From marchywka at hotmail.com Tue Jun 2 13:59:59 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 2 Jun 2009 13:59:59 -0400 Subject: [BiO BB] looking for interactive motif/conserved things or rule site In-Reply-To: References: Message-ID: Hi, I found this site a few years ago, http://www.expasy.ch/prosite/prorule.html and downloaded their rules to generate some tools such as these, http://www.spottext.com/marchywka/annotaters/docs.html I've found it useful to be able to harvest my own rules from literature and wrote a program to convert XML entries including all the source information into "one-liners" that describe each rule as a regular expression along with a terse name and citation. Then, I got the bright idea that I could find many motifs using ncbi's eutils facilities and some scripts. And, indeed this was possible, as I was able to extract perhaps 800 rules but I needed to manually edit them. In any case, I was wondering who else used the prosite facilities or things like it and if there were generated or author deposited pattern libraries somewhere? They do let you enter your own sequence here, http://www.expasy.org/tools/scanprosite/ but not sure if there is any thing more comprehensive for user entered patterns that may be questionable or wrong or just entered for discussion( like the wiki talk pages). As an example, I was reading this article, http://www.jbc.org/cgi/content/full/282/48/34929 and wanted to generate rules from the peptides and maybe put them into some kind of public data file maybe with a discussion page or allow others to curate like a wiki pattern library. Thoughts or comments on existing facilities that may accomplish these results ? Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: hotmail is getting cumbersom, try also marchywka at yahoo.com _________________________________________________________________ Windows Live?: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_BR_life_in_synch_062009 From leo.goodstadt at dpag.ox.ac.uk Mon Jun 1 10:01:49 2009 From: leo.goodstadt at dpag.ox.ac.uk (Leo Goodstadt) Date: Mon, 1 Jun 2009 15:01:49 +0100 Subject: [BiO BB] Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics Message-ID: <016c01c9e2c1$822220d0$86666270$@goodstadt@dpag.ox.ac.uk> A new library called Ruffus is available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html. Ruffus provides easy / lightweight support for running computational pipelines in python. The best way to produce reproducible bioinformatics analyses is by scripting all the stages or tasks which have to be run. Ruffus is designed to allow this to happen in python in the least intrusive manner possible, and without any special (non-python) syntax. Like makefiles (or scons), it helps you to manage task dependencies. However, because it is designed from the start for bioinformatics pipelines (rather than compiling programmes), no ugly syntax / hacking is required. Ruffus provides automatic support for * Managing dependencies * Running tasks in parallel * Re-starting from arbitrary points, especially after errors * Display of the pipeline as a flowchart * Reporting We have been using Ruffus in-house but we would like to see what other scientists think of the design before we bring its attention to a wider audience. (We intend to publish this as an application note in some bioinformatics journal) Please help us by sending feedback to: ruffus at llew.org.uk Extensive documentation, download details and two tutorials are available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html. Leo Goodstadt MRC Functional Genomics Unit University of Oxford From nuin at genedrift.org Tue Jun 2 22:53:53 2009 From: nuin at genedrift.org (Paulo Nuin) Date: Tue, 2 Jun 2009 22:53:53 -0400 Subject: [BiO BB] Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics In-Reply-To: <016c01c9e2c1$822220d0$86666270$@goodstadt@dpag.ox.ac.uk> References: <016c01c9e2c1$822220d0$86666270$@goodstadt@dpag.ox.ac.uk> Message-ID: You just forgot to mention that it's Python 2.6 compatible only. Paulo On 1-Jun-09, at 10:01 AM, Leo Goodstadt wrote: > A new library called Ruffus is available from > http://ruffus.googlecode.com/svn/trunk/doc/html/index.html. > > Ruffus provides easy / lightweight support for running > computational pipelines in python. > > The best way to produce reproducible bioinformatics analyses > is by scripting all the stages or tasks which have to be run. > > Ruffus is designed to allow this to happen in python > in the least intrusive manner possible, and without any > special (non-python) syntax. > > Like makefiles (or scons), it helps you to manage > task dependencies. However, because it is designed > from the start for bioinformatics pipelines (rather than > compiling programmes), no ugly syntax / hacking is > required. > > Ruffus provides automatic support for > > * Managing dependencies > * Running tasks in parallel > * Re-starting from arbitrary points, especially after errors > * Display of the pipeline as a flowchart > * Reporting > > > We have been using Ruffus in-house but we would like to see > what other scientists think of the design before we bring > its attention to a wider audience. (We intend to publish > this as an application note in some bioinformatics journal) > > Please help us by sending feedback to: > ruffus at llew.org.uk > > > Extensive documentation, download details and two tutorials are > available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html > . > > > Leo Goodstadt > MRC Functional Genomics Unit > University of Oxford > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From marty.gollery at gmail.com Wed Jun 3 13:52:50 2009 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 3 Jun 2009 10:52:50 -0700 Subject: [BiO BB] Fwd: Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics In-Reply-To: <1015316567891861630@unknownmsgid> References: <1015316567891861630@unknownmsgid> Message-ID: I took a look at your site, downloaded the source and went through both tutorials. The first 5 minute tutorial took me much more than 5 minutes, the second took me much less! Anyway, I think that this is the Susan Boyle of bioinformatics- I didn't expect much out of it because it was not pretty. I am familiar with the graphic-based pipeline builders like VIBE and Pipeline Pilot, and these are much prettier. Still, I think that what you have created is very valuable for at least a couple of reasons. First, many programmers do not want to use visual 'drag and drop' type tools. These tools are aimed more at non-programmers, but in my experience biologists would rather hire someone to create a pipeline anyway. Second, your module is free and most of the other tools are not. While something like Pipeline Pilot is a wonderful system in the long run, most people just want to get something done today, and don't want to spend money to do it. Third, if I am creating a pipeline in Python, then your module simply makes things easier and more efficient. To switch to another system is an extra learning step that I don't need. Again, people generally want to solve the problem at hand, not to create another issue. Fourth, I like the error-checking and restart capabilities because I have had trouble with that in the past! Best regards, Martin Gollery ---------- Forwarded message ---------- From: Leo Goodstadt Date: Mon, Jun 1, 2009 at 7:01 AM Subject: [BiO BB] Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics To: bbb at bioinformatics.org A new library called Ruffus is available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html. Ruffus provides easy / lightweight support for running computational pipelines in python. The best way to produce reproducible bioinformatics analyses is by scripting all the stages or tasks which have to be run. Ruffus is designed to allow this to happen in python in the least intrusive manner possible, and without any special (non-python) syntax. Like makefiles (or scons), it helps you to manage task dependencies. However, because it is designed from the start for bioinformatics pipelines (rather than compiling programmes), no ugly syntax / hacking is required. Ruffus provides automatic support for * Managing dependencies * Running tasks in parallel * Re-starting from arbitrary points, especially after errors * Display of the pipeline as a flowchart * Reporting We have been using Ruffus in-house but we would like to see what other scientists think of the design before we bring its attention to a wider audience. (We intend to publish this as an application note in some bioinformatics journal) Please help us by sending feedback to: ruffus at llew.org.uk Extensive documentation, download details and two tutorials are available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html. Leo Goodstadt MRC Functional Genomics Unit University of Oxford _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com From tcan at ceng.metu.edu.tr Wed Jun 3 16:16:34 2009 From: tcan at ceng.metu.edu.tr (Tolga Can) Date: Wed, 3 Jun 2009 23:16:34 +0300 Subject: [BiO BB] Call For Papers: Computational Analysis of Biological Networks (Special Issue in Advances in Bioinformatics) Message-ID: <8ad607cb0906031316r46832965l437bef8437a32339@mail.gmail.com> Advances in Bioinformatics Journal Special Issue: Computational Analysis of Biological Networks http://www.hindawi.com/journals/abi/si/cabnet.html Submission Deadline: August 1, 2009 ===================================== Call for Papers One of the fundamental goals of bioinformatics is to understand the biological processes that are the driving forces behind organisms' functions. Biological networks such as metabolic, gene regulatory, and protein interaction networks show how various biochemical entities interact with each other to perform vital functions that they cannot perform alone. A critical common property of biological networks is that although the individual entities of a pathway may have specific functions, they play additional roles in the entire network by communicating with other entities. This Special Issue focuses on novel computational approaches and methods for understanding biological networks. This issue will publish original, high-quality research articles. High-risk/high-gain ideas for understanding biological networks are welcome. Manuscripts should include biological impact and validation as well as technical depth. The topics that are included (but not limited to) in this issue are: * Pathway reconstruction * Comparison and querying of biological networks * Annotation of functional subnetworks * Motif discovery in networks * Steady-state analysis of networks and the whole cell model * Analysis of network-disease family relationships Before submission, authors should carefully read over the journal's Author Guidelines, which are located at http://www.hindawi.com/journals/abi/guidelines.html. Prospective authors should submit an electronic copy of their complete manuscripts through the journal manuscript tracking system at http://mts.hindawi.com/, according to the following timetable: Manuscript Due August 1, 2009 First Round of Reviews November 1, 2009 Publication Date February 1, 2010 Lead Guest Editor * Tamer Kahveci, Computer and Information Sciences and Engineering Department, University of Florida, FL 32610, USA Guest Editors * Tolga Can, Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey * Limsoon Wong, School of Computing, National University of Singapore, Room 3-34, Building COM1, 13 Computing Drive, Singapore, Singapore 117417 * Zhongming Zhao, Virginia Commonwealth University, VA 23284, USA ===================================== From Sudhindra.Gadagkar at notes.udayton.edu Wed Jun 3 22:37:13 2009 From: Sudhindra.Gadagkar at notes.udayton.edu (Sudhindra.Gadagkar at notes.udayton.edu) Date: Wed, 3 Jun 2009 22:37:13 -0400 Subject: [BiO BB] Bioinformatics projects for incoming freshmen Message-ID: Hi all, I need to soon teach a 20-hour summer course for incoming freshmen (STEM students) that needs to end with a capstone project, the results of which they need to present in front of an audience that will include their parents. Any ideas for an entirely computational project? Something fairly simple, but that will keep their interest and make them feel good about it. Would appreciate any suggestions. Thanks! Sudhindra Gadagkar From kanagasa at i2r.a-star.edu.sg Thu Jun 4 13:23:56 2009 From: kanagasa at i2r.a-star.edu.sg (Kanagasabai Rajaraman) Date: Fri, 5 Jun 2009 01:23:56 +0800 Subject: [BiO BB] CFP: Bioinformatics Track @ ACM Symposium on Applied Computing (SAC) 2010 - due Sep 8, 2009 References: <200906041710.n54HAjPl015640@vimes.cs.wisc.edu> Message-ID: <162B8AFBFBBB2148A9A1B8F9C5753428053B5886@mailbe01.teak.local.net> CALL FOR PAPERS - SAC BIO 2010 The 25th ACM Symposium on Applied Computing 22 - 26 March 2010 Sierre, Switzerland Bioinformatics and Computational Systems Biology Track http://www.nrcbioinformatics.ca/acmsac2010/ Track description and motivations The publishing of the draft of the human genome and the recent advancements in high throughput sequencing and functional genomics technologies has ushered in a new era of rapid and exponential growth of data related to how organisms function at the molecular level. A major part of the information to support this understanding is available on large number of heterogeneous databases in both structured and unstructured formats. One challenge is to obtain information and knowledge from these databases and integrate them in a semantically consistent way, in order to be able to analyze them using novel quantitative conceptual and computational approaches smoothly connecting models and experiments. This can offer life scientists a deeper system-level understanding of fundamental biological principles. Examples of computational challenges in this new research paradigm, called systems biology, include identification of biological pathways, structure annotation of proteins, inference ! of biochemical networks and pathways using experimental data, information, and knowledge scattered over heterogeneous databases. The convergence of computer science and biology is both a data- and model- driven new science that necessitates the development of mathematical/computational models and data mining algorithms, that can enable scientists and bio-engineers to analyze with predictive ability biological information that guide the development of therapeutic and biotechnology solutions. This track is motivated by the rapidly growing importance of the informatics vision for novel levels of understanding in complex biological and biomedical systems, and will address research issues related to the whole spectrum of bioinformatics with a particular focus on integrative, inferential and translational bioinformatics. List of topics Papers are solicited in, but not limited to the following areas: * Algebraic biology * Bio imaging * Bioinformatics for drug design & discovery * Biological databases, warehousing and management * Biomedical data integration, metadata & ontologies * Biomarker identification and annotation * Biomedical text mining * Computational and Comparative genomics * Data visualization and visual analytics * Disease informatics * Evolution and phylogenetics * Gene expression/regulation & microarrays * Healthcare applications * High-performance bio-computing * Inference of biochemical network models from experimental data * Integrative bioinformatics * Laboratory information management systems in biology * Model driven analysis of biological systems * Modeling, analysis and Inference of gene and protein networks * Molecular modeling and simulation * Molecular sequence analysis * Pathways identification * Population genetics * Proteomics * Protein & RNA structure and function * Protein structure prediction and modeling * Recognition of genes and regulatory elements * Semantic technologies for life sciences * Sequence analysis & alignment * SNPs, mutations and haplotyping * Structural bioinformatics * Tool integration, web services and workflow systems Papers submission All submissions should represent original and previously unpublished works that are currently not under review in any conference or journal. Both basic and applied research papers are welcome. The author(s) name(s) and address(s) must NOT appear in the body of the submitted paper, and self-references should be in the third person. This is to facilitate blind review required by ACM. All submitted papers must include the paper identification number on the front page, above the title of the paper provided to you by the eCMS when you register your paper. All enquiries and questions should be directed to the Track Chairs. Additional details are available at the track home page at http://www.nrcbioinformatics.ca/acmsac2010/ . Important dates Paper submission: September 8, 2009 Notification of paper acceptance/rejection: October 19, 2009 Camera ready: November 2, 2009 Conference Paper Publication All papers will be fully refereed and undergo a blind review process by at least three referees. The conference proceedings will be published by ACM. Hence, all accepted papers should be submitted in ACM 2-column camera-ready format for publication in the symposium proceedings. The final version of the paper should not be more than 5 pages long. An additional 3 pages are allowed with a charge of 80USD per extra page. Final Camera-ready submissions must follow the template available at: http://www.acm.org/conferences/sac/sac2010/. Journal Paper Publication Expanded version of 4-5 top ranking papers will be accepted for publication in the International Journal of Data Mining and Bioinformatics (ijdmb at inderscience.com). Authors will be contacted after the presentation of these papers at the SAC Conference. Poster Publication of Selected Papers A set of selected papers will be accepted as poster papers by invitation only and will be published as short papers in the symposium proceedings. Track chairs Paola Lecca, Ph.D. Microsoft Research Center University of Trento, Italy. Email: lecca at cosbi.eu Kanagasabai Rajaraman, Ph.D. Institute for Infocomm Research, Singapore. E-mail: kanagasa at i2r.a-star.edu.sg Dan Tulpan, Ph.D. Institute of Information Technology National Research Council of Canada, Canada E-mail: dan.tulpan at nrc-cnrc.gc.ca Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you." From leo.goodstadt at dpag.ox.ac.uk Fri Jun 5 14:16:55 2009 From: leo.goodstadt at dpag.ox.ac.uk (Leo Goodstadt) Date: Fri, 5 Jun 2009 19:16:55 +0100 Subject: [BiO BB] Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics In-Reply-To: References: <016c01c9e2c1$822220d0$86666270$@goodstadt@dpag.ox.ac.uk> Message-ID: <038901c9e609$cea87350$6bf959f0$@goodstadt@dpag.ox.ac.uk> I have changed Ruffus so that it is now compatible with python 2.5 as well, and possibly 2.4 (untested), on Windows and Linux. Please feel free to email me or give me a nudge at http://ruffus.googlecode.com. Leo Goodstadt Functional Genomics Unit University of Oxford Developer of Ruffus: easy support for computational pipelines in python. http://llew.org.uk/ruffus email:ruffus_lib at llew.org.uk From witch_of_agnessi at yahoo.com Sun Jun 7 17:57:03 2009 From: witch_of_agnessi at yahoo.com (Skull Crossbones) Date: Sun, 7 Jun 2009 14:57:03 -0700 (PDT) Subject: [BiO BB] Program for superposition of 3D point sets Message-ID: <108973.43358.qm@web110010.mail.gq1.yahoo.com> Check this: http://boscoh.com/protein/matchpy This is a python program, which accepts a set of equivalent 'atoms'. I beleive this can be modified easily to accept co-ordinates of the equivalent points to be superposed, instead of reading from a pdb file best WoA --- On Tue, 5/12/09, Kalidas Yeturu wrote: > From: Kalidas Yeturu > Subject: [BiO BB] Program for superposition of 3D point sets > To: "General Forum at Bioinformatics.Org" > Date: Tuesday, May 12, 2009, 9:22 AM > Dear All > > I would greatly appreciate if you can give a program that > optimally > superposes a pair of point sets (3D) and outputs rotation > and translation > matrices corresponding to each solution. > > I searched to my best in the web but could not find one. > > Please do NOT point to > - Protein-Protein superposition web-servers/standalone > ones > - Programs that require residues to be contiguous in order > to superpose > - Motif search programs > - IEEE/other literature on point set superposition > algorithms without > corresponding implementation > > I need preferably C/Fortran program or as a last choice a > library function > that I can call from other C programs. > > Thanking You > > -- > With Regards > Kalidas Y > http://ssl.serc.iisc.ernet.in/~kalidas > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From barry.hardy at vtxmail.ch Thu Jun 11 08:20:11 2009 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Thu, 11 Jun 2009 14:20:11 +0200 Subject: [BiO BB] eCheminfo 2009 Community of Practice Meeting Program Message-ID: <4A30F67B.9000202@vtxmail.ch> The eCheminfo 2009 community of practice meeting on drug discovery informatics will take place at Bryn Mawr College, Philadelphia 13-16 October 2009. This annual community of practice meeting is taking place for the fifth time and brings together a unique combination of pharmaceutical and healthcare industry experts, principal investigators and researchers from the academic and government sectors, and leaders from innovative enterprises. The smaller and more intimate meeting format pursued has fostered the type of collaboration not always found at large conferences. The preliminary program with abstracts received so far is now available at http://echeminfo.com/COMTY_conferencesprog09 and will be updated as remaining abstracts are received. The topics addressed this year will include Structure-based Drug Design Applications and Methods, Macromolecular Interactions and Networks, Data Analysis and Visualisation, PDB Ligands, and Predictive Toxicology. A pre-conference best practices workshop on Binding Energy prediction will take place October 12, 2009. This meeting will take place concurrently with the InnovationWell 2009 meeting addressing the topics of Collaboration in Discovery and Development, Translational Bioinformatics, Systems Biology and Biomarkers, Blood Brain Barrier modeling and Predictive Toxicology. Below is a short summary of the eCheminfo program. best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Tel: +41 61 851 0170 email: barry.hardy -(at)- douglasconnect.com Latest Advances in Drug Discovery Informatics eCheminfo 2009 InterAction Meeting October 13-16, 2009 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link with Abstracts: http://echeminfo.com/comty_conferences Program as pdf download: http://barryhardy.blogs.com/files/echeminfoprogrambrynmawr09.pdf Program Summary Monday 12 October Pre-conference Workshop on Drug Binding Affinities Co-Chaired by Scott Brown (Abbott Laboratories) and Judith Lalonde (Bryn Mawr College) Tuesday 13 October Structure-Based Drug Design Applications, Chaired by Alan Cheng (Amgen) Macromolecular Interactions and Networks, Chaired by Emil Alexov (Clemson University) Wednesday 14 October Structure-Based Drug Design Methods, Chaired by Natasja Brooijmans (Wyeth) Data Analysis and Visualisation Applications in Chemical Biology, Chaired by Brian Marsden (Structural Genomics Consortium Oxford) Thursday 15 October PDB Ligands, Chaired by John Westbrook (Rutgers University) Predictive Toxicology, Co-Chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences) Friday 16 October Predictive Toxicology, Co-Chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences) Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo -(at)- douglasconnect.com From christoph.gille at charite.de Thu Jun 11 10:10:57 2009 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 11 Jun 2009 16:10:57 +0200 (CEST) Subject: [BiO BB] For Workshop: Need Proteins with known struct and mutations Message-ID: For our Workshop next week we would like to ask you for your ideas about proteins with known 3D-structure, and known disease causing mutations. Next week we will give a practical workshop in Bioinformatics for postgraduate students of Molecular Medicine. Our plan is that each student chooses a protein. The students will obtain all mutations and SNPs from the literature and from databases. The students should then visualize the mutations on a homologous 3D-structure using the Pymol view (http://en.wikipedia.org/wiki/Pymol) integrated in STRAP ( http://3d-alignment.eu/ ). In the final presentation each student should discuss the function of his/her protein and how the mutation could affect its function in terms of catalysis, ligand binding, 3D-structure stability ... . Do you have ideas for proteins that would be appropriate? Many thanks Christoph From info at bioinformaticsworldwide.com Thu Jun 11 15:26:19 2009 From: info at bioinformaticsworldwide.com (Bioinformatics World Wide) Date: Thu, 11 Jun 2009 14:26:19 -0500 (CDT) Subject: [BiO BB] For Workshop: Need Proteins with known struct and mutations In-Reply-To: References: Message-ID: <4628.84.101.144.242.1244748379.squirrel@bioinformaticsworldwide.com> You can use Balibase benchmark see here http://www-bio3d-igbmc.u-strasbg.fr/balibase/ Regards > For our Workshop next week we would like to ask you for your ideas about > proteins with known 3D-structure, and known disease causing mutations. > > Next week we will give a practical workshop in Bioinformatics for > postgraduate students of Molecular Medicine. > > Our plan is that each student chooses a protein. The students will > obtain all mutations and SNPs from the literature and from databases. > > The students should then visualize the mutations on a homologous > 3D-structure using the Pymol view (http://en.wikipedia.org/wiki/Pymol) > integrated in STRAP ( http://3d-alignment.eu/ ). > > In the final presentation each student should discuss the function of > his/her protein and how the mutation could affect its function in terms of > catalysis, ligand binding, 3D-structure stability ... . > > Do you have ideas for proteins that would be appropriate? > > Many thanks > > Christoph > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From cannataro at unicz.it Sun Jun 14 20:06:30 2009 From: cannataro at unicz.it (Mario Cannataro) Date: Mon, 15 Jun 2009 02:06:30 +0200 (CEST) Subject: [BiO BB] New book: Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare Message-ID: <3a0012ce7f7c3e81b7e3f2e3d3178a6a.squirrel@email.unicz.it> **************************************** New book release Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical Information Science Reference an imprint of IGI Global http://www.igi-global.com/reference/details.asp?id=34292 Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** DESCRIPTION Grids are currently used in many sectors of life sciences, including basic sciences such as genomics, proteomics, and bioinformatics. The Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare brings together state-of-the art methodologies and developments of grid technologies applied in different fields of life sciences. This Handbook of Research considers the use of grid technologies to support research and application of each information level where life science research takes place - a useful reference source for academicians, medical practitioners, and researchers involved in all areas of healthcare technologies. **************************************** "The book surveys state-of-the art research, methodologies and applications of Grid technology in different fields of Life Sciences, from basic science to clinical and healthcare applications." -Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** TOPICS COVERED Biomedical application Data mining in proteomics Data provenance in scientific workflows Docking process in drug discovery Grid-based epidemic surveillance system Grid-based tool for comparative genomics Heart failure awareness management system Managing uncertain data Molecular structure determination Multiple repositories for digital content Polymorph prediction data for drug development Resource discovery in health grids **************************************** For more information about the Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare, you can view the title information sheet at http://www.igi-global.com/downloads/pdf/34292.pdf. To view the Table of Contents and a complete list of contributors online go to http://www.igi-global.com/reference/details.asp?ID=34292&v=tableOfContents. You can also view the first chapter of the publication at http://www.igi-global.com/downloads/excerpts/34292.pdf. **************************************** ABOUT THE EDITOR Mario Cannataro is an Associate Professor of Computer Engineering at University Magna Gr?cia, Catanzaro, Italy, since 2002. He received his Laurea Degree Magna cum Laude in Computer Engineering from the University of Calabria, Rende, Italy, in 1993. He was a researcher at the CRAI Research Consortium and a Senior Researcher at the Italian National Research Council (ICAR-CNR), Rende, Italy, where he worked on parallel computing, massively parallel architectures, parallel implementation of logic programs and cellular automata. He is currently the responsible of the Bioinformatics Laboratory at University Magna Gr?cia of Catanzaro. His current research interests are on grid computing, bioinformatics, computational genomics and proteomics, and ontologies. He authored a book on parallel implementation of logic programs and over 150 scientific papers published on international journals and conference proceedings.. Mario Cannataro is a co-founder of Exeura and is a member of ACM, IEEE Computer Society, BITS (Italian Bioinformatics Society), and HealthGrid. **************************************** To view the full contents of this publication, check for the Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare in your institution?s library. If you library does not currently own this title, please recommend it to your librarian. **************************************** -- Prof. Mario Cannataro, Informatics and Biomedical Engineering, University "Magna Gr?cia" of Catanzaro, Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073, Email: cannataro at unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ From marketing at embl.de Fri Jun 19 08:10:10 2009 From: marketing at embl.de (EMBL Courses & Conferences) Date: Fri, 19 Jun 2009 14:10:10 +0200 Subject: [BiO BB] EMBL Events - Please subscribe Message-ID: <12454134157917575@lxmail02-vm> Dear Colleagues, we would like to invite you to join our mailing list to receive information about events taking place at the European Molecular Biology Laboratory. Please use the following link to subscribe to our mailing list to receive our newsletter, event posters or e-announcements: http://www.embl.de/training/courses_conferences/cco/contact/information/index.html If you do not wish to receive any information from EMBL, please reply with the subject "unsubscribe". Thanks for your interest in our events. Best wishes, the Team of the EMBL Course & Conference Office ......................................................................................................... European Molecular Biology Laboratory Course & Conference Office Meyerhofstr. 2 69117 Heidelberg Germany Email: conferences at embl.de From samal at mis.mpg.de Fri Jun 26 20:47:17 2009 From: samal at mis.mpg.de (Areejit Samal) Date: Sat, 27 Jun 2009 02:47:17 +0200 Subject: [BiO BB] Workshop on metabolic modelling Message-ID: <4A456C15.8080902@mis.mpg.de> Dear Friends, We are organizing a thematic workshop titled "Challenges in experimental data integration within genome-scale metabolic models" to be held in Paris from October 10-11, 2009. This conferences presents an opportunity for the participants to benefit from talks by leading scientists in the community. There is no registration fee for the event but the number of participants is limited to 50. The workshop webpage is here: http://www.mis.mpg.de/calendar/conferences/2009/dimm09.html We request all interested participants to register on the website. Best Regards, Areejit Samal and Pierre-Yves Bourguignon