From gurukatagi at gmail.com Fri Feb 5 00:04:19 2010 From: gurukatagi at gmail.com (gurunath katagi) Date: Fri, 5 Feb 2010 10:34:19 +0530 Subject: [BiO BB] information on domains Message-ID: <87526fc71002042104g764ba3e4sd6b6a8260e7840b1@mail.gmail.com> Dear all, I wanted to make a dataset of proteins with single domains . I wanted to know is there any way that i can get the info. on no. of structural domains given a PDB ID or scop id ? (set of PDB ids) I tried both with PDB and SCOP and i was not successful ? Can any body help me regarding this ? Thank you Gurunath -- Gurunath M Katagi Graduate Research Student Bio molecular computation Laboratory Supercomputer Education & Research Center Indian Institute Of Science, Bangalore- 560012 Karnataka State, India Phone:080-22932737-319,080-22933061 email: gurunath at rishi.serc.iisc.ernet.in From dan.bolser at gmail.com Tue Feb 9 07:23:00 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 9 Feb 2010 12:23:00 +0000 Subject: [BiO BB] information on domains In-Reply-To: <87526fc71002042104g764ba3e4sd6b6a8260e7840b1@mail.gmail.com> References: <87526fc71002042104g764ba3e4sd6b6a8260e7840b1@mail.gmail.com> Message-ID: <2c8757af1002090423t74682432pae6edf3e4c2d1af7@mail.gmail.com> On 5 February 2010 05:04, gurunath katagi wrote: > Dear all, > I wanted to make a dataset of proteins with single domains . > I wanted to know is there any way that i can get the info. on no. of > structural domains given a PDB ID or scop id ? (set of PDB ids) > > I tried both with PDB and SCOP and i was not successful ? > Can any body help me regarding this ? Hi Gurunath, I made a list of single domain proteins for my Ph. D research. I did this by combining the SCOP flat files [1] with the PDB's and MSD's 'biounit' information [2]. I then validated a fraction of them (biounits are notoriously difficult to predict computationally) by checking Pisa [3] and the literature. I'll find where that list is lurking and make it public on PDBWiki [4]. In the mean time, I'd suggest emailing the pdb-l mailing list [5], as I'm sure their will be lots of people there who can help too. Previously I was maintaining a list of 'mailing lists for biologists', but unfortunately that site is down at the moment. HTH, Dan. [1] http://scop.mrc-lmb.cam.ac.uk/scop/parse/index.html [2] http://www.pdbwiki.org/index.php/Biological_unit [3] http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html [4] http://www.pdbwiki.org [5] https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l > Thank you > Gurunath > > -- > Gurunath M Katagi > Graduate Research Student > Bio molecular computation Laboratory > Supercomputer Education & Research Center > Indian Institute Of Science, Bangalore- 560012 > Karnataka State, India > Phone:080-22932737-319,080-22933061 > email: gurunath at rishi.serc.iisc.ernet.in > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From oliviero.carugo at univie.ac.at Tue Feb 9 03:05:57 2010 From: oliviero.carugo at univie.ac.at (Oliviero Carugo) Date: Tue, 9 Feb 2010 09:05:57 +0100 Subject: [BiO BB] information on domains In-Reply-To: <87526fc71002042104g764ba3e4sd6b6a8260e7840b1@mail.gmail.com> References: <87526fc71002042104g764ba3e4sd6b6a8260e7840b1@mail.gmail.com> Message-ID: <6e57a460637019679a6fdc8a1ad3b698.squirrel@webmail.univie.ac.at> Dear Gurunath, unfortunately the definition of "domain" is rather ambiguous. You might try the SCOP and CATH databases (which have different domain boundary definitions). Good luck, Oliviero On Fri, February 5, 2010 06:04, gurunath katagi wrote: > Dear all, > I wanted to make a dataset of proteins with single domains . > I wanted to know is there any way that i can get the info. on no. of > structural domains given a PDB ID or scop id ? (set of PDB ids) > > I tried both with PDB and SCOP and i was not successful ? > Can any body help me regarding this ? > > Thank you > Gurunath > > -- > Gurunath M Katagi > Graduate Research Student > Bio molecular computation Laboratory > Supercomputer Education & Research Center > Indian Institute Of Science, Bangalore- 560012 > Karnataka State, India > Phone:080-22932737-319,080-22933061 > email: gurunath at rishi.serc.iisc.ernet.in > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > From kry.kieslowski at gmail.com Wed Feb 10 15:55:10 2010 From: kry.kieslowski at gmail.com (Ilgar Abdullayev) Date: Wed, 10 Feb 2010 21:55:10 +0100 Subject: [BiO BB] what is the best software/algorithm for miRNA target prediction ? Message-ID: <4B731D2E.3080908@gmail.com> Dear all, I'm a master student who is trying to write a master thesis about predicting miRNA targets. I was wondering if somebody could advise me the best software/algorithm for miRNA target prediction. Or the one that scientific community uses the most. I would really appreciate any kinds of help/advise. Thanks in advance Ilgar Abdullayev Computational and Systems Biology Royal Institute of Technology Stockholm Sweden Tel: +46 707 821 954 From dan.bolser at gmail.com Thu Feb 11 04:10:49 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 11 Feb 2010 09:10:49 +0000 Subject: [BiO BB] what is the best software/algorithm for miRNA target prediction ? In-Reply-To: <4B731D2E.3080908@gmail.com> References: <4B731D2E.3080908@gmail.com> Message-ID: <2c8757af1002110110i7ad007faoda6d6eabbf9a6bba@mail.gmail.com> Hi Ilgar, You could try looking on SEQwiki, a wiki database of software tools for next generation sequencing. http://seqanswers.com/wiki/SEQanswers For anyone who is interested, I'm trying to syndicate the data in SEQwiki onto the Bioinformatics.Org wiki, but for some reason it isn't working. However, a working example of this kind of syndication is available here: http://projects.csail.mit.edu/wibit/wiki/index.php?title=Biotech_Software HTH, Dan. On 10 February 2010 20:55, Ilgar Abdullayev wrote: > Dear all, > > I'm a master student who is trying to write a master thesis about predicting > miRNA targets. ?I was wondering if somebody could advise me the best > software/algorithm for miRNA target prediction. Or the one that scientific > community uses the most. > I would really appreciate any kinds of help/advise. > > Thanks in advance > > Ilgar Abdullayev > Computational and Systems Biology > Royal Institute of Technology > Stockholm Sweden > Tel: +46 707 821 954 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From hlapp at gmx.net Sat Feb 13 18:02:38 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 13 Feb 2010 18:02:38 -0500 Subject: [BiO BB] Registration Open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <2043F7D1-CF3D-4CD9-B308-F1A79901908D@gmx.net> Registration is now open for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://www.evolutionsociety.org/SSE2010/Register.html . iEvoBio aims to bring together biologists working in evolution, systematics, and biodiversity, with software developers, and mathematicians, both to develop new tools, and to increase awareness of existing technologies (ranging from standards and reusable toolkits to mega-scale data analysis to rich visualization). The 2-day meeting will take place June 29-30, 2010, in Portland, OR, jointly with the Evolution Meetings as a satellite conference. The event will feature traditional elements, including a keynote presentation at the beginning of each day and contributed talks, as well as more dynamic and interactive elements, including a challenge, lightning talk-style sessions, a software bazaar, and Birds-of-a- Feather gatherings. Attendees can register jointly for Evolution and iEvoBio at a discount, or only for the iEvoBio conference. For more information about registration, venue, travel, or accommodations visit the Evolution 2010 website at http://www.evolutionsociety.org/SSE2010/. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) From fernandez at noraybio.com Thu Feb 11 06:24:18 2010 From: fernandez at noraybio.com (David Fernandez) Date: Thu, 11 Feb 2010 12:24:18 +0100 Subject: [BiO BB] what is the best software/algorithm for miRNA targetprediction ? In-Reply-To: <4B731D2E.3080908@gmail.com> Message-ID: Dear Ilgar, Depending on your kind of data, you could try miRanalyzer. Have a look at http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyser.php Regards David Fern?ndez Project Manager fernandez at noraybio.com www.noraybio.com Noray Bioinformatics, S.L.U. Parque Tecnol?gico 801 A, 2? 48160 Derio - BIZKAIA T.+34 94 403 69 98 F.+34 94 403 69 99 -----Mensaje original----- De: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] En nombre de Ilgar Abdullayev Enviado el: mi?rcoles, 10 de febrero de 2010 21:55 Para: bbb at bioinformatics.org Asunto: [BiO BB] what is the best software/algorithm for miRNA targetprediction ? Dear all, I'm a master student who is trying to write a master thesis about predicting miRNA targets. I was wondering if somebody could advise me the best software/algorithm for miRNA target prediction. Or the one that scientific community uses the most. I would really appreciate any kinds of help/advise. Thanks in advance Ilgar Abdullayev Computational and Systems Biology Royal Institute of Technology Stockholm Sweden Tel: +46 707 821 954 _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From svtrived at hotmail.com Thu Feb 11 07:36:38 2010 From: svtrived at hotmail.com (Seema Trivedi) Date: Thu, 11 Feb 2010 18:06:38 +0530 Subject: [BiO BB] what is the best software/algorithm for miRNA target prediction ? In-Reply-To: <4B731D2E.3080908@gmail.com> References: <4B731D2E.3080908@gmail.com> Message-ID: Hi Have you tried contacting people at miRBase http://www.mirbase.org/? If you seek their help, they may inform you about the tools that they have used. Moreover, there are web based tools where one can submit the sequence of interest to find whether it is miR target. At present I do not recall which ones they are. I'll post the details as soon as I can remember these links. All the best > Date: Wed, 10 Feb 2010 21:55:10 +0100 > From: kry.kieslowski at gmail.com > To: bbb at bioinformatics.org > Subject: [BiO BB] what is the best software/algorithm for miRNA target prediction ? > > Dear all, > > I'm a master student who is trying to write a master thesis about > predicting miRNA targets. I was wondering if somebody could advise me > the best software/algorithm for miRNA target prediction. Or the one that > scientific community uses the most. > > I would really appreciate any kinds of help/advise. > > Thanks in advance > > Ilgar Abdullayev > Computational and Systems Biology > Royal Institute of Technology > Stockholm Sweden > Tel: +46 707 821 954 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 From jeedward at yahoo.com Fri Feb 12 10:56:58 2010 From: jeedward at yahoo.com (John Edward) Date: Fri, 12 Feb 2010 07:56:58 -0800 (PST) Subject: [BiO BB] Draft paper submission deadline is extended: BCBGC-10, Orlando, USA Message-ID: <259723.98305.qm@web45914.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Draft paper submission deadline is extended: BCBGC-10, Orlando, USA The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields.The following conferences are planned to be organized as part of MULTICONF-10. * International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) * International Conference on Automation, Robotics and Control Systems (ARCS-10) * International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) * International Conference on Computer Communications and Networks (CCN-10) * International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) * International Conference on High Performance Computing Systems (HPCS-10) * International Conference on Information Security and Privacy (ISP-10) * International Conference on Image and Video Processing and Computer Vision (IVPCV-10) * International Conference on Software Engineering Theory and Practice (SETP-10) * International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From barry.hardy at vtxmail.ch Fri Feb 12 15:48:58 2010 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Fri, 12 Feb 2010 21:48:58 +0100 Subject: [BiO BB] Collaboration Pool Formation, Virtual Organisations, ICT Support Message-ID: <4B75BEBA.40804@vtxmail.ch> We are establishing Collaboration Pools of individuals and organisations who have an interest in collaborating together in areas of drug discovery or life science innovation. For example, a selection of Pool members could participate in a collaborative research project, develop a funding proposal or response to a call opportunity together, or develop an innovation or best practice. To join the eCheminfo Collaboration Pool in drug design and discovery, please complete the short form located at https://www.surveymonkey.com/s/V6T2YSD To join the InnovationWell Collaboration Pool in life science innovation please complete the short form located at https://www.surveymonkey.com/s/782L9DZ During April - October 2010 we will be running two pilots which will create two virtual organisations (VOs) of research partners who will collaborate on projects in drug design and predictive toxicology: a) Drug Design project will examine the application of a variety of leading modelling and design approaches to novel target kinases, to experimentally test predictions, and to initiate a best practices virtual screening resource. b) Predictive Toxicology project will apply a combination of in silico and in vitro approaches to predict in vivo toxicity including exposure. Both VOs will be supported by a variety of leading modelling and design software, informatics infrastructure, and collaborative content management and electronic lab notebook systems. The VOs will be created from partners from the Collaboration Pools, who will bring contributing knowledge, computational or experimental capabilities to the partnership for the duration of the projects. We are also currently seeking Expressions of Interest in the ICT support role for the pilots which should be submitted by 17.00 CET, 19 February 2010 through the following form: https://www.surveymonkey.com/s/QSHKDCH The ICT support role will support the informatics requirements of the researchers in organising, processing and sharing data, and in collaborative analysis and decision making. The VOs will also be supported by knowledge-oriented collaboration services developed under the FP7 Synergy research project, including a reactive complex event driven engine, collaboration moderator, collaboration pattern services and partner knowledge base. Summary on Synergy project: http://barryhardy.blogs.com/theferryman/2008/02/knowledge-orien.html The Predictive Toxicology VO will be supported by distributed REST-driven web services for data management, model building, validation and reporting, developed under the OpenTox Framework (http://www.opentox.org/). best regards Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (www.opentox.org) Douglas Connect Switzerland Tel: +41 61 851 0170 Email: barry.hardy -(at)- douglasconnect.com From chang.rui at hotmail.com Mon Feb 15 16:58:47 2010 From: chang.rui at hotmail.com (Rui Chang) Date: Mon, 15 Feb 2010 21:58:47 +0000 Subject: [BiO BB] =?windows-1256?q?CALL_FOR_PAPER=3A_Workshop_at_BIOCOMP?= =?windows-1256?q?=2710_Workshop_on_Novel_algorithms_for_in-silico_modelin?= =?windows-1256?q?g_biological_networks_and_generating_quantitative_predic?= =?windows-1256?q?tions=FE=FE?= Message-ID: [Sorry if you get multiple copies of this message] ============================================= CALL FOR PAPER ========================================== Special session and workshop: ?Novel algorithms for in-silico modeling biological networks and generating quantitative predictions? at BIOCOMP'10 (The 2010 International Conference on Bioinformatics and Computational Biology), July 12-15, 2010, Las Vegas, USA http://www.world-academy-of-science.org/worldcomp10/ws/conferences/biocomp10 Deciphering the biological networks underlying the complex phenotypic traits such as human diseases is no doubt crucial to understand the molecular mechanisms and to develop effective therapeutics. Because of the complexity of the networks and the small number of available functional experiments, in-silico modeling of the underpinning molecular network is challenging. Beyond the structure, the eventual predict of a gene or protein?s function requires accurate mathematical models to parameterize the structure. However, current mainstream algorithms, such as reverse-engineering algorithms, inevitably bear the following disadvantages: i) Structure prediction accuracy is limited due to the availability of functional data. ii) Unable to make accurate quantitative predictions based on the learned network structure. This workshop encourages novel algorithms addressing one or more of the following problems: - Improve networks structure learning accuracy; -Generating accurate quantitative predictions on network behaviors (with known structure) in a relative large biological network; -Inferring network structure and/or parameters by integrating various types of biological data. Full paper submission should follow the format of The 2010 World Congress in Computer Science, Computer Engineering, and Applied Computing WORLDCOMP?10. General information about the conference and format instruction (IEEE style) can be found at the conference website: WORLDCOMP web site: http://www.world-academy-of-science.org Each paper will be peer-reviewed by three independent experts and a decision will be to recommend to the workshop chair based on the paper?s originality, significance, clarity, impact and soundness. If you intend to submit a paper to this special session and workshop, please send your paper to Dr. Rui Chang (chang.rui at hotmail.com). All accepted papers will be published in the conference proceedings in both printed book and online version. The conference proceedings will be will be indexed in Inspec / IET / The Institute for Engineering and Technology, DBLP / Computer Science Bibliography, and others. The printed proceedings will be available for distribution on site at the conference. Please send you paper to Dr. Rui Chang no later than March, 20th, 2010. Notification of acceptance will be send via email by April, 5th, 2010. ------------- Dr. Rui Chang University of California, San Diego email: chang.rui at hotmail.com Tel: +1-646-520-5395 ================================================== _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/ From gzli at tongji.edu.cn Mon Feb 15 20:26:02 2010 From: gzli at tongji.edu.cn (Guo-Zheng Li) Date: Tue, 16 Feb 2010 09:26:02 +0800 Subject: [BiO BB] Extension of submission deadline for ACM-BCB to 15 March References: <4B79DF08.9020705@buffalo.edu> Message-ID: <9E252D4D-A36F-4629-8D5E-DE73402476DE@tongji.edu.cn> Due to holidays and many requests, we are extending the submission deadline to March 15, 2010. Call for Papers and Proposals ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB 2010) August 2-4, Niagara Falls, New York, USA http://www.cse.buffalo.edu/ACM-BCB2010 ACM is pleased to announce that it has taken over sponsorship of the former International Joint Conference on Bioinformatics, Systems Biology, and Intelligent Computing (IJCBS), and will be holding the newly renamed International Conference On Bioinformatics and Computational Biology (ACM-BCB) in August 2010 in Niagara Falls, NY. This conference builds on the success of IJCBS 2009 in Shanghai, and is the start of ACM?s efforts to better support the bioinformatics and computational biology community. We invite you to submit papers with unpublished, original research describing recent advances on all aspects of Bioinformatics and Computational Biology. All papers will undergo peer review by the conference program committee; accepted papers will be published in the conference proceedings (in CD) and in the ACM Digital Library. Authors of selected papers will be invited to extend their papers for submission to several journals. Papers should not exceed 10 pages in ACM template on 8.5 x 11 inch paper (see ACM templates at http://www.acm.org/sigs/publications/proceedings-templates). Papers should be submitted via the link (https://cmt.research.microsoft.com/BCB2010/ ). The topics of relevance for the conference papers include but are not limited to the following: ? Assembly algorithms for the next generation sequencing ? Genome annotations via mass spectrometry ? Gene discovery and protein function prediction ? Functional genomics algorithms for high throughput data generation methods ? DNA and protein motif discovery ? Models of gene expression regulation at RNA level ? Algorithms for comparative and evolutionary genomics ? Molecular evolution and phylogeny reconstruction ? Multiple genome alignment ? Computational genomics for plant and animal genomes ? Engineering of bioinformatic databases ? Models of gene expression networks ? Computational proteomics and methabolomics ? Prediction of protein-protein interactions ? Protein structure prediction and molecular dynamics ? Visualization of biomolecular and cellular structure, dynamics and interactions ? Modeling of methabolic pathways ? Computational epigenomics ? Models of cellular and multicellular systems ? Prediction of cellular network dynamics from incomplete information ? Clinical genomics and proteomics ? Data mining in biomolecular databases ? High performance computing for complex biomolecular and cellular systems . Biomedical imaging Proposals for Tutorials and Workshops: We also invite you to submit tutorial/workshop proposals focusing on problems and new challenges of Bioinformatics and Computational Biology. Submit the proposals by e-mail to Tutorial/Workshop Chairs. Key Dates Paper Submission deadline March 15, 2010 Author Notification May 1, 2010 Workshop proposal Jan. 1, 2010 Tutorial Proposal Jan. 1, 2010 Conference Date 2-4 August, 2010 Organizing Committee *Steering Committee* Joydeep Ghosh, University of Texas at Austin Vipin Kumar, University of Minnesota Meral Ozsoyoglu, Case Western Reserve University Yi Pan, Georgia State University Dong Xu, University of Missouri-Columbia Aidong Zhang, SUNY at Buffalo (co-chair) Joe Zhang, University of Southern Mississippi (co-chair) *General Chairs* Aidong Zhang, SUNY at Buffalo Mark Borodovsky, Georgia Tech *Program Chairs* Gultekin Ozsoyoglu, Case Western Reserve University Armin Mikler, University of North Texas *Treasurer* Joe Zhang, University of Southern Mississippi *Workshop Chairs* Michael Buck, SUNY at Buffalo Vasant Honavar, Iowa State University Zhongming Zhao, Vanderbilt University Medical Center Jason Wang, New Jersey Institute of Technology *Poster Chairs* Tony Hu, Drexel University Sun Kim, Indiana University *Publicity Chairs* Mary Qu Yang, NIH Kebin Jia, Beijing University of Technology *Student Awards Chairs* Susan Bridges, Mississippi State University Parthasarathy Srinivasan, Ohio State University *Best Paper Awards Chairs* Joydeep Ghosh, University of Texas at Austin Wei Wang, University of North Carolina at Chapel Hill *Panel Chair* Vipin Kumar, University of Minnesota *Keynote Chair* Dong Xu, University of Missouri-Columbia *Proceedings Chairs* Li Liao, University of Delaware Guo-zheng Li, Tongji University *Tutorials Chairs* Mohammed Zaki, Rensselaer Polytechnic Institute Bo Yuan, Shanghai Jiaotong University *Registrations Chair* Preetam Ghosh, University of Southern Mississippi *Local Arrangements* Zihua Hu, SUNY at Buffalo Marianne Sullivan, SUNY at Buffalo -------------- next part -------------- From ykalidas at gmail.com Fri Feb 19 01:07:12 2010 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Fri, 19 Feb 2010 11:37:12 +0530 Subject: [BiO BB] [Bio BB] Split a ligand into meaningful fragments Message-ID: <5632703b1002182207m37b93bcfk936fe3e6656d5f04@mail.gmail.com> Dear All, I would like to know if you have come across programs that split a ligand into 'meaningful' fragments. Assuming ligand to be a graph and cutting the non-cyclic edges may lead to fragments containing just one or two atoms that are quite distinct from biologically important fragments. It would greatly help me if you can point me to some stand-alone programs that carry out this task. Thanks in advance. -- With Regards Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas http://proline.physics.iisc.ernet.in/home/User:Kalidas From albert.lai at osumc.edu Tue Feb 23 23:17:00 2010 From: albert.lai at osumc.edu (Albert Lai) Date: Tue, 23 Feb 2010 23:17:00 -0500 Subject: [BiO BB] Call for Papers, 1st ACM International Conference on Health Informatics (IHI) Message-ID: CALL FOR PAPERS, Association for Computing Machinery (ACM) 1st ACM International Conference on Health Informatics (IHI) IHI 2010 November 11-12, 2010 Washington, DC http://ihi2010.sighi.org SCOPE OF THE CONFERENCE We cordially invite you to submit your contribution to the 2010 ACM International Conference on Health Informatics (IHI 2010). IHI 2010 is ACM's premier community forum concerned with the application of computer and information science principles and information and communication technology to problems in healthcare, public health, the delivery of healthcare services and consumer health as well as the related social and ethical issues. For technical contributions, IHI 2010 is primarily interested in end-to-end applications, systems, and technologies, even if available only in prototype form. Therefore, we strongly encourage authors to submit their original contributions describing their algorithmic and methodological contributions providing an application-oriented context. For social/behavioral scientific contributions, we are interested in empirical studies of health-related information needs, seeking, sharing and use, as well as socio-technical studies of heath information technology implementation and use. Topics of interest for this conference cover various aspects of health informatics, including but not limited to the following: * Accessibility and Web-enabled technologies * Analytics applied to direct and remote clinical care * Assistive and adaptive ubiquitous computing technologies * Biosurveillance * Brain computer interface * Cleaning, preprocessing, and ensuring quality and integrity of medical records * Computational support for patient-centered and evidence-based care * Consumer health and wellness informatics applications * Consumer and clinician health information needs, seeking, sharing and use * Continuous monitoring and streaming technologies * Data management, privacy, security, and confidentiality * Display and visualization of medical data * E-communities and networks for patients and consumers * E-healthcare infrastructure design * E-learning for spreading health informatics awareness * Engineering of medical data * Health information system framework and enterprise architecture in the developing world * Human-centered design of health informatics systems * Information retrieval for health applications * Information technologies for the management of patient safety and clinical outcomes * Innovative applications in electronic health records (e.g., ontology or semantic technology, using continuous biomedical signals to trigger alerts) * Intelligent medical devices and sensors * Issues involving interoperability and data representation in healthcare delivery * Keyword and multifaceted search over structured electronic health records * Knowledge discovery for improving patient-provider communication * Large-scale longitudinal mining of medical records * Medical compliance automation for patients and institutions * Medical recommender system (e.g., medical products, fitness programs) * Multimodal medical signal analysis * Natural language processing for biomedical literature, clinical notes, and health consumer texts * Novel health information systems for chronic disease management * Optimization models for planning and recommending therapies * Personalized predictive modeling for clinical management (e.g., trauma, diabetes mellitus, sleep disorders, substance abuse) * Physiological modeling * Semantic Web, linked data, ontology, and healthcare * Sensor networks and systems for pervasive healthcare * Social studies of health information technologies * Survival analysis and related methods for estimating hazard functions * System software for complex clinical studies that involve combinations of clinical, genetic, genomic, imaging, and pathology data * Systems for cognitive and decision support * Technologies for capturing and documenting clinical encounter information in electronic systems * User-interface design issues applied to medical devices and systems Each contribution will be carefully evaluated by a set of reviewers, including experts with multidisciplinary experience spanning computing, information science, social and behavioral sciences, public health, medicine, and nursing as appropriate, to ensure that proper and comprehensive peer-review analysis and feedback can be provided to authors. Submissions will be judged on validity, originality, technical strength, practical and clinical significance, quality of presentation, and relevance to the conference topics. Because of IHI's multidisciplinary nature, the review process will include at least a computing expert and a medical expert as well as a review editor to reconcile the evaluation, making a single recommendation to the Program Committee Co-Chairs. This process is designed to ensure that experts from multiple areas can assess the importance and validity of the work. Therefore, we encourage coherent, application-driven submissions where in-depth ideas from a variety of fields are presented about important problems in health informatics. The conference will accept both regular and short papers. Regular papers (6-10 pages in length) will describe more mature ideas, where a substantial amount of implementation, experimentation, or data collection and analysis will be described. Short papers (1-5 pages) can be less formal and will describe innovative ideas where minimal validation and implementation have occurred and can be described. All papers will appear in the ACM Digital Library. The best papers of IHI 2010 will be considered for a special issue of Springer's Journal of Medical Systems. Submitted papers must not have appeared in, or be under consideration for, another conference, workshop, journal, or other target of publication. All aspects of the submission and notification process will be handled electronically. Submissions must adhere to the following formatting instructions: * Papers must adhere to the ACM Proceedings Format available for LaTex, WordPerfect, WordPerfect 9, and Word. Changing the template's font size, margins, inter-column spacing, or line spacing is prohibited. Each paper must be submitted as a single PDF file, formatted for 8.5" x 11" paper. * The length of submission depends on the type of submission: > - Regular papers must be 6-10 pages long. > - Short papers may be at most 5 pages long. * Each paper must provide an appendix (which is excluded from the page limit) indicating the preferred review approach, including: > - The preferred allocation of reviewing expertise. This can be done by > electing the primary and secondary focus of the paper (e.g., Computing, > Information Science, Medicine, Nursing, and Social/Behavioral Science). > - A bulleted list with up to 3 topics covered in the paper (from the list of > conference topics presented above) IMPORTANT DATES Abstract submission deadline: May 24, 2010 11:30pm EST Paper submission deadline: May 31, 2010 11:30pm EST Notification of acceptance: August 2, 2010 11:30pm EST Camera-ready copy due: August 16, 2010 11:30pm EST General Chair ?mit ?ataly?rek, Ohio State University (catalyurek.1 at osu dot edu) Honorary General Chair Gang Luo, IBM Research (luog at us dot ibm dot com) Program Committee Co-Chairs Henrique Andrade, IBM Research (hcma at us dot ibm dot com) Neil R. Smalheiser, University of Illinois ? Chicago (neils at uic dot edu) Steering Committee Members Dorin Comaniciu, Siemens Corporate Research Michael D. Larsen, George Washington University Ching-Yung Lin, IBM Research Chunqiang Tang, IBM Research YingLi Tian, City College of New York Olivier Verscheure, IBM Research Michael Weiner, Indiana University Honorary Steering Committee members Marion J. Ball, Johns Hopkins University & IBM Research David W. Bates, Partners Healthcare System & Harvard Medical School Joseph A. Konstan, University of Minnesota Blackford Middleton, Partners Healthcare System & Harvard Medical School Joel H. Saltz, Emory University PROGRAM COMMITTEE MEMBERS To be finalized