From owner-srs@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs,bionet.software.general Subject: Re: SRS ODD archive? Date: 5 Apr 1995 11:00:17 GMT Organization: EMBL Heidelberg Lines: 51 Distribution: world Message-ID: <3ltt81$btp@comet.EMBL-Heidelberg.DE> References: <3lh8bm$1as@news.rrz.uni-koeln.de> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b2 (X11; I; IRIX 5.2 IP20) To: sprengel@scan.genetik.uni-koeln.de X-URL: news:3lh8bm$1as@news.rrz.uni-koeln.de joerg, > >two weeks ago I have posted a question about a (non)existing SRS sdl/odd >archive; unfortunately with little response. > Archiving all existing ODD files is not an easy task since these files reflect the structure of the databank but also the requirements of the site ...so the file embl.sdl looks different for sites where the embl databank is stored in the native format or as gcg format ...the fileType object as well as all file names are different ...but it is also a matter of taste ...some sites, such as the ebi prefer to have qualifier names itself in the "features" index ...which makes the index much bigger. There exist also several ways to parse and index individual data-fields; eg, the 'OC' field can be indexed using 'whole' taxa or broken up to all words separated by nonalphabetical characters Well, i don't really know if people do this kind of customizing a lot but theoretically it should be an obstacle towards a central archive. ..to be sure I am in favour of an archive! I posted a short reply to this topic some time ago mentioning experiments to use RCS as a base system for this archive ...this system is now nearing completion - it is a WWW front end to RCS commands that will allow users to display the list of all files in the archive with all their versions. It allows the user to see the revision comment for every version as well as see the differences between a pair of two versions. Using mime types users will be enable to conveniently copy versions to local directories as well as check in files from local directories - so anybody can participate in the maintenance of this archive. I will make an announcement when this system becomes available for testing! 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 Apr 04 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: emnew in status.html Message-ID: <1995Apr5.061433.7515@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 5 Apr 1995 06:14:33 GMT Lines: 33 [to all srswww managers] Colleagues, Reading http://www.embl-heidelberg.de/srs/status.html EMNEW BEN, Brussels | | 44105 | 04-Apr-1995 | ?! BMC, Uppsala, Sweden | | 4128 | 02-Apr-1995 | ?! BiO, Oslo | 43.0 | 18990 | 04-Apr-1995 | ?! Biozentrum, Basel | | 29440 | 04-Apr-1995 | ?! CAOS/CAMM, Nijmegen | | 20 | 03-Apr-1995 | ?! CSC, Finland | 43.0 | 18990 | 03-Apr-1995 | ?! EBI, Hinxton, UK | | 29440 | 03-Apr-1995 | ?! EMBL, Heidelberg | | 40894 | 04-Apr-1995 | ?! INSERM, France | | 44105 | 04-Apr-1995 | ?! Sanger, Hinxton, UK | 43.0 | 29440 | 03-Apr-1995 | ?! Skirbal Inst., NY | | 44105 | 03-Apr-1995 | ?! I get the impression that there are two different parties going along; one being the BiO/CSC/Biozentrum/EBI/Sanger fraction with around 30K entries and one being BEN/EMBL/INSERM/Skirbal. I would suspect that the latter mirrors data from EMBL, and the first mirrors data from EBI. May I kindly ask what duplication occured? Regards Reinhard BEN/ -- 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 Apr 04 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!rodrigol From: rodrigol@bioslave.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: Re: emnew in status.html Date: 5 Apr 1995 10:30:16 GMT Organization: University of Oslo Lines: 36 Message-ID: <3ltrfo$aq6@hermod.uio.no> References: <1995Apr5.061433.7515@comp.bioz.unibas.ch> NNTP-Posting-Host: bioslave.uio.no X-Newsreader: TIN [version 1.2 PL2] Reinhard Doelz (doelz@comp.bioz.unibas.ch) wrote: : [to all srswww managers] : Colleagues, : Reading http://www.embl-heidelberg.de/srs/status.html : EMNEW : BEN, Brussels | | 44105 | 04-Apr-1995 | ?! : BMC, Uppsala, Sweden | | 4128 | 02-Apr-1995 | ?! : BiO, Oslo | 43.0 | 18990 | 04-Apr-1995 | ?! : Biozentrum, Basel | | 29440 | 04-Apr-1995 | ?! : CAOS/CAMM, Nijmegen | | 20 | 03-Apr-1995 | ?! : CSC, Finland | 43.0 | 18990 | 03-Apr-1995 | ?! : EBI, Hinxton, UK | | 29440 | 03-Apr-1995 | ?! : EMBL, Heidelberg | | 40894 | 04-Apr-1995 | ?! : INSERM, France | | 44105 | 04-Apr-1995 | ?! : Sanger, Hinxton, UK | 43.0 | 29440 | 03-Apr-1995 | ?! : Skirbal Inst., NY | | 44105 | 03-Apr-1995 | ?! : I get the impression that there are two different parties going along; : one being the BiO/CSC/Biozentrum/EBI/Sanger fraction with around 30K entries : and one being BEN/EMBL/INSERM/Skirbal. I would suspect that the latter : mirrors data from EMBL, and the first mirrors data from EBI. May I kindly : ask what duplication occured? Actually, you are quite right about two different sites being mirrored. In the process several things happen which do not allow for syncrony between the major sites (EBI, EMBL) and the rest. BiO, for example, mirrors the database at 0200 hours (local time). During the past two days the process has packed up due to networking problems. Some due to satan and others because of yo-yo routers in the Sweden/Netherlands. I suspect the INSERM, Skirbal and EMBL high numbers are due to double accumulation of data. R:) From owner-srs@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS ODD archive? Date: 5 Apr 1995 11:00:35 GMT Organization: EMBL Heidelberg Lines: 51 Distribution: world Message-ID: <3ltt8j$btp@comet.EMBL-Heidelberg.DE> References: <3lh8bm$1as@news.rrz.uni-koeln.de> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b2 (X11; I; IRIX 5.2 IP20) To: sprengel@scan.genetik.uni-koeln.de X-URL: news:3lh8bm$1as@news.rrz.uni-koeln.de joerg, > >two weeks ago I have posted a question about a (non)existing SRS sdl/odd >archive; unfortunately with little response. > Archiving all existing ODD files is not an easy task since these files reflect the structure of the databank but also the requirements of the site ...so the file embl.sdl looks different for sites where the embl databank is stored in the native format or as gcg format ...the fileType object as well as all file names are different ...but it is also a matter of taste ...some sites, such as the ebi prefer to have qualifier names itself in the "features" index ...which makes the index much bigger. There exist also several ways to parse and index individual data-fields; eg, the 'OC' field can be indexed using 'whole' taxa or broken up to all words separated by nonalphabetical characters Well, i don't really know if people do this kind of customizing a lot but theoretically it should be an obstacle towards a central archive. ..to be sure I am in favour of an archive! I posted a short reply to this topic some time ago mentioning experiments to use RCS as a base system for this archive ...this system is now nearing completion - it is a WWW front end to RCS commands that will allow users to display the list of all files in the archive with all their versions. It allows the user to see the revision comment for every version as well as see the differences between a pair of two versions. Using mime types users will be enable to conveniently copy versions to local directories as well as check in files from local directories - so anybody can participate in the maintenance of this archive. I will make an announcement when this system becomes available for testing! 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 Apr 04 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS ODD archive? Date: 5 Apr 1995 11:20:17 GMT Organization: EMBL Heidelberg Lines: 5 Distribution: world Message-ID: <3ltudh$btp@comet.EMBL-Heidelberg.DE> References: <3lh8bm$1as@news.rrz.uni-koeln.de> <3ltt9b$btp@comet.EMBL-Heidelberg.DE> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b2 (X11; I; IRIX 5.2 IP20) X-URL: news:3ltt9b$btp@comet.EMBL-Heidelberg.DE ..oh no ...now the same happened too me ...this time netscape played tricks on me...sorry! Thure From owner-srs@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS ODD archive? Date: 5 Apr 1995 11:00:59 GMT Organization: EMBL Heidelberg Lines: 51 Distribution: world Message-ID: <3ltt9b$btp@comet.EMBL-Heidelberg.DE> References: <3lh8bm$1as@news.rrz.uni-koeln.de> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b2 (X11; I; IRIX 5.2 IP20) X-URL: news:3lh8bm$1as@news.rrz.uni-koeln.de joerg, > >two weeks ago I have posted a question about a (non)existing SRS sdl/odd >archive; unfortunately with little response. > Archiving all existing ODD files is not an easy task since these files reflect the structure of the databank but also the requirements of the site ...so the file embl.sdl looks different for sites where the embl databank is stored in the native format or as gcg format ...the fileType object as well as all file names are different ...but it is also a matter of taste ...some sites, such as the ebi prefer to have qualifier names itself in the "features" index ...which makes the index much bigger. There exist also several ways to parse and index individual data-fields; eg, the 'OC' field can be indexed using 'whole' taxa or broken up to all words separated by nonalphabetical characters Well, i don't really know if people do this kind of customizing a lot but theoretically it should be an obstacle towards a central archive. ..to be sure I am in favour of an archive! I posted a short reply to this topic some time ago mentioning experiments to use RCS as a base system for this archive ...this system is now nearing completion - it is a WWW front end to RCS commands that will allow users to display the list of all files in the archive with all their versions. It allows the user to see the revision comment for every version as well as see the differences between a pair of two versions. Using mime types users will be enable to conveniently copy versions to local directories as well as check in files from local directories - so anybody can participate in the maintenance of this archive. I will make an announcement when this system becomes available for testing! 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 Apr 04 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS ODD archive? Date: 5 Apr 1995 11:00:47 GMT Organization: EMBL Heidelberg Lines: 51 Distribution: world Message-ID: <3ltt8v$btp@comet.EMBL-Heidelberg.DE> References: <3lh8bm$1as@news.rrz.uni-koeln.de> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b2 (X11; I; IRIX 5.2 IP20) To: sprengel@scan.genetik.uni-koeln.de X-URL: news:3lh8bm$1as@news.rrz.uni-koeln.de joerg, > >two weeks ago I have posted a question about a (non)existing SRS sdl/odd >archive; unfortunately with little response. > Archiving all existing ODD files is not an easy task since these files reflect the structure of the databank but also the requirements of the site ...so the file embl.sdl looks different for sites where the embl databank is stored in the native format or as gcg format ...the fileType object as well as all file names are different ...but it is also a matter of taste ...some sites, such as the ebi prefer to have qualifier names itself in the "features" index ...which makes the index much bigger. There exist also several ways to parse and index individual data-fields; eg, the 'OC' field can be indexed using 'whole' taxa or broken up to all words separated by nonalphabetical characters Well, i don't really know if people do this kind of customizing a lot but theoretically it should be an obstacle towards a central archive. ..to be sure I am in favour of an archive! I posted a short reply to this topic some time ago mentioning experiments to use RCS as a base system for this archive ...this system is now nearing completion - it is a WWW front end to RCS commands that will allow users to display the list of all files in the archive with all their versions. It allows the user to see the revision comment for every version as well as see the differences between a pair of two versions. Using mime types users will be enable to conveniently copy versions to local directories as well as check in files from local directories - so anybody can participate in the maintenance of this archive. I will make an announcement when this system becomes available for testing! 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 Sun Apr 09 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Subject: ...getting out what I want... Message-ID: <1995Apr10.111606.18518@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Mon, 10 Apr 1995 11:16:06 GMT Lines: 19 Hi! I am familiar with both versions of SRS: command line and HTTP. During my work with it it became obvious that the features are not identical and that, in fact, only combination of the two would allow me to get what I want from that program. The problem that I face is a simple one: - get out all sequences that contain a signal peptide- only the ACTUAL feature - put it in GCG and do some things on it. The troubles are (for command line interface) - if I do something wrong (like asking FEATURE and PIR- it has no feature field) the program mercilessly crashes (core dump etc.) - I cannot do q1-organism and q2-feature - I cannot do AllText search - some other minor things For the HTTP interface: - I can do all above (except for the q1-organism and q2-feature) - BUT I cannot save my results in a file. What I want is all my seqs- FEATURES ONLY- as a file. One can do it in the command line interface but not HTTP. So, if there is anyone that can help me, please do not hesitate to do so |:) Przemko From owner-srs@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!news.hgmp.mrc.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: ...getting out what I want... Date: 10 Apr 1995 16:00:39 GMT Organization: MRC Human Genome Resource Centre Lines: 80 Message-ID: References: <1995Apr10.111606.18518@reks.uia.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: przemko@reks.uia.ac.be's message of Mon, 10 Apr 1995 11:16:06 GMT In article <1995Apr10.111606.18518@reks.uia.ac.be> przemko@reks.uia.ac.be (Przemko) writes: > I am familiar with both versions of SRS: command line and HTTP. > During my work with it it became obvious that the features are not > identical and that, in fact, only combination of the two would allow > me to get what I want from that program. > The problem that I face is a simple one: > - get out all sequences that contain a signal peptide- only the > ACTUAL feature > - put it in GCG and do some things on it. > The troubles are (for command line interface) > - if I do something wrong (like asking FEATURE and PIR- it has no > feature field) the program mercilessly crashes (core dump etc.) > - I cannot do q1-organism and q2-feature > - I cannot do AllText search > - some other minor things > For the HTTP interface: > - I can do all above (except for the q1-organism and q2-feature) > - BUT I cannot save my results in a file. What I want is all my > seqs- FEATURES ONLY- as a file. One can do it in the command line > interface but not HTTP. > So, if there is anyone that can help me, please do not hesitate > to do so |:) Well, the command line part is in the documentation. You can't use set operators, but you can link the sets to get the result you want. This should be enough to get you started. I also was unable to use "alltext" or "all" from the command line. :Entries and Subentries : :Sets originating from the same databank may have different set types. :Consider the two queries: : : [swissprot-keywords: transmembrane] : [swissprot-features: transmem] : :The first query retrieves all SwissProt entries that have transmembrane :segments, the second finds all transmembrane features contained in :SwissProt entries. The second query will retrieve many more entries :since most transmembrane proteins have more than one membrane spanning :segment. If you requested the sequences for entries in the second set :you would get the transmembrane segments and not the parent entry's :sequence. The first query returns a set of entries whereas the second :returns a set of subentries. The "features" index has a special type: :searches in that index will for all sequence databanks result in sets :of subentries. : :Sets of entries and subentries can not combined be with logical operators! :Only the link operators may be used between them, ie, it is always :possible to link subentries to their respective parent entries. : :Example: : : [swissprot-org:human] > [swissprot-features:transmem] : returns all transmembrane segments found in human proteins. : [swissprot-org:human] < [swissprot-features:transmem] : returns all human proteins that have transmembrane segments. And as for the HTTP part,that is trickier and I can't find a complete solution to the problem. I could use "QueryManager" to enter the query directly - as for the command line but without the quotes (OK, it's a cheat :-) But then it only seems to display complete entries and let you click on the features one at a time. Funny thing though - it seems not to care whether I put "organism" or "features" first in a search. When I look at the query it always looks the same: organism > features (but then displays the sequence of the complete entries rather than the features :-) -- ------------------------------------------------------------------------ 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 Mon Apr 10 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: ...getting out what I want... Date: 11 Apr 1995 14:37:54 GMT Organization: EMBL Heidelberg Lines: 51 Distribution: world Message-ID: <3me482$ltr@comet.EMBL-Heidelberg.DE> References: <1995Apr10.111606.18518@reks.uia.ac.be> NNTP-Posting-Host: falcon.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; IRIX 5.2 IP20) X-URL: news:1995Apr10.111606.18518@reks.uia.ac.be przemko@reks.uia.ac.be (Przemko) wrote: >Hi! >I am familiar with both versions of SRS: command line and HTTP. During my work >with it it became obvious that the features are not identical and that, in fact, >only combination of the two would allow me to get what I want from that program. >The problem that I face is a simple one: >- get out all sequences that contain a signal peptide- only the ACTUAL feature >- put it in GCG and do some things on it. >The troubles are (for command line interface) >- if I do something wrong (like asking FEATURE and PIR- it has no feature field) yes that is true ...srs3.1 supports the PIR feature table and srs4.0 doesn't this is because the feature information in PIR is rather scarce and sometimes difficult to read (for a program) ...but in the near future the PIR feature will be fully supported again >the program mercilessly crashes (core dump etc.) >- I cannot do q1-organism and q2-feature peter rice has already explained how to do this on the command line with the WWW server you just specify the words in the organism and feature fields and then select "sequenceFeature" instead of the default "entries" in the second last line of the query form ...click the ?! there to get more information on that >- I cannot do AllText search this is a new feature in srs4 >- some other minor things >For the HTTP interface: >- I can do all above (except for the q1-organism and q2-feature) >- BUT I cannot save my results in a file. What I want is all my seqs- FEATURES >ONLY- as a file. One can do it in the command line interface but not HTTP. you can do it with the srswww too ...do the query as described above and then, on the next page click "view complete entries" ...this gives you the list of found features plus some but not all of the parent entry's annotation 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 Wed Apr 12 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: solved bugs in SRS4.04 Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 13 Apr 1995 11:09:57 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 107 While searching for another (still unresolved) bug, I found 2 small bugs in SRS 4.02 - 4.04 Here's a list of them, plus the way how I solved them. Possibly there are better solutions Jeroen ========================================================================== 1) Description ----------- '>' signs in the SWISSPROT feature table are not translated to '>' e.g. FT VARIANT 42 42 N -> K (IN RABSON-MENDENHALL SYNDROME). FT VARIANT 55 55 V -> A (IN LEPRECHAUNISM VERONA-1). FT VARIANT 58 58 G -> R (IN LEPRECHAUNISM HELMOND; FT INHIBITS PROCESSING AND TRANSPORT). This could generate problems with HTML parsing Solution -------- This conversion has to be made before adding hyperlinks 2 routines are used to print fields : WwwEntryTextPrint (srswww.c) WwwPrintBuff (srswww.c) I added SmSwapS lines to both: The resulting routines are: .................... static void WwwPrintBuff (char *ln) { SmSwapS (ln, ">", ">"); /* JC */ SmSwapS (ln, "<", "<"); /* JC */ strcat (buff, ln); } ..................... static INT4 WwwEntryTextPrint (ENTRYo *entry) { SLBoFIELD *field; INT4 rv; rv = EntryOpenText (entry); _ErrRet (rv); entry->convertLn = SMxMIXCASE; while ((field = EntryNextField (entry, 0, 1))) { if (field != (SLBoFIELD*) 1L) WwwPrintField (entry, 1); else { if (EntryIsEndLine (entry)) break; SmSwapS (entry->file[0]->ln, "%", "%%"); SmSwapS (entry->file[0]->ln, ">", ">"); /* JC */ SmSwapS (entry->file[0]->ln, "<", "<"); /* JC */ WwwPrintF (entry->file[0]->ln); FilURead (entry->file[0]); } } /* print the data part of ...file per entry type entries (eg, pdb) */ if (ParGetNum ("printData") && LibIsFilePerEntry (entry->lib)) do { WwwPrintF (entry->file[0]->ln); rv = FilURead (entry->file[0]); } while (rv != e__eof); return 1; } ========================================================================== 2) Clicking on feature in swissprot entry generates error messages FT VARIANT 42 42 N -> K (IN RABSON-MENDENHALL SYNDROME). Clicking on VARIANT in the above feature returns a parsing error message Solution -------- in expression.sdl, the %SWISSPROT_FEATURE_PARSER does not define '>' as a valid character in the comment Changed rule comment = ~A-Za-z0-9\-_/. ()'~. to comment = ~A-Za-z0-9\-_/. ()'>:,~. Adding '>' ':' and ',' As I have seen these in Swissprot feature comments Possibly other chars should be added. The errors appear on several servers, but not in Heidelberg. So I guess Thure made this change, but forgot to add the new expression.sdl to the new release (or made the change after the last release) -- ============================================================== . 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 Apr 12 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: unresolved bug on OSF1 3.0 Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 13 Apr 1995 11:09:02 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 56 I have an error when retrieving a large swissprot entry from the EBI SRS server. I tried the same on the Sanger, Heidelberg, and Basel servers, and there everything works fine. So I guess this will be system dependent I run SRS4.04 on Alpha OSF1 rel 3.0. Does anyone else have the same configuration? In that case try http://hostname/srs/srsc?[swissprot-id:insr_human]+-sf+embl on your server On my machine, this ends like ... FT WITH INS-RES DIABETES MELLITUS). FT VARIANT 762 762 R -> S (IN INS-RES ACANTHOSIS NIGRICANS). FT VARIANT 1012 1012 V -> M ( Missing part of the feature table and all of the sequence Observations o Problem exists in SRS4_02 and SRS4_04 o Sometimes I get the error message "error parsing mark, bailing out" on the controlling terminal. I have no idea where this comes from o Changing the format to fasta/gcg/swissprot changes the position of the truncation. o Get the same problem with Netscape, Mosaic, lynx Running Mosaic on Alpha with OSF1 3.0 or 3.2 or Decstation with Ultrix does not change the problem. o When running wgetz from the commandline, the full entry is retrieved. Saving this to a file and loading in Mosaic, displays the full entry o Commenting the SWISSPROT_FEATURE hyperlink in hyperlink.sdl does not solve the problem. It even truncates the entry more. o While tracing this problem, I found several other small bugs. I will report the changes in a seperate post. Jeroen -- ============================================================== . 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 Apr 12 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: unresolved bug on OSF1 3.0 Message-ID: <1995Apr13.161517.27339@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: Date: Thu, 13 Apr 1995 16:15:17 GMT Lines: 24 Jeroen Coppieters (jecop@ebi.ac.uk) wrote: : Does anyone else have the same configuration? [...] : Missing part of the feature table and all of the sequence We're not up to OSF/1 3.0 yet but there's a page on http://www.w3.org/hypertext/WWW/Daemon/Bugs.html which tells Problems with OSF/1 Version 3.0 and Scripts for the CERN daemon. Now as you run presumably NCSA server code it might be different but these colleagues claim that there was a problem with SIGPIPE. Maybe that helps. We're currently finalizing the documentation on how to run SRS under CERN code, if this is of interest to somebody in the readership. 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 Wed Apr 12 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: solved bugs in SRS4.04 Date: 13 Apr 1995 21:17:42 GMT Organization: EMBL Heidelberg Lines: 31 Distribution: world Message-ID: <3mk4dm$gta@comet.EMBL-Heidelberg.DE> References: NNTP-Posting-Host: phenix.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b3 (X11; I; IRIX64 6.0.1 IP21) X-URL: news:D6z0CL.IGB@ebi.ac.uk jecop@ebi.ac.uk (Jeroen Coppieters) wrote: >in expression.sdl, the %SWISSPROT_FEATURE_PARSER does not define >'>' as a valid character in the comment >Changed rule > comment = ~A-Za-z0-9\-_/. ()'~. >to > comment = ~A-Za-z0-9\-_/. ()'>:,~. > >Adding '>' ':' and ',' >As I have seen these in Swissprot feature comments >Possibly other chars should be added. >The errors appear on several servers, but not in Heidelberg. So I guess >Thure made this change, but forgot to add the new expression.sdl to the >new release (or made the change after the last release) > yes i made the change two days ago;-) found some more characters to be included into the rule: comment = ~A-Za-z0-9\-_/. ()&?,;:<>+'~. -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: unresolved bug on OSF1 3.0 Date: 13 Apr 1995 21:23:31 GMT Organization: EMBL Heidelberg Lines: 16 Distribution: world Message-ID: <3mk4oj$gta@comet.EMBL-Heidelberg.DE> References: <1995Apr13.161517.27339@comp.bioz.unibas.ch> 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:1995Apr13.161517.27339@comp.bioz.unibas.ch Jeroen Coppieters (jecop@ebi.ac.uk) wrote: >: Does anyone else have the same configuration? we have osf2.0 and similar problem with very large html files - not generated from SRS ...it is quite unreproducible too ...sometimes the files work and sometimes not ...this 'bailing out' sounds very familiar to me. -- =============================================================================== 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 Thu Apr 13 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!news.vub.ac.be!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Subject: srs problems Message-ID: <1995Apr14.123522.17409@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Fri, 14 Apr 1995 12:35:22 GMT Lines: 20 Hi! I really like that software, thank you for making it available. BUT, I still have some problems with it: -if I do q1 & q2 but they do not have anything in common, I get an empty screen (no message or anything else). Considering that the net may be capricious sometimes, I don't know if that is the net or the SRS. -it is enervating that I cannot compare quesries in some, important, cases (q1 is from a feature, q2 form an organism). I know I have talked about it earlier, and got some answers, but in fact WHY IT IS IMPOSSIBLE TO DO IT? WHY THERE ARE RESTRICTIONS? -a funny thing. When I do feature- signal and organism- eukaryota and compare to feature- signal and alltext- bmp (bone morphogenetic protein- all of them have signal peptide and most of them are eukaryotic) and compare results, here is what is happening. One would expect the second query would be a subset of the first one. Well...it is not! In fact on the first list there is not a SINGLE bmp! That makes me worry about the quality of the other searches. Any comments, help, what do I do wrong this time? ThankX Przemko From owner-srs@net.bio.net Tue Apr 18 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Re: unresolved bug on OSF1 3.0 Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Wed, 19 Apr 1995 08:40:38 GMT References: Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 38 Jeroen Coppieters (jecop@ebi.ac.uk) wrote: : I have an error when retrieving a large swissprot entry from the EBI SRS : server. I tried the same on the Sanger, Heidelberg, and Basel servers, : and there everything works fine. So I guess this will be system dependent : I run SRS4.04 on Alpha OSF1 rel 3.0. : Does anyone else have the same configuration? ...[description deleted] ... : Jeroen It was indeed OSF related. I finally tracked down the problem. Reinhard hinted to httpd. So I had a look at that. From the log files I found out that if data was truncated, it was truncated to multiples of 8192 bytes, which is the copy-buffer size used by httpd. So httpd did not send the last, incomplete buffer. After several tests, I found out that on OSF/1 stdout is not flushed on termination of the program. So adding fflush(stdout) statements to each printing routine could solve the problem. I did not want to scan through the code and do this, so I made stdout unbuffered, by adding setbuf(stdout,NULL); to the main() routine of wgetz. This seems to solve the problem. Jeroen -- ============================================================== . 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 Apr 19 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!clpd-newsserver!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!etzold From: etzold@ebi.ac.uk (Thure) Subject: Re: srs problems Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 20 Apr 1995 14:33:29 GMT References: <1995Apr14.123522.17409@reks.uia.ac.be> Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 21 Przemko (przemko@reks.uia.ac.be) wrote: : Hi! : I really like that software, thank you for making it available. BUT, I still : have some problems with it: : -if I do q1 & q2 but they do not have anything in common, I get an empty screen : (no message or anything else). Considering that the net may be capricious : sometimes, I don't know if that is the net or the SRS. : -it is enervating that I cannot compare quesries in some, important, cases (q1 : is from a feature, q2 form an organism). I know I have talked about it earlier, : and got some answers, but in fact WHY IT IS IMPOSSIBLE TO DO IT? WHY THERE ARE : RESTRICTIONS? : -a funny thing. When I do feature- signal and organism- eukaryota and compare to : feature- signal and alltext- bmp (bone morphogenetic protein- all of them have : signal peptide and most of them are eukaryotic) and compare results, here is : what is happening. One would expect the second query would be a subset of the : first one. Well...it is not! In fact on the first list there is not a SINGLE : bmp! : That makes me worry about the quality of the other searches. : Any comments, help, what do I do wrong this time? : ThankX : Przemko From owner-srs@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!bioftp.unibas.ch!comp.bioz.unibas.ch!redaschi Newsgroups: bionet.software.srs Subject: Direct hypertext links from EMBL to MEDLINE Message-ID: <1995Apr21.172332.9432@comp.bioz.unibas.ch> From: redaschi@comp.bioz.unibas.ch (Nicole Redaschi) Date: Fri, 21 Apr 1995 17:23:32 GMT Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Organization: EMBnet Switzerland [Basel] Nntp-Posting-Host: biox.embnet.unibas.ch Lines: 53 For those of you who are interested in having direct hypertext links to MEDLINE in EMBL entries, the following small modifications will do the job: 1. Edit "hyperlink.sdl" ----------------------- Only if MEDLINE is not installed at your site, edit the "#linkcall": #linkcall /id=%FETCH_MEDLINE /call="%s" Add the new "#hyperlink": #hyperlink /field=@EMBL_RX_FIELD /parse=embl_medline /parser=@INSERTLINK_PARSER Add this line to the "#PARSER": embl_medline = 'RX ' 'MEDLINE;' ~0-9~; 2. Edit "embl.sdl" ------------------ Add this "#field" to "#libformat /id=%EMBL_FORMAT ...": #field /gblid=%EMBL_RX_FIELD /itype=key /ftype=@DF_MEDLINELINK /idtype=@SRSxSEQID /find="medlineid" /begstr="RX "/nextstr="RX " /relIndexSize=0.5 Add a new "#link": #link /id=%EMBL_MEDLINE /lib1=@EMBL_DB /lib2=@MEDLINE_DB /type=index /field1=@EMBL_RX_FIELD /field2=@MEDLINE_ID_FIELD /idtype1=@SRSxSEQID /idtype2=@ENTRY_ID Add this line to the "#PARSER": medlineid = ~0-9~ Regards Nicole Redaschi -------------------------------------------------------------------------------- Nicole Redaschi Biocomputing-Biozentrum der Universitaet Basel-Klingelbergstr.70-CH 4056 Basel -------------------------------------------------------------------------------- From owner-srs@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!bioftp.unibas.ch!redaschi Newsgroups: bionet.software.srs Subject: [TEACHING] Installation of SRSWWW under CERN httpd 3.0 - Part 1 Message-ID: <1995Apr24.164445.5407@comp.bioz.unibas.ch> From: redaschi@comp.bioz.unibas.ch (Nicole Redaschi) Date: Mon, 24 Apr 1995 16:44:45 GMT Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Lines: 392 [ Article crossposted from bionet.software.www ] [ Author was Nicole Redaschi ] [ Posted on Mon, 24 Apr 1995 09:21:17 GMT ] ******************************************************************************** Installation of SRSWWW under CERN httpd 3.0 Part 1: Installation of CERN WWW Server ******************************************************************************** This documentation is a "cookbook recipe" for the installation of CERN httpd 3.0 on UNIX platforms using precompiled binaries. It contains step-by-step instructions for the basic (!) setup of the CERN http server. For more detailed informations read the CERN Server Guide (see below). 1. Getting Informations and the Program --------------------------------------- Go to the directory where you want to install the http server (in this example called "WWW"). % cd WWW The CERN server distribution is available from the "ftp.w3.org" anonymous ftp account. At the date of this writing, informations about the CERN http deamon are located in the directory "pub/www/doc": look for the files "cern-httpd-guide.ps.Z" and "cern-httpd-docs.tar.Z" and 'get' them. The first is a PostScript version of the CERN Server User Guide, the second is a directory comprising a set of HTML documents for the WWW version of the Guide. In this example, the WWW version of the Guide will be used to test the successful installation of the server. To get the httpd binaries you have to go to the directory "pub/www/bin". From there, go to the subdirectory corresponding to your machine architecture (eg. "osf1" if you have an osf1 machine), 'get' the files "cern_httpd_3.0.tar.Z" and "cern_httpd_utils_3.0.tar.Z" and 'quit'. % ftp ftp.w3.org Name: anonymous Password: ftp> cd pub/www/doc ftp> ls -lsa ftp> get cern-httpd-guide.ps.Z ftp> get cern-httpd-docs.tar.Z ftp> cd ../bin ftp> ls -lsa ftp> cd osf1 ftp> ls -lsa ftp> get cern_httpd_3.0.tar.Z ftp> get cern_httpd_utils_3.0.tar.Z ftp> quit Uncompress all files and untar the tar files. "cern-httpd-docs.tar.Z" will form the directory "httpd_docs"; "cern_httpd_3.0.tar.Z" together with "cern_httpd_utils_3.0.tar.Z" will form the common directory tree "cern_httpd_3.0". % uncompress cern-httpd-guide.ps.Z % uncompress cern-httpd-docs.tar.Z % uncompress cern_httpd_3.0.tar.Z % uncompress cern_httpd_utils_3.0.tar.Z % tar xvf cern-httpd-docs.tar % tar xvf cern_httpd_3.0.tar % tar xvf cern_httpd_utils_3.0.tar 2. Customizing the http Configuration File ------------------------------------------ In the subdirectory "config" of your new directory "cern_httpd_3.0" you will find example configuration files. Keep the originals and work on a copy! The "httpd.conf" file is for a regular http server, the "caching.conf" file is for a proxy server and has the advantage that it allows caching. Below are examples of customized versions of the "httpd.conf" and "caching.conf" configuration files. The edited parts are given between pairs of wavy lines (#~~~~~~). Follow these examples to customize your configuration file. EXAMPLE ------------------------------ "httpd.conf"-begin ------------------------------ # # Sample configuration file for cern_httpd for running it # as a normal HTTP server. # # See: # # # for more information. # # Written by: # Ari Luotonen April 1994 # # # Set this to point to the directory where you unpacked this # distribution, or wherever you want httpd to have its "home" # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # ServerRoot /where/ever/server_root ServerRoot /AbsolutePath.../WWW/httpd_docs #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # The default port for HTTP is 80; if you are not root you have # to use a port above 1024; good defaults are 8000, 8001, 8080 # Port 80 # # General setup; on some systems, like HP, nobody is defined so # that setuid() fails; in those cases use a different user id. # UserId nobody GroupId nogroup # # Logging; if you want logging uncomment these lines and specify # locations for your access and error logs # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # AccessLog /where/ever/httpd-log AccessLog /AbsolutePath.../WWW/log/httpd-access # ErrorLog /where/ever/httpd-errors ErrorLog /AbsolutePath.../WWW/log/httpd-error #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LogFormat Common LogTime LocalTime # # User-supported directories under ~/public_html # UserDir public_html #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # The Map-directive maps a virtual URL into a physical path in your file # system. In this example, URLs starting with /httpd-internal-icons/* will # be mapped to the path /cern_icons/*. This address will be passed to the # Exec- and Pass-directives that follow. # Map /httpd-internal-icons/* /cern_icons/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Scripts; URLs starting with /cgi-bin/ will be understood as # script calls in the directory /your/script/directory # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Exec /cgi-bin/* /your/script/directory/* Exec /cgi-bin/* /AbsolutePath.../WWW/cern_httpd_3.0/cgi-bin/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # URL translation rules; If your documents are under /local/Web # then this single rule does the job: # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Pass /* /local/Web/* Pass /* /AbsolutePath.../WWW/httpd_docs/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ "httpd.conf"-end -------------------------------- EXAMPLE ---------------------------- "caching.conf"-begin ------------------------------ # # Sample configuration file for cern_httpd for running it # as a proxy server WITH caching. # # See: # # # for more information. # # Written by: # Ari Luotonen April 1994 # # # Set this to point to the directory where you unpacked this # distribution, or wherever you want httpd to have its "home" # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # ServerRoot /where/ever/server_root ServerRoot /AbsolutePath.../WWW/httpd_docs #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Set the port for proxy to listen to # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Port 8080 Port 80 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # General setup; on some systems, like HP, nobody is defined so # that setuid() fails; in those cases use a different user id. # UserId nobody GroupId nogroup # # Logging; if you want logging uncomment these lines and specify # locations for your access and error logs # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # AccessLog /where/ever/httpd-log AccessLog /AbsolutePath.../WWW/log/httpd-access ProxyAccessLog /AbsolutePath.../WWW/log/proxy-access CacheAccessLog /AbsolutePath.../WWW/log/proxy-cache # ErrorLog /where/ever/httpd-errors ErrorLog /AbsolutePath.../WWW/log/proxy-error #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LogFormat Common LogTime LocalTime # # Proxy protections; if you want only certain domains to use # your proxy, uncomment these lines and specify the Mask # with hostname templates or IP number templates: # # Protection PROXY-PROT { # ServerId YourProxyName # Mask @(*.cern.ch, 128.141.*.*, *.ncsa.uiuc.edu) # } # Protect * PROXY-PROT # # Pass the URLs that this proxy is willing to forward. # Pass http:* Pass ftp:* Pass gopher:* Pass wais:* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # If you want to run a regular http server at the same time, add the # following rules (see the above example for the "http.conf" file) # Map /httpd-internal-icons/* /cern_icons/* Exec /cgi-bin/* /AbsolutePath.../WWW/cern_httpd_3.0/cgi-bin/* Pass /* /AbsolutePath.../WWW/httpd_docs/* #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # Enable caching, specify cache root directory, and cache size # in megabytes # Caching On #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # CacheRoot /your/cache/root/dir CacheRoot /AbsolutePath.../WWW/cache_root #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CacheSize 5 # # Specify absolute maximum for caching time # CacheClean * 2 months # # Specify the maximum time to be unused # CacheUnused http:* 2 weeks CacheUnused ftp:* 1 week CacheUnused gopher:* 1 week # # Specify default expiry times for ftp and gopher; # NEVER specify it for HTTP, otherwise documents generated by # scripts get cached which is usually a bad thing. # CacheDefaultExpiry ftp:* 10 days CacheDefaultExpiry gopher:* 2 days # # Garbage collection controls; daily garbage collection at 3am; # Gc On GcDailyGc 3:00 ---------------------------- "caching.conf"-end -------------------------------- 3. Creating Directories and Symbolic Links ----------------------------------------- If you are not interested in logging information, just leave the corresponding part as it is in the original configuration files. If you copied one of the customized example files above, go to your directory "WWW" and create the subdirectory "log": % cd WWW % mkdir log If you want to run a proxy server with caching, you also had to indicate the "CacheRoot" directory, which is "/AbsolutePath.../WWW/cache_root" in the given example. Create the corresponding directory: % mkdir cache-root In the customized configuration files, the Pass-directive for the regular http server will map all URLs to the directory "/AbsolutePath.../WWW/httpd_docs" (which is the "ServerRoot" directory). If certain URLs have to be mapped to a different directory, you have to do two things: 1. go to your "ServerRoot" directory and add a symbolic link pointing to the respective directory 2. to your httpd configuration file, add a Map-directive which maps all URLs that start with a certain path to that symbolic link Eg. the Map-directive "Map /httpd-internal-icons/* /cern_icons/*" maps all URLs starting with "/httpd-internal-icons/*" to the symbolic link "cern_icons", which shall point to the directory "/AbsolutePath.../WWW/cern_httpd_3.0/icons/". For this to work, you have to add the symbolic link "cern_icons", pointing to the directory "/AbsolutePath.../WWW/cern_httpd_3.0/icons/", to the "ServerRoot" directory. % cd WWW/httpd_docs % ln -s /AbsolutePath.../WWW/cern_httpd_3.0/icons cern_icons 4. Trying It Out in Verbose Mode -------------------------------- In order to check whether everything has been set correctly, start the http server by hand in verbose mode and look what happens when you make a request with your browser. You have to indicate the path of your http configuration file with the command line option "-r". Test servers are typically run on a non- priviledged port above 1024, often 8001, 8080, or such (the official http port is 80). The server port is defined in the configuration file by the Port- directive, but you can override it with the command line option "-p" while testing it. % cd WWW/cern_httpd_3.0/bin % httpd -v -r /AbsolutePath.../WWW/cern_httpd_3.0/config/httpd.conf -p 8080 or: % httpd -v -r /AbsolutePath.../WWW/cern_httpd_3.0/config/caching.conf -p 8080 Now, start your browser and open the URL http://your_server:8080. If everything works fine you should get the CERN "index.html" (-> "Guide.html") page as a Welcome page. There you can read more details about CERN httpd 3.0. 5. Stand-Alone Installation --------------------------- If you are done with testing, stop the test run. Before starting the http server in stand-alone mode, change the protection of the two directories "log" and "cache_root" to allow access by "nobody". % chmod -R 777 log % chmod -R 777 cache_root For the actual installation of httpd in stand-alone mode, you need to create a new startup file. Go to the directory where you keep your system startup files and set up a new file "S_httpd" as described below. ----------------------------- "S_httpd"-begin ---------------------------------- #!/sbin/sh if [ -f /AbsolutePath.../WWW/cern_httpd_3.0/bin/httpd ] ; then if [ -f /AbsolutePath.../WWW/cern_httpd_3.0/config/httpd.conf ] ; then echo "Starting httpd" (/AbsolutePath.../WWW/cern_httpd_3.0/bin/httpd -r /AbsolutePath.../WWW/cern_ httpd_3.0/config/httpd.conf) &> /dev/console else echo "Problem with configuration file: no httpd started" fi else echo "Problem with httpd image: no httpd started" fi ----------------------------- "S_httpd"-end ------------------------------------ Change the protection of the new startup file, then start it. # chmod 744 S_httpd # S_httpd If you did everything correctly, you will get the message "Starting httpd". Have fun! Nicole Redaschi -------------------------------------------------------------------------------- Nicole Redaschi Biocomputing-Biozentrum der Universitaet Basel-Klingelbergstr.70-CH 4056 Basel -------------------------------------------------------------------------------- From owner-srs@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!bioftp.unibas.ch!redaschi Newsgroups: bionet.software.srs Subject: [TEACHING] Installation of SRSWWW under CERN httpd 3.0 - Part 2 Message-ID: <1995Apr24.164510.5474@comp.bioz.unibas.ch> From: redaschi@comp.bioz.unibas.ch (Nicole Redaschi) Date: Mon, 24 Apr 1995 16:45:10 GMT Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Lines: 294 [ Article crossposted from bionet.software.www ] [ Author was Nicole Redaschi ] [ Posted on Mon, 24 Apr 1995 09:23:05 GMT ] ******************************************************************************** Installation of SRSWWW under CERN httpd 3.0 Part 2: Installation of SRS ******************************************************************************** This documentation contains step-by-step instructions, for the basic (!) installation of the SRS software package on UNIX platforms. For details, see the SRS manual at the URL http://www.embl-heidelberg.de/srs/srsman.html. 1. Getting the Program ---------------------- Go to the directory where you want to install SRS (in this example called "SRS"). % cd SRS The SRS package is available from the "ftp.embl-heidelberg.de" anonymous ftp account. At the date of this writing, the most recent version of SRS ("srs4_04.tar.gz") is located in the directory "pub/software/unix/srs". (If you do not find the SRS package there, 'get' the INDEX first and search for the keyword "srs".) 'ftp' to "ftp.embl-heidelberg.de" and go to the directory "pub/software/unix/srs", 'get' the file "srs4_04.tar.gz" and 'quit'. Uncompress ('gunzip' requires modification of the filename extension!) and untar the file. You will get the directory "srs4_04". % ftp ftp.embl-heidelberg.de Name: anonymous Password: ftp> cd pub/software/unix/srs ftp> ls -lsa ftp> bin ftp> get srs4_04.tar.gz ftp> quit % mv srs4_04.tar.gz srs4_04.tar.z % gunzip srs4_04.tar % tar xvf srs4_04.tar 2. Customizing the ODD-Files (".sdl") ------------------------------------- All ".sdl" files are located in the directory "srs4_04/odd". Before you can start to compile the programs, you have to edit the file "srsdb.sdl": 1. Customize the object "#environment" with the name "unix". 2. Remove or outcomment ("!") all "#libenv" definitions of databanks you do not have at your site. 3. For each databank that you would like to index with SRS, modify the given "#libenv" definition if necessary: each databank must be associated with the name of the directory that contains the flatfiles. For databanks not listed in the default "srsdb.sdl" file, add a new "#libenv" definition to the object "#environment" and a new "#libid" definition to the object "#srsdb" (set "n" to a number between 1 and 255 that has not been used yet.) EXAMPLE -------------------------------- "srsdb.sdl" ----------------------------------- ... #environment /name=unix { #libenv /lib=@SWISSPROT_DB /dir="/data/swissprot/" #libenv /lib=@PIR_DB /dir="/data/pir/" ! #libenv /lib=@PIRALN_DB /dir="/data/pir/" #libenv /lib=@EMBL_DB /dir="/data/embl_dna/" #libenv /lib=@EMNEW_DB /dir="/data/emnew/" #libenv /lib=@XEMBL_DB /dir="/data/emnew/" #libenv /lib=@XXEMBL_DB /dir="/data/emnew/" ... #srsdb { #libid /n=1 /library=@SWISSPROT_DB #libid /n=2 /library=@PIR_DB #libid /n=3 /library=@EMBL_DB #libid /n=4 /library=@EMNEW_DB #libid /n=10 /library=@XEMBL_DB #libid /n=11 /library=@XXEMBL_DB ... -------------------------------- "srsdb.sdl" ----------------------------------- Some sequence databanks have a special format when used under GCG (EMBL, Genbank, Swissprot). For each of these you need to edit the respective ".sdl" file ("embl.sdl","genbank.sdl", "swissprot.sdl"). 1. Change the file name(s) that are defined in the "#file" objects. (Eg. the EMBL file "est" is usually called "em_est" in the GCG format) 2. Modify the "#libformat" definition: change the attribute "file_type" so that it points to "GCGREF_FILE" and "GCGSEQ_FILE". All you need to do is to move the outcomment character ("!"). EXAMPLE -------------------------------- "embl.sdl" ------------------------------------ ... #library /id=%EMBL_DB /group=@SEQUENCE_LIBS /name=EMBL /logicname=EM, EMBL /format=@EMBL_FORMAT /cachesize=2048 /maxIndexSizeKb=3200 /oddfile="embl.sdl" !{ ! #file /name=est ! #file /name=patent ... ! #file /name=sts !} !names of the files in GCG format { #file /name=em_est /logicname=EM_EST #file /name=patent /logicname=EM_PAT ... #file /name=em_sts /logicname=EM_STS } ... #libformat /id=%EMBL_FORMAT /parser=@EMBL_PARSER ! /file_type=@EMBLREF_FILE, @EMBLSEQ_FILE !GCG format /file_type=@GCGREF_FILE, @GCGSEQ_FILE /featureExpression=@EMBL_FEATURE_EXPRESSION { ... -------------------------------- "embl.sdl" ------------------------------------ If you have added new databanks to the file "srsdb.sdl", you need to provide corresponding ".sdl" files for the new databanks! Do not start from scratch, look first what you can use from the existing ".sdl" files. Whenever possible copy and paste from what is there and modify where required. If your new databank has the same format as one of those for which you already have an ".sdl" file" you may simply add the following things to this file: 1. a "#library" definition for the new databank 2. a "#libformat" definition for the new databank 3. "#link" definitions if desired As an example, see the file "embl.sdl" which contains data for both EMBL and EMBLNEW. 3. Compilation -------------- Now, you can start with the compilation of the programs. Go to the SRS root directory ("srs4_04") and invoke 'srsinstall'. This script will ask you first for the 'make' and 'cc' commands, then it will compile all programs and create a new binary file with all the data defined by the ".sdl" files. (If you get an ERROR message, you have to edit the appropriate file and recompile the programs.) To build the indices, 'source' the file "etc/prep_srs" and issue the command 'srscheck'. (If you get an ERROR message, you have to edit the appropriate file and then run 'srssection' to recompile the ".sdl" files.) If all worked fine, issue the command 'srsupdate' to start the indexing. % cd srs4_04 % srsinstall all ... [make] (press return) ... [cc] (press return) (% srsinstall all) % source etc/prep_srs % srscheck (% srssection) (% srscheck) % srsupdate To keep the indices up to date automatically, you can create a crontab file with the three commands 'source /AbsolutePath.../etc/prep_srs', 'srscheck' and 'srsupdate'. 4. Installation of SRSWWW under CERN httpd 3.0 ---------------------------------------------- (See Part 1 for the installation of CERN WWW server) On the WWW side: ---------------- Go to your httpd "ServerRoot" directory (in this example "WWW/httpd_docs") and add two symbolic links (srs, srs_map) which point to the SRS home directory "srs4_04/www": % cd WWW/httpd_docs % ln -s /AbsolutePath.../srs4_04/www srs % ln -s /AbsolutePath.../srs4_04/www srs_map Now, you have to edit your httpd configuration file (eg. "httpd.conf" or "caching.conf"). Add the following Map- and Exec-directives: EXAMPLE ---------------------- "httpd.conf"-/"caching.conf"-begin ---------------------- ... Map /srs/ /srs_map/index.html Map /srs/*.html /srs_map/*.html Map /srs/*.gif /srs_map/*.gif Map /cgi-bin/imagemap/srs/* /cgi-bin/htimage/srs_map/* ... Exec /srs/* /AbsolutePath.../srs4_04/www/* ... ---------------------- "httpd.conf"-/"caching.conf"-end ------------------------ Finally, you have to change the format of the image configuration file "srswww.map" (in directory "srs4_04/www") to fit the CERN style: EXAMPLE ----------------------------- "srswww.map"-begin ------------------------------- rect (287,168) (382,195) /srs/srsc?-info%20swissprot rect (80,127) (137,153) /srs/srsc?-info%20embl rect (376,222) (440,253) /srs/srsc?-info%20hssp ... circle (57,100) 5 /srs/srsc?-linfo%20ecd%20embl circle (75,107) 5 /srs/srsc?-linfo%20epd%20embl circle (57,169) 5 /srs/srsc?-linfo%20mimmap%20embl ... default /srs/net.html ----------------------------- "srswww.map"-end --------------------------------- On the SRS side: ---------------- Go to the directory "srs4_04/www" and edit the script "srsc": replace "./wgetz" by the full path name "/AbsolutePath.../srs4_04/www/wgetz". EXAMPLE ------------------------------ "srsc"-begin ------------------------------------ #!/bin/csh set noglob # turn off file name expansion...[]! if (${#argv} == 0) then /AbsolutePath.../srs4_04/www/wgetz -top else /AbsolutePath.../srs4_04/www/wgetz $* endif ------------------------------ "srsc"-end - ------------------------------------ SRSWWW inserts many hypertext links into the entries before display. The configurations of the hypertext links are defined in the file "hyperlink.sdl". You need to edit this file if one or more of the databanks addressed are missing at your site. Eg. if you do not have MEDLINE installed, use the URL given in the example below. In other cases you may address SRSWWW servers installed on other nodes (Eg. replace "/srs/srsc" by "www.embl-heidelberg.de/srs/srsc".) EXAMPLE ------------------------- "hyperlink.sdl"-begin -------------------------------- ... #linkcall /id=%FETCH_MEDLINE /call="%s" ... #linkcall /id=%FETCH_FNUCACCNO /call="%s" ... ------------------------- "hyperlink.sdl"-end-- -------------------------------- After the changes you must run the command "srssection" to recompile the ODD- files! Now, go to the SRS root directory ("srs4_04") and invoke 'srsinstall' with the commandline option "www": % srsinstall www You can now access SRSWWW with the URL "http://your_server/srs/srsc". Have fun! Nicole Redaschi -------------------------------------------------------------------------------- Nicole Redaschi Biocomputing-Biozentrum der Universitaet Basel-Klingelbergstr.70-CH 4056 Basel -------------------------------------------------------------------------------- From owner-srs@net.bio.net Wed Apr 26 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Q: Hardware platforms Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 27 Apr 1995 11:26:12 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 38 If you are willing to share this information, I'm interested in finding out the following o On which machine are you running SRS - make - configuration o which version of SRS - release number - interface o What use do you make of SRS e.g. testing, internal server, external server o is this machine dedicated to SRS o Is your setup sufficient to fullfill your needs I want to use the information to decide what to purchase for a dedicated SRS server Jeroen -- ============================================================== . 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 Apr 27 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!world!uunet!EU.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Q: Hardware platforms Date: 28 Apr 1995 18:18:14 GMT Organization: EMBL Heidelberg Lines: 18 Distribution: world Message-ID: <3nrbh6$b7@comet.EMBL-Heidelberg.DE> References: 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) To: jecop@ebi.ac.uk X-URL: news:D7oyFo.GHr@ebi.ac.uk jeroen, as you probably know we have a power challenge or so (irix64) ...it is nice because it has a big disk cache and a fast bus ...processor is not the problem i have seen SRS on hp machines ...apparently they can be had with a very fast bus which makes SRS as fast as on our silicon graphics but i guess at a much cheaper price 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 Fri Apr 28 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!cs.utexas.edu!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Q: Hardware platforms Message-ID: <1995Apr29.071543.17732@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: Date: Sat, 29 Apr 1995 07:15:43 GMT Lines: 45 Jeroen Coppieters (jecop@ebi.ac.uk) wrote: : If you are willing to share this information, I'm interested in finding : out the following Machine RAM Disks Indigo R3000 48 nfs'ed for data, indices straight (DEC 3.5 GB) Indigo R3000 16 straight (Seagate 2 GB) AXP 3300 LX (*) 64 straight (Barracuda 4GB) AXP 2000 64 straight (Barracuda 4GB) (*) this is www.ch.embnet.org/srs/srsc visible to the outside Software Interface Purpose SRS 4_02 (*) WWW production SRS 4_04 WWW testing SRS 4_04 HASSLE research SRS 4_02 HASSLE research (*) this is www.ch.embnet.org/srs/srsc visible to the outside Purpose Implementation Production Highest availability Testing new sdl files, tests with SRS code Research (severe) manipulation of source code non-WWW networking Dedication All general purpose interactive, SRS, WWW, ftp, etc. Flaws All no SRSWWW or XSRS1/2 service during SRS indexing or data file manipulation Regards Reinhard Doelz EMBnet Switzerland -- 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 Fri Apr 28 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!trane.uninett.no!nntp.uio.no!xyplex25 From: rodrigol@biotek.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: Re: Q: Hardware platforms Date: 29 Apr 1995 18:48:21 GMT Organization: Norwegian EMBnet node Lines: 10 Message-ID: <3nu1ll$fpk@hermod.uio.no> References: NNTP-Posting-Host: xyplex22.uio.no X-Newsreader: News Xpress Version 1.0 Beta #3 In article , jecop@ebi.ac.uk (Jeroen Coppieters) wrote: >If you are willing to share this information, I'm interested in finding >out the following CHALLENGE M (Indigo ^2 R4400 @200 Mhz.) w/128Mb RAM 10Gb total disk space R:)