From jeff at bioinformatics.org Wed Jun 1 17:42:43 2011 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 01 Jun 2011 17:42:43 -0400 Subject: [BiO BB] Course on Protein-Protein Interactions Message-ID: <4DE6B253.6030108@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BI211 Protein-Protein Interactions July 25-29, 2011 Online at Bioinformatics.Org http://www.bioinformatics.org/wiki/BI211_Protein-Protein_Interactions -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: This course will dig into some of the fundamental issues concerning protein-protein interactions (PPIs), including their need and use in research. It will introduce various tools and provide examples for finding true, positive interactors from Web searches and interfaces. The exercises and take-home messages will encourage participants to give the topics some thought and then hopefully build some excitement about the top-down approach of systems biology involving protein-protein interactions. INSTRUCTORS: Prashanth Suravajhala is on the Board of Directors of Bioinformatics.Org. His home page is at http://www.bioinformatics.org/wiki/Prash. Gary D. Bader works on biological network analysis and pathway information resources as an Assistant Professor at The Donnelly Centre at the University of Toronto. His home page is at http://baderlab.org/. TOPICS: * Assays, tools and techniques in PPIs: Pros and Cons * Types of interactions and networks * Data validation and integration * Capabilities of networks * A look at sample PPI data * Future challenges * Introduction to Cytoscape, Osprey and Ingenuity * Networkology: Data representations * Exercises using Osprey: A short project * Exercises with iHOP, String, Bind, PreBind, Genecards, MINT, HPRD REGISTRATION: http://www.bioinformatics.org/edu/ACAA Cheers, Jeff From hlapp at gmx.net Fri Jun 10 18:31:10 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Jun 2011 18:31:10 -0400 Subject: [BiO BB] Birds-of-a-Feather gatherings for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <1213182B-31EE-4E6D-946D-E7711C88ECC6@gmx.net> In anticipation of the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), we solicit all attendees to propose and discuss Birds-of-a-Feather gatherings. See below for details. Birds-of-a-Feather gatherings (BoFs) are informal, ad-hoc, focused face-to-face discussion groups that form around a shared interest. BoFs can also take the form of a hands-on software tutorial on using a tool, or on programming an API. BoFs have a leader (usually, but not necessarily, the proposer) who initiates or moderates the discussion. The topics of BoFs can range widely, including general cultural or computational infrastructure issues, or narrower questions such as how to make the best use of a particular software tool or how to solve a particular computational challenge. Anyone willing to lead such a group can propose a BoF. iEvoBio will provide space that can accommodate up to 8-10 BoFs. Sign-up sheets will be provided on-site on the first day of the conference where attendees can propose a BoF or sign up for one proposed by someone else. BoFs will be about 1-1.5 hours in duration and take place in the afternoon of the second day of the conference. In line with their informal nature, there is no official prior call for or submission of BoFs. However, we encourage those intending to propose one to sound out or rally potential attendees ahead of time. We suggest to employ Twitter (http://twitter.com) for this, using the #ievobioBof tag to mark BoF proposals and comments. Similarly, users interested in seeing a hands-on tutorial BoF about their favorite tool are encouraged to use similar means to give tool developers a sense of the community interest in a tutorial BoF, and what common usage (or programming) questions are. Birds-of-a-Feather gatherings are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Challenge entries, and 4) Software Bazaar entries. All Calls except for Full Talks remain open (see http://ievobio.org/ocs/index.php/ievobio/2011/) . 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 for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) From jnrt.editor at gmail.com Tue Jun 7 16:12:45 2011 From: jnrt.editor at gmail.com (JNRT Editor) Date: Tue, 7 Jun 2011 13:12:45 -0700 Subject: [BiO BB] Canadian Semantic Web Symposium - Call for Paper Message-ID: CALL FOR PAPER ? CSWS2011: Third Canadian Semantic Web Symposium 2011 http://csws2011.uwaterloo.ca/ collocated with SADI workshop. *Vancouver, British Columbia, Canada** ** August 5, 2011 * Paper Submission https://www.easychair.org/account/signin.cgi?conf=cswws11 ================================================= *Important dates:* Submission Deadline: June 20th, 2011 Acceptance Notification: July 15th, 2011 ================================================= The Third Canadian Semantic Web Symposium, will be held in the University of British Columbia, Vancouver, British Columbia (Aug 5, 2011). As a follow-up to the previous symposium, CSWS 2011 aims at bringing together Canadian and international researchers in semantic technologies and knowledge management to discuss about various issues related to the Semantic Web. The Third Canadian Semantic Web Symposium 2011 calls for papers in all topics related to semantic web technologies and their applications. The following are some example topics: ? Languages, tools and methodologies for the Semantic Web ? The application of AI technologies in the Semantic Web ? Searching, querying, visualizing and interpreting the Semantic Web ? Semantic Web-based Knowledge Management; ? Semantic Grid and semantic Grid services ? Trust, privacy, security on the Semantic Web; ? Ontology design, evolution and management ? Ontology mapping and merging ? Semantic Web and uncertainty ? Description logics and frame logics as ontology formalisms ? Modular, distributed, and multi-ontologies ? Semantic Web technologies for collaboration and cooperation ? Semantic Web Services (description, discovery, invocation, composition) ? Semantic Web and databases ? Practical applications of Semantic Web techniques in e-business, e-commerce, e-government and e-learning ? Semantic Web rule languages and engines ? Social Semantic Web (Web 3.0) CSWS 2011 will feature two tracks: a Research and a Work-in-Progress track. The objective of the research track is to solicit original papers that present accomplished research on the area of the Semantic Web. The Work-in-Progress track aims at providing an opportunity for practitioners to present their on-going research on principles and applications of the Semantic Web, even when implementation or deployment has not been completed. Accepted submissions will be published in the symposium Proceeding. Authors are invited to submit full papers in PDF, Postscript or MS-Word RTF electronically. All papers must be written in English. Research papers can be up to 12 pages in length and Work-In-Progress papers can be up to 6 pages. Papers must be formatted according to Springer's LNCS style. Please follow the instructions for authors at Springer's site for authors. To submit papers, please follow visit https://www.easychair.org/conferences/?conf=cswws11 Papers that are not submitted through the automatic procedure cannot be reviewed. *Program Co-Chairs:* Christopher Baker, University of New Brunswick (Saint John) Helen Chen, University of Waterloo *Organization Committee:* Ebrahim Bagheri, Athabasca University Helen Chen, University of Waterloo Weichang Du, University of New Brunswick *Program Committee:* Abdolreza Abhari Ryerson University, Canada Atif Khan University of Waterloo, Canada Alexandre Riazanov University of New Brunswick, Canada Arash Shaban-Nejad McGill University, Canada Babak Esfandiari Carleton University, Canada Bruce Spencer National Research Council Canada, Canada Csaba Huszka Agfa Healthcare, Belgium Christopher Baker University of New Brunswick, Canada Dragan Ga?evi? Simon Fraser University, Canada Ebrahim Bagheri Athabasca University, Canada Faezeh Ensan University of British Columbia, Canada Fred Popowich Simon Fraser University, Canada Hassan Ait-Kaci IBM Canada, Canada Helen Chen University of Waterloo, Canada Leo Ferres Universidad de Concepci?n, Chile Marek Hatala Simon Fraser University, Canada Marek Reformat University of Alberta, Canada Mark Wilkinson University of British Columbia, Canada Marina Sokolova University of Ottawa, Canada Michel Dumontier Carlton University, Canada Ren? Witte Concordia University, Canada Vio Onut IBM Canada, Canada Volker Haarslev Concordia University, Canada Weichang Du University of New Brunswick, Canada Weiming Shen National Research Council, Canada Yevgen Biletskiy University of New Brunswick, Canada From ngadewal at yahoo.com Fri Jun 10 00:24:48 2011 From: ngadewal at yahoo.com (nikhil gadewal) Date: Thu, 9 Jun 2011 21:24:48 -0700 (PDT) Subject: [BiO BB] Ref_seq convertor Message-ID: <691719.24049.qm@web39409.mail.mud.yahoo.com> Dear all, ? I am looking for online tool that converts?Ref_Seq?mRNA (NM_######) into Ref_seq protein (NP_######). I have around 3000 genes to convert. Please let me know. Thanks in?advanced.?? NIKHIL S. GADEWAL ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India From ws1.sadiservices at gmail.com Fri Jun 10 08:47:40 2011 From: ws1.sadiservices at gmail.com (UNBSJ cbrass) Date: Fri, 10 Jun 2011 09:47:40 -0300 Subject: [BiO BB] Training Courses in Web Publishing - Scientific Data and Services in Vancouver, BC, Canada Message-ID: [Apologies for cross posting] Dear Colleague, RE: Training Courses in Web Publishing - Scientific Data and Services in Vancouver, BC, Canada Early Registration Late Registration Until July 15th, 2011 July 16th - August 2nd, 2011 Workshop August 3rd - 4th, 2011 The course provides theory and practical skills in the semantic technologies that underpin the development of semantic web services.The training course is divided into the following modules: - Semantic Web and DL Reasoning - SADI Semantic Web Services The course provides an excellent learning opportunity and serves as a venue for the exchange of ideas among a highly interdisciplinary group of scientists. The intended audience for the course are: - Industry pioneers in workflow, grid and semantic technologies; - Web developers and researchers seeking to ensure the adoption of their technologies as part of a growing ecosystem of easily discoverable and accessible data and services; - Grid computing architects and developers interested in building globally interoperable systems; - Workflow system developers coordinating computational and data resources across the web using semantics; - Researchers involved in web-based knowledge discovery We ask that you broadcast this information widely to your colleagues. Our flyer can be found at http://sadiframework.org/training/WS2/WS2_flyer.pdf. Please do not hesitate to contact us at spaixao at unb.ca should you have any question. Cost The cost per participant is: Early Registration (275 CAN$) Late Registration (375 CAN$) On site Registration (500 CAN$) ** Student discount is available Registration and Further Information To register and for further information please visit the website at: http://sadiframework.org/training/WS2/index.html SADI training course will be co-located with 3rd Canadian Semantic Web Working Symposium 2011 (CSWS2011) in August 5th, lecture theater - UBC,Vancouver. CSWS 2011 aims at bringing together Canadian and international researchers in semantic technologies and knowledge management to discuss about various issues related to the Semantic Web. For further details on CSWS2011, please visit: http://csws2011.uwaterloo.ca/. Sincerely, Silvane Paixao on behalf of the Organizing Committee From bpederse at gmail.com Fri Jun 10 19:21:29 2011 From: bpederse at gmail.com (Brent Pedersen) Date: Fri, 10 Jun 2011 17:21:29 -0600 Subject: [BiO BB] Ref_seq convertor In-Reply-To: <691719.24049.qm@web39409.mail.mud.yahoo.com> References: <691719.24049.qm@web39409.mail.mud.yahoo.com> Message-ID: On Thu, Jun 9, 2011 at 10:24 PM, nikhil gadewal wrote: > Dear all, > > ? I am looking for online tool that converts?Ref_Seq?mRNA (NM_######) into Ref_seq protein (NP_######). I have around 3000 genes to convert. > > Please let me know. > > Thanks in?advanced. > > NIKHIL S. GADEWAL > ACTREC, > Tata Memorial Centre, > Kharghar, > Navi Mumbai, > India > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > see the resources listed here: http://biostar.stackexchange.com/questions/22/gene-id-conversion-tool The biodb net one (http://biodbnet.abcc.ncifcrf.gov/db/db2db.php) listed there seems to be down now, but worked as recently as wednesday. I find it's the nicest to use. -Brent From hlapp at gmx.net Mon Jun 13 22:58:42 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 13 Jun 2011 22:58:42 -0400 Subject: [BiO BB] Deadline extended for Call for Challenge entries for iEvoBio conference Message-ID: <8C9CCC9F-0515-46BD-8D81-88F7B38D96CE@gmx.net> The deadline for submitting entries to the Challenge held by conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended by one week to June 20, 2011. The iEvoBio Challenge is a competition to create a new software tool, or add a new feature or features to an existing platform. Entries to the Challenge need to respond to its theme, which for 2011 is "Data Integration". Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html . Selected candidates will make short oral presentations to demonstrate their work in a "Challenge session" at the conference, and if suitable will automatically be entered into the Software Bazaar track of the conference. The winning entries will be selected by a vote of the iEvoBio meeting participants, and will be awarded cash prizes. Challenge entries are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Software Bazaar entries, and 4) Birds-of-a-Feather gatherings. All tracks except Full Talks remain open(see http://ievobio.org/ocs/index.php/ievobio/2011/) . 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 , or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) From Gaurav.Pradhan at asu.edu Mon Jun 13 18:19:13 2011 From: Gaurav.Pradhan at asu.edu (Gaurav Pradhan) Date: Mon, 13 Jun 2011 15:19:13 -0700 Subject: [BiO BB] CALL FOR PAPERS: 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) References: <499BA5B74640014B9C20CC878F0A85965D3E242C@EX11.asurite.ad.asu.edu> Message-ID: <277C1701239FAE41850579216CE41D79CEA5F86775@EX11.asurite.ad.asu.edu> 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2012) January 28-30, 2012 Miami, Florida, USA http://www.sighit.org/ihi2012 (mirror site: http://www.comp.hkbu.edu.hk/ihi2012/) ________________________________________________________________________________________________________________________________________ CALL FOR PAPERS IMPORTANT DATES Abstract submission deadline: June 23, 2011 11:59pm EST Paper submission deadline: June 30, 2011 11:59pm EST Notification of acceptance: September 1, 2011 11:59pm EST Camera-ready copy due: September 30, 2011 11:59pm EST ABOUT THE CONFERENCE IHI 2012 is the main conference of the newly formed ACM Special Interest Group on Health Informatics (SIGHIT). IHI 2012 is ACM's premier community forum concerned with the application of computer science principles, information science principles, information technology, and communication technology to address problems in healthcare, public health, and everyday wellness. The conference highlights the most novel technical contributions in computing-oriented health informatics and the related social and ethical implications. IHI 2012 will feature keynotes, a multi-track technical program including papers, demonstrations, and panels. New additions to the IHI 2012 program include tutorials and a doctoral consortium. IHI 2012 serves as a venue for the discussion of innovative technical contributions highlighting end-to-end applications, systems, and technologies, even if available only in prototype form (e.g., a system is not deployed in production mode and/or evaluation may be performed by giving examples). We strongly encourage authors to submit their original contributions describing their algorithmic contributions, methodological contributions, and well-founded conjectures based on an application-oriented context. A paper does not have to be comprehensive and can focus on a single aspect of design, development, evaluation, or deployment. Contributions in the realm of social and behavioral issues might include empirical studies of health-related information use and needs, socio-technical studies on the implementation and use of health information technology, studies on health informatics in the context of community impact and implications, studies on public policies on leveraging health informatics infrastructure, among others. SUBMISSION AND PUBLICATION 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 a less degree of validation and implementation have occurred. All papers will appear in the ACM Digital Library. The list of conference topics is available on the conference web site. The best papers of IHI 2012 will also be considered for journal publication in a special issue of the ACM Transactions on Intelligent Systems and Technology (TIST). IHI 2012 has three tracks: analytics, systems, and human factors. " The analytics track focuses on data analysis. " The systems track focuses on building health informatics systems (e.g., architecture, framework, design, engineering, and application). " The human factors track focuses on understanding users or context, interface design, and user studies of health informatics applications. When submitting a paper, the authors must select a track that they regard as the most appropriate one for their paper. Before the review process starts, the PC co-chairs will check each paper and make adjustment if necessary to ensure the submission will be reviewed in the correct track. A subset of highly-ranked papers will have oral presentation slots. The other accepted papers, which are not selected for oral presentation, will be presented as posters. Submitted papers must not have appeared in, or be under consideration for, another conference, workshop, journal, or other target of publication. ________________________________________________________________________________________________________________________________________ CALL FOR DEMOS IMPORTANT DATES Demo paper submission deadline: June 30, 2011 11:59pm EST Notification of acceptance: September 1, 2011 11:59pm EST Camera-ready copy due: September 30, 2011 11:59pm EST SCOPE OF THE DEMO TRACK A submission proposal includes a demo paper and can optionally include a demo video, whose URL should be referred to in the textual demo description for reviewers to take into consideration when analyzing the submission. Note that the demo paper should differ from regular papers in several important aspects. (1) it should clearly describe the overall architecture of the system or technology demonstrated. (2) the paper should put great emphasis on the motivation of the work, on the applications of the presented system or technology, and on the novelty of the work. (3) the proposal should clearly describe the demo scenario. In particular, it should describe how the demo audience can interact with the demo system, to better understand the underlying technology. A list of IHI areas/topics can be found in the Call for Papers. For demos running over the web, a back-up scenario should be described, in case connectivity is limited at the demo venue. The notification for acceptance of demo papers is the same as that for regular papers. Accepted demo proposals will appear in the final proceedings and in ACM digital library. ________________________________________________________________________________________________________________________________________ CALL FOR DOCTORAL CONSORTIUM SUBMISSIONS IMPORTANT DATES Doctoral consortium submission deadline: June 30, 2011 11:59pm EST Notification of acceptance: September 1, 2011 11:59pm EST Camera-ready copy due: September 30, 2011 11:59pm EST SCOPE OF THE DOCTORAL CONSORTIUM The doctorial consortium is expected to offer a supportive learning opportunity for doctoral students in two ways: (1) as a poster presentation during a poster session of the IHI conference and (2) as an article in the SIGHIT Record, the newsletter of SIGHIT (http://www.sighit.org/record/). Extended abstracts will not appear in the IHI conference proceedings. All extended abstract submissions for the doctoral consortium will be formally reviewed by the IHI Program Committee to ensure every accepted submission is appropriate for IHI. The conference organizers will work on ensuring that the doctoral consortium is well attended and have a vibrant discussion environment. ________________________________________________________________________________________________________________________________________ CALL FOR NON-REFEREED EXTENDED ABSTRACTS IMPORTANT DATES Extended abstract submission deadline: September 8, 2011 11:59pm EST Notification of acceptance: September 15, 2011 11:59pm EST Camera-ready copy due: September 30, 2011 11:59pm EST SCOPE OF THE NON-REFEREED EXTENDED ABSTRACT TRACK The non-refereed extended abstract track offers an opportunity for health informatics practitioners and researchers to present their work in progress in two ways: (1) as a poster presentation at the IHI conference and; (2) as an article in the SIGHIT Record, the newsletter of SIGHIT (http://www.sighit.org/record/). Extended abstracts will not appear in the conference proceedings. Although the non-refereed extended abstract submissions will not be formally reviewed, the IHI 2012 conference organizers will read all of the submissions to ensure every accepted submission is appropriate for IHI. The conference organizers will work on ensuring that poster sessions are well attended and have a vibrant discussion environment. ________________________________________________________________________________________________________________________________________ CALL FOR PANEL PROPOSALS IMPORTANT DATES Panel proposal submission deadline: June 30, 2011 11:59pm EST Notification of acceptance: September 1, 2011 11:59pm EST Camera-ready copy due: September 30, 2011 11:59pm EST SCOPE OF PANEL PROPOSALS Panel proposals are expected to address new, exciting, and controversial issues on computing-oriented health informatics and appeal to IHI 2012 attendees with various health informatics-related expertise. The proposed panel should be provocative, insightful, and informative. A mix of industry, government, and academic panel members is encouraged. A panel typically includes approximately 4 panelists and a chair who serves as the moderator. The 90-minute panel should provide a balance between panelists' presentations/debate and audience interactions/discussions. Panelists must make a commitment to participate. If for any reason, one panelist cannot attend the panel, the panel chair must first obtain the approval of the conference general/PC chairs before making another arrangement. Panels will be featured prominently in the conference program. REVIEWING Panel proposals will be reviewed by the PC Co-Chairs and the Conference Leadership, based on the IHI attendees' likely interest in them, the expertise of the chairs and the panelists, and the planned interactivity. ________________________________________________________________________________________________________________________________________ CALL FOR TUTORIAL PROPOSALS IMPORTANT DATES Tutorial proposal submission deadline: June 30, 2011 11:59pm EST Notification of acceptance: September 1, 2011 11:59pm EST Camera-ready copy due: September 30, 2011 11:59pm EST SCOPE OF TUTORIAL PROPOSALS Tutorials at IHI 2012 will be presented by domain experts to cover current topics directly relevant to the conference theme of computing-oriented health informatics (a list of IHI areas/topics can be found in the Call for Papers). Proposed tutorials should be comprehensive, informative, and appealing to IHI 2012 attendees. Each tutorial will be 120-minutes long. Tutorial instructors must make a commitment to prepare the tutorial materials (e.g., slides) that reflect the high quality standard of IHI. Tutorials will be free to all IHI 2012 attendees, and tutorial instructors will receive free registration but not any financial aid from the conference. All tutorials will be featured prominently in the conference program. REVIEWING Tutorial proposals will be reviewed by the PC Co-Chairs and the Conference Leadership, based on the IHI attendees' likely interest in them, the breadth and depth of the topic(s), the planned materials to be used, and the expertise and credential of the instructor. From Phoebe.Chen at latrobe.edu.au Wed Jun 15 08:04:14 2011 From: Phoebe.Chen at latrobe.edu.au (Phoebe Chen) Date: Wed, 15 Jun 2011 22:04:14 +1000 Subject: [BiO BB] Deadline Approaching - APBC2012: The Tenth Asia Pacific Bioinformatics Conference Melbourne Australia Message-ID: Deadline Approaching - APBC2012: The Tenth Asia Pacific Bioinformatics Conference --------------------------------------------------------------------------------------------- The Tenth Asia Pacific Bioinformatics Conference Melbourne, Australia, 17-19 January 2012 http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/ The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development and novel applications of Bioinformatics. Important Dates Paper submission: 20th July 2011 *** Author Notification: 20th Aug 2011 Final Version due on: 1st Oct 2011 Tutorial submission open: 1st July 2011 Poster submission open: 3rd Oct 2011 Registration open: 22nd Aug 2011 From luca at dmi.units.it Mon Jun 20 05:33:58 2011 From: luca at dmi.units.it (Luca Bortolussi) Date: Mon, 20 Jun 2011 11:33:58 +0200 Subject: [BiO BB] HMSB 2011 - Call for Papers Message-ID: <4DFF1406.5060400@dmi.units.it> [We apologize for the reception of multiple copies of this message] ***************************************************************************** Call for Papers HMSB 2011 First International Workshop on Hybrid Modeling in Systems Biology November 12-15, 2011 Atlanta, Georgia, USA Satellite event of BIBM 2011 http://hmsb2011.cs.sunysb.edu/ ***************************************************************************** The goal of systems biology is to provide a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. The intrinsic multi-scale nature of these systems, both in space, in organization levels, and in time, makes extremely difficult to model all of them in a uniform way, e.g. by means of differential equations or discrete stochastic processes. Furthermore such models are often not easily amenable to formal analysis and simulation at the organ or even the cell level is frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale well for both the simulation and formal analysis of biological processes. Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology, and they have been applied to successfully capture the behavior of several biological complex systems, ranging from genetic networks, biochemical reactions, signaling pathways and cardiac tissues electrophysiology. This workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. We solicit the submission of unpublished results that address on both theoretical and applied aspects of hybrid modeling techniques in systems biology. The proceedings will be published in the IEEE BIBM 2011 workshop proceedings volume. A special issue in a journal will be considered at the end of the workshop. Research Topics include (but are not limited to): ? Hybrid models of biological systems (case studies of genetic, biochemical, cellular networks, models of tissues, ecc) ? Computational and mathematical analysis techniques for hybrid systems (i.e. reachability, model checking, abstract interpretation, bifurcation theory for hybrid dynamical systems, etc.), with applications in Systems Biology. ? Hybrid system identification techniques (learning the model from the experimental data) ? Stochastic hybrid systems, applications and analysis techniques ? Efficient simulation techniques for hybrid systems ? Hybrid modeling languages for biological systems ? Hybrid systems coping with incomplete and uncertain information ? Sensitivity analysis for hybrid systems ? Behaviour-driven parameters identification for hybrid systems ? Analysis and simulation tools Paper Submission Please submit a full-length paper (8 page IEEE 2-column format) through the online submission system (you can download the format instruction for Latex or Word at http://wi-lab.com/cyberchair/2011/bibm11/cbc_index.html). Electronic submissions (in PDF or Postscript format) are required. Please refer to the workshop web site for further details on the submission procedure. Important Dates Electronic submission of full papers: September 12, 2011 Notification of paper acceptance: October 1, 2011 Camera-ready version of accepted papers : October 15, 2011 Workshop: November 12-15 Program Co-chairs: Luca Bortolussi, University of Trieste, Italy Ezio Bartocci, University of Stony Brook, USA Program Committee: Marco Antoniotti, University of Milano Bicocca Gregory Batt, INRIA Toulose, France Alberto Casagrande, University of Trieste, Italy Edmund Clarke, Carnegie Mellon, USA Thao Dang, VERIMAG Lab, Grenoble, France Alexandre Donz?, VERIMAG Lab, Grenoble, France James R. Faeder, University of Pittsburgh, USA Jasmin Fisher, Microsoft Research, Cambridge, UK Vashti Galpin, University of Edinburgh, UK Colas Le Guernic, NYU, USA Oded Maler, VERIMAG Lab, Grenoble, France Bud Mishra, NYU, USA Carla Piazza, University of Udine, Italy Scott Smolka, University of Stony Brook, USA Gouhei Tanaka, University of Tokyo, Japan Verena Wolf, Saarland University, Germany Paolo Zuliani, Carnegie Mellon, USA From jlloret at dcom.upv.es Wed Jun 22 05:07:37 2011 From: jlloret at dcom.upv.es (Jaime Lloret Mauri) Date: Wed, 22 Jun 2011 11:07:37 +0200 Subject: [BiO BB] [NPA] CFP: International Journal "Network Protocols and Algorithms" Message-ID: <201106220907.p5M97amv007246@smtp.upv.es> ********************* Call for Papers ********************* Network Protocols and Algorithms ISSN 1943-3581 http://www.macrothink.org/journal/index.php/npa/ Network Protocols and Algorithms is a free-access online international journal, peer-reviewed and published by Macrothink Institute. It publishes papers focused on the design, development, manage, optimize or monitoring any type of network protocol, communication system, algorithm for communication and any protocol and algorithm to communicate network devices. The scope of the journal include, but are not limited to, the following topic areas: - Synchronization Protocols and Algorithms - Security Protocols and Algorithms - QoS Protocols and Algorithms - Ad-Hoc and Sensor Networks Protocols and Algorithms - Content Delivery Networks Protocols and Algorithms - P2P Protocols and Algorithms - Cluster-Based Protocols and Algorithms - Real-Time Protocols and Algorithms - Wireless Protocols and Algorithms - MAC Protocols and Algorithms for Wired Networks - Mobile wireless internet protocols and algorithms - Delay Tolerant protocols and algorithms - Mesh network protocols and algorithms - Protocols and algorithms for Voice over IP delivery - Cognitive Radio Network Protocols and Algorithms - Monitoring and management protocols and algorithms - optical networking protocols and algorithms - Scalable Network Protocols and Algorithms - Protocols and algorithms for Green Computing and Resource Allocation - Routing Protocols and Algorithms - Tree-based Protocols and Algorithms - Distributed/Decentralized Algorithms for Networks - Fault tolerant Protocols and Algorithms - Protocols and algorithms for Mobile and Dynamic Networks - Cross-Layer Collaborative Protocols and Algorithms - Formal methods and cryptographic algorithms for communication - Power Efficient and Energy Saving Network Protocols and Algorithms - Multimedia Network Protocols and Algorithms - Network Protocols and Algorithms for Context-Aware and Semantic Networks - Localized Network Protocols and Algorithms - Transport Layer Protocols - Smart Grids protocols and algorithms Network Protocols and Algorithms has linked its papers to references by DOI (Digital Object Identifier) numbers. Network Protocols and Algorithms appears in the next search engines: Google Scholar, Bing, Yahoo and Ask. Network Protocols and Algorithms is added and indexed in Index Copernicus, ProQuest, EBSCO, Ulrichsweb.com, Directory of Open Access Journals (DOAJ), Open J-Gate, Gale, Socolar, io-port Database, NewJour - Electronic Journals and Newsletters, Public Knowledge Project metadata harvester, Ovid LinkSolver, Genamics JournalSeek and PublicationsList.org. It is also requested to be included in other major Indexing Databases. You are welcome to submit a paper or forward this call for papers to any people working in Network Protocols and Algorithms that may be interested in submitting a paper. The topics suggested by the journal can be discussed in term of concepts, state of the art, standards, implementations, running experiments and applications. Proposals and deployments are also welcome. Submission Information: Only original and unpublished research papers will be considered in this journal. Manuscripts must be writen in English. All submissions will be reviewed based on technical merit and relevance. Instructions for authors and submissions can be found in http://www.macrothink.org/journal/index.php/npa/about/submissions Jaime Lloret Mauri Editor in Chief of the International Journal of Network Protocols and Algorithms Department of Communications Polytechnic University of Valencia, Spain