From owner-bio-srs@hgmp.mrc.ac.uk Mon Jul 14 17:50:28 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 2A7CB7D2D9 for ; Mon, 14 Jul 2003 17:50:28 +0100 (BST) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 907567D2E7 for ; Mon, 14 Jul 2003 17:50:27 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 952117D2D9; Mon, 14 Jul 2003 17:50:26 +0100 (BST) X-Original-To: bionet-software-srs@net.bio.net Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 55FA77D0F8 for ; Mon, 14 Jul 2003 11:16:23 +0100 (BST) Received: from horus.isnic.is (horus.isnic.is [193.4.58.12]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6FF317D0D3 for ; Mon, 14 Jul 2003 11:16:21 +0100 (BST) Received: from mr2.cc.ic.ac.uk (mr2.cc.ic.ac.uk [155.198.5.112]) by horus.isnic.is (8.12.9/8.12.9/isnic) with ESMTP id h6EAGFgO004511 for ; Mon, 14 Jul 2003 10:16:19 GMT (envelope-from news@imperial.ac.uk) Received: from jura.cc.ic.ac.uk ([155.198.5.19]) by mr2.cc.ic.ac.uk with esmtp (Exim 3.36 #1) id 19c0NS-0001zl-02 for bionet-software-srs@moderators.isc.org; Mon, 14 Jul 2003 11:16:14 +0100 Received: from news by jura.cc.ic.ac.uk with local (Exim 2.12 #1) id 19c0NR-0000o1-00 for bionet-software-srs@moderators.isc.org; Mon, 14 Jul 2003 11:16:13 +0100 To: bionet-software-srs@moderators.isc.org From: "James Abbott" Newsgroups: bionet.software.srs Subject: Registering queries within a session from a layout script Organization: Imperial College, London Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 X-Trace: jura.cc.ic.ac.uk 1058177772 3099 155.198.48.115 (14 Jul 2003 10:16:12 GMT) X-Complaints-To: usenet@jura.cc.ic.ac.uk NNTP-Posting-Date: 14 Jul 2003 10:16:12 GMT User-Agent: Pan/0.13.0 (The whole remains beautiful) Date: Mon, 14 Jul 2003 17:50:26 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk I am creating some views of application results databases (under SRS 7.1.1) which require me to retrieve all the results for an application rather than the 30 which are produced by default. I am doing this by using a 'stub' object loader which just contains the job name etc., then within the layout script I can succesfully query the application results database and pull back the data back using a second object loader as follows: $s=CurrSession $set=$s.query:"[$db-id:$job\*]" $data=$set.load:"AppData" This gives me the data I need, however the query carried out during the layout script does not get registered within the users session, even though it is clearly using the right session since the application results are returned correctly. This means that attempts to change the view produce 'Query no. xx does not exist' errors in the browser, and application launching etc. does also not necessarily use the correct sequence. The documentation for the Session object indicates that the 'query' method contains a 'doReg' attribute which is enabled by default, but I've also tried manually registering the results i.e. $set=$s.query:["[$db-id:$job\*]" queryName:"AppData"] $s.registerSet:$set but this also doesn't seem to work. Does anyone have any ideas of how to get round this, or am I trying to do the impossible? Cheers, James -- j.abbott@imperial.NOSPAM.ac.uk Bioinformatics Software Developer, Imperial College, London From owner-bio-srs@hgmp.mrc.ac.uk Tue Jul 15 14:57:32 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 26DD77D393 for ; Tue, 15 Jul 2003 14:57:32 +0100 (BST) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A41B97D398 for ; Tue, 15 Jul 2003 14:57:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id B91FB7D391; Tue, 15 Jul 2003 14:57:30 +0100 (BST) X-Original-To: bionet-software-srs@net.bio.net Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 331D27D36D for ; Tue, 15 Jul 2003 10:10:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id A308B7D36B; Tue, 15 Jul 2003 10:10:43 +0100 (BST) To: bionet-software-srs@net.bio.net From: benedict.arnold@bbsrc.ac.uk ("benedict arnold (JIC)") Newsgroups: bionet.software.srs Subject: Re: Registering queries within a session from a layout script Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Original-To: bio-srs@net.bio.net X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9BDB77D370 for ; Tue, 15 Jul 2003 10:10:42 +0100 (BST) X-Received: from mhub2.bbsrc.ac.uk (mhub2.bbsrc.ac.uk [149.155.202.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9CDC37D36B for ; Tue, 15 Jul 2003 10:10:40 +0100 (BST) X-Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.36 #3) id 19cLo4-0001cb-04; Tue, 15 Jul 2003 10:09:08 +0100 X-Received: from jimserv2.jic.bbsrc.ac.uk ([149.155.120.98]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 3TXRV3ZP; Tue, 15 Jul 2003 10:09:07 +0100 X-Received: by jimserv2.jic.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Tue, 15 Jul 2003 10:09:07 +0100 X-To: "'j.abbott@imperial.NOSPAM.ac.uk'" X-Cc: "'bio-srs@net.bio.net'" X-Mailer: Internet Mail Service (5.5.2653.19) X-ECS-MailScanner-BBSRC: Found to be clean Date: Tue, 15 Jul 2003 14:57:30 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hi James, you're not trying to do the impossible, but the work around will probably mean hacking the standard release page code ;-) As far as I recall, even though you are using $CurrSession, queries from within a layout script aren't registered in the session object (the reason being that some fools (ie me amongst others) use large numbers of queries in layouts) unless queryName is specified. What you might want to do in your layout script is print out the session info where you'll be able to see what the last query done was ... the queryName attribute will give the query a name, however, SRS in it's infinite wisdom rarely uses this to track which query it is on, it uses the queryN attribute of the $UPQ object that refers to query for that results set. I think what you need to do is find out what the queryN is for the query you've just done, something like $query=$s.queryList[$s.queryList.len:[]] will give you the query object, then you can access the queryN attribute using $qn=$query.queryN or you can get it using $qn=$s.queryList[$s.queryList.len:[]].queryN you'll then have to modify all instances where javascript calls like: "javascript:subgif(document.forms[0], '@wwwPageName~@qResult@queryFrom~@viewWith@queryNumber~@22')" occur so that the reflect the query number you want to use. I suspect you may have to do the query you want to use in the page somewhere in the page generation code rather than in the layout, as most of the javascript calls wil have been formed before the layout script is called, so you'll probably have to edit the resultpage.i file and in the context attribute section of the $Page object do the query you want to do and the redo the $qRes=$SpGetQueryResult call. This will set the queryN to the correct value for the query you do in the layout script. At that point you don't need to redo the query with a query string just use : $set=$s.query:[queryName:XXXXX] where XXXXX is the query name you used in the context section. You may be lucky and get $entries reset to the set you want if you use a loader in the contexts chunk of the page. hope that makes sense and you're brave enough to play with the guts of pages :-) all the best Ben --- From owner-bio-srs@hgmp.mrc.ac.uk Tue Jul 29 10:57:58 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 4A8E77D0F3 for ; Tue, 29 Jul 2003 10:57:58 +0100 (BST) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A12C27D35A for ; Tue, 29 Jul 2003 10:57:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id EB9817D37A; Tue, 29 Jul 2003 10:57:49 +0100 (BST) X-Original-To: bionet-software-srs@net.bio.net Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 60DEB7D24D for ; Mon, 28 Jul 2003 14:01:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 688667D248; Mon, 28 Jul 2003 14:00:57 +0100 (BST) To: bionet-software-srs@net.bio.net From: gene.quantification@wzw.tum.de (Gene Quantification Newsletter) Newsgroups: bionet.software.srs Subject: Gene Quantification Newsletter - July/August 2003 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <5.2.1.1.0.20030728150046.0282fb20@pollux.wzw.tum.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_23053765==.ALT" X-Original-To: bio-srs@net.bio.net X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 48AAF7D1CE; Mon, 28 Jul 2003 14:00:54 +0100 (BST) X-Received: from pollux.wzw.tum.de (pollux.edv.agrar.tu-muenchen.de [141.40.103.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 615E47D21A; Mon, 28 Jul 2003 14:00:51 +0100 (BST) X-Received: from pfaffl.wzw.tum.de ([141.40.217.71]) by pollux.wzw.tum.de (AIX4.3/8.9.3/8.9.3) with ESMTP id PAA30876; Mon, 28 Jul 2003 15:00:49 +0200 X-Sender: genequan@pollux.wzw.tum.de X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 X-To: bio-srs@net.bio.net, bionauts@net.bio.net, cellbiol@net.bio.net, immuno@net.bio.net Date: Tue, 29 Jul 2003 10:57:49 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk --=====================_23053765==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Gene Quantification Newsletter - July/August 2003 It is great pleasure for me to invite you to the 1st International qPCR Symposium & Application Workshop Transcriptomics, Clinical Diagnostics & Gene Quantification 3rd - 6th March, 2004 in Freising-Weihenstephan, Germany http://www.w= zw.tum.de/gene-quantification/qpcr2004/index.shtml The Symposium and the Application Workshop presents unbiased international= =20 lectures & posters about quantification strategies, normalisation methods &= =20 new algorithms for exact nucleic acid quantification in the broad range of= =20 qPCR applications: Parallel to the Symposium an Industrial Exhibition will take place along=20 with the congress, where an intensive conversation with numerous companies= =20 is possible (real-time PCR Cyclers, Kit Producers, Nucleic Acid=20 Purification Systems, Enzyme Producers, Plasticware Suppliers, etc.). More than 35 internationally renown speakers will be participating in a=20 lively and exciting programme enabling the valuable exchange of information= =20 in the qPCR field. Confirmed Speakers: Dr. Stephen Bustin Reader in Molecular Medicine, School of=20 Medicine, London Prof. Mikael Kubista TATAA Biocenter, Gothenborg,= Sweden Dr. Udo Reischl Institute of medical Microbiology &= =20 Hygiene, Regensburg, Germany Prof. H.H.D. Meyer Institute of Physiology, ZIEL, Faculty=20 Center of Food & Life Science-Weihenstephan Dr. Michael W. Pfaffl Institute of Physiology, ZIEL, Germany Dr. Olfert Landt TIB Molbiol, Berlin, Germany Dr. Thomas Kaiser Corbett Research R&D, Australia Prof. Hannelore Daniel Molecular Nutrition Unit, ZIEL, Germany,= =20 Center of Food & Life Science-Weihenstephan Dr. Debra Nicksen Invitrogen Dr. David Whitcombe DXS Genotyping Prof. Mario Pazzagli Clinical Biochemistry Unit,=20 Department of Clinical Physiopathology, Florence, Italy Dr. Thomas K=F6hler Roboscreen, Leipzig Anders Stahlberg Chalmers University, Sweden Dr. Pamela Scottie Adams Trudeau Institute, Saranac Lake, NY,,= USA Prof. Lawrence Wangh Brandeis University, Boston, MA, USA Dr. Kristin Brevik Andersson Institute of Experimental Medical= =20 Research, Oslo Dr. Jo Vandesompele Center of Medical Genetics,=20 Ghent University, Belgium Dr. Jim Huggett Center for Infectious Diseases,=20 London, UK N. N. ABI Applied BioSystems Download the actual 2nd announcement flyer, including agenda, important=20 dates, prices, etc: http://www.wzw.tum.de/gene-quantification/qpcr2004/2nd-announcement-qp= cr2004.pdf Symposium organisation & registration: Registration Form=20 (PDF)=20 http://= www.wzw.tum.de/gene-quantification/qpcr2004/registration.pdf Registration Form=20 (DOC)=20 http://= www.wzw.tum.de/gene-quantification/qpcr2004/registration.doc Please send your registration form via: Snail mail Dr. Susanna Wirth, TUM-Tech, Saarstra=DFe 7, D-80797= =20 M=FCnchen, Germany or FAX Dr. Susanna Wirth, TUM-Tech, FAX No. +49-89-306695-66 and e-mail the completed Word document=20 to susanna.wirth@tumtech.de for further information, registration and abstract submission please= contact: qpcr2004@wzw.tum.de ################################################ New features on the Gene-Quantification web page: Further, a lot of NEW real-time PCR workshops http://www.wzw.tu= m.de/gene-quantification/main.shtml#work New Section BioInformatics in real-time PCR http://www.w= zw.tum.de/gene-quantification/bioinformatics.shtml NEW PUBLICATIONS about kinetic PCR http://www.wzw.tum= .de/gene-quantification/real-time.html and http://www.wzw.tu= m.de/gene-quantification/literature.html Please send the NEWSLETTER and the home page links to further scientists=20 and friends who are interested in real-time PCR, new quantification=20 strategies, relative or absolute gene quantification using kinetic PCR. best regards Michael Pfaffl ******************************************************************** Gene Quantification @ wzw.tum.de e-mail: gene.quantification@wzw.tum.de homepage: http://www.wzw.tum.de/gene-quantification/index.shtml homepage: http://www.wzw.tum.de/gene-quantification/physiology.shtml homepage: = http://www.wzw.tum.de/gene-quantification/bioinformatics.shtml responsible Senior Scientist: Dr. Michael W. Pfaffl Institute of Physiology Life Science Center Weihenstephan, Technical University of Munich Weihenstephaner Berg 3 D-85350 Freising-Weihenstephan GERMANY ********************************************************************=20 --=====================_23053765==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Gene Quantification Newsletter - July/August 2003

It is great pleasure for me to invite you to the

1st International qPCR Symposium  &  Application Workshop
Transcriptomics, Clinical Diagnostics  &  Gene Quantification
3rd - 6th March, 2004 in Freising-Weihenstephan, Germany

htt= p://www.wzw.tum.de/gene-quantification/qpcr2004/index.shtml

The Symposium and the Application Workshop presents unbiased international lectures & posters about quantification strategies, normalisation methods & new algorithms for exact nucleic acid quantification in the broad range of qPCR applications:

Parallel to the Symposium an Industrial Exhibition will take place along with the congress, where an intensive conversation with numerous companies is possible (real-time PCR Cyclers, Kit Producers, Nucleic Acid Purification Systems, Enzyme Producers, Plasticware Suppliers, etc.).

More than 35 internationally renown speakers will be participating in a lively and exciting programme enabling the valuable exchange of information in the qPCR field.

Confirmed Speakers:

Dr. Stephen Bustin           &nbs= p;  Reader in Molecular Medicine, School of Medicine, London
Prof. Mikael Kubista           &nb= sp;            TATAA Biocenter, Gothenborg, Sweden
Dr. Udo Reischl           &nb= sp;            Institute of medical Microbiology & Hygiene, Regensburg, Germany
Prof. H.H.D. Meyer           &= nbsp;  Institute of Physiology, ZIEL, Faculty Center of Food & Life Science-Weihenstephan
Dr. Michael W. Pfaffl           =      Institute of Physiology, ZIEL, Germany
Dr. Olfert Landt           &= nbsp;   TIB Molbiol, Berlin, Germany
Dr. Thomas Kaiser           &nbs= p;  Corbett Research R&D, Australia
Prof. Hannelore Daniel            Molecular Nutrition Unit, ZIEL, Germany, Center of Food  & Life Science-Weihenstephan
Dr. Debra Nicksen           = ;            Invitrogen
Dr. David Whitcombe           &= nbsp;      DXS Genotyping
Prof. Mario Pazzagli          &nbs= p;           Clinical Biochemistry Unit, Department of Clinical Physiopathology, Florence, Italy
Dr. Thomas K=F6hler           &n= bsp; Roboscreen, Leipzig
Anders Stahlberg           &= nbsp;        Chalmers University, Sweden
Dr. Pamela Scottie Adams            Trudeau Institute, Saranac Lake, NY,, USA
Prof. Lawrence Wangh            Brandeis University, Boston, MA, USA
Dr. Kristin Brevik Andersson          &nb= sp;  Institute of Experimental Medical Research, Oslo
Dr. Jo Vandesompele          &nbs= p;             Center of Medical Genetics, Ghent University, Belgium
Dr. Jim Huggett           &nb= sp;           Center for Infectious Diseases, London, UK
N. N.            &n= bsp;            =             &nbs= p; ABI Applied BioSystems

Download the actual 2nd announcement flyer, including agenda, important dates, prices, etc:
http://www.wzw.tum.de/gene-quantification/qpcr2004/2nd-announ= cement-qpcr2004.pdf

Symposium organisation & registration:
Registration Form (PDF)            http://www.wzw.tum.de/gene-quantification/qpcr2004/registration.pdf Registration Form (DOC)         http://www.wzw.tum.de/gene-quantification/qpcr2004/registration.doc
 

Please send your registration form via:
Snail mail             Dr. Susanna Wirth, TUM-Tech, Saarstra=DFe 7, D-80797 M=FCnchen, Germany
or
FAX            &= nbsp;     Dr. Susanna Wirth, TUM-Tech, FAX No. +49-89-306695-66
and e-mail            the completed Word document to            susanna.wirth@tumtech.de
for further information, registration and abstract submission please contact:
qpcr2004@wzw.tum.de

################################################

New features on the Gene-Quantification web page:

Further, a lot of NEW real-time PCR workshops
http://w= ww.wzw.tum.de/gene-quantification/main.shtml#work

New Section BioInformatics in real-time PCR
htt= p://www.wzw.tum.de/gene-quantification/bioinformatics.shtml

NEW PUBLICATIONS about kinetic PCR
http://ww= w.wzw.tum.de/gene-quantification/real-time.html
and
http= ://www.wzw.tum.de/gene-quantification/literature.html

Please send the NEWSLETTER and the home page links to further scientists and friends who are interested in real-time PCR, new quantification strategies, relative or absolute gene quantification using kinetic PCR.

best regards

Michael Pfaffl

********************************************************************
Gene Quantification @ wzw.tum.de

e-mail: gene= .quantification@wzw.tum.de
homepage:       http://www.wzw.tum.de/gene-quantification/index.shtml
homepage:       http://www.wzw.tum.de/gene-quantification/physiology.sht= ml
homepage:       http://www.wzw.tum.de/gene-quantification/bioinformatics= .shtml

responsible Senior Scientist:
Dr. Michael W. Pfaffl
Institute of Physiology
Life Science Center Weihenstephan,
Technical University of Munich
Weihenstephaner Berg 3
D-85350 Freising-Weihenstephan
GERMANY

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