From apico at gladstone.ucsf.edu Mon Apr 1 17:12:24 2013 From: apico at gladstone.ucsf.edu (Alexander Pico) Date: Mon, 1 Apr 2013 14:12:24 -0700 Subject: [BiO BB] Call for Abstracts: NetBio SIG at ISMB 2013: DUE APRIL 22ND Message-ID: <9A57DB52-18CF-4C4C-92D1-EB3D86291A4C@gladstone.ucsf.edu> Network Biology SIG at ISMB 2013 in Berlin, Germany, July 19th The Network Biology 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/netbiosig Call for Abstracts We invite abstracts for talks and posters We are seeking a diversity of submissions to represent the breadth and depth of the Network Biology field. Find guidelines at http://nrnb.org/netbiosig Keynote Speakers Natasa Przulj - Computational Systems Biology - Imperial College London, UK Esti Yeger-Lotem - Network Biology of Human Disease - Ben-Gurion University of the Negev, Israel Michael Schroeder - Drug Repositioning with Networks - Biotechnology Center, TU Desden, Germany Benno Schwikowski - Network Inference, CYNI - Pasteur Institute, France Important Dates April 22: Abstract submission deadline May 13: Notification of accepted abstracts June 7: Early registration deadline July 19: NetBio SIG 2013 July 21-23: ISMB 2013 See you there! NetBio SIG Organizing Committee Alexander Pico (apico at gladstone.ucsf.edu), Scooter Morris, Allan Kuchinsky, Gary Bader, Mario Albrecht, Natasa Przulj, Esti Yeger-Lotem, Igor Jurisica From pandey.gaurav at gmail.com Mon Apr 1 15:01:52 2013 From: pandey.gaurav at gmail.com (Gaurav Pandey) Date: Mon, 1 Apr 2013 15:01:52 -0400 Subject: [BiO BB] CFP: 12th International Workshop on Data Mining in Bioinformatics (BIOKDD '13) Message-ID: Dear Colleagues, We welcome your excellent submissions to the BIOKDD 2013 workshop to be held in Chicago, IL along with ACM SIGKDD 2013. Link: http://home.biokdd.org/biokdd13/ The goal of this workshop is to encourage data mining and other researchers to take on the numerous challenges that Bioinformatics offers. This year, the workshop will feature the theme of*Building network and predictive models of biological processes and diseases using complex data*. This field focuses on the use of computational approaches, especially from data mining and machine learning, and the large amount and variety of biological data being generated. The goal here is to build accurate predictive or descriptive network models of biological processes and diseases. These approaches have revolutionized the new age biology by enabling novel discoveries in basic biology and diseases like cancer and diabetes, as well as the development of therapeutics. We encourage papers that propose novel data mining techniques for areas including but not limited to: - Building predictive models for complex phenotypes from large-scale biological data - Discovering biological networks and pathways underlying biological processes and diseases - Processing of new/next-generation sequencing (NGS) data for genome structural variation analysis, discovery of biomarkers and mutations, and disease risk assessment - Discovery of genotype-phenotype associations - Novel methods and frameworks for mining and integrating big biological data - Comparative genomics - Metagenome analysis using sequencing data - RNA-seq and microarray-based gene expression analysis - Genome-wide analysis of non-coding RNAs - Genome-wide regulatory motif discovery - Structural bioinformatics - Correlating NGS with proteomics data analysis - Functional annotation of genes and proteins - Chemo-informatics: Drug discovery, Virtual screening and Combinatorial chemistry - Knowledge discovery in clinical data and electronic medical records - Special biological data management techniques - Information visualization techniques for biological data - Semantic webs and ontology-driven biological data integration methods - Privacy and security issues in mining genomic and health databases Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides. Paper should be submitted in PDF format through CMT at the following link: https://cmt.research.microsoft.com/BIOKDD2013 Dates: 5/10/2013 Paper Submission Due 6/7/2013 Notification of Acceptance 6/17/2013 Camera-ready Paper Due 8/11/2013 Workshop Presentation On Behalf of BioKDD 2013 PC Chairs - Gaurav, Huzefa & George -- Gaurav Pandey, Ph.D. Assistant Professor Institute for Genomics and Multiscale Biology Department of Genetics and Genomic Sciences Mount Sinai School of Medicine, New York City http://www.mssm.edu/profiles/gaurav-pandey From clements at galaxyproject.org Tue Apr 9 02:45:50 2013 From: clements at galaxyproject.org (Dave Clements) Date: Tue, 9 Apr 2013 07:45:50 +0100 Subject: [BiO BB] Fwd: GCC2013 Talk Abstract Submission closes this Friday In-Reply-To: References: Message-ID: Hello all, This is a final reminder that the *deadline for submitting an oral presentation abstract for the 2013 Galaxy Community Conference is this 12 April, this Friday*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. And in case you missed the announcement about GIgaScience and GCC2013 talks: We are pleased to announce that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience * and that BGIwill generously cover the article processing fees for these articles. See the announcement for details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration > and paper and poster abstract submission are > now open for the 2013 Galaxy Community Conference (GCC2013) > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo . > > GCC2013 is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day + > main meeting) starting at ~ ?95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee > > PS: And please help get the word out > ! > -- > http://galaxyproject.org/GCC2013 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > From jlloret at dcom.upv.es Mon Apr 8 17:21:26 2013 From: jlloret at dcom.upv.es (Jaime Lloret Mauri) Date: Mon, 8 Apr 2013 23:21:26 +0200 Subject: [BiO BB] CFP: IEEE HEALTHCOM 2013, Lisbon, Portugal October 09-12, 2013 Message-ID: <201304082121.r38LLQsP004061@smtp.upv.es> CALL FOR PAPERS 15th IEEE International Conference on e-Health Networking, Application & Services (IEEE HEALTHCOM 2013) Lisbon, Portugal ? October 09-12, 2013 http://www.ieee-healthcom.org IEEE Healthcom 2013 is fully sponsored by the IEEE Communications Society. It aims at bringing together interested parties from around the world working in the health care field to exchange ideas, to discuss innovative and emerging solutions, and to develop collaborations. eHealth is defined as the cost-effective and secure use of information and communications technologies in support of health and the related fields, including health-care related services, surveillance, literature, education, knowledge, and research, both at the local site and at a distance. It will make personalised medicine possible and affordable in the near future. The adoption of eHealth technologies in medical fields creates huge opportunities yet lots of challenges still need to be resolved to build reliable, secure, and efficient networks or platforms with great flexibility. Prospective authors are cordially invited to submit their original contributions covering completed or ongoing work related to the eHealth area. The topics include but are not limited to - Biomedical and biosensors engineering - Body sensor networks and wearable sensor systems - Clinical biofeedback, decision support systems, and tools - eHealth information and network Infrastructure - eHealth for public health (including disease prevention, emergency preparedness, epidemiologic interventions) - eHealth for aging (to support quality of life for older adults, aging in place and independence) - Emerging eHealth applications - Health grid and health cloud - Health monitoring, traffic characterisation, & management - ICT-enabled personal health system - Image and video processing on eHealth - Network/Communications Infrastructures and Architectures for Healthcare - New IT-enhanced Models for Healthcare delivery - Pervasive and ubiquitous computing on eHealth - Practical Applications of e-Health - Security and privacy on eHealth - Storage and Display Devices for eHealth - Telemedicine and mobile telemedicine Important dates - Paper Submission: April 30, 2013 - Notification of acceptance: June 30, 2013 - Submission of camera-ready papers: August 31, 2013 PAPER SUBMISSION Perspective authors are invited to submit their papers using EDAS System at http://edas.info/newPaper.php?c=13601&track=26533. A full paper should not have more than five (5) IEEE style pages including results, figures and references. Papers will be reviewed with the standard reviewing procedure (with at least 3 independent anonymous reviews). Accepted papers will be published on IEEExplore (http://ieeexplore.ieee.org/). The best accepted paper will receive the Best Paper Award. Extended version of best papers will be considered for publication on the International Journal on E-Health and Medical Communications (http://www.igi-global.com/IJEHMC) and in the Elsevier IRBM (http://www.elsevier.com/journals/irbm/1959-0318). Note: To be published in the IEEE Healthcom 2013 Conference Proceedings and IEEEXplore, an author of an accepted paper is required to register for the conference at the full (member or non-member) rate and present the paper at the conference. General Chair: Joel Rodrigues, Institute for Telecommunications/ University of Beira Interior, Portugal TPC Chairs: Ricardo Correia, Fac. Medicine, Univ. Porto, Portugal Christos Verikoukis, CTTC, Barcelona, Spain Operations Chairs: Maria Helena Monteiro, ISCSP, Tech. Univ. Lisbon, Portugal Rita Amorim, ISCSP, Tech. Univ. Lisbon, Portugal IEEE HEALTHCOM Steering Committee: Joel Rodrigues (Chair), IT/Univ. of Beira Interior, Portugal Tsong-Ho Wu, Industrial Tech. Research Inst., Taiwan Pradeep Ray, Univ. of New South Wales, Australia Norbert Noury, University of Lyon, France Chi-Ren Shyu, Univ. Missouri, Columbia, MO, USA Portuguese Government Liaison: Henrique Martins, Clinical Information Coordinator, Portugal Industry and Exhibition Chair: Rui Gomes, Fernando Fonseca Hospital, Portugal Industry Forum Chair: Miguel Sales Dias, Microsoft Workshop Chairs: Jos? Neuman de Souza, Federal University of Cear?, Brazil Rui Rijo, Polytechnic Inst. of Leiria, Portugal Tutorial Chairs: Jorge S? Silva, University of Coimbra, Portugal Jos? Carlos Nascimento, University of Minho, Portugal Panel Chair: Eric Addeo, DeVry University, USA Publicity chairs: Jaime Lloret, Univ. Polit?cnica de Valencia, Spain Lei Shu, Guangdong Univ. Petroc. Tech., China Aravind Kailas, Univ. North Carolina Charlotte, USA Scott Fowler, Link?ping University, Sweden Communication Chair: Francisco Roxo, Catholic Univ. of Lisbon, Portugal Web Chair: Vasco Soares, Inst. for Telecom./ IPCB, Portugal From symposium at iscbsc.org Fri Apr 12 08:34:32 2013 From: symposium at iscbsc.org (ISCB Student Council Symposium) Date: Fri, 12 Apr 2013 14:34:32 +0200 Subject: [BiO BB] ISCB SCS 2013 second call for abstracts / Arts & Science exhibition 2013 call for submissions Message-ID: <5167FF58.8030508@iscbsc.org> Dear students and young researchers, The ISMB/ECCB 2013 Conference is just a few months away and the opportunities to participate beyond attending are closing soon. The Student Council Symposium and the Art & Science Exhibition are highlighted below. ****************** _ISCB Student Council Symposium 2013_ *The ISCB Student Council Symposium will be held on July 19th (directly preceding ISMB/ECCB 2013) in Berlin, Germany.* *UPCOMING ABSTRACT SUBMISSIONS DEADLINE: Tuesday, April 16th* The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants have the opportunity to present their work to an international audience, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. We encourage you to submit an abstract and to bring a poster for showcasing your work at the Symposium's poster session. As a central part of the Symposium, ten abstracts will be selected for an oral presentation. We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel fellowships will be available for accepted abstracts, and awards will be given to best posters and presentations. *LINKS* _Symposium website_: http://symposium.iscbsc.org/ _Submission link_: http://www.iscb.org/submissions/index.php?id=156 _Travel Fellowships information_: http://symposium.iscbsc.org/content/travel-fellowships *IMPORTANT DATES* April 16: Abstract submission deadline April 26: Travel Fellowship submission deadline April 30: Abstract acceptance notifications May 14: Travel fellowship acceptance notifications July 19th: Student Council Symposium 2013 ****************** _Art & Science Exhibition_ ISMB/ECCB brings together scientists from a wide range of disciplines, including biology, medicine, computer science, mathematics and statistics. In these fields we are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, and visual aids for problem-solving are omnipresent. For the ISMB/ECCB 2013 Art & Science Exhibition the organizers invite all interested conference attendees to submit such images and videos that have been generated as part of a research project. They are also soliciting images and videos resulting from creative efforts that involve scientific concepts or employ scientific tools and methods. All cover images produced by researchers for scientific journals are welcome as well. A cash award may be given for the winning image as voted by conference attendees. *LINKS* _Website_: https://www.iscb.org/ismbeccb2013-submission/ismbeccb2013-artandscienceexhibition _Submissions link_: http://www.iscb.org/submissions/index.php?id=149 *IMPORTANT DATES* May 13: Submissions deadline ****************** We look forward to receiving your submissions! Tom?s Di Domenico (Chair, SCS2013) Milana Frenkel-Morgenstern (Chair, Art & Science Exhibition 2013) From camda at bioinf.jku.at Fri Apr 19 18:05:19 2013 From: camda at bioinf.jku.at (CAMDA 2013) Date: Sat, 20 Apr 2013 00:05:19 +0200 Subject: [BiO BB] CfP: CAMDA 2013 - 12th International Conference on Critical Assessment of Massive Data Analysis Message-ID: Critical Assessment of Massive Data Analysis (CAMDA2013) An ISMB/ECCB Satellite Meeting, July 19-20, 2013 http://www.camda.info CAMDA focuses on innovative methods to analyze massive data sets from life sciences. Over two days, researchers from bioinformatics, computer sciences, statistics, genetics, molecular biology, and other fields present novel approaches to analyze Big Data. Extracting usable knowledge from Big Data is an extremely pressing topic which requires advanced data mining, machine learning, statistical, and data management techniques that are presented at CAMDA. An essential part of CAMDA is its competitive challenge on big heterogeneous data sets. Academic and industrial researchers worldwide are invited to take the CAMDA challenge, to show their expertise analyzing Big Data. The challenge includes the analysis of a large toxicogenomic and genetic data obtained by Next Generation Sequencing (NGS). Relevant tasks for the toxicogenomics data include, but are not limited to, feature selection, classification, regression, and clustering. To facilitate the data handling, we provide the data set in several formats e.g., CSV and LIBSVM, which are ready to use e.g., for binary classification. Relevant tasks for the NGS data set, include, but are not limited to, variant detection, identical by descent detection, structural variants detection, and population genetics. We provide preprocessed NGS data in VCF format, even merged with data from other populations. The conference consists of keynotes, oral presentations, and a poster session where participants can present their work. As in last years, the prestigious CAMDA prize will be awarded for the best presentation. The contest presentations are complemented by high profile keynotes from: - Atul Butte, Stanford University School of Medicine, CA, USA - Nikolaus Rajewsky, Max-Delbr?ck-Center for Molecular Medicine, Berlin, Germany - Jun Wang, Beijing Genomics Institute (BGI), Shenzhen, China SUBMISSION INFORMATION We solicit submissions, which should include key results, figures, and tables. For original research papers the length of the extended abstract is limited to five pages (12pt Times Roman). Longer submissions cannot be considered. Abstracts must include the title, authors, affiliations, and contact email addresses. The name of the presenting author should be underlined. Abstracts should be submitted electronically as PDF or Microsoft Word online at: https://www.easychair.org/conferences/?conf=camda2013 All accepted abstracts will be published in the conference abstract book. Submission selected for oral presentation will be peer-reviewed and published as full text manuscripts in the CAMDA Proceedings as an open access PubMed indexed special issue of Systems Biomedicine (ISSN:2162-8130). IMPORTANT DATES - Abstract submission deadline for oral presentation / 20 May 2013 - Abstract submission deadline for poster presentation / 25 May 2013 - Notification of accepted contributions / 30 May 2013 - Early registration closes / 1 June 2013 - CAMDA Conference / 19?20 July 2013 - ISMB/ECCB Conference / 21?23 July 2013 - Full paper submission / 25 August 2013 You find additional information about the challenge data sets, submissions, etc. at the conference website: http://www.camda.info We look forward to seeing you in Berlin! The organizers and chairs of CAMDA 2013 12th International Conference on Critical Assessment of Massive Data Analysis Berlin, Germany, July 19-20, 2013 http://www.camda.info camda at bioinf.jku.at From cannataro at unicz.it Fri Apr 19 16:51:29 2013 From: cannataro at unicz.it (Mario Cannataro) Date: Fri, 19 Apr 2013 22:51:29 +0200 (CEST) Subject: [BiO BB] Euro-Par 2013 - 4th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB) In-Reply-To: <8e6a0eaa020399bfb82507040c017757.squirrel@email.unicz.it> References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> <057ca61063d2df86dbfedb3f33fe06f8.squirrel@email.unicz.it> <29b4f0ef371de5adb52505f83a1d153a.squirrel@email.unicz.it> <8a9b80c485a3eac1ad09c3134eb1841d.squirrel@email.unicz.it> <5ef1e4bd7aebe7bd69da47a45ee9d058.squirrel@email.unicz.it> <8e6a0eaa020399bfb82507040c017757.squirrel@email.unicz.it> Message-ID: <5841aa156eb8a359174b4b409bd82f18.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== 4th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB) http://staff.icar.cnr.it/cannataro/hibb2013/ held in conjunction with Euro-Par 2013 Aachen, Germany August 26-30, 2013 http://www.europar2013.org ===================================================================== * * * CALL FOR PAPERS * * * ===================================================================== High-throughput technologies (e.g. microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging) are producing an increasing amount of experimental and clinical data. In such a scenario, large-scale databases and bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine. High-performance computing may play an important role in many phases of life sciences research, from raw data management and processing, to data analysis and integration, till data exploration and visualization. In particular, at the raw data layer, Grid infrastructures may offer the huge data storage needed to store experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data. At an higher layer, emerging biomedical applications need to use in a coordinated way both bioinformatics tools, biological data banks and patient?s clinical data, that require seamless integration, privacy preservation and controlled sharing. Service Oriented Architectures and semantic technologies, such as ontologies, may allow the building and deployment of the so-called "collaboratories" where remote scientists may conduct experimental research in a collaborative way. The goal of HiBB is to bring together scientists in the fields of high performance computing, computational biology and medicine to discuss, among the others, the organization of large-scale biological and biomedical databases and the parallel implementation of bioinformatics algorithms and biomedical applications. 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 applications of parallel and high performance computing to biology and medicine. Topics of interest include, but are not limited to: - Large scale biological and biomedical databases - Data integration and ontologies in biology and medicine - Parallel bioinformatics algorithms - Parallel visualization and exploration of biomedical data - Parallel visualization and analysis of biomedical images - Computing environments for large scale collaboration - Scientific workflows in bioinformatics and biomedicine - (Web) Services for bioinformatics and biomedicine - Grid Computing for bioinformatics and biomedicine - Peer-To-Peer Computing for bioinformatics and biomedicine - Emerging architectures and programming models (e.g. Cell, GPUs) for bioinformatics and biomedicine - Parallel processing of bio-signals - Modeling and simulation of complex biological processes PROGRAM The workshop will take place on August 26 or 27, 2013 (To Be Announced). It is scheduled as half-day. The program is not available yet. PAPER SUBMISSION, REGISTRATION AND PUBLICATION We invite original previously unpublished contributions. Submission implies that at least one author will register for the workshops at Euro-Par 2013 and present the paper in the workshop session, if accepted. Full papers should not exceed 10 pages in the Springer LNCS style (http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0). Download LNCS Latex style here (ftp://ftp.springer.de/pub/tex/latex/llncs/latex2e/llncs2e.zip). Springer's author guidelines are available here. Paper submission has to be performed by using the HiBB-2013 EasyChair submission server (https://www.easychair.org/conferences/?conf=hibb2013). In case of problems, authors may send their manuscript in PDF to the workshop chair: cannataro AT unicz.it. Papers accepted for publication must also be supplied in source form (Latex or Word). All accepted and presented papers will be included in the Workshops proceedings that will be published in a separate Springer LNCS Euro-Par 2013 Workshop volume after the conference. Authors of accepted papers will be required to sign up a Springer copyright form. JOURNAL SPECIAL ISSUE At the end of the workshop, we plan to invite the best 4-6 papers of the workshop for a special section on an international journal. IMPORTANT DATES Workshop papers due: May 31, 2013 Workshop author notification: July 8, 2013 Revised papers to be distributed at the workshop due: July 29, 2013 Workshop session: August 26 or 27, 2013 Important dates for EuroPar Workshop Proceedings preparation Workshop camera-ready papers for Euro-Par Workshop Proceedings due: October 3, 2013 WORKSHOP ORGANIZER Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA 2. David A. Bader, College of Computing, Georgia University of Technology, USA 3. Ignacio Blanquer; Universidad Politecnica de Valencia, Valencia, Spain 4. Daniela Calvetti, Case Western Reserve University, USA 5. Werner Dubitzky, University of Ulster, UK 6. Ananth Y. Grama, Purdue University, USA 7. Concettina Guerra, University of Padova, Italy 8. Vicente Hernandez, Univ. Politecnica de Valencia, Spain 9. Salvatore Orlando, University of Venezia, Italy 10. Horacio Perez-Sanchez, University of Murcia, Spain 11. Omer F. Rana, Cardiff University, UK 12. Richard Sinnott; National e-Science Centre, University of Glasgow, Glasgow, United Kingdom 13. Fabrizio Silvestri, ISTI-CNR, Italy 14. Erkki Somersalo, Case Western Reserve University, USA 15. Paolo Trunfio, University of Calabria, Italy 16. Albert Zomaya, University of Sydney, Australia From djwild at indiana.edu Wed Apr 24 14:09:43 2013 From: djwild at indiana.edu (David Wild) Date: Wed, 24 Apr 2013 14:09:43 -0400 Subject: [BiO BB] New Version 2.0 of Introducing Cheminformatics eBook available Message-ID: I just wanted to let everyone know that a new version 2.0 of the *Introducing Cheminformatics: An Intensive Self-Study Guide* PDF eBook is available The new version contains numerous minor updates, replacement of outdated URL's, and a new section on MOOCs and other online learning resources related to cheminformatics. Those who have already purchased the guide can receive a free update to the new version by sending me a copy of their original version by email to djwild at indiana.edu. I will endeavor to reply within a couple of days with a PDF of the new version. For those who do not already have the eBook, it is available on the Lulu store at http://www.lulu.com/shop/search.ep?contributorId=1065081 The eBook is in the form of a regular (unprotected) PDF, and is available in three versions - an individual version (for personal use), an academic library version (licensed for use in an academic institution) and a corporate version (licensed for use throughout a corporation). The guide gives an intensive introduction to cheminformatics, based on materials used in the Indiana University curriculum, including the history of the field, representing 2D and 3D chemical structures on computer, storing and using databases of chemical and related biological information, handling chemical information on the web and in the scholarly literature, and giving an overview of some advanced topics such as use of cheminformatics in chemistry libraries, clustering and diversity, QSAR and predictive modeling, 3D alignment and docking, and software toolkits cheminformatics software. It is split into 13 lessons, each focusing on a particular area of cheminformatics. Each lesson details learning objectives and concludes with a set of questions that are designed to be thought provoking, with responses and answers in a final chapter. The text is hyperlinked to current resources on the web, with references to pertinent external articles where appropriate. The eBook is designed for computing, biology, bioinformatics, chemistry, library science and other students needing an introduction to the field, and also would be suitable for professional life science or computing practitioners who need a rapid, flexible introduction to cheminformatics. Please let me know if you have questions about the new version David _____________________________________________ Dr. David J. Wild, djwild at indiana.edu, Associate Professor Indiana University School of Informatics & Computing More about me: http://about.me/djwild | Research homepage: http://djwild.info Cheminformatics eBook: http://www.lulu.com/shop/search.ep?contributorId=1065081 Data2Discovery: http://d2discovery.com Mail: 901 E 10th St Rm 207, Bloomington, IN 47408 Phone: +1 812 856 1848 From cannataro at unicz.it Sat Apr 27 11:52:55 2013 From: cannataro at unicz.it (Mario Cannataro) Date: Sat, 27 Apr 2013 17:52:55 +0200 (CEST) Subject: [BiO BB] ACM-BCB 2nd Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio) In-Reply-To: <8e6a0eaa020399bfb82507040c017757.squirrel@email.unicz.it> References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> <057ca61063d2df86dbfedb3f33fe06f8.squirrel@email.unicz.it> <29b4f0ef371de5adb52505f83a1d153a.squirrel@email.unicz.it> <8a9b80c485a3eac1ad09c3134eb1841d.squirrel@email.unicz.it> <5ef1e4bd7aebe7bd69da47a45ee9d058.squirrel@email.unicz.it> <8e6a0eaa020399bfb82507040c017757.squirrel@email.unicz.it> Message-ID: <98ffa7905c49afd30a50480d1812b59f.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio) http://staff.icar.cnr.it/cannataro/parbio2013/ held in conjunction with ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics September 22-25, 2013 Washington DC, USA http://www.cse.buffalo.edu/ACM-BCB2013/ DEADLINE: MAY 30, 2013 ===================================================================== * * * CALL FOR PAPERS * * * ===================================================================== Due to the availability of high-throughput platforms (e.g. next generation sequencing, microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging), a recent trend in Bioinformatics and Biomedicine is the increasing production of experimental and clinical data. Considering the complex analysis pipeline of the biomedical research, the bottleneck is more and more moving toward the storage, integration, and analysis of experimental data, as well as their correlation and integration with publicly available data banks. While Parallel Computing and Grid Computing may offer the computational power and the storage to face this overwhelming availability of data, Cloud Computing is a key technology to hide the complexity of computing infrastructures, to reduce the cost of the data analysis task, and especially to change the overall model of biomedical research and health provision. Grid infrastructures may offer the data storage needed to store the huge experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST, mpiBLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data. On the other hand, these technologies yet require great investments by biomedical and clinical institutions and are based on a traditional model where users often need to be aware and face different management problems, such as hardware and software management, data storage, software ownership, and not scalable costs (different professional-level applications in the biomedical domain have high starting costs that prevent many small laboratories to use them). The Cloud Computing technology, that is able to offer scalable costs and increased reachability, availability and easiness of application use, and also the possibility to enforce collaboration among scientists, is already changing the business model in different domains and now it starts to be used also in the bioinformatics (see for instance the recent JCVI Cloud Bio-Linux initiative) and biomedical domains. However, many problems remain to be solved, such as availability and safety of the data, privacy-related issues, availability of software platforms for rapid deployment, execution and billing of biomedical applications. The goal of ParBio is to bring together scientists in the fields of high performance and cloud computing, computational biology and medicine, to discuss, among the others, the organization of large scale biological and biomedical databases, the parallel/service-based implementation of bioinformatics and biomedical applications, and problems and opportunities of moving biomedical and health applications on the cloud. The workshop will focus on research issues, problems and opportunities of moving biomedical and health applications on the cloud, as well as on the opportunity to define guidelines and minimum requirements for a Biomedical Cloud. Moreover, the workshop will discuss about parallel and distributed management and analysis of molecular and clinical data, that more and more need to be integrated and analysed in a joint way. TOPICS OF INTEREST The main themes and research topics will regard the applications of parallel and high performance computing to biology and medicine, as well as Cloud Computing opportunities and problems for bioinformatics and biomedical applications - Large scale biological and biomedical databases - Data integration and ontologies in biology and medicine - Integration and analysis of molecular and clinical data - Parallel bioinformatics algorithms - Parallel visualization and exploration of omics and clinical data - Parallel visualization and analysis of biomedical images - Computing environments for large scale collaboration - Scientific workflows in bioinformatics and biomedicine - Emerging architectures and programming models for bioinformatics and biomedicine - Parallel processing of bio-signals - Modeling and simulation of complex biological processes - Cloud Computing for bioinformatics and biomedicine - Cloud Computing for health systems - Privacy issues for Cloud-based biomedical applications - (Web) Services for bioinformatics and biomedicine - Grid Computing for bioinformatics and biomedicine - Peer-To-Peer Computing for bioinformatics and biomedicine PROGRAM The workshop will take place on (To Be Announced). It is scheduled as full-day. The program is not available yet. PAPER SUBMISSION, REGISTRATION AND PUBLICATION ParBio 2013 welcomes original submissions that have not been published and that are not under review by another conference or journal. Papers should not exceed 10 pages in ACM template on 8.5 x 11 inch paper (see ACM templates - http://www.acm.org/sigs/publications/proceedings-templates). All submissions will be evaluated on their originality, technical soundness, significance, presentation, and interest to the conference attendees. Submission implies the willingness of at least one of the authors to register and present the work associated with the paper submitted. All submitted papers will be reviewed by ParBio?s technical program committee. All accepted papers of registered authors will be included in the workshop proceedings published by ACM digital libraries. Authors of selected papers may be invited to adapt their papers for their publication in several journals. Authors of accepted papers will be required to submit an online ACM Copyright Form. Authors will be contacted by ACM requesting this information. Authors should submit papers using the Easy Chair System (https://www.easychair.org/conferences/?conf=parbio2013). IMPORTANT DATES Paper submission: May 30, 2013 Notifications sent to authors: July 15, 2013 Camera-ready papers due: August 1, 2013 Conference: September 22-25, 2013 WORKSHOP ORGANIZER Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy PROVISIONAL PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA 2. David A. Bader, College of Computing, Georgia University of Technology, USA 3. Ignacio Blanquer; Universidad Polit?cnica de Valencia, Valencia, Spain 4. Vincent Breton, CNRS/IN2P3, LPC Clermont-Ferrand, France 5. Marian Bubak; AGH Krakow PL and University of Amsterdam NL 6. Rajkumar Buyya, University of Melbourne, Melbourne, Australia 7. Umit Catalyurek, The Ohio State University, USA 8. Tim Clark, Harvard Medical School, USA 9. Giuseppe Di Fatta, University of Reading, UK 10. Werner Dubitzky, University of Ulster, UK 11. Ananth Y. Grama, Purdue University, USA 12. Concettina Guerra, University of Padova, Italy 13. Pietro Hiram Guzzi, University Magna Gr?cia of Catanzaro, Italy 14. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 15. Pilar Herrero, Universidad Politecnica de Madrid, Madrid, Spain 16. Kamer Kaya, The Ohio State University, USA 17. Maria Mirto, University of Salento, Italy 18. Salvatore Orlando, University of Venezia, Italy 19. Maria S. Perez, Universidad Politecnica de Madrid, Madrid, Spain 20. Richard Sinnott, University of Melbourne, Melbourne, Australia 21. Fabrizio Silvestri, ISTI-CNR, Italy 22. Tony Solomonides, University of West of England, Bristol, UK 23. Roberto Tagliaferri, University of Salerno, Italy 24. Paolo Trunfio, University of Calabria, Italy 25. Albert Zomaya, University of Sydney, Australia From Phoebe.Chen at latrobe.edu.au Mon Apr 29 07:30:57 2013 From: Phoebe.Chen at latrobe.edu.au (Phoebe Chen) Date: Mon, 29 Apr 2013 11:30:57 +0000 Subject: [BiO BB] First CFP - APBC2014 The Twelfth Asia Pacific Bioinformatics Conference Message-ID: <406AE3FE9DC1504D9CD42EAE2E589A26478A92B8@MBX02.ltu.edu.au> Dear Colleague, ============================================= Full paper submission deadline is due on 31 July, 2013. *Please send to interested colleagues and students * APBC2014 - The Twelfth Asia Pacific Bioinformatics Conference The Twelfth Asia Pacific Bioinformatics Conference Shanghai, China 17-19 January 2014 http://admis.fudan.edu.cn/apbc2014/ Organization General Co-Chairs Luonan Chen (SIBS, CAS, China) Yixue Li (SIBS, CAS,, China) PC Co-Chairs Phoebe Chen (La Trobe University, Australia) Shuigeng Zhou (Fudan University, China) ============================================ Important Dates * Full Paper submission: 31 July 2013 * Author notification: 15 Sept 2013 * Final version due on: 15 Oct 2013 * Full paper author registration deadline: 31 Oct 2013 The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development and novel applications of Bioinformatics. The past APBC conferences were held in: * APBC2003 4-7 Feb 2003: Adelaide Australia * APBC2004 18-22 Jan 2004: Dunedin, New Zealand * APBC2005 17-21 Jan 2005: Singapore * APBC2006 13-16 Feb, 2006: Taipei Taiwan * APBC2007 15-17 Jan, 2007: Hong Kong * APBC2008 14-17 Jan, 2008: Kyoto Japan * APBC2009 13-16 Jan, 2009: Beijing China * APBC2010 18-21 Jan, 2010: Bangalore, India * APBC2011 11-14 Jan, 2011: Inchon, Korea * APBC2012 17-19 Jan, 2012: Melbourne, Australia * APBC2013 21-23 Jan 2013: Vancouver, BC, Canada ----------------------------------------------------------------------- Call for Papers APBC2014 invites high-quality original full papers on any topic related to Bioinformatics and Computational Biology. The submitted papers must have not been published or under consideration for publication in any other journal or conference with formal proceedings. All accepted papers will have to be presented by one of the authors at the conference. Accepted papers will be invited to be published in the journals BMC Genomics, BMC Bioinformatics, BMC Systems Biology and IEEE/ACM TCCB following the journals' publication policy. Use the following linked site to make your submission https://www.easychair.org/conferences/?conf=apbc2014 From kishor556 at hotmail.com Mon Apr 29 11:59:35 2013 From: kishor556 at hotmail.com (Kishor Shende) Date: Mon, 29 Apr 2013 21:29:35 +0530 Subject: [BiO BB] workshop on Bioinformatics Message-ID: 1. SHORT TERM COURSE ON"FINITE ELEMENT MODELING WITH MATLAB (Under TEQIP-II)" MAY 06-10, 2013 2. NATIONAL WORKSHOP ON BIOINFORMATICSUnder Bioinformatics Infrastructure Facility of Department of Biotechnology, New Delhi&Special Interest Group on Bioinformatics of Computer Society of IndiaMAY 13-17, 2013 Organized byDepartment of MathematicsMaulana AzadNational Institute of TechnologyBhopal 462051 IndiaWebsite: www.manit.ac.in&Department of Applied MechanicsSardar VallabhbhaiNational Institute of TechnologySurat 395007 IndiaWebsite: www.svnit.ac.in CoordinatorsDr. Neeru AdlakhaMr. Mayank Desai Dr. Kishor K. Shende (Information Officer) Dept. of Biotechnology & Bioinformatics Center, Barkatullah Univeristy, Bhopal - 462 026, Madhya Pradesh, India Phone NO:(O) +91-755-2677748-107 Cell. No.: +91-9993421666