From tibs at stat.Stanford.EDU Tue Jul 1 18:55:53 2003 From: tibs at stat.Stanford.EDU (Rob Tibshirani) Date: Tue, 1 Jul 2003 15:55:53 -0700 (PDT) Subject: [BiO BB] data mining short course Message-ID: <200307012255.PAA90415@rgmiller.Stanford.EDU> Short course: Statistical Learning and Data Mining Trevor Hastie and Robert Tibshirani, Stanford University University Park Hotel @ MIT Cambridge, MA, September 15-16, 2003 This two-day course gives a detailed overview of statistical models for data mining, inference and prediction. With the rapid developments in internet technology, genomics and other high-tech industries, we rely increasingly more on data analysis and statistical models to exploit the vast amounts of data at our fingertips. This sequel to our popular "Modern Regression and Classification" course covers many new areas of unsupervised learning and data mining, and gives an in-depth treatment of some of the hottest tools in supervised learning. The first course is not a prerequisite for this new course. Day one focuses on state-of-art methods for supervised learning, including PRIM, boosting, support vector machines, and very recent work on least angle regression and the lasso. Day two covers unsupervised learning, including clustering, principal components, principal curves and self-organizing maps. Many applications will be discussed, including the analysis of DNA expression arrays - one of the hottest new areas in biology! ################################################### Much of the material is based on the best selling book: Elements of Statistical Learning: data mining, inference and prediction Hastie, Tibshirani & Friedman, Springer-Verlag, 2001 http://www-stat.stanford.edu/ElemStatLearn/ A copy of this book will be given to all attendees. ################################################### Go to the site http://www-stat.stanford.edu/~hastie/mrc.html for more information and online registration. ********************************************** Rob Tibshirani, Dept of Health Research & Policy and Dept of Statistics HRP Redwood Bldg Stanford University Stanford, California 94305-5405 phone: HRP: 650-723-7264 (Voice mail), Statistics 650-723-1185 FAX 650-725-8977 tibs at stat.stanford.edu http://www-stat.stanford.edu/~tibs From j.d.tucker at vla.defra.gsi.gov.uk Wed Jul 2 11:21:41 2003 From: j.d.tucker at vla.defra.gsi.gov.uk (Tucker, James) Date: Wed, 2 Jul 2003 16:21:41 +0100 Subject: [BiO BB] DOTPLOTs Message-ID: <104FE795DA19D411A71A0008C733F76404A439C5@vla6> Hi All, I am trying to carry out some dotplots on large seq (around 2.1 Mb). I would therefore appreciate it if any one could suggest any software that I can down load to carry this out, so as to avoid congesting up servers. Regards James James Tucker Brucella Research Group Department of Bacterial Diseases VLA Weybridge Woodham Lane New Haw Addlestone Surrey KT15 3NB Tel: ++44(0)1932 357227 Fax: ++44(0)1932 357873 mailto:j.d.tucker at vla.defra.gsi.gov.uk From pmr at ebi.ac.uk Wed Jul 2 13:24:33 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 02 Jul 2003 18:24:33 +0100 Subject: [BiO BB] DOTPLOTs References: <104FE795DA19D411A71A0008C733F76404A439C5@vla6> Message-ID: <3F031551.2020105@ebi.ac.uk> Tucker, James wrote: > Hi All, > I am trying to carry out some dotplots on large seq (around 2.1 Mb). I would > therefore appreciate it if any one could suggest any software that I can > down load to carry this out, so as to avoid congesting up servers. if you only need word-based matches, especially with a reasonably large word size) then EMBOSS http://www.emboss.org/ will do the job. Hope this helps, Peter From mgollery at unr.edu Wed Jul 2 13:25:01 2003 From: mgollery at unr.edu (Martin Gollery) Date: Wed, 2 Jul 2003 10:25:01 -0700 Subject: [BiO BB] DOTPLOTs In-Reply-To: <104FE795DA19D411A71A0008C733F76404A439C5@vla6> References: <104FE795DA19D411A71A0008C733F76404A439C5@vla6> Message-ID: <1057166701.3f03156d7d595@webmail.unr.edu> Hello James, You can get a program called dotplot at: http://www.ikbar.org/GMS6014/downloads.htm Or as part of a package called 'all-in-One' at: http://134.99.88.55/aio/ Or you can use dotter from the karolinska institute at: http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html I'm sure there are others, but these are some I am aware of. Marty Quoting "Tucker, James" : > Hi All, > I am trying to carry out some dotplots on large seq (around 2.1 Mb). I > would > therefore appreciate it if any one could suggest any software that I can > down load to carry this out, so as to avoid congesting up servers. > Regards > James > > James Tucker > Brucella Research Group > Department of Bacterial Diseases > VLA Weybridge > Woodham Lane > New Haw > Addlestone > Surrey > KT15 3NB > > Tel: ++44(0)1932 357227 > Fax: ++44(0)1932 357873 > > mailto:j.d.tucker at vla.defra.gsi.gov.uk > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS200 (775)784-6048 ------------------------------------------------- This mail sent through https://webmail.unr.edu From carlosandresic at yahoo.com.mx Wed Jul 2 19:33:42 2003 From: carlosandresic at yahoo.com.mx (=?iso-8859-1?q?Carlos=20Andr=E9s=20Iriarte=20Cota?=) Date: Wed, 2 Jul 2003 18:33:42 -0500 (CDT) Subject: [BiO BB] DNA editing software Message-ID: <20030702233342.65409.qmail@web14712.mail.yahoo.com> Hi all of you i'm doing some research on plant DNA editing, and i'm searching for a software that can identify this editing sections on plants' dna, i hope that any of you could tell me please if you know any program that can do this identification, or if you know any web page where i can find more information about this, i'll really appreciate if you help me with this, i'm just beginning on bioinformatics, and i'm pretty interested about this. --------------------------------- Do You Yahoo!? Yahoo! Net: La mejor conexi?n a internet y 25MB extra a tu correo por $100 al mes. -------------- next part -------------- An HTML attachment was scrubbed... URL: From biopolak at yahoo.co.uk Wed Jul 9 12:23:33 2003 From: biopolak at yahoo.co.uk (=?iso-8859-1?q?Peter=20Oledzki?=) Date: Wed, 9 Jul 2003 17:23:33 +0100 (BST) Subject: [BiO BB] BIOMail Message-ID: <20030709162333.12305.qmail@web12203.mail.yahoo.com> Does anybody know what happend to BioMail???? Pete ===== Peter Oledzki Department of Biochemistry and Molecular Biology University of Leeds,UK ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://uk.messenger.yahoo.com/ From jeff at bioinformatics.org Wed Jul 9 12:36:07 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 09 Jul 2003 12:36:07 -0400 Subject: [BiO BB] BIOMail References: <20030709162333.12305.qmail@web12203.mail.yahoo.com> Message-ID: <3F0C4477.2090702@bioinformatics.org> Hi Pete. No. What happened to it? Are you referring to the BioMail running at Bioinformatics.Org or at BioMail.org? Cheers. Jeff Peter Oledzki wrote: > Does anybody know what happend to BioMail???? > > > Pete > > ===== > Peter Oledzki > Department of Biochemistry and Molecular Biology > University of Leeds,UK -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From idoerg at burnham.org Wed Jul 9 12:54:10 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 09 Jul 2003 09:54:10 -0700 Subject: [BiO BB] BIOMail In-Reply-To: <3F0C4477.2090702@bioinformatics.org> References: <20030709162333.12305.qmail@web12203.mail.yahoo.com> <3F0C4477.2090702@bioinformatics.org> Message-ID: <3F0C48B2.2090602@burnham.org> Worked for me just this past Saturday. ./I J.W. Bizzaro wrote: > Hi Pete. > > No. What happened to it? Are you referring to the BioMail running at > Bioinformatics.Org or at BioMail.org? > > Cheers. > Jeff > > Peter Oledzki wrote: > >> Does anybody know what happend to BioMail???? >> >> >> Pete >> >> ===== >> Peter Oledzki >> Department of Biochemistry and Molecular Biology >> University of Leeds,UK > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From biopolak at yahoo.co.uk Wed Jul 9 19:24:41 2003 From: biopolak at yahoo.co.uk (=?iso-8859-1?q?Peter=20Oledzki?=) Date: Thu, 10 Jul 2003 00:24:41 +0100 (BST) Subject: [BiO BB] BIOMail In-Reply-To: <3F0C48B2.2090602@burnham.org> Message-ID: <20030709232441.11993.qmail@web12205.mail.yahoo.com> I had an account on bioinformatics.org but then it stoped working .... it moved to biomail.org i didn't know this .... i will register there..... sorry about the confusion Pete --- Iddo Friedberg wrote: > Worked for me just this past Saturday. > > ./I > > J.W. Bizzaro wrote: > > Hi Pete. > > > > No. What happened to it? Are you referring to > the BioMail running at > > Bioinformatics.Org or at BioMail.org? > > > > Cheers. > > Jeff > > > > Peter Oledzki wrote: > > > >> Does anybody know what happend to BioMail???? > >> > >> > >> Pete > >> > >> ===== > >> Peter Oledzki > >> Department of Biochemistry and Molecular Biology > >> University of Leeds,UK > > > > > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== Peter Oledzki Department of Biochemistry and Molecular Biology University of Leeds,UK ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://uk.messenger.yahoo.com/ From salim at xensia.com Wed Jul 9 13:06:55 2003 From: salim at xensia.com (Salim Badakhchani) Date: Wed, 9 Jul 2003 18:06:55 +0100 (BST) Subject: [BiO BB] BIOMail In-Reply-To: <3F0C48B2.2090602@burnham.org> References: <20030709162333.12305.qmail@web12203.mail.yahoo.com> <3F0C4477.2090702@bioinformatics.org> <3F0C48B2.2090602@burnham.org> Message-ID: <2269.81.5.139.18.1057770415.squirrel@www.xplatform.org> Their web site says the service has ben a bit flaky lately. "Dear BioMail users, Since May 23rd we have been experiencing problems. Beginning June 15th searches seem to be working well. Weekly searches have been moved to Saturdays. Please write to us if you experience problems." -- Salim Badakhchani www.xensia.com Xensia LLP, London UK - Technical Solutions & Hosting From jeff at bioinformatics.org Wed Jul 9 19:37:38 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 09 Jul 2003 19:37:38 -0400 Subject: [BiO BB] Re: BIOMail References: <20030709232441.11993.qmail@web12205.mail.yahoo.com> Message-ID: <3F0CA742.5010201@bioinformatics.org> Wait! :-) BioMail did **NOT** move to BioMail.org. It was there originally, and then Dmitry set it up to run at Bioinformatics.Org **TOO**. If there is a specific reason for thinking BioMail is not working, please report it to Dmitry: dimus at biomail.org Cheers. Jeff Peter Oledzki wrote: > I had an account on bioinformatics.org > but then it stoped working .... it moved to > biomail.org i didn't know this .... i will register > there..... > > sorry about the confusion > > Pete > > > --- Iddo Friedberg wrote: > > Worked for me just this past Saturday. > >>./I >> >>J.W. Bizzaro wrote: >> >>>Hi Pete. >>> >>>No. What happened to it? Are you referring to >> >>the BioMail running at >> >>>Bioinformatics.Org or at BioMail.org? >>> >>>Cheers. >>>Jeff >>> >>>Peter Oledzki wrote: >>> >>> >>>>Does anybody know what happend to BioMail???? >>>> >>>> >>>>Pete >>>> >>>>===== >>>>Peter Oledzki >>>>Department of Biochemistry and Molecular Biology >>>>University of Leeds,UK >>> >>> >>> >>-- >>Iddo Friedberg, Ph.D. >>The Burnham Institute >>10901 N. Torrey Pines Rd. >>La Jolla, CA 92037 >>USA >>Tel: +1 (858) 646 3100 x3516 >>Fax: +1 (858) 646 3171 >>http://ffas.ljcrf.edu/~iddo >> >>_______________________________________________ >>BiO_Bulletin_Board maillist - >>BiO_Bulletin_Board at bioinformatics.org >> > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > ===== > Peter Oledzki > Department of Biochemistry and Molecular Biology > University of Leeds,UK > > ________________________________________________________________________ > Want to chat instantly with your online friends? Get the FREE Yahoo! > Messenger http://uk.messenger.yahoo.com/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From hzi at uol.com.br Wed Jul 9 22:39:05 2003 From: hzi at uol.com.br (hzi at uol.com.br) Date: Wed, 09 Jul 2003 23:39:05 -0300 Subject: [BiO BB] DNA editing software In-Reply-To: <20030702233342.65409.qmail@web14712.mail.yahoo.com> References: <20030702233342.65409.qmail@web14712.mail.yahoo.com> Message-ID: On Wed, 2 Jul 2003 18:33:42 -0500 (CDT), Carlos Andr?s Iriarte Cota wrote: > Hi all of you > i'm doing some research on plant DNA editing, and i'm searching for a > software that can identify this editing sections on plants' dna, i hope > that any of you could tell me please if you know any program that can do > this identification, or if you know any web page where i can find more > information about this, i'll really appreciate if you help me with this, > i'm just beginning on bioinformatics, and i'm pretty interested about > this. > Hi -- I don't know about editing, but the Artemis tool is great for visualization. HTH. http://www.sanger.ac.uk/Software/Artemis/ Bye, Henry From Martin.Leucker at it.uu.se Fri Jul 11 16:31:40 2003 From: Martin.Leucker at it.uu.se (Martin Leucker) Date: Fri, 11 Jul 2003 22:31:40 +0200 Subject: [BiO BB] CFP: Seminar on Testing Message-ID: <20030711203140.GA29737@hamberg.it.uu.se> [Apologies if you receive this more than once] ------------------------------------------------------------------------ Call for Participation GI/Dagstuhl Research Seminar Model-based Testing of Reactive Systems January 12-15, 2004, Schloss Dagstuhl http://www.it.uu.se/research/project/motres/ ------------------------------------------------------------------------ Theme of the seminar Testing is the primary hardware and software validation technique used by industry today. Usually, it is ad hoc, error prone, and very expensive. In recent years, however, many attempts have been made to develop more sophisticated formal testing methods. But a comprehensive account of the area of formal testing is missing. The goal of this seminar is to compile a volume providing an in-depth exposure of this emerging area, especially to make it easily accessible to new researchers in this field. Aim of the seminar The aim of the seminar is to bring together (primarily young) researchers working in or starting to work in this area (PhD students, postdocs, fresh PhDs, or maybe even MSc students; also established researchers might apply). The seminar will be devoted to the assembly of a structured overview (in terms of presentations and papers) of the state-of-the-art. Organisation The organisers will select the participants on the basis of their application (see below). Selected participants will be approached by the coordinators and will be assigned a theme, thereby taking into account the preferences of the applicants as much as possible. The participants will then write an overview paper (up to 30--40 pages) on the assigned theme, supervised by the coordinator; the papers listed below form a starting point for doing so. During the seminar in January 2004 in Dagstuhl, the overview paper has to be presented (45 minutes) and discussed. Some of the themes listed below are so large that working on them in a 2-person group is possible. The seminar papers written will be collected and published with a German publisher. In fact, based on the quality of the final papers, a publication as a tutorial volume in the LNCS series of Springer-Verlag is very likely. In order to ease the publication process, we strongly encourage the papers to be written using LaTeX using Springer's lncs style. In total, we envisage that taking part in the seminar, including the reading, writing, presenting and travelling, will "cost" at least 5 to 6 weeks of work (full time). Note, however, that esp. for PhD students, this type of work has to be done anyway, as part of their PhD studies. Organisers The seminar is organised by * Manfred Broy, Technical University of Munich, Germany * Bengt Jonsson Uppsala University, Sweden * Joost-Pieter Katoen, University of Twente, Netherlands * Martin Leucker, Uppsala University, Sweden, (Coordinator) * Alexander Pretschner, Technical University of Munich, Germany Time and location The seminar is organised as a GI/Dagstuhl-seminar from January 12, 2004 (Monday, arrival) through January 15, 2004 (Thursday) in the International Conference and Research Center for Computer Science at Schloss Dagstuhl. Dagstuhl is located about halfway between Saarbr?cken and Trier and is ideally suited for a research seminar because of its excellent library and special atmosphere. Registration fee for all participants will be 100 Euro; this includes accommodation, all meals and coffee/tea breaks. This extremely low fee is made possible through the sponsorship of the Gesellschaft f?r Informatik. Application Participants are selected on the basis of a good scientific qualification. Participants can apply by sending a short curriculum vitae (with list of publications) and a letter of reference from a professor (in case of MSc or PhD students). Also indicate the topics of your interest! The list of topics can be found on http://www.it.uu.se/research/project/motres/cfp.html Applications (including a list of preferred topics) should be sent electronically (as PS or PDF) by August 30, 2003 to Martin.Leucker at it.uu.se. Time table * July 01: launch of call for participation * August 30: deadline for applications * September 15: notification on participation * November 2003: first version of seminar paper * December 2003: revised versions of seminar paper * January 12-15, 2004: Dagstuhl seminar * March 2004: final camera-ready seminar papers due * Spring 2004: publication of seminar volume List of theme areas and topics We will give an detailed account to formal approaches of testing as well as relations to other validation techniques like model checking. There are several schools of formal testing. We will give an account to some of them providing the basis for a comparison. We will show the similarities and differences in each approach. In general, we concentrate on so-called black-box testing. In this setting, the system under test is not given explicitly but may only be analysed using interaction in terms of input and output actions. The topics comprise the following areas: T1: Testing of finite state machines (3 chapters) T2: Preorder-based testing of labelled transition systems (4 chapters) T3: Further Model-based testing (3 chapters) T4: Test generation tools and case studies (2 chapters) T5: Test execution: TTCN-3 (1 chapter) T6: Test methods (1 chapter) T7: Testing of non-deterministic systems (1 chapter) T8: Model checking and testing (3 chapters) A detailed list of theme areas and topics can be found on http://www.it.uu.se/research/project/motres/cfp.html where furthermore a starting list of references is given. ------------------------------------------------------------------------ Martin Leucker, http://user.it.uu.se/~leucker/ July 01, 2003 ------------------------------------------------------------------------ From pac at bcm.tmc.edu Mon Jul 14 13:26:31 2003 From: pac at bcm.tmc.edu (Pamela Culpepper) Date: Mon, 14 Jul 2003 12:26:31 -0500 Subject: [BiO BB] Bioinformatics Salaries Message-ID: <3F12E7C7.3080308@bcm.tmc.edu> It's budget time and I need to make sure I get my share. I need to know what the going rate for a the following -- Beginning Bioinformatics Programmer, Senior Bioinformatics Programmer, Bioinformatics Web Developer, Bioinformatics Project Manager, Bioinformatics Database Admin, System Admin Bioinformatics Consulting per hour -- Programming and Analysis. Can somebody help me? Thanks, Pam From rls at cin.ufpe.br Mon Jul 14 17:13:11 2003 From: rls at cin.ufpe.br (Rafael Luiz da Silva) Date: Mon, 14 Jul 2003 18:13:11 -0300 (BRT) Subject: [BiO BB] Bioinformatics Salaries In-Reply-To: <3F12E7C7.3080308@bcm.tmc.edu> Message-ID: I would like to know too :) []s Rafael Luiz ["N?o basta persuadir a mente, ? preciso tocar o cora??o."] (www.cin.ufpe.br/~rls) On Mon, 14 Jul 2003, Pamela Culpepper wrote: > It's budget time and I need to make sure I get my share. > > I need to know what the going rate for a the following -- > > Beginning Bioinformatics Programmer, > Senior Bioinformatics Programmer, > Bioinformatics Web Developer, > Bioinformatics Project Manager, > Bioinformatics Database Admin, > System Admin > > Bioinformatics Consulting per hour -- Programming and Analysis. > > Can somebody help me? > > Thanks, > > Pam > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From landman at scalableinformatics.com Tue Jul 15 15:46:14 2003 From: landman at scalableinformatics.com (Joe Landman) Date: 15 Jul 2003 15:46:14 -0400 Subject: [BiO BB] Reorganization of BLAST Bi naries FTP site Message-ID: <1058298374.3556.1.camel@squash.scalableinformatics.com> Thought this would be good to pass on. -----Forwarded Message----- Subject: [blast-announce] [blast-announce #034] Reorganization of BLAST Bi naries FTP site. Date: 15 Jul 2003 15:07:31 -0400 On or about August 15th 2003 NCBI will make changes to the directory structure for the FTP site of BLAST binaries. This will include the Standalone BLAST Binaries, blastcl3 client and the WWW BLAST Server programs. No changes will be made to the database files as they exist now. There will be a subdirectory under the /blast/executables/ FTP directory called /release/. The release/ subdir will contain all releases and will be indexed by version number. Example: /blast/executables/release/2.2.6/ blast-2.2.6-ia32-linux.tar.gz netblast-2.2.6-ia32-win32.tar.gz If major bugs are discovered between releases, fixes will be made available in a /snapshot/ directory. The /snapshot/ directory will contain fixes indexed by date the binary was updated. For example: /blast/executables/snapshot/2003-05-09/ wwwblast-20030509-sparc-solaris.tar.gz These binaries should only be used if the functionality you need is not in the current release. Announcements concerning changes to release will be made through the BLAST-Announce e-mail service (http://www.ncbi.nlm.nih.gov/BLAST/blastannounce.html). Files will also be renamed to better reflect the program, version, and operating system. For example: blast-2.2.6-powerpc-macos9.hqx is the executable for Standalone BLAST version 2.2.6, for Mac OS9. Similarly netblast-2.2.4-powerpc-macos9.hqx and wwwblast-20030509-powerpc-macosx.tar.gz for the blastcl3 client and WWW BLAST server respectively. These changes apply only to the binaries for NCBI tools and programs. If you have any questions please contact blast-help at ncbi.nlm.nih.gov -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From JATP at Lundbeck.com Mon Jul 21 02:03:56 2003 From: JATP at Lundbeck.com (Jan Torleif Pedersen) Date: Mon, 21 Jul 2003 08:03:56 +0200 Subject: [BiO BB] Promoter Analysis Message-ID: Greetings, I hope not everybody is away on vacation ! We are running some custom spotted microarrays in our microbiology department and I would like to run a promoter analysis on all the genes on the chip. To that end I would need a promoter analysis program that I can run in batch-mode and a set of promoter patterns. Could someone advice on the program and library of choice. Many Regards -- Jan Dr. Jan Torleif Pedersen Section head, Bioinformatics Department of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 DK-Valby Denmark phone: +45 36 43 28 87 FAX: 36438271 email: jatp at lundbeck.com From landman at scalableinformatics.com Mon Jul 21 02:58:13 2003 From: landman at scalableinformatics.com (Joseph Landman) Date: 21 Jul 2003 02:58:13 -0400 Subject: [BiO BB] New version of the sge_mpiblast tool Message-ID: <1058770692.3285.13.camel@protein.scalableinformatics.com> Hi Folks: We completely rewrote our sge_mpiblast execution tool into a real program that allows you to run the excellent mpiBLAST (http://mpiblast.lanl.gov) code within the SGE queuing system on a bio-cluster. The new code is named run_mpiblast and is available from our download page (http://scalableinformatics.com/downloads/). Documentation is in process, and the source is heavily commented. The principal differences between the old and new versions are . error detection and problem reporting . file staging . rewritten in a real programming language, no more shell script . works within SGE, or from the command line . uses config files . run isolation . debugging and verbosity controls This is a merge between an internal project and the ideas behind the original code. Please give it a try and let us know how it behaves. The link to the information page is http://scalableinformatics.com/sge_mpiblast.html . Joe -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From dhbsf at mindspring.com Mon Jul 21 16:53:32 2003 From: dhbsf at mindspring.com (David Ballard) Date: Mon, 21 Jul 2003 15:53:32 -0500 (CDT) Subject: [BiO BB] Bioinformatics Projects Message-ID: <2284046.1058817225742.JavaMail.nobody@wamui04.slb.atl.earthlink.net> Hello all, I'm a current grad student in CS and am interested in learning more about bioinformatics - I have a biopsych/neuroscience background. I've looked through the projects on bioinformatics.org and sent some emails, but none seem to have much activity. Anyone with ideas on how I could get involved? Thank you, David From hjm at tacgi.com Mon Jul 21 18:28:47 2003 From: hjm at tacgi.com (Harry Mangalam) Date: Mon, 21 Jul 2003 15:28:47 -0700 Subject: [BiO BB] Promoter Analysis In-Reply-To: References: Message-ID: <3F1C691F.6000002@tacgi.com> sounds like tacg might be of use. it can take an arbitrary number of patterns formatted as IUPAC patterns, regular expressions, or transfac matrices (altho not mixed) and search large numbers of input sequences. Especially useful for your search, it can also search for pattern /sets/ that you define as useful or interesting - ie: if A, B, C, D, E, and F represent IUPAC patterns such as gyrnngttgtynnng, you could search for (A AND ((B XOR C) OR (D AND F)) NOT (E OR A)) Look at tacg.sf.net and if it looks interesting, let me know and I'll send you version 4 which is just about finished. harry Jan Torleif Pedersen wrote: > Greetings, > > I hope not everybody is away on vacation ! > > We are running some custom spotted microarrays in our microbiology > department and > I would like to run a promoter analysis on all the genes on the chip. To > that end I would need > a promoter analysis program that I can run in batch-mode and a set of > promoter patterns. > > Could someone advice on the program and library of choice. > > Many Regards -- Jan > > Dr. Jan Torleif Pedersen > Section head, Bioinformatics > Department of Molecular Genetics > H. Lundbeck A/S > Ottiliavej 9, 2500 DK-Valby > Denmark > phone: +45 36 43 28 87 > FAX: 36438271 > email: jatp at lundbeck.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> Go Dennis! http://www.kucinich.us From jeff at bioinformatics.org Mon Jul 21 18:47:20 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 21 Jul 2003 18:47:20 -0400 Subject: [BiO BB] Bioinformatics Projects References: <2284046.1058817225742.JavaMail.nobody@wamui04.slb.atl.earthlink.net> Message-ID: <3F1C6D78.60805@bioinformatics.org> Hi David. You can also try subscribing to the mailing lists of projects that interest you. There are some very active projects here: ICIS, Ghemical, E-Cell2, BioPHP, polyxmass, R-nova, Sight, etc. But there are some that are essentially archived. If you find that there are no posts to a mailing list in a few weeks time, chances are the project is not active :-) But posting a message here is a good start. If you could list your skills and interests, perhaps you'll find a match. Cheers. Jeff David Ballard wrote: > Hello all, > > I'm a current grad student in CS and am interested in learning more about bioinformatics - I have a biopsych/neuroscience background. I've looked through the projects on bioinformatics.org and sent some emails, but none seem to have much activity. Anyone with ideas on how I could get involved? > > Thank you, > David > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From rwang at bccancer.bc.ca Tue Jul 22 12:25:05 2003 From: rwang at bccancer.bc.ca (Renxue Wang) Date: Tue, 22 Jul 2003 09:25:05 -0700 Subject: [BiO BB] which one is the "best" protein sequence when multiple entries ar e found? Message-ID: <6BAF4D075F07D411B30900508B94CBA00D84647C@SERVER20> Hi, Everyone, In protein databases such as NCBI and others. The same protein often has many different entries (different accession numbers deposited by different authors at different time). To avoid the redundancy, I need to pick one entry for each protein to work with. What is the criteria to pick the "best" one (the most accurate)? Any rule of thumb for a programmer? Thanks a lot. Ren (rxwang1 at aol.com) -------------- next part -------------- An HTML attachment was scrubbed... URL: From bkutlu at ulb.ac.be Tue Jul 22 04:49:15 2003 From: bkutlu at ulb.ac.be (Burak Kutlu) Date: Tue, 22 Jul 2003 10:49:15 +0200 Subject: [BiO BB] Promoter Analysis In-Reply-To: References: Message-ID: <3F1CFA8B.9090706@ulb.ac.be> Dear Jan Why don't you try RSAT tools. rsat.ulb.ac.be/rsat/ I don't which organism you work with; I hope it helps burak Jan Torleif Pedersen wrote: >Greetings, > >I hope not everybody is away on vacation ! > >We are running some custom spotted microarrays in our microbiology >department and >I would like to run a promoter analysis on all the genes on the chip. To >that end I would need >a promoter analysis program that I can run in batch-mode and a set of >promoter patterns. > >Could someone advice on the program and library of choice. > > Many Regards -- Jan > >Dr. Jan Torleif Pedersen >Section head, Bioinformatics >Department of Molecular Genetics >H. Lundbeck A/S >Ottiliavej 9, 2500 DK-Valby >Denmark >phone: +45 36 43 28 87 >FAX: 36438271 >email: jatp at lundbeck.com > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Burak Kutlu Laboratory of Experimental Medicine Universit? Libre de Bruxelles 808 route de Lennik CP618 B-1070 Bruxelles Belgium http://student.ulb.ac.be/~bkutlu http://msite.nl/burak From mgollery at unr.edu Tue Jul 22 15:12:43 2003 From: mgollery at unr.edu (Martin Gollery) Date: Tue, 22 Jul 2003 12:12:43 -0700 Subject: [BiO BB] Promoter Analysis In-Reply-To: References: Message-ID: <1058901163.3f1d8cab66859@webmail.unr.edu> Hi Jan, Download the Promoter database (EPD) to your local server, then run formatdb on it. This will allow you to do a local Batch BLAST search. Quite quickly too, as EPD is rather small. Marty Quoting Jan Torleif Pedersen : > Greetings, > > I hope not everybody is away on vacation ! > > We are running some custom spotted microarrays in our microbiology > department and > I would like to run a promoter analysis on all the genes on the chip. To > that end I would need > a promoter analysis program that I can run in batch-mode and a set of > promoter patterns. > > Could someone advice on the program and library of choice. > > Many Regards -- Jan > > Dr. Jan Torleif Pedersen > Section head, Bioinformatics > Department of Molecular Genetics > H. Lundbeck A/S > Ottiliavej 9, 2500 DK-Valby > Denmark > phone: +45 36 43 28 87 > FAX: 36438271 > email: jatp at lundbeck.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS200 (775)784-6048 ------------------------------------------------- This mail sent through https://webmail.unr.edu From Joel.Dudley at asu.edu Tue Jul 22 17:30:33 2003 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Tue, 22 Jul 2003 14:30:33 -0700 Subject: [BiO BB] which one is the "best" protein sequence when multip le entries ar e found? Message-ID: <9EAE2E44897BC749ACB3A62683B2C8D112FB8A@ex4.asurite.ad.asu.edu> I would suggest picking the longest version of the protein. - Joel -----Original Message----- From: Renxue Wang [mailto:rwang at bccancer.bc.ca] Sent: Tuesday, July 22, 2003 9:25 AM To: 'bio_bulletin_board at bioinformatics.org' Subject: [BiO BB] which one is the "best" protein sequence when multiple entries ar e found? Hi, Everyone, In protein databases such as NCBI and others. The same protein often has many different entries (different accession numbers deposited by different authors at different time). To avoid the redundancy, I need to pick one entry for each protein to work with. What is the criteria to pick the "best" one (the most accurate)? Any rule of thumb for a programmer? Thanks a lot. Ren (rxwang1 at aol.com) -------------- next part -------------- An HTML attachment was scrubbed... URL: From mkgovindis at yahoo.com Tue Jul 22 22:16:10 2003 From: mkgovindis at yahoo.com (govind mk) Date: Tue, 22 Jul 2003 19:16:10 -0700 (PDT) Subject: [BiO BB] which one is the "best" protein sequence when multip le entries ar e found? In-Reply-To: <9EAE2E44897BC749ACB3A62683B2C8D112FB8A@ex4.asurite.ad.asu.edu> Message-ID: <20030723021610.43151.qmail@web40106.mail.yahoo.com> Hi IF you find a hit with a Refseq entry then I would suggest you to go with it as Refseq entries have undergone some level of curation and standardisation. -Govind --- Joel Dudley wrote: > I would suggest picking the longest version of the > protein. > > - Joel > > -----Original Message----- > From: Renxue Wang [mailto:rwang at bccancer.bc.ca] > Sent: Tuesday, July 22, 2003 9:25 AM > To: 'bio_bulletin_board at bioinformatics.org' > Subject: [BiO BB] which one is the "best" protein > sequence when multiple > entries ar e found? > > > > Hi, Everyone, In protein databases such as NCBI and > others. The same protein > often has many different entries (different > accession numbers deposited by > different authors at different time). To avoid the > redundancy, I need to > pick one entry for each protein to work with. What > is the criteria to pick > the "best" one (the most accurate)? Any rule of > thumb for a programmer? > Thanks a lot. Ren (rxwang1 at aol.com) > > __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From ngadewal at yahoo.com Wed Jul 23 05:31:34 2003 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 23 Jul 2003 02:31:34 -0700 (PDT) Subject: [BiO BB] which one is the "best" protein sequence when multiple entries ar e found? In-Reply-To: <6BAF4D075F07D411B30900508B94CBA00D84647C@SERVER20> Message-ID: <20030723093134.99178.qmail@web40911.mail.yahoo.com> Hi, If u are looking for gene/protein seq from particular organism source than go to 'map viewer' in NCBI. In Map viewer gives a single gene entry for an organsim. Single gene entry is derived for multiple sequence of different seqs of same gene in a database. Check for locus name of the gene. bye.. Nikhil --- Renxue Wang wrote: > Hi, Everyone, In protein databases such as NCBI and > others. The same protein > often has many different entries (different > accession numbers deposited by > different authors at different time). To avoid the > redundancy, I need to > pick one entry for each protein to work with. What > is the criteria to pick > the "best" one (the most accurate)? Any rule of > thumb for a programmer? > Thanks a lot. Ren (rxwang1 at aol.com) > > ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Tata Memorial centre, Kharghar, Navi Mumbai E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From jccostel at indiana.edu Wed Jul 23 15:19:46 2003 From: jccostel at indiana.edu (jccostel at indiana.edu) Date: Wed, 23 Jul 2003 14:19:46 -0500 Subject: [BiO BB] Bioinformtics Projects Message-ID: <1058987986.3f1edfd2cab50@webmail.iu.edu> Hello all, I will be entering my second year as a Master?s student in Bioinformatics at Indiana University. I have a Biology and CS background. I am currently looking for ideas for my Capstone Project/Master?s Thesis. I have interests in proteomics, data mining, algorithm development and application, and bioinformatics software applications, just to name a few. I was wondering if anyone out there had projects they needed help on or had ideas that they wanted to see come to life. This could be a very good opportunity for all you out there with some great ideas and concepts. The way I see it, you can get a whole lot of research done for free (done by myself, of course) and possibly a published article. The investment by you would be minimal and the payoffs (I hope) would far exceed the amount of time that will be required of you. If anyone has any thoughts, comments, or suggestions, please contact me at: jccostel at indiana.edu Thanks to all, Jim Costello From b.d.vanschaik at amc.uva.nl Thu Jul 24 04:13:08 2003 From: b.d.vanschaik at amc.uva.nl (Barbera van Schaik) Date: Thu, 24 Jul 2003 10:13:08 +0200 Subject: [BiO BB] Comparison HGP and Celera Message-ID: <3F1F9514.7030100@amc.uva.nl> Hello, In 2001 an article was published where the annotated genes of the Celera draft sequence were compared with the annotated genes of the HGP draft sequence (Hogenesch et al (2001) A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell, 106(4), 413-415) I was wondering if someone else has made a comparison more recently with the new databases. I couldn't find an article about an update anywhere. With kind regards, Barbera -- ._._._._._._._._._._._._._._._._._._._._._._. Barbera D.C. van Schaik Academic Medical Center (K2.207) Postbus 22660 1100 DD Amsterdam The Netherlands DivG/BioInformatics Laboratory DivC/Human Genetics Room: K2.207 Phone: (+31) 20 - 566 25 18 Email: B.D.vanSchaik at amc.uva.nl _._._._._._._._._._._._._._._._._._._._._._._ -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Thu Jul 24 16:49:51 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 24 Jul 2003 21:49:51 +0100 (BST) Subject: [BiO BB] Bioinformtics Projects In-Reply-To: <1058987986.3f1edfd2cab50@webmail.iu.edu> Message-ID: I have a huge list of projects, if you are interested.... Dan. On Wed, 23 Jul 2003 jccostel at indiana.edu wrote: > Hello all, > > I will be entering my second year as a Master?s student in Bioinformatics at > Indiana University. I have a Biology and CS background. I am currently > looking for ideas for my Capstone Project/Master?s Thesis. I have interests in > proteomics, data mining, algorithm development and application, and > bioinformatics software applications, just to name a few. I was wondering if > anyone out there had projects they needed help on or had ideas that they wanted > to see come to life. This could be a very good opportunity for all you out > there with some great ideas and concepts. The way I see it, you can get a > whole lot of research done for free (done by myself, of course) and possibly a > published article. The investment by you would be minimal and the payoffs (I > hope) would far exceed the amount of time that will be required of you. > > If anyone has any thoughts, comments, or suggestions, please contact me at: > jccostel at indiana.edu > > Thanks to all, > Jim Costello > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From cat_worth at hotmail.com Fri Jul 25 05:45:39 2003 From: cat_worth at hotmail.com (Catherine Worth) Date: Fri, 25 Jul 2003 09:45:39 +0000 Subject: [BiO BB] Microarray Analysis of Twin Data Message-ID: An HTML attachment was scrubbed... URL: From srivaths at engineering.ucsb.edu Sun Jul 27 01:48:44 2003 From: srivaths at engineering.ucsb.edu (Srivatsan Pallavaram) Date: Sat, 26 Jul 2003 22:48:44 -0700 Subject: [BiO BB] Industry standard References: Message-ID: <028301c35402$c354d3d0$be1410ac@Srivathsan> Hi all, I am interested in knowing the industry standard for gene classification (Intron/exon). I am working on classification using neural networks and am interested in comparing my results with an industry standard. Help in this regard will be deeply appreciated. Thank You Srivathsan --- -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Sun Jul 27 15:26:49 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sun, 27 Jul 2003 20:26:49 +0100 (BST) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <1059146891.3f214c8b4bc10@webmail.iu.edu> Message-ID: Great!, and thanks for the responses! I hope you don't mind, but I have opened this up to the BB for discussion. I have worked on and with MS bioinfo projects before, so I have some idea of what is required / what can be reasonably acheived. In this case I doubt the same kind of close collaboration will be possible, where our unit was able to fund students. I know what you meen about getting 'outside ideas', the broader your input the better in all fields I guess. I think it is definatly worth while in the bioinfo community, as this area of science more closly resembles the sofware engineering community than most. I think the best way to procede is to make the projects clearly open source, so ideas, progress and results can be made available to the community. I guess this would work well within the framework of bioinformatics.org, but I have no practical experience of setting up / running open source projects! I.E. I have no clue what kind of admin this involves / where responsibility lies etc. I imagine this should not be too much of a problem if you and other students are willing to work togeher to get the projects off the ground within this framework (maby including university admin where you are?). I will prepare a list of projects which I think are reasonable, and then I guess we should initiate some kind of open discussion on the relevance / previous work in the area / statement of aims and objectives / etc. Is this kind of forum available at bioinfo.org? I would really like to see an open forum for 'modular' project discussion, where people can add relevant papers / link / etc. to form a knowledge base for further work. Anyway, I will first have to run the list by the people in my lab to be sure that they are happy having these ideas made open (as I have a terrible habbit of jumping on good ideas which are not my own!). I will look forward to further comments / suggestions. P.S. do you have a time frame for project selection, as I could send one-at-a-time if that would help? Thanks very much for your idea, Dan. On Fri, 25 Jul 2003 jccostel at indiana.edu wrote: > > > Dan, > > I read your post saying you have lots of projects. I would be interested in a > project if it were something that I could use as my Master's Capstone Project > (I am currently working towards my Master's degree in Bioinformatics). I am > also interested in seeing what other people are working on outside of > Bloomington Indiana (Indiana University). There are very interesting projects > and research going on at Indiana University, but it is also a pretty small and > often secluded community. It would be nice to get a different perspective on > Bioinformatics and possible work with people, again, outside of Bloomington > Indiana. Also, I know there will be other students looking for ideas for their > Master's project and I could pass the project information on to them, if you > would like. I am not sure how you would like to proceed, but please email me > back with any input. > > Thanks, > Jim Costello > From srivaths at engineering.ucsb.edu Sun Jul 27 19:49:48 2003 From: srivaths at engineering.ucsb.edu (Srivatsan Pallavaram) Date: Sun, 27 Jul 2003 23:49:48 -0000 Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: Message-ID: Hi all, This open source projects, forum like environment, links, papers, etc sounds like a great idea to me. I am game! Srivatsan Pallavaram --- Dan Bolser said: > > Great!, and thanks for the responses! > > I hope you don't mind, but I have opened > this up to the BB for discussion. > > I have worked on and with MS bioinfo projects > before, so I have some idea of what is required / > what can be reasonably acheived. In this case I > doubt the same kind of close collaboration will > be possible, where our unit was able to fund students. > > I know what you meen about getting 'outside ideas', > the broader your input the better in all fields > I guess. I think it is definatly worth while in > the bioinfo community, as this area of science > more closly resembles the sofware engineering > community than most. > > I think the best way to procede is to make the > projects clearly open source, so ideas, progress and > results can be made available to the community. > > I guess this would work well within the framework of > bioinformatics.org, but I have no practical experience > of setting up / running open source projects! I.E. I > have no clue what kind of admin this involves / where > responsibility lies etc. > > I imagine this should not be too much of a problem if > you and other students are willing to work togeher to > get the projects off the ground within this framework > (maby including university admin where you are?). > > I will prepare a list of projects which I think are > reasonable, and then I guess we should initiate > some kind of open discussion on the relevance / > previous work in the area / statement of aims and > objectives / etc. > > Is this kind of forum available at bioinfo.org? > > I would really like to see an open forum for 'modular' > project discussion, where people can add relevant > papers / link / etc. to form a knowledge base for > further work. > > Anyway, I will first have to run the list by the > people in my lab to be sure that they are happy > having these ideas made open (as I have a terrible > habbit of jumping on good ideas which are not my own!). > > I will look forward to further comments / suggestions. > > P.S. do you have a time frame for project selection, as > I could send one-at-a-time if that would help? > > Thanks very much for your idea, > Dan. > > > > On Fri, 25 Jul 2003 jccostel at indiana.edu wrote: > > > > > > > Dan, > > > > I read your post saying you have lots of projects. I would be interested in a > > project if it were something that I could use as my Master's Capstone Project > > (I am currently working towards my Master's degree in Bioinformatics). I am > > also interested in seeing what other people are working on outside of > > Bloomington Indiana (Indiana University). There are very interesting projects > > and research going on at Indiana University, but it is also a pretty small and > > often secluded community. It would be nice to get a different perspective on > > Bioinformatics and possible work with people, again, outside of Bloomington > > Indiana. Also, I know there will be other students looking for ideas for their > > Master's project and I could pass the project information on to them, if you > > would like. I am not sure how you would like to proceed, but please email me > > back with any input. > > > > Thanks, > > Jim Costello > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Srivatsan Pallavaram Graduate Student Researcher Image Processing Research Lab (Prof. Sanjit K Mitra group) Dept. of Electrical and Computer Engineering (ECE) University of California, Santa Barbara (UCSB) From jeff at bioinformatics.org Sun Jul 27 23:17:59 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 27 Jul 2003 23:17:59 -0400 Subject: [BiO BB] Re: Bioinformatics Project References: Message-ID: <3F2495E7.3080301@bioinformatics.org> Hi Dan. Dan Bolser wrote: > I will prepare a list of projects which I think are > reasonable, and then I guess we should initiate > some kind of open discussion on the relevance / > previous work in the area / statement of aims and > objectives / etc. > > Is this kind of forum available at bioinfo.org? If the project requires software development, the Biodevelopers forum would be a good place to go: biodevelopers at bioinformatics.org http://bioinformatics.org/lists/biodevelopers > I would really like to see an open forum for 'modular' > project discussion, where people can add relevant > papers / link / etc. to form a knowledge base for > further work. I'd been thinking along these lines too. I often get e-mail messages from students looking for ideas to pursue, and I have to tell them that most scientists have very few leads and thus covet them (i.e., good luck getting anyone to give them away). I also know of many knowledgebase projects to archive things that we know. But, how about things that we **DON'T KNOW**? How about developing a "lack-of-knowledge-base" or "questionbase", where the literature is mined for unanswered questions (perhaps from the "future directions" sections in published articles)? Does anyone know if anything like that exists (specifcally one where the questions have **NEVER** been answered)? If not, maybe it should be made (and then, for everyone out there who has asked me for ideas, there you go ;-)) Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From bioinfo_india at yahoo.com Mon Jul 28 07:45:39 2003 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Mon, 28 Jul 2003 04:45:39 -0700 (PDT) Subject: [BiO BB] HMMER on genomes In-Reply-To: Message-ID: <20030728114539.86742.qmail@web41107.mail.yahoo.com> Hi Group, Did any one tried to build HMMs (using HMMER) for any gene class and then search genomes over this HMM. Although this is more perfect for proteins, how one can cope the problem of introns when you search genomic DNA where you build and train HMM on mRNAs (Exons). Can it be done. Unfortunately the makers of HMMER are politely denying to respond to such specific questions. Can any one please help. Thanks Suraj. ===== Suraj Peri Ph.D. Student School of Medicine Johns Hopkins University 600 North Wolfe Street Baltimore, MD 21287 Phone:410-502-6665 E-mail: peri at jhmi.edu __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From mgollery at unr.edu Mon Jul 28 12:42:04 2003 From: mgollery at unr.edu (Martin Gollery) Date: Mon, 28 Jul 2003 09:42:04 -0700 Subject: [BiO BB] HMMER on genomes In-Reply-To: <20030728114539.86742.qmail@web41107.mail.yahoo.com> References: <20030728114539.86742.qmail@web41107.mail.yahoo.com> Message-ID: <1059410524.3f25525c8046d@webmail.unr.edu> Hi Suraj, Try GeneWise- you can download it at ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ But I will warn you- it is quite slow! Marty Quoting Peri Suraj : > Hi Group, > Did any one tried to build HMMs (using HMMER) for any > gene class and then search genomes over this HMM. > Although this is more perfect for proteins, how one > can cope the problem of introns when you search > genomic DNA where you build and train HMM on mRNAs > (Exons). Can it be done. Unfortunately the makers of > HMMER are politely denying to respond to such specific > questions. Can any one please help. > Thanks > > Suraj. > > > ===== > Suraj Peri > Ph.D. Student > School of Medicine > Johns Hopkins University > 600 North Wolfe Street > Baltimore, MD 21287 > Phone:410-502-6665 > E-mail: peri at jhmi.edu > > __________________________________ > Do you Yahoo!? > Yahoo! SiteBuilder - Free, easy-to-use web site design software > http://sitebuilder.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 New phone number! 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From vamsally at yahoo.com Mon Jul 28 16:27:57 2003 From: vamsally at yahoo.com (Sally Lee) Date: Mon, 28 Jul 2003 13:27:57 -0700 (PDT) Subject: [BiO BB] Request for Information... Message-ID: <20030728202757.25467.qmail@web13507.mail.yahoo.com> Hello, I am hoping someone might be able to point me in the right direction. I hope to apply to a graduate program in Bioinformatics this fall and looking for professors in universities/institutes that might be working on research in the areas that I am interested in. Since my background is both in Biology and Computer Science, the areas I am mostly interested in are protein modeling or genome data mining. I have found BMERC site at Boston University and few others, but I thought someone in the field would know more about what I seek. Thank you for your help! Sally ===== ~~Sally~~ www.cafedeminuit.com __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From MRR at unex.berkeley.edu Mon Jul 28 16:38:01 2003 From: MRR at unex.berkeley.edu (Michelle Ragozzino) Date: Mon, 28 Jul 2003 13:38:01 -0700 Subject: [BiO BB] Request for Information... Message-ID: Have you tried: http://123genomics.homestead.com/files/courses.html Good luck! m >>> vamsally at yahoo.com 07/28/03 01:27PM >>> Hello, I am hoping someone might be able to point me in the right direction. I hope to apply to a graduate program in Bioinformatics this fall and looking for professors in universities/institutes that might be working on research in the areas that I am interested in. Since my background is both in Biology and Computer Science, the areas I am mostly interested in are protein modeling or genome data mining. I have found BMERC site at Boston University and few others, but I thought someone in the field would know more about what I seek. Thank you for your help! Sally ===== ~~Sally~~ www.cafedeminuit.com __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From pfern at igc.gulbenkian.pt Tue Jul 29 05:47:46 2003 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Tue, 29 Jul 2003 10:47:46 +0100 Subject: [BiO BB] Request for Information... grad prog References: <20030728202757.25467.qmail@web13507.mail.yahoo.com> Message-ID: <00d101c355b6$771d8ce0$4d1a7ec1@biocasept> Hello You may be interested in applying to PGBIOINF in Portugal. The next call is in Jan 2004 http://bioinfomatics.fc.ul.pt Thank you P. Fernandes ---------------------------------------------------------------------------- - Pedro Fernandes E-mail: pfern at igc.gulbenkian.pt Instituto Gulbenkian de Ciencia pen - No Portugues da Rede EMBnet Unidade de Bioinformatica URL: http://www.igc.gulbenkian.pt Apartado 14 Telephone (switchboard): +351 21 4407900 2781-901 OEIRAS Telephone (direct) : +351 21 4407912 PORTUGAL Fax : +351 21 4407970 From dmb at mrc-dunn.cam.ac.uk Tue Jul 29 07:56:52 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 29 Jul 2003 12:56:52 +0100 Subject: [BiO BB] Re: Bioinformatics Project References: <3F2495E7.3080301@bioinformatics.org> Message-ID: <3F266104.9020002@mrc-dunn.cam.ac.uk> J.W. Bizzaro wrote: > Hi Dan. > > Dan Bolser wrote: > >> I will prepare a list of projects which I think are >> reasonable, and then I guess we should initiate >> some kind of open discussion on the relevance / previous work in the >> area / statement of aims and objectives / etc. >> Is this kind of forum available at bioinfo.org? > > > If the project requires software development, the Biodevelopers forum > would be a good place to go: > > biodevelopers at bioinformatics.org > http://bioinformatics.org/lists/biodevelopers Cheers, I am sure that development will be involved, but I don't see the production of 'one off' applications as the main aim. One unifying principal of the work I have in mind is knowledge modelling (through data modelling). I see this as a kind of ontology of bioinformatics, but of course this isn't an implicitly correct or static model of the domain. It makes sense for this mode to be openly developed (along the lines of an integrated database system?). Various projects could 'plug in' to the main system in the form of specific databases and analysis pipelines, but there is a unified (but as yet unknown) whole. I was thinking that we should start a new project with this aim (building towards and defining the 'whole'). >> I would really like to see an open forum for 'modular' >> project discussion, where people can add relevant >> papers / link / etc. to form a knowledge base for further work. > > > I'd been thinking along these lines too. I often get e-mail messages > from students looking for ideas to pursue, and I have to tell them > that most scientists have very few leads and thus covet them (i.e., > good luck getting anyone to give them away). Sadly I have discovered that the ideas in my head are not my property. However, I am confident that my mind reading alter ego is a free man, and he should be able to get my ideas across. > I also know of many knowledgebase projects to archive things that we > know. But, how about things that we **DON'T KNOW**? How about > developing a "lack-of-knowledge-base" or "questionbase", where the > literature is mined for unanswered questions (perhaps from the "future > directions" sections in published articles)? I always get the impression that this knowledge is only available to experts in the field. It takes knowledge of the domain to know which 'next step' out of the many is the most relevant for the field. This relates to the idea of getting people to post up projects that they would like to see done, an expert wish list. This inherently comes with background information to motivate why the project should be taken on, what can be gained, and what related work exists etc. > Does anyone know if anything like that exists (specifcally one where > the questions have **NEVER** been answered)? If not, maybe it should > be made (and then, for everyone out there who has asked me for ideas, > there you go ;-)) Great! phrased like this I am sure people would be happy to contribute... 'What do you think are the biggest open questions in bioinf?' 'What question would you ask God about Bioinformatics?' > > Cheers. > Jeff Ta, Dan. From lxyiwc at yahoo.com Tue Jul 29 19:17:18 2003 From: lxyiwc at yahoo.com (l x yi) Date: Tue, 29 Jul 2003 16:17:18 -0700 (PDT) Subject: [BiO BB] protein profile statistics question Message-ID: <20030729231718.78478.qmail@web21205.mail.yahoo.com> Does anyone know if there has been any work on modelling the correlations between multiple alignment protein profiles? Thanks very much. Lily --------------------------------- Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software -------------- next part -------------- An HTML attachment was scrubbed... URL: From pfern at igc.gulbenkian.pt Wed Jul 30 05:59:22 2003 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Wed, 30 Jul 2003 10:59:22 +0100 Subject: [BiO BB] sorry, my last message was a mistake Message-ID: <00ee01c35681$404af510$4d1a7ec1@biocasept> An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Wed Jul 30 06:26:50 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 30 Jul 2003 11:26:50 +0100 Subject: [BiO BB] protein profile statistics question References: <20030729231718.78478.qmail@web21205.mail.yahoo.com> Message-ID: <3F279D6A.4060201@mrc-dunn.cam.ac.uk> protein profiles? l x yi wrote: > Does anyone know if there has been any work on modelling the > correlations between multiple alignment protein profiles? > > Thanks very much. > > Lily > ------------------------------------------------------------------------ > Do you Yahoo!? > Yahoo! SiteBuilder > - > Free, easy-to-use web site design software -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Wed Jul 30 07:56:47 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 30 Jul 2003 12:56:47 +0100 Subject: [BiO BB] Re: Bioinformatics Project References: Message-ID: <3F27B27F.90202@mrc-dunn.cam.ac.uk> Srivatsan Pallavaram wrote: > Hi all, > > This open source projects, forum like environment, links, papers, etc sounds > like a great idea to me. I am game! > > Srivatsan Pallavaram > --- I started working on a 'journal magement system' in PHP, maby this would be a good inital project to start to help admin. The implemented system uploads a journal in pdf / ps format and then converts the document to text. The text of the document is then displayed alongside a form, to help the user fill in the various fields i.e. author, title, date, journal, etc. Then there is another form to handle multiple authors .... Thinking about this it is really clunky - we could have a system to query MEDLINE and parse the reference tag into a local database of journals. Can we do this with PHP? I.E. PHP - SOAP? I started to implement browsing of the database, but didn't get very far. I am sure there is plenty of stuff we could take from 'on line shopping' modules. Searching, reader comments and ratings need to be implemented, as well as a system to link various journals with various projects / sub sections of projects. In this way you could click on a project, and search all the associated papers for user comments like 'a good introduction'. Later you could use the system to search medline and add a paper to the project. We could list the 'most popular read' in each project. Can we borrow some of the infra from BMC ? Cheers, Dan. >Dan Bolser said: > > > >>Great!, and thanks for the responses! >> >>I hope you don't mind, but I have opened >>this up to the BB for discussion. >> >>I have worked on and with MS bioinfo projects >>before, so I have some idea of what is required / >>what can be reasonably acheived. In this case I >>doubt the same kind of close collaboration will >>be possible, where our unit was able to fund students. >> >>I know what you meen about getting 'outside ideas', >>the broader your input the better in all fields >>I guess. I think it is definatly worth while in >>the bioinfo community, as this area of science >>more closly resembles the sofware engineering >>community than most. >> >>I think the best way to procede is to make the >>projects clearly open source, so ideas, progress and >>results can be made available to the community. >> >>I guess this would work well within the framework of >>bioinformatics.org, but I have no practical experience >>of setting up / running open source projects! I.E. I >>have no clue what kind of admin this involves / where >>responsibility lies etc. >> >>I imagine this should not be too much of a problem if >>you and other students are willing to work togeher to >>get the projects off the ground within this framework >>(maby including university admin where you are?). >> >>I will prepare a list of projects which I think are >>reasonable, and then I guess we should initiate >>some kind of open discussion on the relevance / >>previous work in the area / statement of aims and >>objectives / etc. >> >>Is this kind of forum available at bioinfo.org? >> >>I would really like to see an open forum for 'modular' >>project discussion, where people can add relevant >>papers / link / etc. to form a knowledge base for >>further work. >> >>Anyway, I will first have to run the list by the >>people in my lab to be sure that they are happy >>having these ideas made open (as I have a terrible >>habbit of jumping on good ideas which are not my own!). >> >>I will look forward to further comments / suggestions. >> >>P.S. do you have a time frame for project selection, as >>I could send one-at-a-time if that would help? >> >>Thanks very much for your idea, >>Dan. >> >> >> >> From mgruenb at gmx.net Wed Jul 30 09:15:15 2003 From: mgruenb at gmx.net (Michael Gruenberger) Date: 30 Jul 2003 13:15:15 +0000 Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <3F27B27F.90202@mrc-dunn.cam.ac.uk> References: <3F27B27F.90202@mrc-dunn.cam.ac.uk> Message-ID: <1059570915.4442.36.camel@vogel> Hello everyone, you can have some of my code: I wrote a PHP system for a news web site. It allows users to submit news and attach files (Images, PDFs, Docs,etc). It also has a comments system. It can have different categories and it has a (simple) search engine. It uses Sybase as backend, but it should be quite easy to modify it for MySQL or Postgresql. It should also be quite easy to add some fields (e.g. for Medline references etc). If you are interested I would be more than happy to contribute to your project! Ohh.. you can see how it works here (except for the admin bit): http://www.euradnews.org Cheers, Michael. On Wed, 2003-07-30 at 11:56, Dan Bolser wrote: > Srivatsan Pallavaram wrote: > > > Hi all, > > > > This open source projects, forum like environment, links, papers, etc sounds > > like a great idea to me. I am game! > > > > Srivatsan Pallavaram > > --- > > > I started working on a 'journal magement system' in PHP, > maby this would be a good inital project to start to help > admin. > > The implemented system uploads a journal in pdf / ps > format and then converts the document to text. > > The text of the document is then displayed alongside > a form, to help the user fill in the various fields > > i.e. author, title, date, journal, etc. > > Then there is another form to handle > multiple authors .... > > Thinking about this it is really clunky - we could have > a system to query MEDLINE and parse the reference > tag into a local database of journals. Can we do this with > PHP? I.E. PHP - SOAP? > > I started to implement browsing of the database, but > didn't get very far. I am sure there is plenty of stuff > we could take from 'on line shopping' modules. > > Searching, reader comments and ratings need to be > implemented, as well as a system to link various > journals with various projects / sub sections of > projects. > > In this way you could click on a project, and search > all the associated papers for user comments like > 'a good introduction'. Later you could use the system > to search medline and add a paper to the project. > > We could list the 'most popular read' in each project. > > Can we borrow some of the infra from BMC ? > > Cheers, > Dan. > > >Dan Bolser said: > > > > > > > >>Great!, and thanks for the responses! > >> > >>I hope you don't mind, but I have opened > >>this up to the BB for discussion. > >> > >>I have worked on and with MS bioinfo projects > >>before, so I have some idea of what is required / > >>what can be reasonably acheived. In this case I > >>doubt the same kind of close collaboration will > >>be possible, where our unit was able to fund students. > >> > >>I know what you meen about getting 'outside ideas', > >>the broader your input the better in all fields > >>I guess. I think it is definatly worth while in > >>the bioinfo community, as this area of science > >>more closly resembles the sofware engineering > >>community than most. > >> > >>I think the best way to procede is to make the > >>projects clearly open source, so ideas, progress and > >>results can be made available to the community. > >> > >>I guess this would work well within the framework of > >>bioinformatics.org, but I have no practical experience > >>of setting up / running open source projects! I.E. I > >>have no clue what kind of admin this involves / where > >>responsibility lies etc. > >> > >>I imagine this should not be too much of a problem if > >>you and other students are willing to work togeher to > >>get the projects off the ground within this framework > >>(maby including university admin where you are?). > >> > >>I will prepare a list of projects which I think are > >>reasonable, and then I guess we should initiate > >>some kind of open discussion on the relevance / > >>previous work in the area / statement of aims and > >>objectives / etc. > >> > >>Is this kind of forum available at bioinfo.org? > >> > >>I would really like to see an open forum for 'modular' > >>project discussion, where people can add relevant > >>papers / link / etc. to form a knowledge base for > >>further work. > >> > >>Anyway, I will first have to run the list by the > >>people in my lab to be sure that they are happy > >>having these ideas made open (as I have a terrible > >>habbit of jumping on good ideas which are not my own!). > >> > >>I will look forward to further comments / suggestions. > >> > >>P.S. do you have a time frame for project selection, as > >>I could send one-at-a-time if that would help? > >> > >>Thanks very much for your idea, > >>Dan. > >> > >> > >> > >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Michael Gruenberger Computer Officer, University of Cambridge Webmaster, European Late Effects Project, http://www.eulep.org Developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From gary at www.bioinformatics.org Wed Jul 30 10:51:55 2003 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Wed, 30 Jul 2003 10:51:55 -0400 (EDT) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <3F27B27F.90202@mrc-dunn.cam.ac.uk> Message-ID: Hey Gang, You might want to check out 'Librarian' http://bioinformatics.org/librarian/ Librarian is a free tool for self-creation of virtual annotated library of PDF articles, designed for small trusted groups, e.g. science labs. Regards, g. On Wed, 30 Jul 2003, Dan Bolser wrote: > Srivatsan Pallavaram wrote: > > > Hi all, > > > > This open source projects, forum like environment, links, papers, etc sounds > > like a great idea to me. I am game! > > > > Srivatsan Pallavaram > > --- > > > I started working on a 'journal magement system' in PHP, > maby this would be a good inital project to start to help > admin. > > The implemented system uploads a journal in pdf / ps > format and then converts the document to text. > > The text of the document is then displayed alongside > a form, to help the user fill in the various fields > > i.e. author, title, date, journal, etc. > > Then there is another form to handle > multiple authors .... > > Thinking about this it is really clunky - we could have > a system to query MEDLINE and parse the reference > tag into a local database of journals. Can we do this with > PHP? I.E. PHP - SOAP? > > I started to implement browsing of the database, but > didn't get very far. I am sure there is plenty of stuff > we could take from 'on line shopping' modules. > > Searching, reader comments and ratings need to be > implemented, as well as a system to link various > journals with various projects / sub sections of > projects. > > In this way you could click on a project, and search > all the associated papers for user comments like > 'a good introduction'. Later you could use the system > to search medline and add a paper to the project. > > We could list the 'most popular read' in each project. > > Can we borrow some of the infra from BMC ? > > Cheers, > Dan. > > >Dan Bolser said: > > > > > > > >>Great!, and thanks for the responses! > >> > >>I hope you don't mind, but I have opened > >>this up to the BB for discussion. > >> > >>I have worked on and with MS bioinfo projects > >>before, so I have some idea of what is required / > >>what can be reasonably acheived. In this case I > >>doubt the same kind of close collaboration will > >>be possible, where our unit was able to fund students. > >> > >>I know what you meen about getting 'outside ideas', > >>the broader your input the better in all fields > >>I guess. I think it is definatly worth while in > >>the bioinfo community, as this area of science > >>more closly resembles the sofware engineering > >>community than most. > >> > >>I think the best way to procede is to make the > >>projects clearly open source, so ideas, progress and > >>results can be made available to the community. > >> > >>I guess this would work well within the framework of > >>bioinformatics.org, but I have no practical experience > >>of setting up / running open source projects! I.E. I > >>have no clue what kind of admin this involves / where > >>responsibility lies etc. > >> > >>I imagine this should not be too much of a problem if > >>you and other students are willing to work togeher to > >>get the projects off the ground within this framework > >>(maby including university admin where you are?). > >> > >>I will prepare a list of projects which I think are > >>reasonable, and then I guess we should initiate > >>some kind of open discussion on the relevance / > >>previous work in the area / statement of aims and > >>objectives / etc. > >> > >>Is this kind of forum available at bioinfo.org? > >> > >>I would really like to see an open forum for 'modular' > >>project discussion, where people can add relevant > >>papers / link / etc. to form a knowledge base for > >>further work. > >> > >>Anyway, I will first have to run the list by the > >>people in my lab to be sure that they are happy > >>having these ideas made open (as I have a terrible > >>habbit of jumping on good ideas which are not my own!). > >> > >>I will look forward to further comments / suggestions. > >> > >>P.S. do you have a time frame for project selection, as > >>I could send one-at-a-time if that would help? > >> > >>Thanks very much for your idea, > >>Dan. > >> > >> > >> > >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From sookjc at yahoo.com Wed Jul 30 11:29:20 2003 From: sookjc at yahoo.com (Sook Jung) Date: Wed, 30 Jul 2003 08:29:20 -0700 (PDT) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: Message-ID: <20030730152920.28300.qmail@web20912.mail.yahoo.com> Hi, Is there anythink like it for Unix? Thanks, Sook --- Gary Van Domselaar wrote: > Hey Gang, > > You might want to check out 'Librarian' > http://bioinformatics.org/librarian/ > > Librarian is a free tool for self-creation of > virtual annotated library of > PDF articles, designed for small trusted groups, > e.g. science labs. > > Regards, > > g. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From dmb at mrc-dunn.cam.ac.uk Wed Jul 30 10:37:20 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 30 Jul 2003 15:37:20 +0100 (BST) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <20030730152920.28300.qmail@web20912.mail.yahoo.com> Message-ID: It works in linux! PHP is so cool! On Wed, 30 Jul 2003, Sook Jung wrote: > Hi, > > Is there anythink like it for Unix? > Thanks, > > Sook > --- Gary Van Domselaar > wrote: > > Hey Gang, > > > > You might want to check out 'Librarian' > > http://bioinformatics.org/librarian/ > > > > Librarian is a free tool for self-creation of > > virtual annotated library of > > PDF articles, designed for small trusted groups, > > e.g. science labs. > > > > Regards, > > > > g. > > > __________________________________ > Do you Yahoo!? > Yahoo! SiteBuilder - Free, easy-to-use web site design software > http://sitebuilder.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From steletch at biomedicale.univ-paris5.fr Wed Jul 30 13:00:25 2003 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: 30 Jul 2003 19:00:25 +0200 Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <3F27B27F.90202@mrc-dunn.cam.ac.uk> References: <3F27B27F.90202@mrc-dunn.cam.ac.uk> Message-ID: <1059584425.11527.7.camel@pc-54-149.kj.uib.no> Le mer 30/07/2003 ? 13:56, Dan Bolser a ?crit : > Srivatsan Pallavaram wrote: > > > Hi all, > > > > This open source projects, forum like environment, links, papers, etc sounds > > like a great idea to me. I am game! > > > > Srivatsan Pallavaram > > --- > > > I started working on a 'journal magement system' in PHP, > maby this would be a good inital project to start to help > admin. Have you looked at : http://refdb.sourceforge.net/ I think it would be a good starting point for covering much of the areas you describe ... Stef -- Teletch?a St?phane -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From dmb at mrc-dunn.cam.ac.uk Wed Jul 30 12:09:00 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 30 Jul 2003 17:09:00 +0100 (BST) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <1059584425.11527.7.camel@pc-54-149.kj.uib.no> Message-ID: On 30 Jul 2003, [ISO-8859-1] Teletch?a St?phane wrote: > Le mer 30/07/2003 ? 13:56, Dan Bolser a ?crit : > > Srivatsan Pallavaram wrote: > > > > > Hi all, > > > > > > This open source projects, forum like environment, links, papers, etc sounds > > > like a great idea to me. I am game! > > > > > > Srivatsan Pallavaram > > > --- > > > > > > I started working on a 'journal magement system' in PHP, > > maby this would be a good inital project to start to help > > admin. > > Have you looked at : > > http://refdb.sourceforge.net/ > > I think it would be a good starting point for covering much of the areas > you describe ... > > Stef > From gary at www.bioinformatics.org Wed Jul 30 13:58:03 2003 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Wed, 30 Jul 2003 13:58:03 -0400 (EDT) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <20030730152920.28300.qmail@web20912.mail.yahoo.com> Message-ID: Hi Sook, It runs as a server (Apache/PHP/MySQL), so yes, definitely it will run on Unix/Linux. Regards, g. On Wed, 30 Jul 2003, Sook Jung wrote: > Hi, > > Is there anythink like it for Unix? > Thanks, > > Sook > --- Gary Van Domselaar > wrote: > > Hey Gang, > > > > You might want to check out 'Librarian' > > http://bioinformatics.org/librarian/ > > > > Librarian is a free tool for self-creation of > > virtual annotated library of > > PDF articles, designed for small trusted groups, > > e.g. science labs. > > > > Regards, > > > > g. > > > __________________________________ > Do you Yahoo!? > Yahoo! SiteBuilder - Free, easy-to-use web site design software > http://sitebuilder.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From shenhav at wicc.weizmann.ac.il Wed Jul 30 04:15:51 2003 From: shenhav at wicc.weizmann.ac.il (Barak Shenhav) Date: Wed, 30 Jul 2003 10:15:51 +0200 Subject: [BiO BB] protein profile statistics question Message-ID: <3F210CC4@wiccweb> Look at the work by Dr. Shmuel Pietrokovski (shmuel.pietrokovski at weizmann.ac.il) from the Weizmann Institute of Science. His URL is: http//bioinformatics.weizmann.ac.il/~pietro/ best Barak >===== Original Message From bio_bulletin_board at bioinformatics.org ===== >--0-257339235-1059520638=:76355 >Content-Type: text/plain; charset=us-ascii > >Does anyone know if there has been any work on modelling the correlations between multiple alignment protein profiles? > >Thanks very much. > >Lily > > >--------------------------------- >Do you Yahoo!? >Yahoo! SiteBuilder - Free, easy-to-use web site design software >--0-257339235-1059520638=:76355 >Content-Type: text/html; charset=us-ascii > >
Does anyone know if there has been any work on modelling the correlations between multiple alignment protein profiles?
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Thanks very much.
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Lily


>Do you Yahoo!?
>Yahoo! SiteBuilder - Free, easy-to-use web site design software >--0-257339235-1059520638=:76355-- >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Wed Jul 30 20:05:00 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 31 Jul 2003 01:05:00 +0100 (BST) Subject: [BiO BB] protein profile statistics question In-Reply-To: <3F210CC4@wiccweb> References: <3F210CC4@wiccweb> Message-ID: <38308.213.107.104.145.1059609900.squirrel@www.mrc-dunn.cam.ac.uk> This paper is good... Revealing the set of mutually correlated positions for the protein families of immunoglobulin fold Boris Galitsky In Silico Biology 3, 0022 (2003) http://www.bioinfo.de/isb/2003/03/0022/ The link below just redirects for some reason? Barak Shenhav said: > Look at the work by Dr. Shmuel Pietrokovski > (shmuel.pietrokovski at weizmann.ac.il) from the Weizmann Institute of Science. His > URL is: > > http//bioinformatics.weizmann.ac.il/~pietro/ > > best > > Barak > >>===== Original Message From bio_bulletin_board at bioinformatics.org >> ====>--0-257339235-1059520638=:76355 Content-Type: text/plain; charset=us-ascii >> >>Does anyone know if there has been any work on modelling the correlations > between multiple alignment protein profiles? >> >>Thanks very much. >> >>Lily >> >> >>--------------------------------- >>Do you Yahoo!? >>Yahoo! SiteBuilder - Free, easy-to-use web site design software >>--0-257339235-1059520638=:76355 >>Content-Type: text/html; charset=us-ascii >> >>
Does anyone know if there has been any work on modelling the > correlations between multiple alignment protein profiles?
>>
>>
Thanks very much.
>>
>>
Lily


>>Do you Yahoo!?
>> href="http://us.rd.yahoo.com/evt=10469/*http://sitebuilder.yahoo.com">Yahoo! > SiteBuilder - Free, easy-to-use web site design software >>--0-257339235-1059520638=:76355-- >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From gary at www.bioinformatics.org Thu Jul 31 14:32:11 2003 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Thu, 31 Jul 2003 14:32:11 -0400 (EDT) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <3F27B27F.90202@mrc-dunn.cam.ac.uk> Message-ID: Hey Gang, I'm not sure how relevant this is for PHP, but I thought I would mention this kind of cool idea: A while back my colleague J.W. Bizzaro suggested a P2P system for distribution of scientific articles in PDF (and perhaps other) formats. Users of the system would store their favorite articles locally on their server, but make them accessible to others through the P2P system. The system would allow the articles to be restricted to certain authenticated groups (eg lab members). Type checking could be enforced so only 'document file formats' would be distributed, reducing the potential for abuse. A system like this combined with the features you describe, like automatic field retrieval and population from PubMed would be a very useful system indeed. Like the MPAA and RIAA, most journal publishing companies would feel threatened by a distribution system like this, but others such as BMC and PLoS would likely embrace it, and might even help out with some funding. There is an interesting article by Robert Cringely on how a system like this might possibly be implemented with some protection from litigation: http://www.pbs.org/cringely/pulpit/pulpit20030724.html 'Soulseek' is a P2P system for music distribution that has some nice features, including 'rooms' for people with similar musical interests. This would be like the 'labs' feature I mentioned above. www.slsk.org/ I think a system like this would be popular and successful. Regards, g. ------------------ On Wed, 30 Jul 2003, Dan Bolser wrote: > Srivatsan Pallavaram wrote: > > > Hi all, > > > > This open source projects, forum like environment, links, papers, etc sounds > > like a great idea to me. I am game! > > > > Srivatsan Pallavaram > > --- > > > I started working on a 'journal magement system' in PHP, > maby this would be a good inital project to start to help > admin. > > The implemented system uploads a journal in pdf / ps > format and then converts the document to text. > > The text of the document is then displayed alongside > a form, to help the user fill in the various fields > > i.e. author, title, date, journal, etc. > > Then there is another form to handle > multiple authors .... > > Thinking about this it is really clunky - we could have > a system to query MEDLINE and parse the reference > tag into a local database of journals. Can we do this with > PHP? I.E. PHP - SOAP? > > I started to implement browsing of the database, but > didn't get very far. I am sure there is plenty of stuff > we could take from 'on line shopping' modules. > > Searching, reader comments and ratings need to be > implemented, as well as a system to link various > journals with various projects / sub sections of > projects. > > In this way you could click on a project, and search > all the associated papers for user comments like > 'a good introduction'. Later you could use the system > to search medline and add a paper to the project. > > We could list the 'most popular read' in each project. > > Can we borrow some of the infra from BMC ? > > Cheers, > Dan. > > >Dan Bolser said: > > > > > > > >>Great!, and thanks for the responses! > >> > >>I hope you don't mind, but I have opened > >>this up to the BB for discussion. > >> > >>I have worked on and with MS bioinfo projects > >>before, so I have some idea of what is required / > >>what can be reasonably acheived. In this case I > >>doubt the same kind of close collaboration will > >>be possible, where our unit was able to fund students. > >> > >>I know what you meen about getting 'outside ideas', > >>the broader your input the better in all fields > >>I guess. I think it is definatly worth while in > >>the bioinfo community, as this area of science > >>more closly resembles the sofware engineering > >>community than most. > >> > >>I think the best way to procede is to make the > >>projects clearly open source, so ideas, progress and > >>results can be made available to the community. > >> > >>I guess this would work well within the framework of > >>bioinformatics.org, but I have no practical experience > >>of setting up / running open source projects! I.E. I > >>have no clue what kind of admin this involves / where > >>responsibility lies etc. > >> > >>I imagine this should not be too much of a problem if > >>you and other students are willing to work togeher to > >>get the projects off the ground within this framework > >>(maby including university admin where you are?). > >> > >>I will prepare a list of projects which I think are > >>reasonable, and then I guess we should initiate > >>some kind of open discussion on the relevance / > >>previous work in the area / statement of aims and > >>objectives / etc. > >> > >>Is this kind of forum available at bioinfo.org? > >> > >>I would really like to see an open forum for 'modular' > >>project discussion, where people can add relevant > >>papers / link / etc. to form a knowledge base for > >>further work. > >> > >>Anyway, I will first have to run the list by the > >>people in my lab to be sure that they are happy > >>having these ideas made open (as I have a terrible > >>habbit of jumping on good ideas which are not my own!). > >> > >>I will look forward to further comments / suggestions. > >> > >>P.S. do you have a time frame for project selection, as > >>I could send one-at-a-time if that would help? > >> > >>Thanks very much for your idea, > >>Dan. > >> > >> > >> > >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From steletch at biomedicale.univ-paris5.fr Thu Jul 31 16:50:09 2003 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: 31 Jul 2003 22:50:09 +0200 Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: References: Message-ID: <1059684608.14462.8.camel@pc-54-149.kj.uib.no> Le jeu 31/07/2003 ? 20:32, Gary Van Domselaar a ?crit : > Hey Gang, > > I'm not sure how relevant this is for PHP, but I thought I would mention > this kind of cool idea: > > A while back my colleague J.W. Bizzaro suggested a P2P system for > distribution of scientific articles in PDF (and perhaps other) formats. > Users of the system would store their favorite articles locally on their > server, but make them accessible to others through the P2P system. The > system would allow the articles to be restricted to certain authenticated > groups (eg lab members). Type checking could be enforced so only 'document > file formats' would be distributed, reducing the potential for abuse. A > system like this combined with the features you describe, like automatic > field retrieval and population from PubMed would be a very useful system > indeed. Have alook at refdb, it will allow exactly what you are displaying, the peer-to-peer solution is nevertheless a bad thing when it is used for a large scale exchange, MPAA or RIAA or whatever company/group is involved in the treatment of the problem (they should find a way to distribute their contents more logically and the peer-to-peer system would stop by itself). To be short, linking pybliographic to lyx and refdb is actually a working system for publication-class paper, but you can imagine much more : on this database, everyone could add its comments on a specific paper, like this, you're beginning to have a real database of knowledge based on publication, and experience from users (some tricks for improving scales for examples). You'll begin to use a computer at its real power ... Stef -- Teletch?a St?phane -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From dig at bioinformatics.org Thu Jul 31 17:52:38 2003 From: dig at bioinformatics.org (Dmitri I GOULIAEV) Date: Thu, 31 Jul 2003 16:52:38 -0500 Subject: [BiO BB] bad signature from steletch@biomedicale.univ-paris5.fr Message-ID: <20030731165238.B21368@lifebook> Hi! ,---[ output ]--- | [-- PGP output follows (current time: Thu Jul 31 16:24:08 2003) --] | gpg: Signature made Thu Jul 31 15:50:08 2003 CDT using DSA key ID F44CAE88 | gpg: BAD signature from "Teletch\xc3\xa9a St\xc3\xa9phane (perso) " | [-- End of PGP output --] `---[ ]--- I would like to ask others on this list: has anyone the same problem as I do (I mean -- "BAD signature")? Or I should look closer to my gpg configuration file? Thanks for any tips. Best regards, -- DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 From dmb at mrc-dunn.cam.ac.uk Thu Jul 31 18:18:57 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 31 Jul 2003 23:18:57 +0100 (BST) Subject: [BiO BB] Re: Bioinformatics Project In-Reply-To: <1059684608.14462.8.camel@pc-54-149.kj.uib.no> References: <1059684608.14462.8.camel@pc-54-149.kj.uib.no> Message-ID: <32864.213.107.104.145.1059689937.squirrel@www.mrc-dunn.cam.ac.uk> Teletch?a St?phane said: > Le jeu 31/07/2003 ? 20:32, Gary Van Domselaar a ?crit : >> Hey Gang, >> >> I'm not sure how relevant this is for PHP, but I thought I would mention this >> kind of cool idea: >> >> A while back my colleague J.W. Bizzaro suggested a P2P system for distribution >> of scientific articles in PDF (and perhaps other) formats. Users of the system >> would store their favorite articles locally on their server, but make them >> accessible to others through the P2P system. The system would allow the >> articles to be restricted to certain authenticated groups (eg lab members). Type >> checking could be enforced so only 'document file formats' would be distributed, >> reducing the potential for abuse. A system like this combined with the >> features you describe, like automatic field retrieval and population from >> PubMed would be a very useful system indeed. > > Have alook at refdb, it will allow exactly what you are displaying, the > peer-to-peer solution is nevertheless a bad thing when it is used for a large > scale exchange, MPAA or RIAA or whatever company/group is involved in the > treatment of the problem (they should find a way to distribute their contents more > logically and the peer-to-peer system would stop by itself). > > To be short, linking pybliographic to lyx and refdb is actually a > working system for publication-class paper, but you can imagine much more : on > this database, everyone could add its comments on a specific paper, like this, > you're beginning to have a real database of knowledge based on publication, and > experience from users (some tricks for > improving scales for examples). You'll begin to use a computer at its real power > ... This would be really great, a discussion group for each paper, including the authors and critics. I have thought the same thing would be usefull for 'open' database systems, a particular sequence could have its own discussion group debating the sequence annotation. > > Stef > > > > -- > Teletch?a St?phane From dmb at mrc-dunn.cam.ac.uk Thu Jul 31 18:45:08 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 31 Jul 2003 23:45:08 +0100 (BST) Subject: [Biophp-dev] Re: [BiO BB] Re: Bioinformatics Project In-Reply-To: Message-ID: Sounds like a great project On Thu, 31 Jul 2003, Gary Van Domselaar wrote: > Hey Gang, > > I'm not sure how relevant this is for PHP, but I thought I would mention > this kind of cool idea: > > A while back my colleague J.W. Bizzaro suggested a P2P system for > distribution of scientific articles in PDF (and perhaps other) formats. > Users of the system would store their favorite articles locally on their > server, but make them accessible to others through the P2P system. The > system would allow the articles to be restricted to certain authenticated > groups (eg lab members). Type checking could be enforced so only 'document > file formats' would be distributed, reducing the potential for abuse. A > system like this combined with the features you describe, like automatic > field retrieval and population from PubMed would be a very useful system > indeed. > > Like the MPAA and RIAA, most journal publishing companies would feel > threatened by a distribution system like this, but others such as BMC and > PLoS would likely embrace it, and might even help out with some funding. > There is an interesting article by Robert Cringely on how a system like > this might possibly be implemented with some protection from litigation: > > http://www.pbs.org/cringely/pulpit/pulpit20030724.html > > 'Soulseek' is a P2P system for music distribution that has some nice > features, including 'rooms' for people with similar musical interests. > This would be like the 'labs' feature I mentioned above. > > www.slsk.org/ > > I think a system like this would be popular and successful. > > Regards, > > g. > ------------------ > > > On Wed, 30 Jul 2003, Dan Bolser wrote: > > > Srivatsan Pallavaram wrote: > > > > > Hi all, > > > > > > This open source projects, forum like environment, links, papers, etc sounds > > > like a great idea to me. I am game! > > > > > > Srivatsan Pallavaram > > > --- > > > > > > I started working on a 'journal magement system' in PHP, > > maby this would be a good inital project to start to help > > admin. > > > > The implemented system uploads a journal in pdf / ps > > format and then converts the document to text. > > > > The text of the document is then displayed alongside > > a form, to help the user fill in the various fields > > > > i.e. author, title, date, journal, etc. > > > > Then there is another form to handle > > multiple authors .... > > > > Thinking about this it is really clunky - we could have > > a system to query MEDLINE and parse the reference > > tag into a local database of journals. Can we do this with > > PHP? I.E. PHP - SOAP? > > > > I started to implement browsing of the database, but > > didn't get very far. I am sure there is plenty of stuff > > we could take from 'on line shopping' modules. > > > > Searching, reader comments and ratings need to be > > implemented, as well as a system to link various > > journals with various projects / sub sections of > > projects. > > > > In this way you could click on a project, and search > > all the associated papers for user comments like > > 'a good introduction'. Later you could use the system > > to search medline and add a paper to the project. > > > > We could list the 'most popular read' in each project. > > > > Can we borrow some of the infra from BMC ? > > > > Cheers, > > Dan. > > > > >Dan Bolser said: > > > > > > > > > > > >>Great!, and thanks for the responses! > > >> > > >>I hope you don't mind, but I have opened > > >>this up to the BB for discussion. > > >> > > >>I have worked on and with MS bioinfo projects > > >>before, so I have some idea of what is required / > > >>what can be reasonably acheived. In this case I > > >>doubt the same kind of close collaboration will > > >>be possible, where our unit was able to fund students. > > >> > > >>I know what you meen about getting 'outside ideas', > > >>the broader your input the better in all fields > > >>I guess. I think it is definatly worth while in > > >>the bioinfo community, as this area of science > > >>more closly resembles the sofware engineering > > >>community than most. > > >> > > >>I think the best way to procede is to make the > > >>projects clearly open source, so ideas, progress and > > >>results can be made available to the community. > > >> > > >>I guess this would work well within the framework of > > >>bioinformatics.org, but I have no practical experience > > >>of setting up / running open source projects! I.E. I > > >>have no clue what kind of admin this involves / where > > >>responsibility lies etc. > > >> > > >>I imagine this should not be too much of a problem if > > >>you and other students are willing to work togeher to > > >>get the projects off the ground within this framework > > >>(maby including university admin where you are?). > > >> > > >>I will prepare a list of projects which I think are > > >>reasonable, and then I guess we should initiate > > >>some kind of open discussion on the relevance / > > >>previous work in the area / statement of aims and > > >>objectives / etc. > > >> > > >>Is this kind of forum available at bioinfo.org? > > >> > > >>I would really like to see an open forum for 'modular' > > >>project discussion, where people can add relevant > > >>papers / link / etc. to form a knowledge base for > > >>further work. > > >> > > >>Anyway, I will first have to run the list by the > > >>people in my lab to be sure that they are happy > > >>having these ideas made open (as I have a terrible > > >>habbit of jumping on good ideas which are not my own!). > > >> > > >>I will look forward to further comments / suggestions. > > >> > > >>P.S. do you have a time frame for project selection, as > > >>I could send one-at-a-time if that would help? > > >> > > >>Thanks very much for your idea, > > >>Dan. > > >> > > >> > > >> > > >> > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > Biophp-dev mailing list > Biophp-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biophp-dev > From dmb at mrc-dunn.cam.ac.uk Thu Jul 31 18:48:13 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 31 Jul 2003 23:48:13 +0100 (BST) Subject: [Biophp-dev] Re: [BiO BB] Re: Bioinformatics Project In-Reply-To: <1059684608.14462.8.camel@pc-54-149.kj.uib.no> Message-ID: On 31 Jul 2003, [ISO-8859-1] Teletch?a St?phane wrote: > Le jeu 31/07/2003 ? 20:32, Gary Van Domselaar a ?crit : > > Hey Gang, > > > > I'm not sure how relevant this is for PHP, but I thought I would mention > > this kind of cool idea: > > > > A while back my colleague J.W. Bizzaro suggested a P2P system for > > distribution of scientific articles in PDF (and perhaps other) formats. > > Users of the system would store their favorite articles locally on their > > server, but make them accessible to others through the P2P system. The > > system would allow the articles to be restricted to certain authenticated > > groups (eg lab members). Type checking could be enforced so only 'document > > file formats' would be distributed, reducing the potential for abuse. A > > system like this combined with the features you describe, like automatic > > field retrieval and population from PubMed would be a very useful system > > indeed. > > Have alook at refdb, it will allow exactly what you are displaying, the > peer-to-peer solution is nevertheless a bad thing when it is used for a > large scale exchange, MPAA or RIAA or whatever company/group is involved > in the treatment of the problem (they should find a way to distribute > their contents more logically and the peer-to-peer system would stop by > itself). Is this implementation? Scientists tend to have good internet connections, as compared to biology they are cheap. It is just a matter of getting them to integrate and communicate. > To be short, linking pybliographic to lyx and refdb is actually a > working system for publication-class paper, but you can imagine much > more : on this database, everyone could add its comments on a specific > paper, like this, you're beginning to have a real database of knowledge > based on publication, and experience from users (some tricks for > improving scales for examples). You'll begin to use a computer at its > real power ... > > Stef > > > > From steletch at biomedicale.univ-paris5.fr Thu Jul 31 20:34:25 2003 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: 01 Aug 2003 02:34:25 +0200 Subject: [BiO BB] bad signature from steletch@biomedicale.univ-paris5.fr In-Reply-To: <20030731165238.B21368@lifebook> References: <20030731165238.B21368@lifebook> Message-ID: <1059698065.14749.1.camel@pc-54-149.kj.uib.no> Le jeu 31/07/2003 ? 23:52, Dmitri I GOULIAEV a ?crit : It it just that for the moment nobody has signed my key with its, i must diffuse it, i should be done by the bext month. If you come in Paris, we could exchange keys and sign them ... Stef > Hi! > > ,---[ output ]--- > | [-- PGP output follows (current time: Thu Jul 31 16:24:08 2003) --] > | gpg: Signature made Thu Jul 31 15:50:08 2003 CDT using DSA key ID F44CAE88 > | gpg: BAD signature from "Teletch\xc3\xa9a St\xc3\xa9phane (perso) " > | [-- End of PGP output --] > `---[ ]--- > > I would like to ask others on this list: has anyone the same problem as I do (I mean -- "BAD signature")? Or I should look closer to my gpg configuration file? > > Thanks for any tips. > > > Best regards, -- Teletch?a St?phane -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From wzh0032002 at yahoo.com Thu Jul 31 13:50:38 2003 From: wzh0032002 at yahoo.com (wh z) Date: Thu, 31 Jul 2003 10:50:38 -0700 (PDT) Subject: [BiO BB] Homology Message-ID: <20030731175038.22348.qmail@web20713.mail.yahoo.com> hello, there! is there anyone have some experience on protein homology using Biopolymer and Charmm ? did you get good results ? As we don't have more efficient software right now ,I have to use the traditional way. but the result is not good. What I am doing is using Biopolymer to build the model and Charmm to do energy minimization and annealing. Is there some steps missing? I am a beginner on this, I have no progress for some time. any of your advice will be truely appreciated. Thank you. Gracia __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From idoerg at burnham.org Thu Jul 31 17:34:32 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 31 Jul 2003 14:34:32 -0700 Subject: [BiO BB] GRAVY index program anyone? Message-ID: <3F298B68.4060200@burnham.org> Hi, Does anybody have a program which calculates a sequence's Grand average of hydropathicity (GRAVY)? TIA, ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo