From red from nospam.com Tue Dec 4 07:58:12 2007 From: red from nospam.com (Red) Date: Tue Dec 4 11:49:12 2007 Subject: [Bioforum] Bioinformatics question: Use eUtils for BlastN-type query Message-ID: Is there any practical way to use NCBI's "eUtil" code to send a nucleotide sequence to NCBI to get a list of proteins back? Like a BlastN query. Thanks for any info! From Hongbo_Gu from brown.edu Wed Dec 5 09:42:53 2007 From: Hongbo_Gu from brown.edu (Gu, Hongbo) Date: Thu Dec 6 19:12:34 2007 Subject: [Bioforum] immunoprecipitation problems Message-ID: <91C1AD5E37A96E42B8A200E334370A9C06B8F67C@MAIL2.AD.Brown.Edu> Hello, I recently met an problem with IP, I tried 2 commercial Abs try to pull down one membrane receptor, but both of them falied, but they can successfully pull down this receptor in the mimic experiment (I have some recombinant receptor proteins expressed from E. Coli), I have tried different lysis buffer, different amount of Ab and other conditions. Because the MW of this receptor is about 25KDa, which is closer to the light chain of Ab, so I used protein G-HRP to detect the receptor by western. I am wondering is there something wrong with sample preparation, I added the lysis buffer to cells, sonicate them briefly, incubate on ice for 1h, centrifuge and pre-clear it by preimmune IgG and protein G bead, after all above steps, the receptor still present by western, but cannnot be pulled down by IP. The only reason I could think of is that the potential PTMs of the receptor block the epitopes of both Abs, is there other potential reasons for my problem? Thanks a lot! Hongbo Gu Graduate student of Chemistry Department Box H Brown University 324 Brook Street Providence, RI 02912 Office: GC332 Office Phone: 401-863-9162 From Red from nospam.com Sat Dec 8 19:08:03 2007 From: Red from nospam.com (Red) Date: Sat Dec 8 19:22:42 2007 Subject: [Bioforum] Re: Bioinformatics question: Automate Blast query References: Message-ID: I'd like to find source code for accessing Blast databases. Pref C/C++/C#, but anything will help. Thanks From dorjetarap from googlemail.com Sun Dec 9 05:57:15 2007 From: dorjetarap from googlemail.com (kdt) Date: Sun Dec 9 14:42:03 2007 Subject: [Bioforum] Re: Bioinformatics question: Automate Blast query References: Message-ID: <225e4b5a-5b2f-4191-a48b-a4b66eb40cb2@x69g2000hsx.googlegroups.com> On Dec 9, 12:08 am, Red wrote: > I'd like to find source code for accessing Blast databases. Pref > C/C++/C#, but anything will help. > > Thanks Not sure about mid level languages, but the bioperl library has a module called remoteblast that does what you need. http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast It may be worth checking out biopython, bioruby or biojava if you are more familiar with any of these languages. I think they should have some similar module. From idees from videotron.qc.ca Wed Dec 12 22:43:11 2007 From: idees from videotron.qc.ca (=?iso-8859-1?b?SWTpZXM=?=) Date: Thu Dec 13 00:14:06 2007 Subject: [Bioforum] Re: Bioinformatics question: Automate Blast query References: Message-ID: Le Sat, 08 Dec 2007 19:08:03 -0500, Red nous a dit: > I'd like to find source code for accessing Blast databases. Pref > C/C++/C#, but anything will help. > > Thanks You might want to check the source code of bibus (http://sourceforge.net/ projects/bibus-biblio/). It's in python, but you said that anything would help! From wce_2008 from iaeng.org Thu Dec 13 12:36:36 2007 From: wce_2008 from iaeng.org (wce_2008@iaeng.org) Date: Thu Dec 13 13:50:19 2007 Subject: [Bioforum] Last Call for Papers (extended): The IAENG International Conference on Bioinformatics (ICB 2008) Message-ID: CFP: IAENG International Conference on Bioinformatics ICB 2008 From: International Association of Engineers The 2008 IAENG International Conference on Bioinformatics 19-21 March, 2008, Hong Kong http://www.iaeng.org/IMECS2008/ICB2008.html The conference ICB'08 is held under the International MultiConference of Engineers and Computer Scientists 2008. The IMECS 2008 is organized by the International Association of Engineers (IAENG), and serves as good platforms for the engineering community members to meet with each other and to exchange ideas. The last conference in 2007 has attracted a total of over one thousand participants from over 50 countries. All submitted papers will be under peer review and accepted papers will be published in the conference proceeding (ISBN: 978-988-98671-8-8). The abstracts will be indexed and available at major academic databases. The accepted papers will also be considered for publication in the special issues of the journal Engineering Letters, in IAENG journals and in edited books. Revised and expanded version of the selected papers may also be included as book chapters in the standalone edited books under the framework of cooperation between IAENG and Springer. For reference, the following post conference edited books of our recent IAENG 2007 conferences have been scheduled to be published by Springer in early 2008: Trends in Intelligent Systems and Computer Engineering, Advances in Communication Systems and Electrical Engineering, and Advances in Industrial Engineering and Operations Research. Important Dates: Draft Manuscript submission deadline (extended): 30 December, 2007 Camera-Ready papers & Pre-registration due: 12 January, 2007 ICB 2008: 19-21 March, 2008 Submission: ICB 2008 is now accepting manuscript submissions. Prospective authors are invited to submit their draft paper in full paper (any appropriate style) to imecs{at}iaeng.org by 30 December, 2007. The submitted file can be in MS Word format, PS format, or PDF formats. The first page of the draft paper should include: (1) Title of the paper; (2) Name, affiliation and e-mail address for each author; (3) A maximum of 5 keywords of the paper. Also, the name of the conference that the paper is being submitted to should be stated in the email. The topics of the ICB'08 include, but not limited to, the following: Sequence analysis Sequence alignment Sequence database Sequence profiling tools Sequence motif RNA interference analysis High throughput screening Gene network and pathway analysis Genome annotation Gene finding Computational evolutionary biology Gene expression analysis Analysis of mutations in cancer and other diseases Structure prediction Structural motif Preserving biodiversity Modeling biological systems Software tools Protein expression analysis Single nucleotide polymorphism analysis And other applications ICB Conference Co-Chairs and Committee Members: Dechang Chen Assistant professor, Department of Preventive Medicine and Biometrics, Uniformed Services University of the Health Sciences, USA Dr. Qingfeng Chen (co-chair) School of Information Technology Deakin University, Australia I-Jen Chiang Associate Professor, Graduate Institute of Medical Informatics, Taipei Medical University Adjunct Associate Professor, Graduate Institute of Biomedical Engineering, National Taiwan University, Taiwan Wallace Choy (co-chair) Research Ass. Professor, Department of Electrical and Electronic Engineering The University of Hong Kong, Hong Kong Jui-chien Hsieh (co-chair) Assistant Professor, Department of Bioinformatics Chung Hua University, Taiwan Hsueh-Fen Juan Assistant Professor, Department of Life science National Taiwan University, Taiwan Xueliang Li Deputy Director and Professor Center for Combinatorics, Nankai University, China Chiung Moon Associate Professor, Department of Information & Industrial Engineering, Yonsei University, Seoul, South Korea Area Editor of the Journal of Industrial Engineering & Management Systems Alejandro Murua (co-chair) Associate Professor, Department of Mathematics and Statistics, University of Montreal, Canada Associate Editor, International Journal of Tomography and Statistics Dr. Dat Tran Senior Lecturer in Computing, School of Information Sciences and Engineering, University of Canberra, Australia Lin-Yu Tseng (co-chair) Professor, Department of Computer Science National Chung Hsing University, Taiwan Jer-Shyan Wu (co-chair) Associate Professor, Department of Bioinformatics Chung Hua University, Taiwan Cheng-Hong Yang Professor, Department of Electronics Engineering, National Kaohsiung University of Applied Sciences, Taiwan Dr. Xiaohua (Douglas) Zhang Senior biometrician, Merck Research Laboratories, West Point, PA, USA ICB'07 Special session: Pharmacogenomics Special session chair: Xiaohua (Douglas) Zhang, Ph.D. Carnegie Mellon University Senior biometrician, Merck Research Laboratories, West Point, PA, USA More details about the IMECS 2008 can be found at: http://www.iaeng.org/IMECS2008/index.html http://www.iaeng.net/IMECS2008/index.html http://www.iaeng.com/IMECS2008/index.html It is our target that the reviewing process and the result notification for each submitted manuscript can be completed within one month from its submission. The reviewing process is to ensure the quality of the accepted papers in the WCE congress. The conferences have enjoyed high reputation among many research colleagues ( for example, see the http://cs.conference-ranking.net/ or http://www.conference-ranking.com/ or http://www.conference-ranking.org/cs.html ). More details about the International Association of Engineers, the journal Engineering Letters and the IAENG International Journal of Computer Science can be found at: http://www.iaeng.org/about_IAENG.html http://www.iaeng.org/IJCS/index.html http://www.iaeng.org/IJAM/index.html http://www.iaeng.net/ http://www.iaeng.com/ The official journal web site of Engineering Letters at: http://www.engineeringletters.com Other Engineering Letters web sites at: http://www.engineeringletters.com http://www.engineeringletters.net http://www.engineeringletters.org http://www.engineeringletter.com ******** It will be highly appreciated if you can circulate these calls for papers to your colleagues. From hra from pixel.cviog.uga.edu Mon Dec 17 11:52:25 2007 From: hra from pixel.cviog.uga.edu (Hamid R. Arabnia) Date: Mon Dec 17 14:35:25 2007 Subject: [Bioforum] Call For Papers: WORLDCOMP'08 - Computer Science and Engineering Conferences, USA, July 2008. Message-ID: <20071217165225.23BBB2245EF6@pixel.cviog.uga.edu> Dear Colleagues: Please disseminate the following announcement to those who may be interested. I would be grateful. I hope you have a wonderful Christmas. Thank you, Hamid ----- CALL FOR PAPERS and Call For Workshop Proposals WORLDCOMP'08 The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing July 14-17, 2008, Las Vegas, USA (composed of 25 Joint Conferences) ACADEMIC SPONSORS: Research labs at Harvard University, UCLA, Georgia Institute of Technology, University of Texas at Austin, University of Iowa, and others (see below). You are invited to submit a paper (and/or a proposal to organize a session/workshop). All accepted papers will be published in the respective conference proceedings. The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'08) is composed of the following 25 conferences (all will be held simultaneously, same location and dates: July 14-17, 2008, USA): o BIOCOMP'08: The 2008 International Conference on Bioinformatics and Computational Biology o CDES'08: The 2008 International Conference on Computer Design o CGVR'08: The 2008 International Conference on Computer Graphics and Virtual Reality o CIC'08: The 2008 International Conference on Communications in Computing o CSC'08: The 2008 International Conference on Scientific Computing o DMIN'08: The 2008 International Conference on Data Mining o EEE'08: The 2008 International Conference on e-Learning, e-Business, Enterprise Information Systems, and e-Government o ERSA'08: The 2008 International Conference on Engineering of Reconfigurable Systems and Algorithms o ESA'08: The 2008 International Conference on Embedded Systems and Applications o FCS'08: The 2008 International Conference on Foundations of Computer Science o FECS'08: The 2008 International Conference on Frontiers in Education: Computer Science and Computer Engineering o GCA'08: The 2008 International Conference on Grid Computing and Applications o GEM'08: The 2008 International Conference on Genetic and Evolutionary Methods o ICAI'08: The 2008 International Conference on Artificial Intelligence o ICOMP'08: The 2008 International Conference on Internet Computing o ICWN'08: The 2008 International Conference on Wireless Networks o IKE'08: The 2008 International Conference on Information and Knowledge Engineering o IPCV'08: The 2008 International Conference on Image Processing, Computer Vision, and Pattern Recognition o ITSL'08: The 2008 International Conference on Information Theory and Statistical Learning o MLMTA'08: The 2008 International Conference on Machine Learning; Models, Technologies and Applications o MSV'08: The 2008 International Conference on Modeling, Simulation and Visualization Methods o PDPTA'08: The 2008 International Conference on Parallel and Distributed Processing Techniques and Applications o SAM'08: The 2008 International Conference on Security and Management o SERP'08: The 2008 International Conference on Software Engineering Research and Practice o SWWS'08: The 2008 International Conference on Semantic Web and Web Services (a link to each conference's URL can be found at http://www.world-academy-of-science.org) General Co-Chair and Coordinator: H. R. Arabnia, PhD Professor, Computer Science Editor-in-Chief, The Journal of Supercomputing (Springer) Vice President, Int'l Society of Intelligent Biological Medicine The University of Georgia Department of Computer Science 415 Graduate Studies Research Center Athens, Georgia 30602-7404, USA Tel: (706) 542-3480 Fax: (706) 542-2966 E-mail: hra@cs.uga.edu PURPOSE / HISTORY: This set of joint conferences is the largest annual gathering of researchers in computer science, computer engineering and applied computing. Many of the 25 joint conferences in WORLDCOMP are the premier conferences for presentation of advances in their respective fields. We anticipate to have 2,600 or more attendees from over 80 countries participating in the 2008 joint conferences. The motivation is to assemble a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. The main goal is to provide a forum for exchange of ideas in a number of research areas that interact. The model used to form these annual conferences facilitates communication among researchers from all over the world in different fields of computer science, computer engineering and applied computing. Both inward research (core areas of computer science and engineering) and outward research (multi-disciplinary, inter-disciplinary, and applications) will be covered during the conferences. WORLCOMP'08 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations. In recent past, keynote and/or tutorial speakers included: Prof. Michael J. Flynn (Stanford U.); Prof. John H. Holland (U. of Michigan, Ann Arbor); Prof. H. J. Siegel (Colorado State U.); Prof. Barry Vercoe (MIT); Prof. Ruzena Bajcsy (U. of California, Berkeley); Prof. David Cheriton (Stanford U.), Prof. A. K. Dunker (Indiana U. and Purdue U.); Prof. Jun Liu (Harvard U.); Dr. Jim Gettys (developer of X Window, ...); Dr. Chris Rowen (President and CEO, Tensilica, Inc.); and many other distinguished speakers. SUBMISSION OF PAPERS: Prospective authors are invited to submit their draft paper (about 5 to 7 pages - single space, font size of 10 to 12) to H. R. Arabnia by Feb. 25, 2008. email submissions in MS document or PDF formats are preferable (Fax or postal submissions are also fine.) All reasonable typesetting formats are acceptable (later, the authors of accepted papers will be asked to follow a particular typesetting format to prepare their papers for publication.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, email address, and telephone number for each author. The first page should also identify the name of the Contact Author and a maximum of 5 topical keywords that would best represent the content of the paper. Finally, the name of the conference that the paper is being submitted to must be stated on the first page. Papers will be evaluated for originality, significance, clarity, impact, and soundness. Each paper will be refereed by two experts in the field who are independent of the conference program committee. The referees' evaluations will then be reviewed by two members of the program committee who will recommend a decision to the chair of the track that the paper has been submitted to. The chair will make the final decision. Lastly, the Camera-Ready papers will be reviewed by one member of the program committee. PROPOSAL FOR ORGANIZING SESSIONS/WORKSHOPS: Each session will have at least 6 paper presentations from different authors (12 papers in the case of workshops). The session chairs will be responsible for all aspects of their sessions; including, soliciting papers, reviewing, selecting, ... The names of session chairs will appear as Associate Editors in the conference proceedings and on the cover of the books. Proposals to organize sessions should include the following information: name and address (+ email) of proposer, title of session, a 100-word description of the topic of the session, the name of the conference the session is submitted for consideration, and a short description on how the session will be advertised (in most cases, session proposers solicit papers from colleagues and researchers whose work is known to the session proposer). email your proposal to H. R. Arabnia (address is given above). We would like to receive the proposals by January 16, 2008. IMPORTANT DATES: Jan. 16, 2008: Proposals for organizing/chairing sessions/workshops Feb. 25, 2008: Submission of papers (about 5 to 7 pages) March 25, 2008: Notification of acceptance April 25, 2008: Camera-Ready papers and Registration due July 14-17, 2008: The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'08 - 25 joint conferences) MEMBERS OF PROGRAM AND ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; AI; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being formed. Those interested in joining the Program Committee should email H. R. Arabnia (hra@cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, a short biography together with research interests and the name of the conference offering to help with. Many who have already joined the committees of individual tracks are renowned leaders, scholars, researchers, scientists and practitioners of the highest ranks; many are directors of research laboratories, fellows of various societies, heads/chairs of departments, deans and provosts. LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). This is a mega hotel with excellent conference facilities and over 3,000 rooms. It is minutes from the airport with 24-hour shuttle service to and from the airport. This hotel has many recreational attractions, including: waterfalls, spa, pools, sunning decks, Easy River, wave pool, lighted tennis courts, health spa, nightly shows, a number of restaurants, ... The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions (recreational destinations, Golf courses, ...) SPONSORS: (this is a partial list) Academic Co-sponsors include: - Computational Biology and Functional Genomics Laboratory, Harvard University, Cambridge, Massachusetts, USA http://compbio.dfci.harvard.edu/ - Horvath Laboratory, University of California, Los Angeles (UCLA), USA http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ - BioMedical Informatics & Bio-Imaging Laboratory, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA http://www.bio-miblab.org/ - Intelligent Data Exploration and Analysis Laboratory, University of Texas at Austin, Austin, Texas, USA http://www.ideal.ece.utexas.edu/ - Center for the Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA http://opal.biology.gatech.edu/GeneMark/ - Hawkeye Radiology Informatics, Department of Radiology, College of Medicine, University of Iowa, Iowa, USA http://www.uiowa.edu/~hri/ - Medical Image HPC & Informatics Lab (MiHi Lab), University of Iowa, Iowa, USA http://www.uiowa.edu/mihpclab/ - The University of North Dakota, Grand Forks, North Dakota, USA http://www.und.edu - International Society of Intelligent Biological Medicine http://www.isibm.org/ - Institute for Informatics Problems of the Russian Academy of Sciences, Moscow, Russia. Other Co-sponsors: - NIIT Technologies http://www.niit-tech.com/ - High Performance Computing for Nanotechnology (HPCNano) http://www.hpcnano.org - International Technology Institute (ITI) http://www.itiworld.org/ - GridToday http://www.gridtoday.com/gridtoday.html - HPCwire http://www.hpcwire.com/ - Hodges' Health (H2CM), UK http://www.p-jones.demon.co.uk Future Announcements: If you do not wish to receive future announcements about this event, please send an email to hra@cs.uga.edu. From akhtung from gmail.com Mon Dec 17 22:15:15 2007 From: akhtung from gmail.com (akhtung@gmail.com) Date: Tue Dec 18 13:24:01 2007 Subject: [Bioforum] Gemini: Free Software for Mining Gene Expression Data and Other High Dimensional Datasets Message-ID: <6cbca022-d18d-4ee5-9f65-65720970d480@e25g2000prg.googlegroups.com> We are happy to announce the immediate availability of a set of gene expression mining tools that we have researched and developed over the past few years under the project "GEMINI: Gene Expression Mining". These tools include: CARPENTER: A closed pattern mining algorithm that is specially catered to mine tables with large number of columns (10,000-100,000) and small number of rows (200-1000) using a concept call row enumeration or samle enumeration under the gene expression context. TopkIRG: An efficient rule extraction and classifier construction algorithm that find top-k covering rules for each row/sample in the gene expression in order to construct a highly accurate rule-based classifier. RegMiner: A gene clustering algorithm that group coherent genes together even if they are shifted and scaled version of a common pattern. More details of GEMINI are available at http://nusdm.comp.nus.edu.sg/. To obtain the software, please click on "Resources" at the website. Anthony K. H. Tung School of Computing National University of Singapore(NUS) From jaume.bacardit from nottingham.ac.uk Thu Dec 20 09:48:02 2007 From: jaume.bacardit from nottingham.ac.uk (Jaume Bacardit) Date: Thu Dec 20 11:25:42 2007 Subject: [Bioforum] Call for papers for the 11th International Workshop on Learning Classifier Systems Message-ID: <476A80A2.3070902@nottingham.ac.uk> Our apologies if you receive multiple copies of this announcement. -------------------------------------------------------------------------------- 11th International Workshop on Learning Classifier Systems to be held as part of the 2008 GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE (GECCO-2008) July 12-16, 2008 (Saturday-Wednesday) Renaissance Atlanta Hotel Atlanta, Georgia, USA Sponsored by ACM SIGEVO www.sigevo.org/GECCO-2008 PAPER SUBMISSION DEADLINE FOR WORKSHOP: March 26th, 2008 Workshop Website: http://www.psychologie.uni-wuerzburg.de/i3pages/butz/IWLCS2008 -------------------------------------------------------------------------------- The Eleventh International Workshop on Learning Classifier Systems (IWLCS 2008) will be held in Atlanta, Georgia, USA, Sunday, July 13, 2008 during the Genetic and Evolutionary Computation Conference (GECCO-2008), July 12-16, 2008. Originally, Learning Classifier Systems (LCSs) were introduced by John H. Holland as a way of applying evolutionary computation to machine learning and adaptive behavior problems. Sine then, the LCS paradigm has broadened greatly into a framework that encompasses many representations, rule discovery mechanisms, and credit assignment schemes. Current LCS applications range from data mining, to automated innovation and the on-line control of cognitive systems. LCS research includes various actual system approaches: While Wilson's accuracy-based XCS system (1995) has received the highest attention and gained the highest reputation, studies and developments of other LCSs are usually discussed and contrasted. Advances in machine learning, and reinforcement learning in particular, as well as in evolutionary computation have brought LCS systems the necessary competence and guaranteed learning properties. Novel insights in machine learning and evolutionary computation are being integrated into the LCS framework. Thus, we invite submissions that discuss recent developments in all areas of research on, and applications of, Learning Classifier Systems. IWLCS is the event that brings together most of the core researchers in classifier systems. Moreover, a free introductory tutorial on LCSs is presented the day before the workshop at GECCO 2008. Tutorial and IWLCS workshop thus also provide an opportunity for researchers interested in LCSs to get an impression of the current research directions in the field as well as a guideline for the application of LCSs to their problem domain. Submissions and Publication --------------------------- Submissions will be short-papers up to 8 pages in ACM format. Please see the GECCO 2008 information for authors for further details. All accepted papers will be presented at IWLCS 2008 and will appear in the GECCO workshop volume. Proceedings of the workshop will be published on CD-ROM, and distributed at the conference. Authors will be invited after the workshop to submit revised (full) papers for publication in the next post-workshop proceedings volume (scheduled for 2009), in the Springer LNCS/LNAI book series. All papers should be submitted in PDF format and e-mailed to: esterb[at]salle.url.edu. Important dates --------------- * Paper submission deadline: Wednesday, March 26, 2008 * Notification to authors: Wednesday, April 2, 2008 * Submission of camera-ready material: by Friday, April 18, 2008 * Conference registration by Monday, April 21, 2008 * Workshop date: Sunday, July 13, 2008 Committees ---------- - Organizing Commitee * Jaume Bacardit, University of Nottingham (UK). E-mail: jaume.bacardit@nottingham.ac.uk * Ester Bernad-Mansilla, Universitat Ramon Llull (Spain). E-mail: esterb@salle.url.edu * Martin V. Butz, Universitat Wurzburg (Germany). E-mail: mbutz@psychologie.uni-wuerzburg.de - Advisory Committee * Tim Kovacs, University of Bristol (UK) * Xavier Llor University of Illinois at Urbana-Champaign (USA) * Pier Luca Lanzi, Politechnico de Milano (Italy) * Wolfgang Stolzmann, Daimler Chrysler AG (Germany) * Keiki Takadama, Tokyo Institute of Technology (Japan) * Stewart Wilson, Prediction Dynamics (USA) Further information ------------------- For more details, please visit the workshop website at: http://www.psychologie.uni-wuerzburg.de/i3pages/butz/IWLCS2008 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From atglab from vsnl.net Fri Dec 21 02:25:04 2007 From: atglab from vsnl.net (Mol biol training) Date: Fri Dec 21 12:53:16 2007 Subject: [Bioforum] Mol bio training Message-ID: To bridge the gap between academics and industries and to provide quality industry oriented wet lab biotech education, we have started training students in various skill sets. Major objectives are 1. To provide cutting edge hands on training for young biotechnologists 2. To built a talented human resource pool in cell and molecular biology 3. To create a dedicated work force for research and development in various life science areas. We have successfully completed batches of four weeks and two weeks training program since June 2007 with the training theme .... Polymerase chain reaction and molecular diagnostics we are specialized in Virology and Human Genetics. We also carry out six months project in biotechnology and bioinformatics for final year students. For recent update and detailed course contents, six months projects details, and free demo of the working of PCR programming visit out laboratory. With best wishes! D.P. Lingojwar Director, ATG Biosystems, Pune, INDIA Mobile 9921446321 email atglab@vsnl. net From Red from nospam.com Sun Dec 23 01:25:16 2007 From: Red from nospam.com (Red) Date: Sun Dec 23 18:20:23 2007 Subject: [Bioforum] Re: Bioinformatics question: Automate Blast query References: <225e4b5a-5b2f-4191-a48b-a4b66eb40cb2@x69g2000hsx.googlegroups.com> Message-ID: On Sun, 9 Dec 2007 02:57:15 -0800 (PST), kdt wrote: >On Dec 9, 12:08 am, Red wrote: >> I'd like to find source code for accessing Blast databases. Pref >> C/C++/C#, but anything will help. >> >> Thanks > >Not sure about mid level languages, but the bioperl library has a >module called remoteblast that does what you need. > >http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast > >It may be worth checking out biopython, bioruby or biojava if you are >more familiar with any of these languages. I think they should have >some similar module. A belated thanks for your reply! I never saw it until today. My other ISP probably filtered it (the sporge floods don't show up there either, but I guess their filter is too aggressive). I'll definitely check the links that you recommended. Probably easy enough to translate to C++ or C#. From javeda from cs.rpi.edu Fri Dec 28 18:16:02 2007 From: javeda from cs.rpi.edu (javeda@cs.rpi.edu) Date: Sat Dec 29 12:48:26 2007 Subject: [Bioforum] workshop on Data Mining for Biomedical Informatics at SDM08 In-Reply-To: <2204.72.230.6.173.1197307563.squirrel@webmail.cs.rpi.edu> References: <2204.72.230.6.173.1197307563.squirrel@webmail.cs.rpi.edu> Message-ID: <2391.72.230.6.173.1198883762.squirrel@webmail.cs.rpi.edu> Dear Colleague: We would like to bring to your attention a workshop on Data Mining for Biomedical Informatics at the SIAM International Conference on Data Mining (SDM08), in Atlanta, Georgia, April 24 - 26, 2008. This is the second workshop in the series of Data Mining for Biomedical Informatics workshops held in conjunction with SDM. The URL for the workshop is: http://www.cs.rpi.edu/DMBIO08/ This workshop intends to provide a venue to facilitate the exchange of ideas between scientists in computer science, biology, mathematics and clinical research by bringing together researchers to discuss and present sources of data, research topics that may be addressed by such data, and data mining algorithms that may be used to analyze them. We encourage the submission of papers that use techniques from disciplines such as statistics, linear algebra, functional analysis, and signal processing, applied in some biomedical domain, as well as papers exposing rich sources of publicly available biomedical data that are of interest to the data mining community. Important Dates =============== Papers due: January 11, 2008 Notification of acceptance: January 20, 2008 Final version: February 4, 2008 Workshop: April 26, 2008 We are looking forward to receiving your submission. With best regards, Asif Javed, Publicity Chair javeda@cs.rpi.edu On behalf of the organizers Petros Drineas drinep@cs.rpi.edu Michael W. Mahoney mahoney@yahoo-inc.com Rui Kuang kuang@cs.umn.edu From scimedweb from mail.com Mon Dec 31 05:59:25 2007 From: scimedweb from mail.com (scimedweb@mail.com) Date: Mon Dec 31 13:12:17 2007 Subject: [Bioforum] Tumor suppressor genes in breast cancer: an update. Message-ID: <686038bb-9d72-4426-b5d5-5521b93d9c84@y5g2000hsf.googlegroups.com> An update on tumor suppressor genes in breast cancer. by Marc Lacroix InTextoResearch, Baelen (Wallonia), Belgium in Tumor Suppressor Genes, Nova Sciences Publishers, ISBN 1-60021-693-5 (2007), pp. 177-251 Breast cancer is characterized by the accumulation of genetic alterations, including point mutations and loss of entire DNA regions ("loss of heterozygosity" or LOH). Among genes that are affected by such events, the "tumor suppressor genes" (TSGs) have a peculiar interest since they often occupy pivotal positions in regulatory networks that control the cell cycle and/or encompass various signal transduction cascades. While a number of genes have been suggested as candidate TSGs in breast cancer, only a few of them have been confirmed in this status. They include TP53, BRCA1, BRCA2...and are mainly involved in the control of DNA repair, cell proliferation, apoptosis and signaling. Some TSGs are linked to familial (hereditary) forms of breast cancer. The exact definition of what is a TSG is still debated. Recently, genes not affected by mutation or even LOH, but occasionally methylated have been considered as TSGs. Genes discussed: On chromosome 1: CLCA2, DIRAS3 (ARHI, RHOI, NOEY2), LPHH1, TTC4, RAD54L (RAD54), FABP3 (MDGI), RUNX3 (CBFA3, AML2), PRDM2 transcript 1 (RIZ transcript 1), SFN (14-3-3s) On chromosome 3: ROBO1 (DUTT1), PTPG (PTPRG); FHIT (FRA3B, included), PB1 (BAF180), RASSF1 transcript A, RBM5 (LUCA-15, H37), TUSC4 (NPRL2), TMEM158 (RIS1), SEMA3B, TGFBR2 (HNPCC6), APRG1 (C3ORF35), RARB transcript 2, VHL, ATR (FRP1) On chromosome 4: SLIT2, PRDM5, HPGD (PGDH1) On chromosome 5: DAB2 (C9), APC, IRF1 On chromosome 6: PLAGL1 (ZAC, LOT1), LATS1 (WARTS), IGF2R (MPRI) On chromosome 7: ST7 (TSG7, RAY1, FAM4A1, HELG) On chromosome 8: SFRP1 (FRP), DLC1 (ARHGAP7), BNIP3L, RHOBTB2 (DBC2), LZTS1 (FEZ1, F37), MTUS1 (ATIP), MCPH1 (BRIT1), ST18 On chromosome 9: CDKN2A (p16INK4A, p14ARF), SYK, DAB2IP (AIP1), TSC1 On chromosome 10: PTEN (MMAC1), PDCD4, MGMT On chromosome 11: WT1, TSG101, CDKN1C (BWS), CST6, IGSF4 (ST17, NECL2, TSLC1), ATM, LOH11CR2A (BCSC1) On chromosome 12: CCND2 On chromosome 13: LATS2, BRCA2 (FANCD1), RB1, ARL11 (ARLTS1) On chromosome 15: RAD51 (RECA) On chromosome 16: TSC2, CYLD, CTCF, CDH1, TERF2 (TRF2), TERFIP, FBXL8, LRRC29, ATBF1, WWOX, FBXO31, CBFA2T3 transcript B (MTG16), CPNE7, CDK10 (PISSLRE), FANCA, GAS11, C16ORF3 On chromosome 17: MAP2K4 (SERK1, SEK1, PRKMK4, MEK4), GABARAP, TP53, IC1, OVCA1(DPH2L1, DPH1), BRCA1, BECN1, SLC9A3R1 On chromosome 18: EPB41L3, SMAD4 (ELAC1, DPC4), DCC On chromosome 19: STK11 (LKB1) On chromosome 22: SMARCB1 (BAF47, SNF5), RRP22, TMPRSS6, CHEK2 (CHK2, RAD53), NF2, PRR5