From rwagner at faw.jku.at Tue Jan 11 06:46:54 2011 From: rwagner at faw.jku.at (Roland Wagner) Date: Tue, 11 Jan 2011 12:46:54 +0100 Subject: [BiO BB] Call for Papers ITBAM 2011 Message-ID: <4D2C432E.6010205@faw.jku.at> Preliminary Call for Papers and Posters International Conference on Information Technology in Bio- and Medical Informatics ITBAM 2011 In conjunction with DEXA 2011 www.dexa.org 29 August ? 2 September 2011, Toulouse, France Data intensive disciplines like life sciences and medicine are promoting vivid research activities in the area of databases. Modern technologies such as high-throughput mass-spectrometry and sequencing, micro-arrays, high-resolution imaging, etc. produce enormous and continuously increasing amounts of data. Huge public databases provide access to aggregated and consolidated information on genome and protein sequences, biological pathways, diseases, anatomy atlases, and scientific literature. There has never been more potentially available information to study biomedical systems ranging from single cells to complete organisms. However, it is a non-trivial task to transform the vast amount of biomedical data into actionable information triggering scientific progress and supporting patient management. Major biomedical application scenarios for research in the database community include but are not limited to: * Systems biology, * Genomics, proteomics, and metabolomics, * Genome-wide association studies, * Drug target discovery and personalized medicine, * Neuroscience, * Electronic patient records, * Patient monitoring, * Surgery planning and support, * etc. Various emerging database technologies for coping with the challenges of these application scenarios have been developed and are an active area of research in information technology: * Administration of vast amounts of data, * Integration of heterogeneous data sources, * Federated and distributed databases, * Data warehouses, * Data mining techniques like classification, clustering, association rule mining, etc. * Decision support systems, * Information and image retrieval, * Signal processing and streaming databases, * Privacy protection and data security, * Data quality assurance, * Process management and collaborative work, * User interfaces and visualization, * etc. Designing database technology to support applications in life sciences and medicine is an inspiring field of interdisciplinary research. Often there is a long way from an idea to practical application which involves intensive discussion between experts in information technology, life sciences and medicine. ITBAM accompanies and supports this way by providing an excellent venue for the exchange of ideas, fruitful discussion, and effective interaction among interdisciplinary researchers. In addition to the regular conference program featuring presentations of full and short research papers published in the proceedings, ITBAM encourages the submission of posters reporting work in progress. All accepted posters will be displayed during the whole event and abstracts will also be included in the proceedings. Important Dates: ITBAM conference papers and poster submissions: * Paper submission deadline (firm): March 7, 2011 * Notification of acceptance: May 11, 2011 * Poster submission deadline (firm): May 16, 2011 * Camera-ready copies due: June 9, 2011 Paper Submission Details: Authors are invited to submit electronically original contributions or experience reports in English. The submitted manuscript should closely reflect the final paper as it will appear in the proceedings. * Paper submissions should not exceed 15 pages in LNCS format. Poster submissions are expected to consist of 1 page Abstract (http://www.springer.de/comp/lncs/authors.html). * Any submission that exceeds length limits or deviates from formatting requirements may be rejected without review. * For registration and electronic submission see: http://confdriver.ifs.tuwien.ac.at/ * The submission system will be open starting from January 2011. * Submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of exposition. * Duplicate submissions are not allowed. Authors are expected to agree to the following terms: "I understand that the paper being submitted must not overlap substantially with any other paper that I am a co-author of and that is currently submitted elsewhere. Furthermore, previously published papers with any overlap are cited prominently in this submission." Accepted Papers: All accepted conference papers will be published in "Lecture Notes in Computer Science" (LNCS) by Springer Verlag. Accepted full papers will be of 15 pages length, short papers 8 pages. Authors of accepted papers must sign a Springer copyright release form. For further inquiries, please contact the Conference Organisation Office (gabriela at dexa.org). General Chairperson: Christian B?hm, University of Munich, Germany Program Committee Co-chairpersons: Sami Khuri, San Jos? State University, USA Lenka Lhotska, Czech Technical University Prague, Czech Republic Nadia Pisanti, University of Pisa, Italy Program Committee: tbd From chaouki.amir at gmail.com Fri Jan 21 10:10:50 2011 From: chaouki.amir at gmail.com (amir chaouki) Date: Fri, 21 Jan 2011 16:10:50 +0100 Subject: [BiO BB] (no subject) Message-ID: hello, i am a member in bioinformatics organisation and i have created a new tool, named gCut, for restriction analysis and i will appreciate if you can just check it and tell me what you think about it, i have posted it in bioinformatics.org but i just need some body with a lot of experience in this field to tell me what he thinks about this. you can find it in: gcut.sourceforge.net please help me i will be grateful if you respond to this message. thank you, tell me also what are the functionalities that i can add in the future. From Alex.Bossers at wur.nl Sat Jan 22 10:44:04 2011 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Sat, 22 Jan 2011 16:44:04 +0100 Subject: [BiO BB] (no subject) In-Reply-To: References: Message-ID: <605CF62A79C32E4AA0CC741FD84D4E7425D3D9EA90@scomp0536.wurnet.nl> Amir, nice going. I wondered what your initial use case was before you started the project? Some rapid remarks by just browing the manual; - having to remove Fasta headers? are you serious? A cmdline tool like yours is build to use many sequences right? Skipping headers or stripping some usefull info from it would be the first to fix. - It analyses 4 and 6 mers.... what about the other enzymes also having cleavage outside the recognition sequences? 4-6 simple enzymes can be done with a single regexp. - What about methylation dam/dcm and/or CpG in eukaryotes? Looong time ago we made an online tool for such a thing as this using the complete REBASE 3700+ enzymes. We started with a proper use-case and requirements analysis. you might be able to get some ideas from that if they overlap. You can find it here: http://biolinux.smith.man.ac.uk/~campus13ab/ToolREA/ Good luck. Alex ________________________________________ Van: bbb-bounces at bioinformatics.org [bbb-bounces at bioinformatics.org] namens amir chaouki [chaouki.amir at gmail.com] Verzonden: vrijdag 21 januari 2011 16:10 Aan: bbb at bioinformatics.org Onderwerp: [BiO BB] (no subject) hello, i am a member in bioinformatics organisation and i have created a new tool, named gCut, for restriction analysis and i will appreciate if you can just check it and tell me what you think about it, i have posted it in bioinformatics.org but i just need some body with a lot of experience in this field to tell me what he thinks about this. you can find it in: gcut.sourceforge.net please help me i will be grateful if you respond to this message. thank you, tell me also what are the functionalities that i can add in the future. _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From daniele.gianni at gmail.com Sun Jan 23 11:51:25 2011 From: daniele.gianni at gmail.com (Daniele Gianni) Date: Sun, 23 Jan 2011 17:51:25 +0100 Subject: [BiO BB] COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - Call for Papers In-Reply-To: References: Message-ID: Please accept our apologies if you receive multiple copies of this CfP) ################################################################# IEEE WETICE 2011 2nd International Track on Collaborative Modeling and Simulation CALL FOR PAPERS ################################################################# June 27 - June 29, 2011, Paris (France) http://www.sel.uniroma2.it/CoMetS11 ################################################################# # Papers Due: *** March 5, 2011 *** # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. ################################################################# Modeling and Simulation (M&S) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, M&S is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of M&S activities increases for the more complex models and for the communications among a wider number and variety of M&S stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of M&S activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among M&S stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to M&S activities, the track seeks innovative contributions that deal with the application of M&S practices to the design of collaborative environments. These environments are continuously becoming more complex and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. M&S offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non?exhaustive list of topics of interest includes: * collaborative environments for M&S * collaborative Systems of Systems M&S * workflow modelling for collaborative environments and processes * agent-based M&S * collaborative distributed simulation * collaborative component-based M&S * net-centric M&S * web-based M&S * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environments * domain specific languages for collaborative M&S * databases and repositories for M&S * distributed virtual environments * virtual research environment for M&S To stimulate creativity, however, the track maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and M&S. +++++++++++++++++++++++++++++++++++ On-Line Submissions and Publication +++++++++++++++++++++++++++++++++++ CoMetS'11 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the track research area. Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Accepted full papers will be included in the proceedings and published by the IEEE Computer Society Press (IEEE approval pending). Please note that at least one author for each accepted paper should register to attend WETICE 2011 to have the paper published in the proceedings. Authors may contact the organizers for expression of interests and content appropriateness at any time. Papers can be submitted in PDF format at the submission site (https://www.easychair.org/conferences/?conf=comets2011), which is supported by the EasyChair conference management system. Please contact the track chairs (comets2011 at easychair.org) if you experience problems with the EasyChair Web site. +++++++++++++++ Important Dates +++++++++++++++ * Submission Deadline: March 5, 2011 * Decision to paper authors: April 4, 2011 * Final version of accepted papers due to IEEE: April 29, 2011 * Conference dates: June 27 - June 29, 2011 ++++++++++++++++++++ Organizing Committee ++++++++++++++++++++ * Andrea D'Ambrogio, University of Roma TorVergata, Italy * Daniele Gianni, European Space Agency, The Netherlands * Joachim Fuchs, European Space Agency, The Netherlands * Giuseppe Iazeolla, University of Roma TorVergata, Italy +++++++++++++++++ Program Committee +++++++++++++++++ * Santiago Balestrini, Georgia Institute of Technology, USA * Torsten Bieler, European Space Agency, The Netherlands * Olivier Dalle, University of Nice Sophia Antipolis, CNRS & INRIA, France * Joseph Giampapa, SEI, Carnegie Mellon University, USA * Ralph Huntsinger, Beijng University of Aeronautics and Astronautics, China and California State University, USA * Axel Lehmann, Universitaet der Bundeswehr Muenchen, Germany * Cristiano Leorato, Rhea, The Netherlands * Brian Lewis, Vanguard Software Corporation, USA * Steve McKeever, University of Oxford, UK * David Nickerson, Auckland Bioengineering Institute, NZ * Alfred Park, IBM T.J. Watson Research Center, USA * Wolfgang Prinz, Fraunhofer FIT and RWTH Aachen, Germany * Jos? L. Risco-Martin, Universidad Complutense de Madrid, Spain * Maarten Sierhuis, NASA and Palo Alto Research Center, USA * Hans Vangheluwe, University of Antwerp, Belgium, and McGill University, Canada * Gabriel Wainer, Carleton University, Canada * Quirien Wijnands, European Space Agency, The Netherlands * Heming Zhang, Tsinghua University, China *** Contact Information *** Daniele Gianni (track co-chair) Email: daniele.gianni at esa.int From harry.mangalam at uci.edu Sun Jan 23 13:38:00 2011 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Sun, 23 Jan 2011 10:38:00 -0800 Subject: [BiO BB] (no subject) In-Reply-To: References: Message-ID: <201101231038.01256.harry.mangalam@uci.edu> Hi Amir, I don't want to dampen your enthusiasm for programming in this domain, but while there may be reason to do this, there are a number of such tools already extant that seem to have many more features already: - the ugene GUI tool is one - the webcutter web interface - NEB's own Web RE mapper - the EMBOSS RE modules - and even (immodestly, my own) tacg Many of these are open source and if you're interested in the field, you'd be welcome to use your talents to expand or enhance these existing tools rather than start yet another from scratch. If you want to remain programming in Python, the BioPython project would be happy to have your help to improve their modules and you would be in the company of some brilliant programmers who would be (mostly) happy to exchange their insights for some sweat equity. Just sayin... Best Harry On Friday 21 January 2011 07:10:50 amir chaouki wrote: > hello, i am a member in bioinformatics organisation and i > have created a new tool, named gCut, for restriction analysis > and i will appreciate if you can just check it and tell me > what you think about it, i have posted it in > bioinformatics.org but i just need some body with a lot of > experience in this field to tell me what he thinks about > this. you can find it in: gcut.sourceforge.net > please help me i will be grateful if you respond to this > message. thank you, tell me also what are the functionalities that > i can add in the future. > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine [ZOT 2225] / 92697 Google Voice Multiplexer: (949) 478-4487 MSTB=Bldg 415 (G-5 on Lat/Long: 33.642025,-117.844414 (paste into google maps) -- Like the autumn leaves / Our rights flutter to the ground / So too, our trousers. From cannataro at unicz.it Sun Jan 23 17:26:22 2011 From: cannataro at unicz.it (Mario Cannataro) Date: Sun, 23 Jan 2011 23:26:22 +0100 (CET) Subject: [BiO BB] Last CfP: 4th Workshop on Biomedical and Bioinformatics Challenges to Computer Science In-Reply-To: References: <503239aa165f7384cfd05fe975b6d169.squirrel@email.unicz.it> Message-ID: <8714cc3a577511f1aa9ad468b57a60fe.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. SUBMISSION DEADLINE EXTENDED TO JANUARY 31, 2011 ===================================================================== ICCS 2011 4th Workshop on Biomedical and Bioinformatics Challenges to Computer Science http://staff.icar.cnr.it/cannataro/iccs2011/ "The Ascent of Computational Excellence in the Land of the Rising Sun" Computational Science Tsukuba International Congress Center, Tsukuba Japan June 1 - June 3, 2011 http://www.iccs-meeting.org/ ===================================================================== * * * CALL FOR PAPERS - Submission Deadline January 31, 2011 * * * ===================================================================== CALL FOR PAPERS Bioinformatics is providing the foundation for fast and reliable data analysis. Genomics, interactomics, proteomics, epidemiological, clinical and text mining applications have made essential progress through using bioinformatics tools. Standard tools are usually offered through the Web. This is no longer sufficient with more complex analysis and simulation tasks from emerging research fields like systems biology, image analysis, biomedical applications or data management. In recent years Grid and Web services based approaches have been developed to face the new challenges. Moreover, emerging life sciences applications need to use in a coordinated way both bioinformatics tools, biological data banks, and patient?s clinical data, that requires seamless integration, privacy preservation and controlled sharing. This 4th Workshop on Biomedical and Bioinformatics Challenges to Computer Science will bring together scientists from computer and life sciences to discuss future directions of bioinformatics algorithms, applications, and data management. Questions to be looked at are whether wrapping existing algorithms as Grid or Web service will be sufficient to cope with the more complex applications and the increasing volume of data to be processed or which applications would profit from being redeveloped as native parallel or distributed application. Furthermore, the use of novel parallel architectures and dedicated hardware to implement bioinformatics and biomedical algorithms will be discussed. TOPICS OF INTEREST The workshop is seeking original research papers presenting innovative solutions from parallel, distributed and Grid computing applied to bioinformatics algorithms and life sciences applications. Specifically we are interested in the following topics: - sequence and structure bioinformatics - genomics, proteomics, interactomics - systems biology - biomedical image analysis - biomedical simulation - data management - data integration - data visualization - workflow modelling - distributed biomedical applications - high performance computing - dedicated hardware and architectures - parallelisation techniques - service orientation - volunteer computing - peer-to-peer computing PAPER SUBMISSION AND PUBLICATION The submitted paper must be camera-ready and formatted according to the rules of Procedia Computer Science. Please use this file for a Latex template plus instructions and click here for an MS word template file. Submission implies the willingness of at least one of the authors to register and present the paper. PostScript and source versions of your paper must be submitted electronically through the paper submission system. Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format. Dates of deadlines for draft paper submission (full paper), notification of acceptance, deadline for camera-ready paper submission and registration may be found in the Important Dates section of the ICCS Web site. Papers must be based on unpublished, mature and original work and must be submitted to ICCS only. After the conference, selected papers may be invited for a special issue of the Journal of Computational Science ICCS is an ERA 2010 A-ranked conference series. JOURNAL SPECIAL ISSUE After the workshop, selected papers may be invited for a special issue of the Journal of Computational Science. Selected papers (extended and revised version) accepted on the 1st edition of the workshop have been published on a special section of Future Generation Computer Systems, Elsevier. IMPORTANT DATES Full papers submission: January 31, 2011 (EXTENDED) Notification of acceptance: February 20, 2011 Camera ready papers: March 7, 2011 Early registration opens: February 15, 2011 Early registration closes: March 31, 2011 Conference sessions: June 1-3, 2011 WORKSHOP CO-ORGANIZERS Mario Cannataro, University Magna Graecia of Catanzaro, Italy Joakim Sundnes, Simula Research Laboratory, Norway Rodrigo Weber dos Santos, Federal University of Juiz de Fora, Brazil PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Dave Angulo, DePaul University, Chicago, USA 2. Rui Brito, University of Coimbra, Portugal 3. Tim Clark, Harvard Medical School, USA 4. Giuseppe Di Fatta, University of Reading, UK 5. Werner Dubitzky, University of Ulster, UK 6. Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI, Orsay, France 7. Alan Garny, University of Oxford, Department of Physiology, Anatomy & Genetics 8. Concettina Guerra, University of Padova, Italy 9. Pietro Hiram Guzzi, University Magna Graecia of Catanzaro, Italy 10. Ulrich Hansmann, Research Centre Juelich, Germany 11. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 12. Pilar Herrero, Universidad Polit?cnica de Madrid, Madrid, Spain 13. Ela Hunt, SystemsX.ch, ETHZ, Switzerland 14. Glenn Terje Lines, Simula Research Laboratory, Norway 15. Marcelo Lobosco, Federal University of Juiz de Fora, Brazil 16. Uko Maran, University of Tartu, Estonia 17. Wagner Meira Jr., Federal University of Minas Gerais, Brazil 18. Maria Mirto, University of Salento, Italy 19. Hartmut Mix, University of Technology Dresden, Germany 20. Salvatore Orlando, University of Venezia, Italy 21. Mar?a S. P?rez, Universidad Polit?cnica de Madrid, Madrid, Spain 22. Gernot Plank, University of Graz, Austria 23. Omer F. Rana, Cardiff University, UK 24. Blanca Rodriguez, University of Oxford, UK 25. Luis Paulo da Silva Barra, Federal University of Juiz de Fora, Brazil 26. Fabrizio Silvestri, ISTI-CNR, Italy 27. Raymond Spiteri, University of Saskatchewan, Canada 28. Roberto Tagliaferri, University of Salerno, Italy 29. El-Ghazali Talbi, Universit? des Sciences et Technologies de Lille, France 30. Paolo Trunfio, University of Calabria, Italy 31. Pierangelo Veltri, University Magna Graecia of Catanzaro, Italy 32. Edward J. Vigmond, University of Calgary, Canada 33. Albert Zomaya, University of Sydney, Australia From apico at gladstone.ucsf.edu Mon Jan 31 18:20:48 2011 From: apico at gladstone.ucsf.edu (Alexander Pico) Date: Mon, 31 Jan 2011 15:20:48 -0800 Subject: [BiO BB] Announcing: Network Biology SIG at ISMB 2011 in Vienna, July 16th Message-ID: Announcing: Network Biology SIG at ISMB 2011 in Vienna, July 16th The Network Biology (NetBio) SIG will focus on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology, synthetic biology and medicine. The meeting will provide a unique interface between tool developers and users in the field of network biology. Through these complementary lenses, the SIG will bring into focus the current state of the field, its future promise and how to get there. http://nrnb.org/netbiowiki == Keynote speakers == Trey Ideker, ?Rewiring of Genetic Networks by DNA Damage? ? ???University of California at San Diego Alfonso Valencia, ?Using and Completing Cancer Networks? ???Spanish National Cancer Research Centre Gary Bader ???University of Toronto TBA == Call for Abstracts == We invite abstracts for talks at one of the two main sessions: Tools & Resources or Applied Research. We are seeking a diversity of submissions to represent the breadth and depth of Network Biology. Find guidelines at http://nrnb.org/netbiowiki/Abstract_submission == Important Details == Date: July 16, 2010 Location: Vienna, Austria ISMB site: http://www.iscb.org/ismbeccb2011-program/satellite-meetings#network NetBio wiki: http://nrnb.org/netbiowiki Mailing list: http://groups.google.com/group/netbio Abstract submission: http://nrnb.org/netbiowiki/Abstract_submission == Important Dates == Feb 7: Open for submissions April 8: Abstract deadline April 29: Notification of accepted abstracts July 16: NetBio SIG 2011 See you there! NetBio Organizing Committee Alexander Pico (apico at gladstone.ucsf.edu), Scooter Morris, Allan Kuchinsky, Annette Adler, Gary Bader, Mario Albrecht, Diego di Bernardo, Ian Donaldson, Hana El-Samad From Gaurav.Pradhan at asu.edu Sun Jan 30 18:50:48 2011 From: Gaurav.Pradhan at asu.edu (Gaurav Pradhan) Date: Sun, 30 Jan 2011 16:50:48 -0700 Subject: [BiO BB] FW: CALL FOR PAPERS: 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) Message-ID: <277C1701239FAE41850579216CE41D79CE915D855F@EX11.asurite.ad.asu.edu> CALL FOR PAPERS 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) November 9-11, 2011 Miami, Florida, USA http://sites.google.com/site/web2011ihi/ (mirror site: http://www.comp.hkbu.edu.hk/ihi2011/) ABOUT THE CONFERENCE We cordially invite you to submit your contribution to the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011). IHI 2011 is the main conference of the newly formed ACM Special Interest Group on Health Informatics (SIGHIT). IHI 2011 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 2011 will feature keynotes, a multi-track technical program including papers, demonstrations, and panels. New additions to the IHI 2011 program include tutorials and a doctoral consortium. IHI 2011 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. CONFERENCE TOPICS Specific topics of interest for this conference cover various facets of health informatics research, including but not limited to the following: 1. Information technologies for healthcare delivery and management - Comparative effectiveness research - Consumer health and wellness informatics applications - E-commerce in health informatics - Economics of health computing (e.g., cost-benefit analysis) - E-learning for spreading health informatics awareness - Health informatics education - Healthcare delivery in developing countries - Healthcare workflow management - Information technologies for alternative medicine - Information technologies for healthcare service delivery - Information technologies for hospital management - Information technologies for the management of patient safety and clinical outcomes - Medical compliance automation for patients and institutions - Organizational impacts of health information technologies - Public health informatics - Social studies of health information technologies - Technology informatics guiding educational reform - Telecare - Telemedicine - Virtual conferencing systems for healthcare 2. Health data acquisition, management, and visualization - Continuous monitoring and streaming technologies for healthcare - Data model for health information system - Disease profiling and personalized treatment - Display and visualization of medical data - Intelligent medical devices and sensors - Medical data management - Medical signal acquisition, archiving, and communication - RFID solutions for healthcare - Technologies for capturing and documenting clinical encounter information in electronic systems - Virtual and augmented reality for healthcare - Virtual patients 3. Healthcare knowledge management and decision support - Business intelligence and data warehousing for healthcare - Cognitive and decision support systems - Computational intelligence methodologies for healthcare - Computational support for patient-centered and evidence-based care - Computer support for surgical intervention - Computer-aided diagnosis - Healthcare knowledge abstraction, classification, and summarization - Healthcare knowledge computerization, execution, inference, management, and representation - Medical recommender systems - Semantic Web, linked data, ontology, and healthcare 4. Healthcare modeling and simulation - Biomedical modeling and simulation - Disease diagnostic models - Disease prognostic models - Epidemiological modeling - Health risk evaluation and modeling - Operations research methods for healthcare - Optimization models for planning and recommending therapies - Personalized predictive modeling for clinical management (e.g., cancer, trauma, diabetes mellitus, sleep disorders, substance abuse) - Physiological modeling 5. Data analytics, data mining, and machine learning - Analytics for clinical care - Biomarker discovery and biomedical model development - Biomedical data mining - Biomedical pattern recognition - Cleaning, pre-processing, and ensuring quality and integrity of medical data - Data analytics for healthcare quality assurance - Healthcare workflow mining - Large-scale longitudinal mining of medical records - Medical insurance fraud detection - Medical signal analysis and processing - Natural language processing and text mining for biomedical literature, clinical notes, and health consumer texts - Statistics and quality of medical data - Survival analysis and health hazard evaluations - Visual analytics for healthcare 6. Health information system engineering - Acceptance testing for healthcare systems and applications - Cloud computing for healthcare - Database design for health information systems - Experiences of building health information systems - Health IT project management - Health software architecture, framework, design, and engineering - Health systems simulation - High-performance computing for healthcare - Multi-agent systems for healthcare - System integration for healthcare - Trustworthy and secure infrastructures for health information systems 7. Health information systems - Applications in electronic health records - Clinical information systems - Consumer and clinician health information needs, seeking, sharing, and use - Development and implementation of medical data and vocabulary standards - Evaluation of health information systems - E-visit system - Health digital library - Health information systems for chronic disease management - Information retrieval for health applications - Intelligent personal health records - Issues involving interoperability and data representation in healthcare delivery - Keyword and multifaceted search over structured electronic health records - Open-source software for healthcare - Pharmaco- and pharmacy informatics systems - Privacy in healthcare - Security in healthcare - System software for clinical studies and translational research 8. Healthcare communication networks and environments - Assistive and adaptive ubiquitous computing technologies for healthcare - Collaboration technologies for healthcare - Computer games for healthcare - E-communities, social networks, and social media for patients and caregivers - Health portals - Healthcare communication system performance and adaptability - Peer-to-peer networks for healthcare - Sensor networks and systems for pervasive healthcare - Social media analysis and mining for healthcare applications 9. Interactions with health information technologies - Accessibility and Web-enabled technologies for healthcare - Affective computing for healthcare - Automated generation of textual document and multimedia content for healthcare - Biological effects of medical devices - Bio-surveillance - Communication interventions between patients and care providers - Consumer health literacy, numeracy, and graphicacy - Human factors (ergonomics) in health information systems - Medical biometrics - Medical robotics - Physiological computing (e.g., brain computer interface) - Speech, gesture, and handwriting acquisition and recognition for healthcare - Usability studies in healthcare - User-interface design for medical devices and health software 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 best papers of IHI 2011 will also be considered for journal publication in a special issue of the ACM Transactions on Intelligent Systems and Technology (TIST). IHI 2011 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. The conference organizers will work on ensuring that poster sessions are well attended and have a vibrant discussion environment. 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 track (analytics, systems, or human factors) - 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) REVIEWING Each contribution will be carefully evaluated by a group 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 health 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. IMPORTANT DATES Abstract submission deadline: May 23, 2011 11:59pm EST Paper submission deadline: May 30, 2011 11:59pm EST Notification of acceptance: August 1, 2011 11:59pm EST Camera-ready copy due: August 30, 2011 11:59pm EST CONFERENCE ORGANIZERS General Chairs (contact email: 2011.ihi at gmail.com) Jiming Liu, Hong Kong Baptist University Sanjay Ranka, University of Florida Program Committee Co-Chairs (contact email: 2011.ihi at gmail.com) Katie A. Siek, University of Colorado at Boulder (human factors track) Annie Lau, University of New South Wales, Australia (human factors track) Christopher C. Yang, Drexel University (systems track) Albert M. Lai, Ohio State University (systems track) Shusaku Tsumoto, Shimane University, Japan (analytics track) Aur?lie N?v?ol, National Library of Medicine/NCBI (analytics track) Steering Committee Members Henrique Andrade, Goldman Sachs Umit Catalyurek, Ohio State University Michael D. Larsen, George Washington University Ching-Yung Lin, IBM Research Gang Luo, IBM Research (SIGHIT chair) Andrew Sears, UMBC Neil R. Smalheiser, University of Illinois - Chicago Chunqiang Tang, IBM Research Olivier Verscheure, IBM Research Michael Weiner, Indiana University Osmar R. Zaiane, University of Alberta, Canada Program Committee Members Listed on the conference web site _________________________________________________________________________________________ CALL FOR DEMOS 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) November 9-11, 2011 Miami, Florida, USA http://sites.google.com/site/web2011ihi/ (mirror site: http://www.comp.hkbu.edu.hk/ihi2011/) SCOPE OF THE DEMO TRACK We cordially invite you to submit your contribution to the demo track of the 2011 ACM SIGHIT International Health Informatics Symposium (IHI 2011). The IHI demo track is an exciting and highly interactive way to demonstrate your health informatics system or application. Because of IHI's focus on end-to-end systems, whereby applied informatics is used to address the needs of health and healthcare applications, demos of innovative systems are solicited, which illustrate practical research or engineering contributions in an interesting and interactive manner. The demo program will be featured prominently in the conference program and should be seen as a vehicle for researchers, practitioners, and commercial/industrial/non-profit institutions to showcase innovative new technologies or applications in health informatics. The demo review process will look for practical uses of technology and also for a "wow" factor in all submissions. We encourage the description of prototypes as long as they clearly present a coherent, end-to-end view of what the application might become once it gets deployed in production. 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. First, it should clearly describe the overall architecture of the system or technology demonstrated. Second, 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. Third, 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. For demos running over the web, a back-up scenario should be described, in case connectivity is limited at the demo venue. All topics described in the Call for Papers are eligible for demo track submissions. WHAT SHOULD BE SUBMITTED All aspects of the submission and notification process will be handled electronically. Submissions must adhere to the following guidelines: " The author(s) name and affiliation(s) must be present in the submitted document. Any submitted demo proposal violating the length, file type, or formatting requirements will be rejected without review. " 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 is 4 pages. This page limit includes all parts of the proposal: title, abstract, body, and bibliography. " 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) The optional demo video should focus on illustrating the demo scenario and the interactive nature of the demo system. The video must be no more than three minutes in length and should start by clearly identifying the authors and title of the proposal. The video should be in common video format (e.g., MPEG, AVI), and should be playable on a wide variety of media players. We strongly encourage authors to produce and submit a demo video that will be linked off of the final program on the conference website (e.g., YouTube, Vimeo). 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. Note that all deadlines are the same as for regular paper submissions. IMPORTANT DATES Demo paper submission deadline: May 30, 2011 11:59pm EST Notification of acceptance: August 1, 2011 11:59pm EST Camera-ready copy due: August 30, 2011 11:59pm EST _________________________________________________________________________________________ CALL FOR DOCTORAL CONSORTIUM SUBMISSIONS 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) November 9-11, 2011 Miami, Florida, USA http://sites.google.com/site/web2011ihi/ (mirror site: http://www.comp.hkbu.edu.hk/ihi2011/) SCOPE OF THE DOCTORAL CONSORTIUM We cordially invite doctoral students to submit their extended abstracts to, and participate in, the doctoral consortium of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011). The doctorial consortium is expected to offer a supportive learning opportunity for doctoral students in the early stage of their research on health informatics related problems to discuss their work in progress and to receive feedback and guidance from the IHI audience 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 topics described in the Call for Papers are eligible for extended abstract submissions. SUBMISSION PROCESS Each extended abstract should be 2-page in length, containing title, motivation, problem statement, proposed methodology, progress/results so far, outstanding issues, and related work and references. Submissions 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: " Submissions 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 extended abstract must be submitted as a single PDF file, formatted for 8.5" x 11" paper. " Submissions should not list keywords, general terms, and categories and subject descriptions. In addition, submissions should not have the copyright notice located at the bottom of the left column of the first page of the ACM Proceedings template. 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. IMPORTANT DATES Doctoral consortium submission deadline: May 30, 2011 11:59pm EST Notification of acceptance: August 1, 2011 11:59pm EST Camera-ready copy due: August 30, 2011 11:59pm EST _________________________________________________________________________________________ CALL FOR PANEL PROPOSALS 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) November 9-11, 2011 Miami, Florida, USA http://sites.google.com/site/web2011ihi/ (mirror site: http://www.comp.hkbu.edu.hk/ihi2011/) SCOPE OF PANEL PROPOSALS We cordially invite you to submit your panel proposal to the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011). Panel proposals are expected to address new, exciting, and controversial issues on computing-oriented health informatics and appeal to IHI 2011 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. SUBMISSION PROCESS Each panel proposal should have two parts: " Part 1: A 1-page extended abstract that includes: the title of the panel, the names and affiliations of the panelists and the chair, a description of the topic and what insights the audience will gain by attending the panel, and short biographies of the panelists. This extended abstract will appear in the conference proceedings. " Part 2: A session proposal that is at most 4 pages long and includes: a. The main topics to be discussed/debated during the panel session; b. A description of the presentation of each panelist; c. The panel format with an emphasis on how interactivity will be integrated into the panel (e.g., question and answer session; voting); d. More information on the panelists and the chair (e.g., biographies/awards/home page); e. Any other information that will assist the PC Co-Chairs and Conference Leadership to adequately review the panel proposal. All aspects of the submission and notification process will be handled electronically. Submissions must adhere to the following formatting instructions: " Submissions 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 panel proposal must be submitted as a single PDF file, formatted for 8.5" x 11" paper. " Submissions should not list keywords, general terms, and categories and subject descriptions. In addition, submissions should not have the copyright notice located at the bottom of the left column of the first page of the ACM Proceedings template. " Each accepted panel will appear in the conference proceedings as a 1-page extended abstract. 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. IMPORTANT DATES Panel proposal submission deadline: May 30, 2011 11:59pm EST Notification of acceptance: August 1, 2011 11:59pm EST Camera-ready copy due: August 30, 2011 11:59pm EST _________________________________________________________________________________________ CALL FOR TUTORIAL PROPOSALS 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) November 9-11, 2011 Miami, Florida, USA http://sites.google.com/site/web2011ihi/ (mirror site: http://www.comp.hkbu.edu.hk/ihi2011/) SCOPE OF TUTORIAL PROPOSALS We cordially invite you to submit your tutorial proposal to the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011). Tutorials at IHI 2011 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 2011 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 2011 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. SUBMISSION PROCESS Each tutorial proposal should have two parts: " Part 1: A 1-page extended abstract that includes: the title of the tutorial, the name and affiliation of the instructor(s), a description of the tutorial scope, the intended audience, and what new knowledge and perspectives the audience will gain by attending the tutorial, and a short biography of the instructor(s). This extended abstract will appear in the conference proceedings. " Part 2: A full tutorial proposal that is at most 4 pages long and includes: a. A description of the main topics to be covered during the tutorial; b. Targeted audience and aims/objectives; c. If relevant, a description of real-world systems, experiences, and/or case studies to be discussed; d. More information on the instructor (e.g., biography/awards/home page); e. Any other information (e.g., previous tutorials given) that will assist the PC Co-Chairs and Conference Leadership to adequately review the tutorial proposal. All aspects of the submission and notification process will be handled electronically. Submissions must adhere to the following formatting instructions: " Submissions 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 tutorial proposal must be submitted as a single PDF file, formatted for 8.5" x 11" paper. " Submissions should not list keywords, general terms, and categories and subject descriptions. In addition, submissions should not have the copyright notice located at the bottom of the left column of the first page of the ACM Proceedings template. " Each accepted tutorial will appear in the conference proceedings as a 1-page extended abstract. 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. IMPORTANT DATES Tutorial proposal submission deadline: May 30, 2011 11:59pm EST Notification of acceptance: August 1, 2011 11:59pm EST Camera-ready copy due: August 30, 2011 11:59pm EST _________________________________________________________________________________________ CALL FOR NON-REFEREED EXTENDED ABSTRACTS 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011) November 9-11, 2011 Miami, Florida, USA http://sites.google.com/site/web2011ihi/ (mirror site: http://www.comp.hkbu.edu.hk/ihi2011/) SCOPE OF THE NON-REFEREED EXTENDED ABSTRACT TRACK We cordially invite you to submit your contribution to the non-refereed extended abstract track of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011). 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. All topics described in the Call for Papers are eligible for extended abstract submissions. SUBMISSION PROCESS Each extended abstract should be 1 page in length. Submissions 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: " Submissions 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 extended abstract must be submitted as a single PDF file, formatted for 8.5" x 11" paper. " Submissions should not list keywords, general terms, and categories and subject descriptions. In addition, submissions should not have the copyright notice located at the bottom of the left column of the first page of the ACM Proceedings template. The conference organizers will work on ensuring that poster sessions are well attended and have a vibrant discussion environment. Although the non-refereed extended abstract submissions will not be formally reviewed, the IHI 2011 conference organizers will read all of the submissions to ensure every accepted submission is appropriate for IHI. IMPORTANT DATES Extended abstract submission deadline: August 8, 2011 11:59pm EST Notification of acceptance: August 15, 2011 11:59pm EST Camera-ready copy due: August 30, 2011 11:59pm EST