From idoerg at burnham.org Tue May 1 01:07:47 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon, 30 Apr 2007 22:07:47 -0700 Subject: [BiO BB] AFP / Biosapiens 2007: submission deadline extension Message-ID: <4636CB23.3080808@burnham.org> CALL FOR TALKS & CALL FOR POSTERS (Please forward as appropriate) THERE IS STILL TIME TO SEND IN YOUR WORK. Due to many requests, the abstract submission deadline has been extended to May 6, 2007 The Automated Function Prediction Special Interest Group (AFP SIG) and the Biosapiens European network of excellence in genome annotation are teaming up to hold a two-day Special Interest Group (SIG) meeting July 19-20, 2007 alongsideISMB/ECCB 2007 in Vienna Austria. Two page abstracts for posters or short talks will be accepted for consideration. Please go to: http://2007.BioFunctionPrediction.org/node/2 to submit your abstracts. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through to predicting the function from protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations. Talks are sought in, but not limited to: * Various aspects of gene and protein function prediction o Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity. o Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss. o Phylogeny based methods o Function from molecular interactions o Function from structure o Function prediction using combined methods o "Meta-talks" discussing the limitations and horizons of computational function prediction. o Assessing function prediction programs * Genomic annotation o Gene finding o Genome visualization o Collaborative annotation o Cooperation between experimental and computational biologists Confirmed speakers include: * Janet Thornton, European Bioinformatics Institute, Cambridge, UK * David Jones University College, London, UK * Rob Russell EMBL, Heidelberg, Germany * Christine Orengo, University College London, UK * Alfonso Valencia, Centro Nacional de Biotecnologia, Madrid, Spain * Ewan Birney, European Bioinformatics Institute, Cambridge, UK * Shoshana Wodak, University of Toronto, Canada * Russ Altman, Stanford University, USA Organizers: Iddo Friedberg, Burnham Institute for Medical Research, La Jolla, CA, USA Adam Godzik, Burnham Institute for Medical Research and University of California, San Diego Christine Orengo, University College, London Important dates: NEW AND FINAL DEADLINE: May 6 2007: Talk and poster abstracts due May 21 2007: notification of acceptance May 28, 2007: final correction for accepted abstracts due July 19-20, 2007: AFP-Biosapiens SIG alongside ISMB/ECCB 2007 in Vienna, Austria. Contact us: afp.biosap.2007 at gmail.com For more information: http://2007.BioFunctionPrediction.org -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From varvenne at genoway.com Wed May 2 03:40:09 2007 From: varvenne at genoway.com (Benoit VARVENNE) Date: Wed, 02 May 2007 09:40:09 +0200 Subject: [BiO BB] Can you explain theses results? In-Reply-To: Message-ID: Hi all, I want to apologize for having posted such a foolish and too-fast answer to Daniel's email last time. Really sorry for that. Cheers, Beno?t -- Benoit Varvenne, Bioinformatics, GenOway - Lyon (France) From dsousa at inf.puc-rio.br Wed May 2 10:29:13 2007 From: dsousa at inf.puc-rio.br (dsousa at inf.puc-rio.br) Date: Wed, 2 May 2007 11:29:13 -0300 (BRT) Subject: [BiO BB] Can you explain theses results? In-Reply-To: References: Message-ID: <53478.139.82.100.131.1178116153.squirrel@webmail.inf.puc-rio.br> Ok Benoit, Dont worry about this. In the first moment I thought that you could be rigth too. But, after I saw which very hits of good qaulity will stay out. In this moment I am couting the cust of function (in source) to first phase or match words and to second phase or extension. To explain that resuls... By, Daniel > Hi all, > > I want to apologize for having posted such a foolish and too-fast answer > to > Daniel's email last time. > > Really sorry for that. > > Cheers, > Beno?t > > -- > Benoit Varvenne, > Bioinformatics, > GenOway - Lyon (France) > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Daniel Xavier de Sousa Laboratorio de Bioinformatica - PUC-Rio From lijo.skb at gmail.com Thu May 3 07:06:35 2007 From: lijo.skb at gmail.com (lijo skb) Date: Thu, 3 May 2007 16:36:35 +0530 Subject: [BiO BB] GCG gap program and emboss In-Reply-To: <87614.55710.qm@web51403.mail.re2.yahoo.com> References: <87614.55710.qm@web51403.mail.re2.yahoo.com> Message-ID: Hello Hongyu, This link may be helpful http://helix.nih.gov/apps/bioinfo/emboss-gcg.html Li On 4/30/07, Hongyu Zhang wrote: > > Dear all, > > I am wondering which program in the EMBOSS package is closest to the GCG > gap program? and how similar is their performance in terms of sequence > alignment and score? > > Thanks! > > Hongyu > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Lijo From aloraine at gmail.com Thu May 3 22:51:37 2007 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 3 May 2007 21:51:37 -0500 Subject: [BiO BB] discrepancy between probe sets for same gene in microarray In-Reply-To: <4596.10.10.118.126.1177752128.squirrel@webmail.sibs.ac.cn> References: <4596.10.10.118.126.1177752128.squirrel@webmail.sibs.ac.cn> Message-ID: <83722dde0705031951x1c614cbctf9c15c626238359b@mail.gmail.com> Dear Lichun, This happens quite a lot, but it isn't clear what to do about it. These probe sets are sometimes called "redundant probe sets" because they are annotated as targeting the same gene. If you look at them in the Integrated Genome Browser (tool for visualizing genes, tiling array data, probe sets, etc.) you find that they map to different regions near the three-prime ends of known gene structures. (You can view the probe set alignments by clicking the links labeled "IGB" that appear on Affy's probe set level Web pages in the NetAffx Analysis Center section of the Affymetrix Web site.) One would like to think that differential readings from redundant probe sets indicate something interesting - such as regulated alternative 3-prime end processing. But...you have to be a bit careful, because sometimes the probe set-to-target gene annotations are imperfect. For some discussion of all this, see: Cui & Loraine http://www.lifesciencessociety.org/CSB2006/toc/223.2006.html (sorry ... I can't resist citing our paper!) and to get related articles, follow the "related links" from here: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17369640&query_hl=7&itool=pubmed_docsumu Best, Ann -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From dsousa at inf.puc-rio.br Fri May 4 07:47:56 2007 From: dsousa at inf.puc-rio.br (dsousa at inf.puc-rio.br) Date: Fri, 4 May 2007 08:47:56 -0300 (BRT) Subject: [BiO BB] words-hit and neighborhood of BLAST Message-ID: <2954.139.82.100.131.1178279276.squirrel@webmail.inf.puc-rio.br> Hi, Please, How can I count or just see the number of word-hit and neighborhood match in one comparation of BLAST? out file of blast ?? or variable in source code?? Thanks for all Daniel Xavier de Sousa Laboratorio de Bioinformatica - PUC-Rio From Sterten at aol.com Sun May 6 03:28:20 2007 From: Sterten at aol.com (Sterten at aol.com) Date: Sun, 6 May 2007 03:28:20 EDT Subject: [BiO BB] kalign Message-ID: hello, has someone succeeded to compile kalign2 under Windows ? I'd like a Windows - executable which runs under DOS or Windows-XP or Windows-vista . Best on all 3, of course, but either would be fine for now. Guenter From christoph.gille at charite.de Sun May 6 19:04:26 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 7 May 2007 01:04:26 +0200 (CEST) Subject: [BiO BB] kalign no problem under MS-Windows. In-Reply-To: References: Message-ID: <64609.84.190.62.192.1178492666.squirrel@webmail.charite.de> I found no problem to compile kalign under windows. It is included in the STRAP package and will be downloaded and installed automatically when it is used for the first time. From christoph.gille at charite.de Sun May 6 19:52:39 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 7 May 2007 01:52:39 +0200 (CEST) Subject: [BiO BB] kalign no problem under MS-Windows. Message-ID: <64791.84.190.70.246.1178495559.squirrel@webmail.charite.de> I found no problem to compile kalign under windows. It is included in the STRAP package and will be downloaded and installed automatically when it is used for the first time. From Sterten at aol.com Mon May 7 00:03:55 2007 From: Sterten at aol.com (Sterten at aol.com) Date: Mon, 7 May 2007 00:03:55 EDT Subject: [BiO BB] kalign no problem under MS-Windows. Message-ID: In einer eMail vom 07.05.2007 01:53:10 Westeurop?ische Normalzeit schreibt christoph.gille at charite.de: > I found no problem to compile kalign under windows. > It is included in the STRAP package and will be downloaded and installed > automatically when it is used for the first time. so, can you send or upload kalign2.exe , please ? From ykalidas at gmail.com Mon May 7 01:03:59 2007 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Mon, 7 May 2007 10:33:59 +0530 Subject: [BiO BB] [CNS] How to pass command line arguments to cns-scripts Message-ID: <5632703b0705062203j2795946cv86f079fe49471e7a@mail.gmail.com> Hi All I am trying to use CNS-crystallography s/w for the task of computing interaction energy between a ligand and a protein. For this, I need to pass and as parameters to required for 'cns_solve'. Can anyone please let me know how to accomplish the following simple task: Example: cns_solve < test.inp where: test.inp (looks shall look like this) define(...) ... var1= var2= ... stop Thanking You With Regards Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From tejalonline at gmail.com Sat May 5 04:27:55 2007 From: tejalonline at gmail.com (T Joshi) Date: Sat, 5 May 2007 10:27:55 +0200 Subject: [BiO BB] Extraction of 5' & 3' UTR sequences Message-ID: <11417a880705050127u438bb6d2h81b468cbbb859c96@mail.gmail.com> Hi ! I am searching for efficient ways to extract 5' & 3' UTR sequences from the DNA sequence database. I have tried to use BioMart's package, which gives the sequence in FASTA format. Actually, I want to store these sequences automatically (through some software tool) into MySQL database. BioMart's martview allows to query one chromosome sequence, and either 5' UTR or 3' UTR at a time. The tool MartJ doesn't support retrival of sequences from the database. Can you suggest me such tools through which I can automatically create database scheme and import the UTR sequence dataset into the database? Thanks & Regards, T Joshi From swhwang10 at yahoo.com Sun May 6 22:18:35 2007 From: swhwang10 at yahoo.com (Seungwoo Hwang) Date: Sun, 6 May 2007 19:18:35 -0700 (PDT) Subject: [BiO BB] [Announcement] International Openfree Bioinformation Contents Competition Message-ID: <743059.75443.qm@web43133.mail.sp1.yahoo.com> International Openfree Bioinformation Contents Competition (Biowiki contest) User-driven web authoring processes (such as Web 2.0, UCC, and wiki) have achieved significant improvements on the process of collecting and distributing a variety of information on the internet. In order to adopt the new paradigm of web contents authoring and exchange towards collaborative development of biological knowledge data base, we thus hold the first International Openfree Bioinformation Contents Competition. The objective of this event is to promote knowledge exchange through participation and discussion among life scientists from diverse disciplines. Sponsor: This competition is supported by ASEAN countries and operated by EABN (East Asia Bioinformation Network) organizers. KOBIC (Korean Bioinformation Center), provides fund and bioinformatics infrastructure for this competition. Venue: This contest is held through the internet. Schedule - Registration: 2007/05/03 - 2007/05/13 - Final Result Due: 2007/06/06 - Award Notification: 2007/06/14 Awards and prizes - 1st runner: Free-knowledge award: $500 USD - 2nd runner: Open-sharing award: $200 USD - 3rd runner: Truthful-work award: $100 USD - Prize will be paid through PayPal Event URL: http://www.biowikicontest.net Contact: biowikicontest at biomaillist.org ____________________________________________________________________________________ Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html From arnec at bio.umass.edu Mon May 7 11:10:09 2007 From: arnec at bio.umass.edu (Arne Christensen) Date: Mon, 7 May 2007 11:10:09 -0400 Subject: [BiO BB] Short peptide sequence comparison Message-ID: I'm wondering if anyone can recommend an application to analyze the conservation between two short, <20 amino acids, with comprehensive information on charge, hydrophobicity, etc. I have two sequences I believe are functionally conserved, but not particularly well conserved in terms of identity. I'm trying to get to the bottom of the discrepancies in the pepties. Thank you , arnec -- From claudio.forcato at poste.it Wed May 9 06:30:12 2007 From: claudio.forcato at poste.it (Claudio Forcato) Date: Wed, 09 May 2007 12:30:12 +0200 Subject: [BiO BB] Whole genome alignment Message-ID: <1178706612.5811.20.camel@jonny> Dear all, I'm Claudio and I'm searching for softwares to align whole genomes. Could you suggest me the best tools or algorithms for this purpose? Where can I find documentation, papers or reviews where it's explained advantages and disadvantages of the different softwares? Thank you From jeff at bioinformatics.org Wed May 9 20:27:56 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 09 May 2007 20:27:56 -0400 Subject: [BiO BB] Course on genome browsers Message-ID: <4642670C.9060503@bioinformatics.org> Bioinformatics Organization Data Discovery & Acquisition Series CS111A Introduction to Genome Browsers (on-line) May 14-18, 2007 http://edu.bioinformatics.org/AT "Introduction to Genome Browsers" is a Web seminar course co-sponsored by Bioinformatics.Org and presented by OpenHelix. This course covers powerful, popular, and free Web-based genome browsers including UCSC Genome Browser, Ensembl, Map Viewer, and Integrated Microbial Genome (IMG) system -- all critical bioinformatics and genomic research tools. As genome browsers become a more and more critical tool for life science research, the need to learn the features and functionality of the browsers is important for biologists, medical researchers, and others in life sciences. To meet that need, OpenHelix and Bioinformatics.Org announce a comprehensive Web seminar course on "Introduction to Genome Browsers," May 14-18, 2007. Genome browsers enable researchers to access annotated data on a large number of genomes. These genome browsers are excellent resources for data discovery and analysis. This course is targeted towards researchers who are not acquainted with these genome browsers or who wish to learn to use these tools more effectively. The course will go over the basic use of each genome browser and some of the data and tools available to them. The user will also get a good overview of comparisons and contrasts between the browsers. Each class is approximately 90 minutes long, starting each day at 11:30 AM US EDT. Classes include about 45 minutes of introduction (where attendees can follow along on the browser) and another 45 minutes of hands-on project exercises. In addition, each class will be recorded for later use or for attendees that can't attend certain classes. The topics covered are: - General overview of genome browsers and their characteristics - Introduction to UCSC Genome Browser - Advanced Topics of the UCSC Genome Browser - Introduction to the Ensembl Genome Browser - Introduction to NCBI's MapViewer - Introduction to the Integrated Microbial Genomes system (IMG) PREREQUISITES: Attendees should have knowledge of genomic/biological concepts, however, no programming skills are required. Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and the Adobe Flash plugin. TUITION: Cost for the complete course is $397 for non-profit/academic and $595 for commercial attendees. FOR MORE INFORMATION: For further information, visit http://www.openhelix.com/ or http://edu.bioinformatics.org/AT. From Sterten at aol.com Wed May 9 20:32:09 2007 From: Sterten at aol.com (Sterten at aol.com) Date: Wed, 9 May 2007 20:32:09 EDT Subject: [BiO BB] Whole genome alignment Message-ID: what sort of genomes ? I recently found this: _http://align.bmr.kyushu-u.ac.jp/mafft/online/server/_ (http://align.bmr.kyushu-u.ac.jp/mafft/online/server/) which worked fine for flu. But I align each segement and then merge them with my own software From sbotond at gmail.com Thu May 10 10:47:42 2007 From: sbotond at gmail.com (Sipos Botond) Date: Thu, 10 May 2007 16:47:42 +0200 Subject: [BiO BB] Whole genome alignment In-Reply-To: References: Message-ID: <80797a220705100747h7cc09203xed57e225146e17f0@mail.gmail.com> Hi all! (As this is my first post here :) ) When I have been searching for similar applications I found this: http://mummer.sourceforge.net/ greetings. sb. On 5/10/07, Sterten at aol.com wrote: > > what sort of genomes ? > I recently found this: > _http://align.bmr.kyushu-u.ac.jp/mafft/online/server/_ > (http://align.bmr.kyushu-u.ac.jp/mafft/online/server/) > > which worked fine for flu. > But I align each segement and then merge them with my own software > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From aloraine at gmail.com Fri May 11 19:31:42 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 11 May 2007 16:31:42 -0700 Subject: [BiO BB] need help w/ VRML viewer for big graphs - Mozilla plug-in? Message-ID: <83722dde0705111631p4e4c1a38vdbdefb5593a19e38@mail.gmail.com> Hi all, This is a question for list members who may have worked with large graphs or network files and who wouldn't mind sharing some experience and advice! I'm trying to display a whole-genome network of correlated expression using output from LGL (Large Graph Layout - see: http://apropos.icmb.utexas.edu/lgl/), which generates layouts for very big graphs. (Take a look at the image gallery if you have some spare time -- some of the images are quite impressive!) I'm just getting started with LGL, but it looks like it can give me a VRML document that specifies the layout of large graphs (my biggest is 500K edges, 9k nodes), and I'd like to find a VRML viewer that might be able to handle such a large graph. (I've got a machine w/ 3 gig memory, and access to a few others with even more memory, but I don't have admin privs on those, so I'd like to avoid bugging the sysadmins about installing new software until I'm sure I've got something that will work...) If anyone on the list can recommend a good VRML plug-in (for Mozilla) or stand-alone viewer that might work for this application, I would be very grateful! Also, if you have any tips on visualizing large graphs, I'd be grateful for those as well! So far the only thing I've been able to find that appears capable of laying out big graphs is LGL...but maybe there are some others? Thank you in advance for your help!!! -Ann -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From landman at scalableinformatics.com Fri May 11 19:38:52 2007 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 11 May 2007 19:38:52 -0400 Subject: [BiO BB] need help w/ VRML viewer for big graphs - Mozilla plug-in? In-Reply-To: <83722dde0705111631p4e4c1a38vdbdefb5593a19e38@mail.gmail.com> References: <83722dde0705111631p4e4c1a38vdbdefb5593a19e38@mail.gmail.com> Message-ID: <4644FE8C.70906@scalableinformatics.com> Hi Ann Ann Loraine wrote: > I'm just getting started with LGL, but it looks like it can give me a VRML > document that specifies the layout of large graphs (my biggest is 500K > edges, 9k nodes), and I'd like to find a VRML viewer that might be able to > handle such a large graph. (I've got a machine w/ 3 gig memory, and access > to a few others with even more memory, but I don't have admin privs on > those, so I'd like to avoid bugging the sysadmins about installing new > software until I'm sure I've got something that will work...) > > If anyone on the list can recommend a good VRML plug-in (for Mozilla) or > stand-alone viewer that might work for this application, I would be very > grateful! Hmmm... Maybe my info is dated, but I had used inventor viewer (the VRML 1.0 spec was effectively OpenInventor's spec) to view some molecular structures I created out of PDB and other coordinates. Calls these fairly simple graphs, several thousand nodes, and tens of thousands of edges. Inventor viewer worked fine for these, though I ran them on an SGI at the time. I have run ivview recently on the same files on my laptop without problem. So if they are v1.0 VRML compliant, you might try the OpenInventor viewer as a stand-alone. > Also, if you have any tips on visualizing large graphs, I'd be grateful for > those as well! Get lots of RAM. And a fast graphics card (accelerated OpenGL) with lots of RAM :( > So far the only thing I've been able to find that appears capable of laying > out big graphs is LGL...but maybe there are some others? There are some hyperbolic space viewers for large connected graphs, though these are more for drilling in to specific nodes, than seeing the large scale structure of the system. > > Thank you in advance for your help!!! > > -Ann > -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615 From aloraine at gmail.com Sat May 12 01:34:24 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 11 May 2007 22:34:24 -0700 Subject: [BiO BB] need help w/ VRML viewer for big graphs - Mozilla plug-in? In-Reply-To: <4644FE8C.70906@scalableinformatics.com> References: <83722dde0705111631p4e4c1a38vdbdefb5593a19e38@mail.gmail.com> <4644FE8C.70906@scalableinformatics.com> Message-ID: <83722dde0705112234y6436ab2fq78f0f75f162361be@mail.gmail.com> A hyperbolic viewer might be just the thing. We do want to "drill down" into specific components of the graph. So that could be what we need... Let me know if you would recommend a particular one (or two) to try out first. Maybe some-one on the list would know, as well? One nice side benefit of LGL is that in the process of building layouts for the graph, it seems to separate them into separate components, which is useful. Thanks for the suggestions! -Ann On 5/11/07, Joe Landman wrote: > > Hi Ann > > Ann Loraine wrote: > > > I'm just getting started with LGL, but it looks like it can give me a > VRML > > document that specifies the layout of large graphs (my biggest is 500K > > edges, 9k nodes), and I'd like to find a VRML viewer that might be able > to > > handle such a large graph. (I've got a machine w/ 3 gig memory, and > access > > to a few others with even more memory, but I don't have admin privs on > > those, so I'd like to avoid bugging the sysadmins about installing new > > software until I'm sure I've got something that will work...) > > > > If anyone on the list can recommend a good VRML plug-in (for Mozilla) or > > stand-alone viewer that might work for this application, I would be very > > grateful! > > Hmmm... Maybe my info is dated, but I had used inventor viewer (the VRML > 1.0 spec was effectively OpenInventor's spec) to view some molecular > structures I created out of PDB and other coordinates. Calls these > fairly simple graphs, several thousand nodes, and tens of thousands of > edges. Inventor viewer worked fine for these, though I ran them on an > SGI at the time. I have run ivview recently on the same files on my > laptop without problem. So if they are v1.0 VRML compliant, you might > try the OpenInventor viewer as a stand-alone. > > > Also, if you have any tips on visualizing large graphs, I'd be grateful > for > > those as well! > > Get lots of RAM. And a fast graphics card (accelerated OpenGL) with > lots of RAM :( > > > So far the only thing I've been able to find that appears capable of > laying > > out big graphs is LGL...but maybe there are some others? > > There are some hyperbolic space viewers for large connected graphs, > though these are more for drilling in to specific nodes, than seeing the > large scale structure of the system. > > > > > Thank you in advance for your help!!! > > > > -Ann > > > > -- > Joseph Landman, Ph.D > Founder and CEO > Scalable Informatics LLC, > email: landman at scalableinformatics.com > web : http://www.scalableinformatics.com > phone: +1 734 786 8423 > fax : +1 734 786 8452 or +1 866 888 3112 > cell : +1 734 612 4615 > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From wiiat at kis-lab.com Sat May 12 02:09:56 2007 From: wiiat at kis-lab.com (Jia Hu) Date: Sat, 12 May 2007 15:09:56 +0900 Subject: [BiO BB] CFP: Biomedicine Applications of Web technologies 2007 Message-ID: <20070512061640.5E1FB368727@primary.bioinformatics.org> ================================================================================ Call for Papers International Workshop on BioMedicine applications of Web Technologies in conjunction with WI/IAT 2007 Silicon Valley, CA, USA, November 2-5, 2007 http://chunnan.iis.sinica.edu.tw/BMWT2007.html ======================================================================== ========================= Topics of the workshop ========================= BMWT 2007 will be part of events of the WI-IAT conference and will be arranged for a date during November 2-5. This workshop will cover interesting topics of applications of intelligent Web technologies in bio-medicine, including Web Ontology, Semantic Web, Web Usage Mining, Web Search and Intelligent Agents. Original contributions will be solicited in the following subjects (but not necessarily limited to): * Web information extraction and wrapper generation * Applications of Web taxonomies and ontologies in bio-medicine * Web-based service-oriented architecture in bio-medicine * Integration and maintenance of bio-medicine taxonomies and ontologies * Web content and structure mining , Web Information retrieval and filtering * Web-based data collection, curation and analysis * Text mining for metadata creation * Multimedia contents in bio-medicine on the Web * Web search engines, meta-search engines and inference engine * Semantic Web * Intelligent Web agents * Knowledge community formation and support This workshop intends to bring together researchers and practitioners to foster the exchange of ideas and the dissemination of emerging techniques on intelligent Web technology in bio-medicine applications. The workshop will capture current important developments of new models, new methodologies and new tools for building a variety of embodiments of scalable, effective and intelligent Web-based information systems for the ever-increasing needs of bio-medicine applications. ================== Type of workshop ================== The workshop will run as a half-day workshop for approximately 5 hours with 1~2 keynote speeches and 8~12 paper presentations. ================== Important dates ================== June 20, 2007: Due date for full workshop papers submission August 1, 2007: Final acceptance by Workshop Co-Chairs August 2, 2007: Notification of paper acceptance to authors August 17, 2007: Camera-ready of accepted papers November 2-5, 2007: Workshops ========================== Paper submission guideline ========================== (1) All submitted papers will be reviewed on the basis of technical quality, relevance, significance, and clarity by at least two reviews for each paper. (2) We will use WI-IAT 2007 Cyberchair system for on-line paper submission and review process. Details to be announced. (3) The length of accepted papers should NOT exceed 4 pages (IEEE-CS format, extra payment is only available for one more extra page). (4) We will not have a separate workshop registration fee this year. (i.e., only one conference registration covers everything). ================= Program committee ================= (Tentative) Howard CT Ho, IBM Almaden, USA Chun-Nan Hsu, Academia Sinica, Taiwan Chung-Yen Lin, Academia Sinica, Taiwan Wen-Hsiang Lu, NCKU, Taiwan Louiqa Raschid, U of Maryland, USA Shin-Mu Tseng, NCKU, Taiwan Samson Tu, Stanford, USA Qiang Yang, HKUST, Hong Kong, China Ueng-Cheng Yang, NYMU, Taiwan ==================== Organizing committee ==================== Chun-Nan Hsu (Co-Chair) Institute of Information Science Academia Sinica, Taipei, Taiwan chunnan at iis.sinica.edu.tw Vincent Shin-Mu Tseng (Co-Chair) Department of Computer Science and Information Engineering National Cheng Kung University, Tainan, Taiwan tsengsm at mail.ncku.edu.tw Wen-Hsiang Lu (Co-Chair) Department of Computer Science and Information Engineering National Cheng Kung University, Tainan, Taiwan whlu at mail.ncku.edu.tw From asidhu at biomap.org Sat May 12 18:19:27 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Sun, 13 May 2007 08:19:27 +1000 Subject: [BiO BB] CFP: 2nd IEEE International Workshop on Data Mining in Bioinformatics (DMB 2007) Message-ID: <1179008367.46463d6f7a005@mail.opentransfer.com> 2nd International Workshop on Data Mining in Bioinformatics (DMB 2007) With IEEE/WIC/ACM WI-IAT-BIBM 2007 & IEEE GrC 2007 http://dmb07.swbio.org/ MOTIVATION Data Mining deals with the use of data analysis techniques and methodologies in the design, development and assessment of data and information systems for biomedical computing. The goal of this workshop is to share research solutions using data mining approaches to problems of today's biomedical systems and to identify new issues and directions for future research in biomedical data mining. Techniques and Methodologies proposed in this workshop will help addressing two major challenges to incorporate this vast biological knowledge into the data mining cycle: (i) designing efficient the data mining frameworks; and (ii) adapting existing data mining algorithms to understand constantly varying and changing biomedical data. In this workshop we hope to present to the audience, the state-of-the-art frameworks for bringing the background biomedical knowledge into the pattern recognition task for biomedical data. THEMES In DMB 2007, complementary to main themes of IEEE BIBM 2007, special focus is aimed at looking on the evolving areas of interest for Application of Data Mining in Bioinformatics, namely Semantic Biomedicine, Biomedical Privacy and Security, Biometrics and Health Informatics. Thus as part of DMB 2007, there are four special tracks on: 1. Biomedical Data Mining: Theory and Applications 2. Semantics in Biomedicine 3. Biomedical Privacy, Security and Biometric Authentication 4. Health Informatics IMPORTANT DATES August 10, 2007 Paper Submission Deadline September 10, 2007 Notification of acceptance September 17, 2007 Final camera-ready paper due November 2 - 5, 2007 Workshop Days TOPICS Authors are invited to submit original papers to the workshop exploring data mining theories, techniques, and applications for Bioinformatics. Papers are invited (but not limited) to the following topics: ? Biomedical Data Mining Theory and Applications o Genomics and Proteomics o Comparative Genomics o Microarray Data Analysis o Protein/RNA Structure Prediction o Phylogenetics o Drug Design o Feature selection and pattern discovery in biological data o Biomedical Literature Mining o System Biology and Pathways o Data mining applications in bioinformatics, biomedicine, health care and other biomedical domain areas ? Semantics in Biomedicine o Conceptual Models for Biological and Medical Data o Modeling of Biochemical Pathways o Biological Data Visualization o Biomedical Ontologies o Biomedical Data Engineering using Ontologies o Biological Database Management o Biomedical Data Warehousing o Interoperation of Biomedical Databases o Biomedical Query Processing, Query Optimization, and Information Retrieval ? Biomedical Data Privacy and Security o Trusted Systems for Biomedical Data Frameworks o Secure e-science protocols and web services o Soft Computing methods in biomedical privacy and security o Management of emerging health care technologies ? Heath Informatics o Electronic Health Records o Clinical Assessment and Patient Diagnosis o Disease Control and Prevention o Medical informatics o Clinical decision support design, development and implementation o e-health and m-health o Virtual health technologies PAPER SUBMISSION Please submit a full length paper (not exceeding 5000 words) thorough the online submission system (http://kis-lab.com/cyberchair/bibm07/scripts/submit.php). Electronic submissions (in PDF or Postscript format) are required. Selected participants will be asked to submit their revised papers in a format to be specified at the time of acceptance. Extended versions of selected papers will be published in a Special Issues of International Journal of Data Mining and Bioinformatics (IJDMB) and International Journal of Computer Systems Science & Engineering (CSSE). Selected high quality submissions will be published as book chapters in an edited book entitled: "Annual Review of Biomedical Knowledge Discovery and Data Mining: Enriching Biomedical Data Mining with Ontologies" in Studies in Computational Intelligence Series by Springer. For further questions, please contact technical program chair: dmb07 at swbio.org ORGANIZATION General Chairs: Tharam S. Dillon Curtin University of Technology, Australia Elizabeth Chang Curtin University of Technology, Australia Program Chairs: Amandeep S. Sidhu Curtin University of Technology, Australia Farookh K. Hussain Curtin University of Technology, Australia Steering Committee: ? Alexey Tysmbal (Siemens, Germany) ? Amandeep S. Sidhu (Curtin University of Technology, Perth, Australia) ? Elizabeth Chang (Curtin University of Technology, Perth, Australia) ? Farookh K. Hussain (Curtin University of Technology, Perth, Australia) ? Jake Chen (Indiana University, USA) ? Jason Wang (New Jersey Institute of Technology, USA) ? Mykola Pechenizkiy (Eindhoven University of Technology, Netherlands) ? Mohammed J. Zaki (Rensselaer Polytechnic Institute, USA) ? T. Y. Lin (San Jose State University, USA) ? Tharam S. Dillon (Curtin University of Technology, Perth, Australia) ? Tony Hu (Drexel University, USA) ? Yi Pan (Georgia State University, USA) Special Track Chairs: ? Biomedical Data Mining ? Tony Hu ? Semantics in Biomedicine ? Amandeep S. Sidhu ? Biomedical Privacy, Security and Biometric Authentication ? Farookh K. Hussain ? Health Informatics ? Maja Hadzic From harry.mangalam at uci.edu Mon May 14 14:15:26 2007 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Mon, 14 May 2007 11:15:26 -0700 Subject: [BiO BB] need help w/ VRML viewer for big graphs - Mozilla plug-in? In-Reply-To: <83722dde0705112234y6436ab2fq78f0f75f162361be@mail.gmail.com> References: <83722dde0705111631p4e4c1a38vdbdefb5593a19e38@mail.gmail.com> <4644FE8C.70906@scalableinformatics.com> <83722dde0705112234y6436ab2fq78f0f75f162361be@mail.gmail.com> Message-ID: <200705141115.26269.harry.mangalam@uci.edu> Depending on how much programming you're willing to do, it sounds like some of the CAIDA tools may be of interest, particularly their java3d walrus visualizer (based on Tamara Munzner's work) http://www.caida.org/tools/visualization/walrus/ Right now it doesn't support much support for identification of the nodes themselves but it provides a good framework for writing in your own node-handling functions. We're evaluating it for doing some large network (IP as well as semantic) visualizations. hjm On Friday 11 May 2007 22:34, Ann Loraine wrote: > A hyperbolic viewer might be just the thing. We do want to "drill > down" into specific components of the graph. So that could be what > we need... > > Let me know if you would recommend a particular one (or two) to try > out first. Maybe some-one on the list would know, as well? > > One nice side benefit of LGL is that in the process of building > layouts for the graph, it seems to separate them into separate > components, which is useful. > > Thanks for the suggestions! > > -Ann > > On 5/11/07, Joe Landman wrote: > > Hi Ann > > > > Ann Loraine wrote: > > > I'm just getting started with LGL, but it looks like it can > > > give me a > > > > VRML > > > > > document that specifies the layout of large graphs (my biggest > > > is 500K edges, 9k nodes), and I'd like to find a VRML viewer > > > that might be able > > > > to > > > > > handle such a large graph. (I've got a machine w/ 3 gig memory, > > > and > > > > access > > > > > to a few others with even more memory, but I don't have admin > > > privs on those, so I'd like to avoid bugging the sysadmins > > > about installing new software until I'm sure I've got something > > > that will work...) > > > > > > If anyone on the list can recommend a good VRML plug-in (for > > > Mozilla) or stand-alone viewer that might work for this > > > application, I would be very grateful! > > > > Hmmm... Maybe my info is dated, but I had used inventor viewer > > (the VRML 1.0 spec was effectively OpenInventor's spec) to view > > some molecular structures I created out of PDB and other > > coordinates. Calls these fairly simple graphs, several thousand > > nodes, and tens of thousands of edges. Inventor viewer worked > > fine for these, though I ran them on an SGI at the time. I have > > run ivview recently on the same files on my laptop without > > problem. So if they are v1.0 VRML compliant, you might try the > > OpenInventor viewer as a stand-alone. > > > > > Also, if you have any tips on visualizing large graphs, I'd be > > > grateful > > > > for > > > > > those as well! > > > > Get lots of RAM. And a fast graphics card (accelerated OpenGL) > > with lots of RAM :( > > > > > So far the only thing I've been able to find that appears > > > capable of > > > > laying > > > > > out big graphs is LGL...but maybe there are some others? > > > > There are some hyperbolic space viewers for large connected > > graphs, though these are more for drilling in to specific nodes, > > than seeing the large scale structure of the system. > > > > > Thank you in advance for your help!!! > > > > > > -Ann > > > > -- > > Joseph Landman, Ph.D > > Founder and CEO > > Scalable Informatics LLC, > > email: landman at scalableinformatics.com > > web : http://www.scalableinformatics.com > > phone: +1 734 786 8423 > > fax : +1 734 786 8452 or +1 866 888 3112 > > cell : +1 734 612 4615 > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) harry.mangalam at uci.edu From Reactome-Knowledgebase at reactome.org Tue May 15 09:24:42 2007 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Tue, 15 May 2007 09:24:42 -0400 Subject: [BiO BB] New version of Reactome knowledgebase released Message-ID: <000c01c796f4$6606b250$51f5308f@DFWFS881> Version 21 of the Reactome Knowledgebase has been released and is accessible at http://www.reactome.org. Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute). Reactome covers human biological processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, HapMap, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). The web interface allows users to view the curated annotations of human biological processes and orthology-based electronic inferences from these annotations for 22 other species). New topics released in Version 21 include the Rho GTPase cycle, Wnt regulation of beta-catenin, gap junction turnover, pathways for steroid hormone biosynthesis, metabolism of bile acids and bile salts and snRNP assembly. An outline of the entire influenza virus infection cycle has been completed. Updated release statistics and the Editorial Calendar are available. Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. A description of Reactome was published in March, 2007, in Genome Biology; the PDF version is available here: http://genomebiology.com/2007/8/3/r39. Reactome is seeking expert help for the curation of new modules. The Reactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key biological processes, and to integrate these with other processes already in Reactome. We are seeking new author-collaborators. If you're interested, or would like more information about our data acquisition process, please contact us at editorial at reactome.org. For questions and comments please reply to this message or write to help at reactome.org. From smagarwal at yahoo.com Tue May 15 04:57:33 2007 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Tue, 15 May 2007 09:57:33 +0100 (BST) Subject: [BiO BB] Sequence similarity Message-ID: <841464.37275.qm@web31502.mail.mud.yahoo.com> Hi all I would like to know regarding the names of programs that are capable of identifying similarity of sequences (global and not local) within a large given dataset and subsequently it should also be capable of clustering these sequences. Thanks Subhash Agarwal --------------------------------- Office firewalls, cyber cafes, college labs, don't allow you to download CHAT? Here's a solution! From Sterten at aol.com Wed May 16 12:50:29 2007 From: Sterten at aol.com (Sterten at aol.com) Date: Wed, 16 May 2007 12:50:29 EDT Subject: [BiO BB] Sequence similarity Message-ID: OK, I wrote one for influenza. It's "beta" , description in bird-flu forums... I could search for description, if someone is interested. _http://magictour.free.fr/seqa.zip_ (http://magictour.free.fr/seqa.zip) (C-sourcecode attached to the executable) runs under Windows or DOS seqa.exe (for viruses, 8 segments) seq1.exe (for single segments) qingh6.3w3 (Qinghai-viruses) egy7s.10 (HA-Segments) seqa qingh6.3w3 > xx stores the lists of distances and mutations in file xx seqa without Parameter gives Menu extra Programme for Horizontal Sorting etc. other files etc. on demand From wilfred at sdsc.edu Wed May 16 13:18:04 2007 From: wilfred at sdsc.edu (Wilfred Li) Date: Wed, 16 May 2007 10:18:04 -0700 (PDT) Subject: [BiO BB] [NBCR Announce] Call for Participation: NBCR Summer Institute 2007 -- Cyberinfrastructure and Multiscale Modeling Approaches Message-ID: The National Biomedical Computation Resource (http://nbcr.net , NBCR) is pleased to present its second annual Summer Institute (http://nbcr.net/si/2007) to be held July 30 - August 3, 2007. This training program provides an overview of cyberinfrastructure and multiscale modeling approaches, and includes plenary sessions and hands-on training sessions using the tools essential for cutting edge biomedical research. NBCR's goal in offering this Summer Institute is to broaden the impact of these tools and work closely with the biomedical community in future developments, while offering significant opportunities for networking among researchers and participants. Each of the following topics represents a parallel track that will meet half days, for four days. Each participant may sign up for up to two tracks. Some tracks may offer extended sessions for advanced users. * Cluster and grid computing * Programming scalable scientific applications * Computational cardiac electrophysiology and mechanics * Molecular electrostatics and diffusion * Molecular visualization and virtual screening * Integrative studies: translational biomedical research For online access of training session materials, please visit the NBCR Public Wiki for the Summer Institute (https://nbcr.net/pub/wiki/index.php?title=NBCR_Summer_Institute). The workshop is geared toward graduate students, postdocs and researchers interested in learning how to use specific tools addressed by this workshop and/or who are interested in understanding the role of cyberinfrastructure in biomedical research. Registration fees are $400 for two tracks, or $250 for one track. Registration fees are waived for out of town participants using the campus lodging and meals plan. The campus lodging and meals plan is $660 (6 nights), plus $110 for each additional night. For individuals who require campus housing and meals, the registration deadline is July 16th. For individuals who do NOT need campus housing and meals, the registration deadline is July 23rd. All tracks are free to UCSD affiliated participants subject to space availability, with paying participants and those with accepted posters given higher priority. There are a number of scholarships awarded to defray the costs of attending the Summer Institute. Applicants are encouraged to apply early. The deadline for application is May 31, 2007. Notifications will be given by June 14, 2007. Please send your CV, poster abstract, and one letter of recommendation from or contact info for your Ph.D. advisor or immediate supervisor to Wilfred Li (wilfred at sdsc.edu). Awardees are required to present a poster during the poster sessions. For the names of the recipients of the 2006 Summer Institute, please visit the NBCR Summer Institute Forum (https://nbcr.net/forum/viewforum.php?f=14). Enrollment is limited. To ensure your place in the Summer Institute program and to help us accommodate you, we ask that you register as early as possible. Please contact Teri Simas (858.534.5034, tgraysimas at ucsd.edu) if you need additional information. From chenmengen at yahoo.com.cn Wed May 16 16:38:20 2007 From: chenmengen at yahoo.com.cn (chenmengen) Date: Wed, 16 May 2007 16:38:20 -0400 Subject: [BiO BB] NOC 3.0 is released Message-ID: <20070516204506.3D67A368788@primary.bioinformatics.org> New version NOC-3.0 is released for Windows/Linux/Mac OSX/FreeBSD/Solaris with source code. Downloading is available at http://noch.sourceforge.net NOC is: a easy and fast protein explorer for structure visulization, analysis; a powerful tool for crystallographic mapping, modeling and refinement; a efficient viwer for GROMACS/AMBER MD trajectories; From pmr at ebi.ac.uk Fri May 18 04:14:09 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 18 May 2007 09:14:09 +0100 Subject: [BiO BB] GCG gap program and emboss In-Reply-To: <87614.55710.qm@web51403.mail.re2.yahoo.com> References: <87614.55710.qm@web51403.mail.re2.yahoo.com> Message-ID: <464D6051.50200@ebi.ac.uk> Hongyu Zhang wrote: > Dear all, > > I am wondering which program in the EMBOSS package is closest to the GCG gap program? and how similar is their performance in terms of sequence alignment and score? Two EMBOSS programs have the same function (global alignment of nucleotide or protein sequences). needle is a straight implementation of the Needleman Wunsch alignment algorithm An alternative is stretcher, which is a port of the global alignment code in the FASTA package and can handle longer sequences by using a more memory-efficient order of processing. The score is fixed by the algorithm so you should get the same results. regards, Peter Rice From christoph.gille at charite.de Fri May 18 12:36:02 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 18 May 2007 18:36:02 +0200 (CEST) Subject: [BiO BB] proteolytic cleavage site prediction ? Message-ID: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> I am looking for a tool to predict proteases that can cut my amino acid sequence. Many Thanks ! From marty.gollery at gmail.com Fri May 18 12:49:11 2007 From: marty.gollery at gmail.com (Martin Gollery) Date: Fri, 18 May 2007 09:49:11 -0700 Subject: [BiO BB] proteolytic cleavage site prediction ? In-Reply-To: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> References: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> Message-ID: Hi Christoph, Try PeptideCutter or PoPS http://pops.csse.monash.edu.au Cheers, Marty On 5/18/07, Dr. Christoph Gille wrote: > I am looking for a tool to > predict proteases that can cut my > amino acid sequence. > Many Thanks ! > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif 775-833-9113 880 Northwood Blvd. Suite 7 Incline Village, NV 89451 From idoerg at burnham.org Fri May 18 13:42:56 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 18 May 2007 10:42:56 -0700 Subject: [BiO BB] proteolytic cleavage site prediction ? References: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> Message-ID: <1F97379A556D0946AAEFE3F63FD6F5744D46D7@MAIL.burnham.org> You should contact the center on proteolytic pahtways at the Burnham Institute. there are several tools there at various stages of development. http://cpp.burnham.org/metadot/index.pl CutDB is produciton level: http://cutdb.burnham.org/ -----Original Message----- From: bio_bulletin_board-bounces+idoerg=burnham.org at bioinformatics.org on behalf of Dr. Christoph Gille Sent: Fri 5/18/2007 9:36 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] proteolytic cleavage site prediction ? I am looking for a tool to predict proteases that can cut my amino acid sequence. Many Thanks ! _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From gigi at biocomp.unibo.it Fri May 18 12:45:10 2007 From: gigi at biocomp.unibo.it (gigi) Date: Fri, 18 May 2007 18:45:10 +0200 Subject: [BiO BB] proteolytic cleavage site prediction ? In-Reply-To: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> References: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> Message-ID: <464DD816.60509@biocomp.unibo.it> Maybe you can find some useful tool in Merops http://merops.sanger.ac.uk/ in the "searches" section Dr. Christoph Gille wrote: >I am looking for a tool to >predict proteases that can cut my >amino acid sequence. >Many Thanks ! > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From vxg189 at bham.ac.uk Sat May 19 05:39:55 2007 From: vxg189 at bham.ac.uk (Vibhor Gupta) Date: Sat, 19 May 2007 10:39:55 +0100 Subject: [BiO BB] proteolytic cleavage site prediction ? References: <45035.141.42.56.114.1179506162.squirrel@webmail.charite.de> <1F97379A556D0946AAEFE3F63FD6F5744D46D7@MAIL.burnham.org> Message-ID: Hello all, Is anyone aware of a freely available tool that allows me to submit a list of Gene IDs/symbols and determines which genes in the list are known transcription factors? Moreover, if such a tool exists, does it also report the targets of these known transcription factors? Thanks a lot. Best Wishes Vibhor _____ _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lixue at iastate.edu Tue May 22 08:54:39 2007 From: lixue at iastate.edu (Li Xue) Date: Tue, 22 May 2007 20:54:39 +0800 Subject: [BiO BB] need suggestions on how to start on Bioinformatics with data mining background Message-ID: <200705221255.l4MCt58G006846@mailhub-3.iastate.edu> Hello all, I am a graduate student with data mining background. My supervisor and I want to do some research on drug discovery. Recently, I have been reading nature and nature review. However I find out it is hard to find data mining topic in this journal. How should I start Bioinformatics? Should I begin with reading popular journals? Would you please recommend some journals to me? Thanks. Xue, Li Bioinformatics and Computational Biology Program Iowa State University 1-515-5201676 From rafael.najmanovich at ebi.ac.uk Tue May 22 06:48:07 2007 From: rafael.najmanovich at ebi.ac.uk (Rafael Najmanovich) Date: Tue, 22 May 2007 11:48:07 +0100 Subject: [BiO BB] Structural bioinformatics and computational biophysics ISMB satellite meeting Message-ID: <3A8BF064-36A8-458B-8A5B-92441AC6122A@ebi.ac.uk> On behalf of the 3DSig organising committee, I would like to bring to your attention the approaching deadline to submit an abstract to the forthcoming 3DSig 2007: Structural bioinformatics and computational biophysics ISMB satellite meeting to be held on July 19-20 in Vienna, Austria. http://structure.bu.edu/3DSig/ The deadline for abstract submissions is June 1st. Authors can choose to present their contribution as a laptop presentation and/or a poster (which may be the same as that to be presented in the main ISMB event). Furthermore, contributions can be selected for oral presentations. Registration for 3DSig does not require registration for the main ISMB event. The third 3Dsig meeting will consist of two full days with a balance of invited talks, short oral presentations, two laptop/poster- sessions, critical, topic-focused discussions and a dinner session. A truly unique event bringing together in one place the structural computational biology community. Relevant topics include among others: Structure representation, structure prediction, structural genomics Structural databases and 3D data mining Structure-based function prediction Evolution studied through structure Protein-protein, protein-ligand, and protein-RNA/DNA interactions (docking, analysis & prediction) Prediction and analysis of domains Membrane protein structure prediction and analysis The role of geometry and energetics in protein and RNA structure and function Protein and RNA dynamics and simulation: folding, stability, interactions, conformational gating Computer-aided protein and RNA design Structure-based drug design and pharmacophore analysis Chemoinformatics 3Dsig 2007 is continuing the tradition established through the successful 3Dsig 2006 and 3Dsig 2004. To better appreciate the wealth of leading topics and presenters, please explore the programs and proceedings from past 3Dsig 2004 and 2006 meetings. The program will be built around talks from accepted abstracts and invited speakers. The scientific committee is looking for fresh, effective voices with new, high impact ideas. Accepted abstracts will fall into two categories: oral presentation and laptop/poster presentation. Participants with accepted abstracts for the latter type will have the choice of presenting their work as either a regular poster, a laptop presentation, or a combination thereof. Those choosing to use a laptop to substitute or augment their poster presentation will have a stand or table and electric socket for a personal laptop (presenters must bring their own laptops). The aim of the poster/ laptop session is to facilitate interactions between the presenter and the viewers. http://structure.bu.edu/3DSig/ Looking forward to seeing you in Vienna! Dr. Rafael Najmanovich European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom rafael.najmanovich [at] ebi.ac.uk - www.ebi.ac.uk/~rafi +44-1223-492599 (voice) +44-7951-394145 (mobile) +44-1223-494468 (fax) From duangdao.wic at gmail.com Tue May 22 11:13:19 2007 From: duangdao.wic at gmail.com (Duangdao Wichadakul) Date: Tue, 22 May 2007 22:13:19 +0700 Subject: [BiO BB] need suggestions on how to start on Bioinformatics with data mining background In-Reply-To: <200705221255.l4MCt58G006846@mailhub-3.iastate.edu> Message-ID: You might search PubMed for "data mining" key word. You will get thousands of papers from there. For specific journals, I would recommend you to start from the following journals: "Nucleic Acid Research" (NAR), "Bioinformatics", "BMC Bioinformatics", "Genome Biology". Best, --Duangdao. On 5/22/07 7:54 PM, "Li Xue" wrote: > Hello all, > > I am a graduate student with data mining background. My supervisor > and I want to do some research on drug discovery. > > Recently, I have been reading nature and nature review. However I > find out it is hard to find data mining topic in this journal. > > How should I start Bioinformatics? Should I begin with reading > popular journals? Would you please recommend some journals to me? Thanks. > > Xue, Li > Bioinformatics and Computational Biology Program > Iowa State University > 1-515-5201676 > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Lambert at Chatham.edu Tue May 22 13:32:56 2007 From: Lambert at Chatham.edu (Lambert, Lisa) Date: Tue, 22 May 2007 13:32:56 -0400 Subject: [BiO BB] need suggestions on how to start on Bioinformatics with data mining background[Scanned] References: <200705221255.l4MCt58G006846@mailhub-3.iastate.edu> Message-ID: <7980CF1A43C6564184A9A92D278F839E0CA2AF56@hickory.chatham.local> Have you also looked at the following? Both have free subscriptions for academics: Genetic Engineering News http://www.genengnews.com/ Drug Discovery and Development http://www.dddmag.com/Subscribe.aspx?CommonCount=0 Lisa A. Lambert, Ph.D. Associate Professor of Biology Director, Graduate Biology Programs Chatham University Pittsburgh, PA 15232 412-365-1217 lambert at chatham.edu -----Original Message----- From: bio_bulletin_board-bounces+lambert=chatham.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+lambert=chatham.edu at bioinformatics.or g] On Behalf Of Li Xue Sent: Tuesday, May 22, 2007 8:55 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] need suggestions on how to start on Bioinformatics with data mining background[Scanned] Hello all, I am a graduate student with data mining background. My supervisor and I want to do some research on drug discovery. Recently, I have been reading nature and nature review. However I find out it is hard to find data mining topic in this journal. How should I start Bioinformatics? Should I begin with reading popular journals? Would you please recommend some journals to me? Thanks. Xue, Li Bioinformatics and Computational Biology Program Iowa State University 1-515-5201676 _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Wed May 23 19:14:30 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 23 May 2007 19:14:30 -0400 Subject: [BiO BB] Late spring Perl and R courses at BiO Message-ID: <4654CAD6.8040909@bioinformatics.org> Here are the upcoming Perl and R scripting courses from Bioinformatics.Org: PERL FOR BIOLOGISTS, LEVEL 1 May 28-June 1, 2007 http://edu.bioinformatics.org/CG R FOR BIOLOGISTS, LEVEL 1 May 28-June 1, 2007 http://edu.bioinformatics.org/CT PERL FOR BIOLOGISTS, LEVEL 2 June 11-15, 2007 http://edu.bioinformatics.org/GA R FOR BIOLOGISTS, LEVEL 2 June 11-15, 2007 http://edu.bioinformatics.org/GC Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From lixue at iastate.edu Wed May 23 22:55:31 2007 From: lixue at iastate.edu (Li Xue) Date: Thu, 24 May 2007 10:55:31 +0800 Subject: [BiO BB] need suggestions on how to start on Bioinformatics with data mining background In-Reply-To: References: <200705221255.l4MCt58G006846@mailhub-3.iastate.edu> Message-ID: <200705240255.l4O2tgpa013019@mailhub-3.iastate.edu> Thank you all for helpful information. :) Regards, Li At 23:13 2007-5-22, Duangdao Wichadakul wrote: >You might search PubMed for "data mining" key word. >You will get thousands of papers from there. >For specific journals, I would recommend you to start from the following >journals: "Nucleic Acid Research" (NAR), "Bioinformatics", "BMC >Bioinformatics", "Genome Biology". > >Best, >--Duangdao. > >On 5/22/07 7:54 PM, "Li Xue" wrote: > > > Hello all, > > > > I am a graduate student with data mining background. My supervisor > > and I want to do some research on drug discovery. > > > > Recently, I have been reading nature and nature review. However I > > find out it is hard to find data mining topic in this journal. > > > > How should I start Bioinformatics? Should I begin with reading > > popular journals? Would you please recommend some journals to me? Thanks. > > > > Xue, Li > > Bioinformatics and Computational Biology Program > > Iowa State University > > 1-515-5201676 > > > > > > _______________________________________________ > > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Xue, Li Bioinformatics and Computational Biology Program Iowa State University 1-515-5201676 From rres.bab-announce at bbsrc.ac.uk Fri May 25 06:50:41 2007 From: rres.bab-announce at bbsrc.ac.uk (rres bab-announce (RRes-Roth)) Date: Fri, 25 May 2007 11:50:41 +0100 Subject: [BiO BB] 4th Integrative Bioinformatics Workshop - 3rd call for papers - EXTENDED DEADLINE - 11 JUNE 2007 Message-ID: Subject: 4th Integrative Bioinformatics Workshop - 3rd call for papers - EXTENDED DEADLINE - 11 JUNE 2007 THIRD CALL FOR PAPERS - EXTENDED DEADLINE - 11 JUNE 2007 4th Integrative Bioinformatics Workshop September 10-12, 2007 University of Ghent, Belgium http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib07/ Papers are invited for oral presentations. Submission must be through the workshop web site. Accepted papers will also appear in the Journal of Integrative Bioinformatics http://journal.imbio.de/ DESCRIPTION Biological data are scattered across hundreds of biological databases and thousands of scientific journals. Current high throughput genomics technologies generate large quantities of high dimensional data. Microarray, NMR, mass spectrometry, protein chips, gel electrophoresis data, Yeast-Two-Hybrid, QTL mapping, gene silencing and knockout experiments are all examples of technologies that capture thousands of data points, often in single experiments. The challenge for Integrative Bioinformatics is to capture, model, integrate and analyse these data in a consistent way to provide new and deeper insights into complex biological systems. This, fourth workshop on Integrative Bioinformatics will be of interest to Bioinformaticians, Computer Scientists and others working in, or interested in finding out more about, the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches or their practical applications. SPONSORS The European Science Foundation have kindly agreed to sponsor this workshop as part of their functional genomics programme. This enables us to extend the workshop programme and we are able to offer some travel and subsistence bursaries for research students. TOPICS Database Integration Combined dry and wetlab studies Molecular Databases / Data Warehouses Errors and inconsistencies in biological databases Prediction and Integration of Metabolic and Regulatory Networks Genotype - phenotype linkage Protein-Protein-Interactions Microarray Modeling and Analyses Integrative Approaches for Drug Design Computational Infrastructure for Biotechnology Text and data mining Virtual Cell Modeling Gene Identification, Regulation and Expression Identification of Gene Regulatory Networks Computational Systems Biology Computational Proteomics Optimization of Workflow Management in Bioinformatics Bio Ontologies Quality and consistency of ontologies Integrative modeling and simulation frameworks Integrative data and text mining approaches IMPORTANT DATES - EXTENDED DEADLINES: June 11: Paper submission deadline July 16: Notification of acceptance for papers July 30: Camera ready paper submission deadline August 13: Registration deadline August 27: Poster submission deadline KEYNOTE TALKS Prof Carole Goble, School of Computer Science, University of Manchester, UK "myExperiment: A MySpace for the Self-serving Bioinformatician" Prof S?ren Brunak, BioCentrum-DTU, Technical University of Denmark, Denmark "Integrating data for interactome analysis across organisms" Dr David Searls, Senior Vice President, Informatics, GlaxoSmithKline Pharmaceuticals, USA "Integrative Drug Discovery" Dr Luis Serrano, EMBL, Heidelberg, Germany "Structure-based prediction of protein-protein and protein-DNA interactions" ORGANISING COMMITTEE Ralf Hofest?dt Bielefeld University, Germany Jacob Koehler Rothamsted Research, UK Martin Kuiper University of Gent, Belgium Paul Verrier Rothamsted Research, UK CONTACT Karen Morris, BAB Division, Rothamsted Research, West Common, Harpenden, Herts. AL5 2JQ, UK karen.morris at bbsrc.ac.uk tel: 01582 763133 ext 2813 fax: 01582 467907 From ieee820 at gmail.com Fri May 25 08:45:55 2007 From: ieee820 at gmail.com (Yang JingJing) Date: Fri, 25 May 2007 20:45:55 +0800 Subject: [BiO BB] Problem about comparing two TFBS In-Reply-To: References: Message-ID: Dear Sir: I have a problem about how to compare two transcription factors binding sites (i.e. CWTCC to CTTCC ) to determine if the two are the same or different using bioperl modules . Can you recommend me some useful bioperl modules to solve this problem ? Thank you very much . Best Regards James Yang From marchywka at hotmail.com Sat May 26 09:22:28 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 26 May 2007 09:22:28 -0400 Subject: [BiO BB] anyone have experience with un-annotated AFFX probes? In-Reply-To: <464DD816.60509@biocomp.unibo.it> Message-ID: Hi, I'm trying to follow up on results originally reported in http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16881841&query_hl=9&itool=pubmed_docsum Am J Vet Res. 2006 Aug;67(8):1307-18. Genomic expression patterns of mitral valve tissues from dogs with degenerative mitral valve disease.Oyama MA, Chittur SV. The authors reported this probe as being upregulated: 1586963 DG2−131f15 11.4 but even today it is not identified: ( you need to register but this is free) https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=CANINE%3A1586963_AT I'm trying to get any suggestive information on what this could possibly be. There is no link to "probe set display" as suggested here, http://www.affymetrix.com/support/technical/whitepapers/Sleuthing_NetAffx_whitepaper.pdf I wrote a script to run blast searches on the reverse complements probes listed on the above page and then found one human hit that turned up in most of the blasts, http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=116174854 If I grep for match locations I find that the hits are all reasonably close to each other, ( I tested this on a grade A annotation and it did find all the probes ) $ cat *.out | grep -A 10 ">.*AC004686"| grep Sbjct | sort -g -k 2 Sbjct: 109088 aggaacagatgtccaatgtttc 109109 Sbjct: 109124 ttgtggatttggctgacaaac 109144 Sbjct: 109137 tgacaaactctctaagctgcattt 109160 Sbjct: 109168 gttcccatagagtcagctagccact 109192 Sbjct: 109264 tcaaatgaatccagggtg 109281 Sbjct: 109376 tagtgggtcaaagagaatgagcaaa 109400 Sbjct: 109393 tgagcaaacagttggcacctgcc 109415 Sbjct: 109437 taaaggcaatgagtaagcagct 109458 Sbjct: 109527 tttgctgcaattcaaggcctc 109547 Hoping this may be a feature of the dog genome that for whatever reason was missed, I decide to investigate further. So, I cut an enclosing sequence from the NCBI entry, 109081 aattaagagg aacagatgtc caatgtttca aaaagccaca catttgtgga tttggctgac 109141 aaactctcta agctgcattt tatttctgtt cccatagagt cagctagcca cttgcaactg 109201 actcacttct ctctgggcca cagtttgggc cagtctcctg actacagaat tagaatccag 109261 atatcaaatg aatccagggt gcttgggtgg agagcaggtg ttaaaagcca tctaaaacca 109321 ccccttccct gctttaattt aggagtatca acacccacac agcaaactgc aaggctagtg 109381 ggtcaaagag aatgagcaaa cagttggcac ctgccaatcc cagcaccacg caattttaaa 109441 ggcaatgagt aagcagctgt ctggaacagg tttttgtata atccttctta agagtactgg 109501 ttaaatatgc aaatacacac aggttatttg ctgcaattca aggcctcgcc cccaaggcaa and tried to run a translated blast. First, it is worth noting that running clustalw against the AFFX target sequence (reverse complement ) showed a reasonable match to the above sequence I pulled out. While blast did find the above entry in various reading frames, nothing else of significance turned up. Any thoughts on a way to proceed? I have a ribosome script and will try various translations and see if an automated function prediction system can notice anything. Conserved domain searches on some of the above blast hits didn't turn up anything. Perhaps if I take a cleaner section of the gene I could get something more meaningful? Maybe I should download the IGB and play with the transcript a little? Thoughts or better approaches? Thanks. I sent a similar request to Affymetrix support- they have been very helpful in checking my earlier efforts and they provide a lot of great support but I thought someone here may be able to help as they are probably gone for the weekend. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com _________________________________________________________________ Like the way Microsoft Office Outlook works? You?ll love Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_outlook_0507 From rafael.najmanovich at ebi.ac.uk Tue May 29 13:11:25 2007 From: rafael.najmanovich at ebi.ac.uk (Rafael Najmanovich) Date: Tue, 29 May 2007 18:11:25 +0100 Subject: [BiO BB] Approaching Deadline: 3DSig: Structural bioinformatics and Computational Biophysics Message-ID: <6AD303C1-F891-4715-B3B3-542046A17F8F@ebi.ac.uk> On behalf of the 3DSig organising committee, I would like to bring to your attention the approaching deadline to submit an abstract to the forthcoming 3DSig 2007: Structural bioinformatics and computational biophysics ISMB satellite meeting to be held on July 19-20 in Vienna, Austria. http://structure.bu.edu/3DSig/ The deadline for abstract submissions is June 1st. Authors can choose to present their contribution as a laptop presentation and/or a poster (which may be the same as that to be presented in the main ISMB event). Furthermore, contributions can be selected for oral presentations. Registration for 3DSig does not require registration for the main ISMB event. The third 3Dsig meeting will consist of two full days with a balance of invited talks, short oral presentations, two laptop/poster- sessions, critical, topic-focused discussions and a dinner session. A truly unique event bringing together in one place the structural computational biology community. Relevant topics include among others: Structure representation, structure prediction, structural genomics Structural databases and 3D data mining Structure-based function prediction Evolution studied through structure Protein-protein, protein-ligand, and protein-RNA/DNA interactions (docking, analysis & prediction) Prediction and analysis of domains Membrane protein structure prediction and analysis The role of geometry and energetics in protein and RNA structure and function Protein and RNA dynamics and simulation: folding, stability, interactions, conformational gating Computer-aided protein and RNA design Structure-based drug design and pharmacophore analysis Chemoinformatics 3Dsig 2007 is continuing the tradition established through the successful 3Dsig 2006 and 3Dsig 2004. To better appreciate the wealth of leading topics and presenters, please explore the programs and proceedings from past 3Dsig 2004 and 2006 meetings. The program will be built around talks from accepted abstracts and invited speakers. The scientific committee is looking for fresh, effective voices with new, high impact ideas. Accepted abstracts will fall into two categories: oral presentation and laptop/poster presentation. Participants with accepted abstracts for the latter type will have the choice of presenting their work as either a regular poster, a laptop presentation, or a combination thereof. Those choosing to use a laptop to substitute or augment their poster presentation will have a stand or table and electric socket for a personal laptop (presenters must bring their own laptops). The aim of the poster/ laptop session is to facilitate interactions between the presenter and the viewers. http://structure.bu.edu/3DSig/ Looking forward to seeing you in Vienna! Dr. Rafael Najmanovich European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD United Kingdom rafael.najmanovich [at] ebi.ac.uk - www.ebi.ac.uk/~rafi +44-1223-492599 (voice) +44-7951-394145 (mobile) +44-1223-494468 (fax)