn't yet any standard
way of doing HTML forms between two programs on a Mac or PC,
which is what would be needed for this latter. But the "getz"
searching functionality would be a useful way to make bio
databases available in non-Internet settings.
When will these changes be available to the public? It will be a little
while yet till I can get back to this (a week at least). But as soon
as I can, it will be available to the rest of you.
-- Don
P.S., SRS doesn't seem to do quite as good a job as WAIS in finding all
matches for some simple queries of SwissProtein, and probably also
GenBank/other data. I hope to do some more comparison testing soon, and
to see if the problem areas can be tracked down. It may be only a
matter of writing those odd sdl definitions better (e.g., many matches
were lost because the comment field wasn't indexed in the swissprot.sdl
I used at first, and the "AllText" index I used didn't really search
all the other indices).
--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet
From: Thure Etzold
Newsgroups: bionet.software.srs
Subject: SRS release 4.04
Date: 31 Mar 1995 16:08:30 GMT
Organization: EMBL Heidelberg
Lines: 39
Distribution: world
Message-ID: <3lh9du$ijc@comet.EMBL-Heidelberg.DE>
NNTP-Posting-Host: phenix.embl-heidelberg.de
I just finished the release SRS4.04. login as ftp on
felix.embl-heidelberg.de
and get the file
pub/software/unix/srs/srs4_04.tar.gz
there are only some minor changes ...including the fix for
the problem don gilbert had on sunos.
No ODD file has changed except "expression.sdl" ...for those who
want to upgrade their system.
here is some lists of changes between srs4_03 and srs4_04:
1995/03/22
fixed a problem that occurs when indexing the embl feature table.
IDSxTMPSETSIZE is exceeded - the set grows now dynamically
1995/03/30
Fixed a serious bug in the index caching (this bug occured for the first
time when indexing the embl feature table)
1995/03/30
fixed a few problems when extracting sequence features when begin and end
positions are shifted
1995/03/30
fixed the problem that links crash on some combination of gcc compiler and
sunos
1995/03/30
some changes in the documentation
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 Fri Mar 31 23:00:00 1995
Path: biosci!agate!library.ucla.edu!csulb.edu!csus.edu!news.starnet.net!wupost!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: Re: SRS on Mac and PC
Date: 1 Apr 1995 00:36:28 GMT
Organization: Biology, Indiana University - Bloomington
Lines: 17
Message-ID: <3li76c$285@usenet.ucs.indiana.edu>
References: <3lf0q7$j6v@hermod.uio.no> <3lfgbr$lbs@usenet.ucs.indiana.edu> <1995Mar31.214143.44651@yogi.urz.unibas.ch>
NNTP-Posting-Host: sunflower.bio.indiana.edu
>which configuration/compiler was used? I'd be interested in Think C.
CodeWarrior, of course.
There is a compiler-dependent trick involved in getting this to
work right on Macs. Mac and Unix are at odds about what a newline
character is: 0x0D on a Mac, and 0x0A on Unix. I had problems until
I use a compiler switch for Codewarrior, which is also standard w/
MPW, to make 0x0d == '\n'. You also have to link w/ libraries in
Codewarrior built /w this option, which wasn't available until CW version 5.
Last time I used Think C, it didn't have a newline option like this.
You could still get SRS to work but you would have to make all the
data & sdl files have 0x0A as newlines, and they wouldn't look good
in standard mac editors.
--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!RRZ.Uni-Koeln.DE!usenet
From: Joerg Sprengel
Newsgroups: bionet.software.srs,bionet.software.general
Subject: SRS ODD archive?
Date: 31 Mar 1995 15:50:14 GMT
Organization: Regional Computing Center, University of Cologne
Lines: 51
Message-ID: <3lh8bm$1as@news.rrz.uni-koeln.de>
NNTP-Posting-Host: gz.genetik.uni-koeln.de
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 7bit
To: sprengel@scan.genetik.uni-koeln.de
X-URL: news:bionet.software.srs
Dear SRS maintainers/users/programmers/lovers/...
two weeks ago I have posted a question about a (non)existing SRS sdl/odd
archive; unfortunately with little response.
Anyway I will ask the question again:
--------- more or less cited from the previous posting ----
It seems to me, that with the increasing interest in SRS and more
programmers writing their own sdl definitions, it becomes really
difficult to incorporate new definitions in a "running" installation.
Thure also confirmed that the situation tends to develop in an
"chaotic" direction. Obviously there are no separately maintained
srs-source-xxx.tar and srs-odd.xxx.tar archives available.
What do you think about the idea to maintain such an archive to
prevent the diverging of the definition files?
One could collect all sdl/odd definitions in addition with an
(SHORT) documentation file and kind of a changelog (author,
version, like all these nice gnu programs)? The local
dependencies, like file paths, which are defined in srsdb.sdl
could go into a srsdb.new.sdl to prevent the accidental
overwriting of an existing one. Once in a while one could release
a complete set of definitions and make them available per ftp and
W3 (isn't this U6?), and SRS form itself.
------------
Yes I saw Peter Rice's posting about the info collected and provided at
http://www.sanger.ac.uk/srs/....
What I'm looking for is a tar'red archive of all (?) ODDs of databases
currently available AND usable 'out of the box'. The local maintainer
should define the local databases and where they can be found and
voil`a the systems runs fine. I have had some problems in fetching
sdl Files conflicting with the local sdl's (hypertext.sdl).
Is there any
-x- Interest in this?
-x- Need to maintain such an archiv?
-x- Did I missed something?
Greetings,
//
Jorg
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!RRZ.Uni-Koeln.DE!usenet
From: Joerg Sprengel
Newsgroups: bionet.software.srs,bionet.software.general
Subject: SRS ODD archive?
Date: 31 Mar 1995 15:48:56 GMT
Organization: Regional Computing Center, University of Cologne
Lines: 51
Message-ID: <3lh898$1as@news.rrz.uni-koeln.de>
NNTP-Posting-Host: gz.genetik.uni-koeln.de
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 7bit
To: sprengel@scan.genetik.uni-koeln.de
X-URL: news:bionet.software.srs
Dear SRS maintainers/users/programmers/lovers/...
two weeks ago I have posted a question about a (non)existing SRS sdl/odd
archive; unfortunately with little response.
Anyway I will ask the question again:
--------- more or less cited from the previous posting ----
It seems to me, that with the increasing interest in SRS and more
programmers writing their own sdl definitions, it becomes really
difficult to incorporate new definitions in a "running" installation.
Thure also confirmed that the situation tends to develop in an
"chaotic" direction. Obviously there are no separately maintained
srs-source-xxx.tar and srs-odd.xxx.tar archives available.
What do you think about the idea to maintain such an archive to
prevent the diverging of the definition files?
One could collect all sdl/odd definitions in addition with an
(SHORT) documentation file and kind of a changelog (author,
version, like all these nice gnu programs)? The local
dependencies, like file paths, which are defined in srsdb.sdl
could go into a srsdb.new.sdl to prevent the accidental
overwriting of an existing one. Once in a while one could release
a complete set of definitions and make them available per ftp and
W3 (isn't this U6?), and SRS form itself.
------------
Yes I saw Peter Rice's posting about the info collected and provided at
http://www.sanger.ac.uk/srs/....
What I'm looking for is a tar'red archive of all (?) ODDs of databases
currently available AND usable 'out of the box'. The local maintainer
should define the local databases and where they can be found and
voil`a the systems runs fine. I have had some problems in fetching
sdl Files conflicting with the local sdl's (hypertext.sdl).
Is there any
-x- Interest in this?
-x- Need to maintain such an archiv?
-x- Did I missed something?
Greetings,
//
Jorg
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!RRZ.Uni-Koeln.DE!usenet
From: Joerg Sprengel
Newsgroups: bionet.software.srs,bionet.software.general
Subject: SRS ODD archive?
Date: 31 Mar 1995 15:47:57 GMT
Organization: Regional Computing Center, University of Cologne
Lines: 51
Message-ID: <3lh87d$1as@news.rrz.uni-koeln.de>
NNTP-Posting-Host: gz.genetik.uni-koeln.de
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 7bit
To: sprengel@scan.genetik.uni-koeln.de
X-URL: news:bionet.software.srs
Dear SRS maintainers/users/programmers/lovers/...
two weeks ago I have posted a question about a (non)existing SRS sdl/odd
archive; unfortunately with little response.
Anyway I will ask the question again:
--------- more or less cited from the previous posting ----
It seems to me, that with the increasing interest in SRS and more
programmers writing their own sdl definitions, it becomes really
difficult to incorporate new definitions in a "running" installation.
Thure also confirmed that the situation tends to develop in an
"chaotic" direction. Obviously there are no separately maintained
srs-source-xxx.tar and srs-odd.xxx.tar archives available.
What do you think about the idea to maintain such an archive to
prevent the diverging of the definition files?
One could collect all sdl/odd definitions in addition with an
(SHORT) documentation file and kind of a changelog (author,
version, like all these nice gnu programs)? The local
dependencies, like file paths, which are defined in srsdb.sdl
could go into a srsdb.new.sdl to prevent the accidental
overwriting of an existing one. Once in a while one could release
a complete set of definitions and make them available per ftp and
W3 (isn't this U6?), and SRS form itself.
------------
Yes I saw Peter Rice's posting about the info collected and provided at
http://www.sanger.ac.uk/srs/....
What I'm looking for is a tar'red archive of all (?) ODDs of databases
currently available AND usable 'out of the box'. The local maintainer
should define the local databases and where they can be found and
voil`a the systems runs fine. I have had some problems in fetching
sdl Files conflicting with the local sdl's (hypertext.sdl).
Is there any
-x- Interest in this?
-x- Need to maintain such an archiv?
-x- Did I missed something?
Greetings,
//
Jorg
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!daresbury!sunsite.doc.ic.ac.uk!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet
From: Thure Etzold
Newsgroups: bionet.software.srs
Subject: Re: SRS on Mac and PC
Date: 31 Mar 1995 15:46:50 GMT
Organization: EMBL Heidelberg
Lines: 23
Distribution: world
Message-ID: <3lh85a$ijc@comet.EMBL-Heidelberg.DE>
References: <3lf0q7$j6v@hermod.uio.no>
NNTP-Posting-Host: phenix.embl-heidelberg.de
rodrigol@biotek.uio.no (Rodrigo Lopez) wrote:
>
>
> Having read Don's short message stating he's got SRS working on Mac I would
> like to inquire further about it. Would Don be so kind as to provide the
> readership with some background/details about his SRS on the Mac. Perhaps,
> Thure could let us know about on-going work to get SRS to work on PC's too?
>
> These are very exciting improvements!
>
> R:)
>
John Smith at the EBI is working with the SRS software on a pc. He
uses the (32bit) whatcom compiler. There are compiler flags for
the pc in the distributed software but NO makefiles ...so please
ask me or john (smith@ebi.ac.uk) if you want to start on the pc ...
another idea would be to modify the makefiles for unix
Thure
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!daresbury!sunsite.doc.ic.ac.uk!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet
From: Thure Etzold
Newsgroups: bionet.software.srs
Subject: Re: SRS on Mac and PC
Date: 31 Mar 1995 15:41:58 GMT
Organization: EMBL Heidelberg
Lines: 41
Distribution: world
Message-ID: <3lh7s6$ijc@comet.EMBL-Heidelberg.DE>
References: <3lf0q7$j6v@hermod.uio.no> <3lfgbr$lbs@usenet.ucs.indiana.edu>
NNTP-Posting-Host: phenix.embl-heidelberg.de
gilbertd@sunflower.bio.indiana.edu (Don Gilbert) wrote:
>
>
> The "odd" and "srsbuild" functions both work properly -- one
> can build a full set of srs indices on a mac. But one can also
> transfer indices from another system and have them work right (as
> I did from Sun to Mac). "wgetz" does properly spit out HTML versions
> of the data.
>
great! did you compile with a 32bit compiler?
The indices are platform independent so once built they
can be used on any operating system
> I don't yet see a good way of having "wgetz" functionalilty running t
> his on a Mac -- that would involve rewriting an HTML browser to
> work with "wgetz". As far as I know there isn't yet any standard
> way of doing HTML forms between two programs on a Mac or PC,
I don't understand that ..all you would need is a httpd on the mac that
talks to wgetz?
> P.S., SRS doesn't seem to do quite as good a job as WAIS in finding all
> matches for some simple queries of SwissProtein, and probably also
> GenBank/other data. I hope to do some more comparison testing soon, and
> to see if the problem areas can be tracked down. It may be only a
> matter of writing those odd sdl definitions better (e.g., many matches
> were lost because the comment field wasn't indexed in the swissprot.sdl
> I used at first, and the "AllText" index I used didn't really search
> all the other indices).
can you send me the queries you have done? there should be really
no difference ...and if there is it can be all configured.
Alltext is a virtual data-field, ie, a group of indices that will
be all searched - those index groups can be added and modified -
the Alltext field is defined in srsgeneral.sdl - other data-fields
that want to be part of Alltext must point to the Alltext definition
..and yes, i should index the comment data-field in swissprot
thure
From owner-srs@net.bio.net Fri Mar 31 23:00:00 1995
Path: biosci!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!clpd-newsserver!news.sprintlink.net!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!RRZ.Uni-Koeln.DE!usenet
From: Joerg Sprengel
Newsgroups: bionet.software.srs,bionet.software.general
Subject: SRS SDL ODD archive?
Date: 31 Mar 1995 15:57:20 GMT
Organization: Regional Computing Center, University of Cologne
Lines: 56
Message-ID: <3lh8p0$1as@news.rrz.uni-koeln.de>
NNTP-Posting-Host: gz.genetik.uni-koeln.de
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 7bit
To: sprengel@scan.genetik.uni-koeln.de
X-URL: news:bionet.software.srs
Dear SRS maintainers/users/programmers/lovers/...
two weeks ago I have posted a question about a (non)existing SRS sdl/odd
archive; unfortunately with little response.
Anyway I will ask the question again:
--------- more or less cited from the previous posting ----
It seems to me, that with the increasing interest in SRS and more
programmers writing their own sdl definitions, it becomes really
difficult to incorporate new definitions in a "running" installation.
Thure also confirmed that the situation tends to develop in an
"chaotic" direction. Obviously there are no separately maintained
srs-source-xxx.tar and srs-odd.xxx.tar archives available.
What do you think about the idea to maintain such an archive to
prevent the diverging of the definition files?
One could collect all sdl/odd definitions in addition with an
(SHORT) documentation file and kind of a changelog (author,
version, like all these nice gnu programs)? The local
dependencies, like file paths, which are defined in srsdb.sdl
could go into a srsdb.new.sdl to prevent the accidental
overwriting of an existing one. Once in a while one could release
a complete set of definitions and make them available per ftp and
W3 (isn't this U6?), and SRS form itself.
------------
Yes I saw Peter Rice's posting about the info collected and provided at
http://www.sanger.ac.uk/srs/....
What I'm looking for is a tar'red archive of all (?) ODDs of databases
currently available AND usable 'out of the box'. The local maintainer
should define the local databases and where they can be found
in srsdb.sdl, a global switch decides whether one would like to index
just everything, what system one uses VMS/U*ix/PC/MAC (filenames) and
voil`a the systems runs fine. I have had some problems in fetching
sdl Files conflicting with the local sdl's (hypertext.sdl).
Is there any
-x- Interest in this?
-x- Need to maintain such an archiv?
-x- Suggestions?
-x- Did I missed something?
Greetings,
//
Jorg