From cannataro at unicz.it Fri May 4 18:38:50 2012 From: cannataro at unicz.it (Mario Cannataro) Date: Sat, 5 May 2012 00:38:50 +0200 (CEST) Subject: [BiO BB] CfP: 3rd Workshop on High Performance Bioinformatics and Biomedicine - Euro-Par 2012 In-Reply-To: References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> Message-ID: <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB) http://staff.icar.cnr.it/cannataro/hibb2012/ held in conjunction with Euro-Par 2012 Rhodes Island, Greece August 27th - 31st, 2012 http://europar2012.cti.gr/ ===================================================================== * * * 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 experimental research may be conducted by remote scientists 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 (To Be Announced). It is scheduled as full-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 2012 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. Paper submission has to be performed by using the HiBB EasyChair submission server (https://www.easychair.org/conferences/?conf=hibb2012). 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 2012 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 Full papers submission: June 4, 2012, Decision Notification: July 6, 2012 Final papers due: July 20, 2012 Workshop session: To Be Announced Camera ready papers for EuroPar Workshop Proceedings: October 1, 2012 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 Polit?cnica 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 Hern?ndez, Univ. Polit?cnica de Valencia, Spain 9. Salvatore Orlando, University of Venezia, Italy 10. Omer F. Rana, Cardiff University, UK 11. Richard Sinnott; National e-Science Centre, University of Glasgow, Glasgow, United Kingdom 12. Fabrizio Silvestri, ISTI-CNR, Italy 13. Erkki Somersalo, Case Western Reserve University, USA 14. Paolo Trunfio, University of Calabria, Italy 15. Albert Zomaya, University of Sydney, Australia --------------------------------------------------------------------------------- 5x1000 Sostieni la Ricerca e le iniziative dell'Universit? degli Studi Magna Graecia di Catanzaro. Apponi la tua firma nel riquadro della dichiarazione dei redditi alla voce "Finanziamento agli enti della ricerca scientifica e della universit?", sia che si tratti del Modello 730, del Modello Unico 2012 oppure del CUD 2012. Trascrivi il codice fiscale dell'Universit?: 97026980793 From hlapp at gmx.net Thu May 10 14:32:06 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 10 May 2012 14:32:06 -0400 Subject: [BiO BB] Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: Many trees enter. Fresh analysis ensues. New insights emerge. As a reminder, the iEvoBio conference is again holding a Challenge competition in 2012, this time on the theme, "Synthesizing Phylogenies." Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Also, alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The deadline for the Geneious Challenge is the same as for the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information. More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign From bmcmutations at gmail.com Wed May 9 07:40:58 2012 From: bmcmutations at gmail.com (Christopher Baker) Date: Wed, 9 May 2012 08:40:58 -0300 Subject: [BiO BB] Mutation: Annotation, Interpretation and Management of (AIMM2012) Message-ID: *AIMM 2012 - CALL FOR PAPERS* Annotation, Interpretation and Management of Mutations (AIMM2012), a workshop at the European Conference on Computational Biology (ECCB12) Sept 9th 2012, Basel, Switzerland. http://www.eccb12.org/workshops#ws2 http://www.unbsj.ca/sase/csas/data/aimm2012/ *Keynote Speaker* - Mauno Vihinen PhD, Professor of Medical Structural Biology (Lund). VARIATION ONTOLOGY: ontology for standardized, systematic description of effects and consequences of variations. *Important Dates* Abstract submission June 15 2012 Full paper submission July 1 2012 Acceptance notification July 30 2012 Final manuscript Aug 15 2012 AIMM2012 Workshop Sept 9 2012 *Workshop Themes* * Mutation Nomenclature, Databases and Metadata: Design, Content, Accuracy. * Mutation Data Integration, Phenotype Ontologies, Semantic Services and Reuse. * Semantic Integration and Interpretation of data linked to mutations and diseases * Impacts of Mutations: Prediction and Bootstrapping. * Extraction and grounding of mutations and impact annotations from scientific literature * System Evaluations and Benchmarking http://www.unbsj.ca/sase/csas/data/aimm2012/themes.html http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html http://www.ebi.ac.uk/Rebholz-srv/aimm.html *Submissions* We invite workshop papers (3000 words / 8 pages) and demonstrations. Early Abstracts should be no more than 500 words. Manuscripts should be focused around a specific challenge with a biomedical context where they suggest a solution, demonstrate feasibility and possibly also a meaningful evaluation. Pre-submission enquiries and variations to the deadlines above may be made in consultation with the Chris Baker bakerc at unb.ca * Author instructions can be obtained by sending an email to bmcmutations at gmail.com an automated reply will be sent and complete submissions should be uploaded to Easychair:https://www.easychair.org/conferences/?conf=aimm2012 *Journal Special Issue* A special issue in a biomedical scientific journal will be produced of the best contributions to the Workshop Proceedings. Papers have to address genuine themes relevant to the: Annotation, Interpretation and Management of Mutations (see below)* * Workshop Organizers / Special Issue Editors* - Christopher J. O. Baker - University of New Brunswick, Canada - Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, UK From grlmc at urv.cat Wed May 9 11:01:27 2012 From: grlmc at urv.cat (URV - RESEARCH GROUP ON MATHEMATICAL LINGUISTICS) Date: Wed, 09 May 2012 17:01:27 +0200 Subject: [BiO BB] TPNC 2012: last submission deadline extension Message-ID: *To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject* ********************************************************************* LAST SUBMISSION DEADLINE EXTENSION: May 21, 2012 (23:59h, CET) ********************************************************************* 1st INTERNATIONAL CONFERENCE ON THE THEORY AND PRACTICE OF NATURAL COMPUTING TPNC 2012 Tarragona, Spain October 1-5, 2012 http://grammars.grlmc.com/tpnc2012/ ********************************************************************* AIMS: TPNC is the first event in a series to cover the wide spectrum of computational principles, models and techniques inspired by information processing in nature. TPNC 2012 will reserve significant room for young scholars at the beginning of their career. It aims at attracting contributions about nature-inspired models of computation, synthesizing nature by means of computation, nature-inspired materials, and information processing in nature. VENUE: TPNC 2012 will take place in Tarragona, less than 100 kms. to the south of Barcelona. SCOPE: Topics of either theoretical, experimental or applied interest include, but are not limited to: * Nature-inspired models of computation: - amorphous computing - cellular automata - chaos and dynamical systems based computing - evolutionary computing - membrane computing - neural computing - optical computing - swarm intelligence * Synthesizing nature by means of computation: - artificial chemistry - artificial immune systems - artificial life * Nature-inspired materials: - computing with DNA - nanocomputing - physarum computing - quantum computing and quantum information - reaction-diffusion computing * Information processing in nature: - developmental systems - fractal geometry - gene assembly in unicellular organisms - rough/fuzzy computing in nature - synthetic biology - systems biology * Applications of natural computing to: algorithms, bioinformatics, control, cryptography, design, economy, graphics, hardware, learning, logistics, optimization, pattern recognition, programming, robotics, telecommunications etc. A flexible "theory to/from practice" approach would be the perfect focus for the expected contributions. STRUCTURE: TPNC 2012 will consist of: ? invited talks ? invited tutorials ? peer?reviewed contributions INVITED SPEAKERS: Christian Blum (Barcelona), tutorial tba Andrew Childs (Waterloo), tba Max H. Garzon (Memphis), A Geometric Approach to DNA Codeword Design and Applications Faustino G?mez (IDSIA, Manno-Lugano), Scalable Neuroevolution for Reinforcement Learning Ponnuthurai N. Suganthan (Singapore), Differential Evolution: Recent Advances Barbara M. Terhal (Aachen), Fragility of Quantum Information and Quantum Error Correction Peter Ti?o (Birmingham), Computational Intelligence in Astronomy - Win-Win Situation PROGRAMME COMMITTEE: Ajith Abraham (Auburn) Selim G. Akl (Kingston CA) Enrique Alba (M?laga) Artiom Alhazov (Chi?in?u) Peter J. Bentley (London) Mauro Birattari (Brussels) Christian Blum (Barcelona) ?scar Castillo (Tijuana) Weng-Long Chang (Kaohsiung) Parimal Pal Chaudhuri (Calcutta) Carlos A. Coello Coello (Mexico DF) Kalyanmoy Deb (Kanpur) Peter Dittrich (Jena) Andries Petrus Engelbrecht (Pretoria) Toshio Fukuda (Nagoya) Enrique Herrera-Viedma (Granada) C?sar Herv?s-Mart?nez (C?rdoba) Julia Kempe (Tel Aviv & Paris) Elmar Wolfgang Lang (Regensburg) Pier Luca Lanzi (Milan) Vincenzo Manca (Verona) Maurice Margenstern (Metz) Carlos Mart?n-Vide (Tarragona, chair) Kaisa Miettinen (Jyv?skyl?) Michael O'Neill (Dublin) Ferdinand Peper (Kobe) Ion Petre (Turku) Carla Piazza (Udine) A.C. Cem Say (Istanbul) J?rgen Schmidhuber (Lugano) Moshe Sipper (Beer-Sheva) El-Ghazali Talbi (Lille) Kay Chen Tan (Singapore) Jir? Wiedermann (Prague) Takashi Yokomori (Tokyo) Ivan Zelinka (Ostrava) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Peter Leupold (Tarragona) Carlos Mart?n?Vide (Tarragona, chair) Bianca Truthe (Magdeburg) Florentina Lilica Voicu (Tarragona) SUBMISSIONS: Authors are invited to submit papers presenting original and unpublished research. Papers should not exceed 12 single?spaced pages (including eventual appendices) and should be formatted according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0). Submissions have to be uploaded at: https://www.easychair.org/conferences/?conf=tpnc2012 PUBLICATIONS: A volume of proceedings published by Springer in the LNCS series will be available by the time of the conference. A special issue of a major journal will be later published containing peer?reviewed extended versions of some of the papers contributed to the conference. Submissions to it will be by invitation. REGISTRATION: The period for registration is open from February 25 to October 1, 2012. The registration form can be found at the website of the conference: http://grammars.grlmc.com/tpnc2012/ Early registration fees: 500 Euro Early registration fees (PhD students): 400 Euro Late registration fees: 540 Euro Late registration fees (PhD students): 440 Euro On?site registration fees: 580 Euro On?site registration fees (PhD students): 480 Euro At least one author per paper should register. Papers that do not have a registered author who paid the fees by July 1, 2012 will be excluded from the proceedings. Fees comprise access to all sessions, one copy of the proceedings volume, coffee breaks and lunches. PhD students will need to prove their status on site. PAYMENT: Early (resp. late) registration fees must be paid by bank transfer before July 1, 2012 (resp. September 21, 2012) to the conference bank account: Uno-e Bank bank?s address: Julian Camarillo 4 C, 28037 Madrid, Spain IBAN: ES3902270001820201823142 SWIFT/BIC code: UNOEESM1 account holder: Carlos Mart?n-Vide GRLMC account holder?s address: Av. Catalunya 35, 43002 Tarragona, Spain Please mention TPNC 2012 and your name in the subject. A receipt will be provided on site. Remarks: - Bank transfers should not involve any expense for the conference. - People claiming early registration will be requested to prove that the bank transfer order was carried out by the deadline. People registering on site must pay in cash. For the sake of local organization, however, it is much recommended to do it earlier. Besides paying the registration fees, it is required to fill in the registration form at the website of the conference. IMPORTANT DEADLINES: Paper submission: May 21, 2012 (23:59h, CET) Notification of paper acceptance or rejection: June 18, 2012 Final version of the paper for the LNCS proceedings: June 25, 2012 Early registration: July 1, 2012 Late registration: September 21, 2012 Starting of the conference: October 1, 2012 Submission to the post?conference special issue: January 5, 2013 FURTHER INFORMATION: florentinalilica.voicu at urv.cat POSTAL ADDRESS: TPNC 2012 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34?977?559543 Fax: +34?977?558386 From smeganck at vub.ac.be Wed May 9 04:45:54 2012 From: smeganck at vub.ac.be (Stijn Meganck) Date: Wed, 9 May 2012 10:45:54 +0200 Subject: [BiO BB] CFP: CSBio 2012 : 3rd International Conference on Computational Systems-Biology and Bioinformatics Message-ID: <69CD380E-44A2-4618-BCA7-A737B1C1916D@vub.ac.be> * Apologies if you received multiple copies of this announcement. * Kindly forward to those who may be interested. Thanks. ********** CSBio 2012 - Call for Papers ********* CSBio 2012 : 3rd International Conference on Computational Systems-Biology and Bioinformatics Bangkok, Thailand, October 3-5, 2012 http://www.csbio.org/ Important Dates =============== Regular paper submission deadline: May 31, 2012 Notification of acceptance: June 30, 2012 Camera-ready paper: July 31, 2012 ORGANIZERS - National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) - King Mongkut University of Technology Thonburi (KMUTT) TECHNICAL SPONSORS - International Neural Network Society (INNS) - ACM Thailand Chapter Aims and Scope ============== With the advent of technologies like DNA sequencing and DNA microarray, an enormous amount of information has been generated that can only be efficiently analyzed with computers. As the information becomes ever larger and more complex, more computational tools are needed to sort through the data. These include: * Development of new algorithms and statistics to assess biological information, such as relationships among members of very large data sets. * Development of computational methodologies to perform systematic studies of complex interactions in biological systems to enable discovery of new emergent properties that may arise from the integrated systemic view. * Development and implementation of tools that enable efficient access and management of different types of information, such as various databases, integrated mapping information. * Visualization of various types of biological data to aid in analysis and interpretation of nucleotide and amino acid sequences, protein domains, and protein structures. Topics of interest include, but are not limited to: * Adaptive computation in bioinformatics * Translational bioinformatics * Medical and biomedical informatics * DNA, RNA and protein sequence analysis * Gene expression analysis * Biomarker discovery * Disease classification * Modeling and simulation of biological processes, pathways, networks, and so on * Parallel and grid computing * Molecular evolution and phylogeny * Functional genomics * Proteomics & other omics * Protein folding * Drug discovery and validation * Biological network reconstruction and analysis * Bio-inspired computing * Bio-data visualization Paper Submission ================ The CSBio 2012 online submission system is opened at EasyChair (http://www.easychair.org/conferences/?conf=csbio2012). Prospective authors are invited to submit original, high quality full papers of up to twelve (12) pages electronically. Short papers of 4-6 pages will also be considered. The submission must conform to the Elsevier Procedia Computer Science format (http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description ). All accepted papers will be published in the proceedings of CSBio 2012 as an Elsevier Procedia Computer Science open access volume (indexed by EI, Scopus and Conference Proceedings Citation Index - formerly ISI Proceedings). Extended version of selected papers will be invited for publication in special issues of international journals after the conference. All submissions will be checked by VeriGuide for originality (http://veriguide1.cse.cuhk.edu.hk/portal/page/index.jsp). Journal versions of selected papers from the conference proceedings will be invited to the following thematic issues: - Journal of Biomedical Informatics (Elsevier) - "Computational Advances in Translational Bioinformatics" - Memetic Computing (Springer) - "Modern Applications of Adaptive Computation in Bioinformatics" Collocated Conferences ===================== - The 11th International Conference on Bioinformatics (InCoB 2012 - www.incob2012.org) - The 3rd Winter Conference of the International Neural Network Society (INNS-WC 2012 - http://inns.sit.kmutt.ac.th/wc2012/) From clements at galaxyproject.org Mon May 14 16:43:48 2012 From: clements at galaxyproject.org (Dave Clements) Date: Mon, 14 May 2012 13:43:48 -0700 Subject: [BiO BB] 2012 Galaxy Community Conference (GCC2012) Update Message-ID: Hello all, The 2012 Galaxy Community Conference (GCC2012), being held in Chicago, Illinois, July 25-27, is now 10 weeks away. *About the meeting: * GCC2012 is about integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. This is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy is an open web-based platform for data intensive biomedical research (http://galaxyproject.org) that is widely used and deployed at research organizations of all sizes and around the world. *Updates since the initial announcement: * 1) A day of tutorials has been added to the agenda this year. The GCC2012 Training Day has 3 parallel tracks, each featuring four, 90 minute workshops and covering between and 7 and 12 different topics. Please take a few minutes to vote on topics that you would like to see presented: *The survey ends this Friday, May 18*, so please provide your feedback now. http://bit.ly/GCC2012TDSurvey 2) The GCC2012 early registration deadline is June 11, which is just 4 weeks away. Registering early saves* 36 to 42%* on registration costs, and allows you to book discounted conference lodging before it fills up. *Register now at* http://wiki.g2.bx.psu.edu/Events/GCC2012/Register ** 3) A list of confirmed speakers and abstracts are now available on the conference web site. This list is not yet finished, but will give you a pretty accurate idea of the range of topics that will be discussed during the meeting. http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers Hope to see you in Chicago, Dave Clements, on behalf of the GCC2012 Organizing Committee On Tue, Mar 20, 2012 at 1:39 PM, Dave Clements wrote: > Hello all, > > We are pleased to announce that early registration for the 2012 Galaxy > Community Conference (GCC2012, http://galaxyproject.org/GCC2012) is > now open. GCC2012 will be held July 25-27, at the UIC Forum, in > Chicago, Illinois. The conference will feature two full days of > presentations, discussions, lightning talks, and breakouts. We have > also added a new full day of training this year, featuring 3 parallel > tracks with four workshops each, covering seven different topics. > > The Galaxy Community Conference is for: > * Sequencing core facility staff > * Bioinformatics core staff > * Bioinformatics tool and workflow developers > * Bioinformatics focused principal investigators and researchers > * Data producers > * Power bioinformatics users > > This event is about integrating, analyzing, and sharing the diverse > and very large datasets that are now typical in biomedical research. > GCC2012 is an opportunity to share best practices with, and learn > from, a large community of researchers and support staff who are > facing the challenges of data-intensive biology. Galaxy is an open > web-based platform for data intensive biomedical research > (http://galaxyproject.org) that is widely used and deployed at > research organizations of all sizes and around the world. > > Registration is very affordable, especially for post-docs and > students. You can can save an additional 40% by registering on or > before June 11. > > Conference lodging can also be booked. Low-cost rooms have been > reserved on the UIC campus. You can also stay at the official > conference hotel, at a substantial discount arranged for conference > attendees. There are a limited rooms available in both, and you are > encouraged to register early, if you would like to take advantage of > these. > > Abstract submission is also open, from now through April 16. Abstract > submissions on any topic of interest to the Galaxy community are > strongly encouraged. See the Abstracts page for details. > > Dave Clements, on behalf of the GCC2012 Organizing Committee > > PS: Please help get the word out. A flyer and graphics are at > http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion. > > -- > http://galaxyproject.org/GCC2012 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://galaxyproject.org/wiki/ > -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ From grlmc at urv.cat Sun May 13 05:07:26 2012 From: grlmc at urv.cat (GRLMC) Date: Sun, 13 May 2012 11:07:26 +0200 Subject: [BiO BB] SSMBio 2012: 2nd announcement Message-ID: <1EF0DAC8118D461DA25D10CF3F859CB7@Carlos1> *To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject* ********************************************************************* 2012 INTERNATIONAL SUMMER SCHOOL IN METHODS IN BIOINFORMATICS SSMBio 2012 Tarragona, Spain August 27-31, 2012 Organized by: Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/ssmbio2012/ ********************************************************************* AIM: SSMBio 2012 offers a broad and intensive series of lectures at different levels on bioinformatics. The students choose their preferred courses according to their interests and background. Instructors are top names in their respective fields. The School intends to help students initiate and foster their research career. The previous event in this series was WSMBio 2012: http://grammars.grlmc.com/wsmbio2012/ ADDRESSED TO: Graduate (and advanced undergraduate) students from around the world. Most appropriate degrees include: Computer Science, Biology and Medicine. Other students (for instance, from Engineering or Mathematics) are welcome too. The School is appropriate also for people more advanced in their career who want to keep themselves updated on developments in the field. There is no overlap in the class schedule. COURSES AND PROFESSORS: - Rita Casadio (U Bologna), Human Protein Variants: Structural and Functional Annotation [advanced, 8 hours] - David Gilbert (Brunel U, London), Multiscale Modelling for Systems Biology [intermediate/advanced, 6 hours] - Minoru Kanehisa (Kyoto U), Translational Bioinformatics: From Genomes to Diseases and Drugs [introductory/intermediate, 4 hours] - Bin Ma (U Waterloo), Mass Spectrometry Data Analysis for Proteomics [introductory/intermediate, 6 hours] - Luay Nakhleh (Rice U), Gene Tree Reconciliations: Incomplete Lineage Sorting, Duplication/Loss, and Reticulation [introductory/intermediate, 4 hours] - Gajendra P.S. Raghava (Institute of Microbial Technology, Chandigarh), Bioinformatics Approach for Designing Therapeutic Peptides, particularly Subunit Vaccines [intermediate/advanced, 8 hours] - Joachim Selbig (University of Potsdam & Max Planck Institute of Molecular Plant Physiology), Integrative 'Omics' Data and Network Analysis [intermediate/advanced, 6 hours] - Wing-Kin Sung (National U Singapore), Extracting Information from Next Generation Sequencing Data [introductory/intermediate, 6 hours] - Michael Zhang (U Texas Dallas), From Computational -Omics to Systems Biology [intermediate, 6 hours] REGISTRATION: It has to be done on line at http://grammars.grlmc.com/ssmbio2012/Registration.php FEES: They are variable, depending on the number of courses each student takes. The rule is: 1 hour = - 10 euros (for payments until June 2, 2012), - 15 euros (for payments after June 2, 2012). PAYMENT PROCEDURE: The fees must be paid to the School's bank account: Uno-e Bank bank?s address: Julian Camarillo 4 C, 28037 Madrid, Spain IBAN: ES3902270001820201823142 BIC/SWIFT: UNOEESM1 account holder: C. Martin ? GRLMC account holder?s address: Av. Catalunya 35, 43002 Tarragona, Spain Please mention SSMBio 2012 and your name in the subject. A receipt will be provided on site. Remarks: - Bank transfers should not involve any expense for the School. - People claiming early registration will be requested to prove that the bank transfer order was carried out by the deadline. - Students may be refunded only in the case when a course gets cancelled due to the unavailability of the instructor. People registering on site at the beginning of the School must pay in cash. For the sake of local organization, however, it is much recommended to do it earlier. ACCOMMODATION: Information about accommodation is available on the website of the School. CERTIFICATE: Students will be delivered a certificate stating the courses attended, their contents, and their duration. IMPORTANT DATES: Announcement of the programme: April 21, 2012 Starting of the registration: April 21, 2012 Early registration deadline: June 2, 2012 Starting of the School: August 27, 2012 End of the School: August 31, 2012 QUESTIONS AND FURTHER INFORMATION: Lilica Voicu: florentinalilica.voicu at urv.cat WEBSITE: http://grammars.grlmc.com/ssmbio2012/ POSTAL ADDRESS: SSMBio 2012 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-558386 ACKNOWLEDGEMENTS: Diputaci? de Tarragona Universitat Rovira i Virgili From price at uchicago.edu Thu May 10 16:40:43 2012 From: price at uchicago.edu (Phoebe Rice) Date: Thu, 10 May 2012 15:40:43 -0500 (CDT) Subject: [BiO BB] help with bacterial protein sequence comparisons Message-ID: <20120510154043.BJU04978@mstore01.uchicago.edu> I need some hints from people who really know how to deal with the burgeoning database (I'm a crystallographer / biochemist): I'm interested in the catalytic domain of a protein found on many plasmids & transposons. I'd like to make a "sequence logo" or other informative-at-a-glance display of which residues are most conserved. Blast gives me pages of 99% identical proteins (mostly from other S. aureus strains), and I'm too lazy to pick "representatives" manually from further down the list. What is the best way to get a list of related proteins that are all, say, <90% identical to other proteins in the list? many thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp From tdmlwilo at yahoo.com Sun May 13 13:24:36 2012 From: tdmlwilo at yahoo.com (Twaha Daudi) Date: Sun, 13 May 2012 10:24:36 -0700 (PDT) Subject: [BiO BB] Bioinformatics Career Message-ID: <1336929876.34206.YahooMailNeo@web163103.mail.bf1.yahoo.com> Dear all, Good day.? Iam doing Master's in Public Health, and would like to do project in Bioinformatics .Can any help to me shed light which area is good,especially in africa. Genetic epidemiology vs bioinformatics. or molecular epidemiology vs bionformatics. Thank you in advance. T From ss2489 at cornell.edu Mon May 14 22:53:56 2012 From: ss2489 at cornell.edu (Surya Saha) Date: Mon, 14 May 2012 22:53:56 -0400 Subject: [BiO BB] Internships: Applications open now! Message-ID: Internships: Applications open now! There are currently two internship positions on offer for students from developing nations: 1. Rost Lab, Technische Universit?t M?nchen, Munich, Germany 2. Diagnostic Genomics Group, NICTA, The University of Melbourne, Melbourne, Australia Read more details at http://www.iscbsc.org/content/internships-0 From ketil.malde at imr.no Tue May 15 03:10:56 2012 From: ketil.malde at imr.no (Ketil Malde) Date: Tue, 15 May 2012 09:10:56 +0200 Subject: [BiO BB] help with bacterial protein sequence comparisons In-Reply-To: <20120510154043.BJU04978@mstore01.uchicago.edu> (Phoebe Rice's message of "Thu, 10 May 2012 22:40:43 +0200") References: <20120510154043.BJU04978@mstore01.uchicago.edu> Message-ID: <87aa192a2n.fsf@nmd999X.imr.no> Phoebe Rice writes: > Blast gives me pages of 99% identical proteins (mostly from other > S. aureus strains), and I'm too lazy to pick "representatives" > manually from further down the list. What is the best way to get a > list of related proteins that are all, say, <90% identical to other > proteins in the list? I don't know if these are in UniProt, but if they are, you can search the UniRef 90 (or 50) database, which consists of proteins with at most 90 (50) percent similarity. -k -- If I haven't seen further, it is by standing in the footprints of giants From m.francescatto at vumc.nl Tue May 15 09:14:56 2012 From: m.francescatto at vumc.nl (Francescatto, M.) Date: Tue, 15 May 2012 13:14:56 +0000 Subject: [BiO BB] ISCB Student Council Symposium 2012 - Call for Late Posters Message-ID: <8890C124EDA3C04189F7F22B2039EE4009065C50@SP-MX-MBX3.vumc.nl> Dear all, The 8th Symposium of ISCB Student Council 2012 will be held on July 13 in Long Beach, California, as a satellite meeting of the ISMB conference. In case you have not submitted an abstract for SCS 2012 yet, there is still time! The extended deadline for Late Poster submission is Sunday, May 20th 2012. The ISCB Student Council Symposium 2012 will bring together an international audience of over 100 students and young scientists in Computational Biology and Bioinformatics. We welcome abstracts covering both scientific studies as well as novel tools and applications in this field. As in previous years, awards will be given to outstanding posters and presentations. The confirmed keynotes are Jonathan Eisen, University of California Davis, USA Matthew Hibbs, The Jackson Laboratory, USA Robin Dowell, University of Colorado, USA. If you are also planning to attend ISMB, remember that June 1st is the deadline for receiving the early registration discount. You may also register only for the Student Council Symposium. Late Poster submission deadline: May 20st ISMB Early registration deadline: June 1st Submission information: http://symposium.iscbsc.org/content/submissions Symposium website: http://symposium.iscbsc.org/ ISMB registration: http://www.iscb.org/ismb2012-registration Please help spread the word by sharing this mail with your colleagues and collaborators. We look forward to receiving your abstract! Alexander Goncearenco Chair, SCS2012 Olga Botvinnik Co-Chair, SCS2012 From hlapp at gmx.net Wed May 16 14:20:58 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 16 May 2012 14:20:58 -0400 Subject: [BiO BB] Mentorship program at the 2012 iEvoBio conference Message-ID: The iEvoBio Mentorship Program pairs undergraduate and graduate students with faculty who have extensive experience in evolution, systematics, biodiversity, mathematics and/or software development to enhance their experience at iEvoBio 2012. Mentors will guide participants in collaborative and networking opportunities throughout the two-day conference. If you would like to gain the wisdom of your colleagues' experiences by participating in this program, please email the iEvoBio 2012 organizing committee at committee at ievobio.org by June 1, indicating if you have any activities you would like to be included in the mentorship program, or a particular field of interest. You can find more information about the meeting and registration at http://ievobio.org/. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign From Sterten at aol.com Wed May 16 03:36:33 2012 From: Sterten at aol.com (Sterten at aol.com) Date: Wed, 16 May 2012 03:36:33 -0400 (EDT) Subject: [BiO BB] help with bacterial protein sequence comparisons Message-ID: <4c6a3.506d0c25.3ce4b300@aol.com> hmm, I just downloaded all bacterial sequences from genbank (~20GB) you can always easily search these files for a keyword (sub-protein-sequence) or search for sets of such subsequences simultaneously with viruses I did build a binary database of 16-nucleotide-subsequences and was searching all 24-subsequences all of whose 9 subsubsequences were marked. This was pretty fast. I'm not sure yet what to do with bacteria and amino acids A blast for all bacterial sequences must be quite slow ?!? From jprudhomme at healthtech.com Thu May 17 14:56:53 2012 From: jprudhomme at healthtech.com (James Prudhomme) Date: Thu, 17 May 2012 14:56:53 -0400 Subject: [BiO BB] Structure-Based Drug Design, June 4-5, Cambridge, MA Message-ID: <006f01cd345e$d2c37f10$784a7d30$@com> *** Please distribute this message to your colleagues. Thank you. *** Register Today! CHI and Bio-IT World Present the Twelfth Annual Structure-Based Drug Design: Predicting Biological and Kinetic Profiles from Structure June 6-8, 2012 Royal Sonesta Hotel Boston, Cambridge, MA http://www.healthtech.com/sbd About the event: Structure-based drug design took nearly two decades of multiple, parallel technological improvements to arrive at its current mainstream position in medicinal chemistry. Developments in computer graphics, high-power radiation sources, computational processing power, refinement protocols, virtual screening and crystallography were all necessary to create the environment for rapid, iterative structure-based drug discovery. Given the crisis facing the pharmaceutical industry in the translation of early stage drug discovery results, a different set of tools, concerned with algorithms and methods for developing best in class drugs that engage biological targets with kinetically optimized potency and selectivity will need to be refined. In this conference, we bring to focus recent advancements in this field from an experienced faculty. Keynote Address: Binding Kinetics in Drug Discovery David Swinney, Ph.D., CEO, Institute for Rare and Neglected Diseases Drug Discovery (iRND3) Themed Sessions: - Structure to Function - Free Energy Calculation and Molecular Dynamics Simulation - GPCR - Fragment-Based Design - Druggability and Kinetics-Based Drug Design - Trends and Advances Download a PDF brochure at http://www.healthtech.com/Conferences_Overview.aspx?ekfrm=111573&libID=11152 8 Register at https://chidb.com/register/2012/sbd/reg.asp or call 781-972-5400. To inquire about sponsoring and/or exhibiting, contact Jon Stroup at 781-972-5483, jstroup at healthtech.com Please contact me with any questions. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme at healthtech.com From Sterten at aol.com Thu May 17 02:00:19 2012 From: Sterten at aol.com (Sterten at aol.com) Date: Thu, 17 May 2012 02:00:19 -0400 (EDT) Subject: [BiO BB] help with bacterial protein sequence comparisons Message-ID: thinking more about it ... task: --------------------------------------- given two strings of amino-acids, S1 and S2. Typically the lengths are ~100-~million bytes for S1 and ~100M-~4B bytes for S2, where e.g. S2 is the list of all bacterial amino-acid sequences from genbank, joined together. Given threshold D , find all triples(s1,s2,L) of lengths L and subsequences s1 of length L from S1 and subsequences s2 of length L from S2 such that p-value(|s1-s2|) < D . Typically this is done for several Ds simultaneously, basically trying to find the n best subsequences for some given n. Solve that task as quickly as possible. ----------------------------------- algorithm suggestion: ---------------------------------------------------- for all length=(4?) subsequences s1 from S1 make a table T[s1] of addresses where that subsequence occurs in S1 walk through all length=4 subsequences s2 of S2 (load S2 into a cyclic 256 byte-buffer) whenever s2 is marked in T (T[s2]>0), check the extended subsequences x1 bytes forward, x2 bytes backward from s2 , enter it into the best(L) lists for the various lengths L=x1+x2+4. Print those that are replying to myself again ... (posts appear with a lag, when the opinion may have already changed) ok, that's basically what blast is doing. I didn't know about blast. _http://en.wikipedia.org/wiki/BLAST_ (http://en.wikipedia.org/wiki/BLAST) most cited paper in the 90s ! But I wanted a small program that I understand and can easily manipulate for different formats and additional features and without copyright,licence, so I wrote my own. For the original problem (as I understood it) - I would send the blast output to a file and filter the output for representatives. There should be a tool for that, (I don't know) Mine is again selfwritten. Hmm, sequences that are 99% identical to the original can't be only 90% identical to each other, so maybe I misunderstood. In a message dated 18.05.2012 04:17:35 Westeurop?ische Normalzeit, Sterten at aol.com writes: thinking more about it ... task: --------------------------------------- given two strings of amino-acids, S1 and S2. Typically the lengths are ~100-~million bytes for S1 and ~100M-~4B bytes for S2, where e.g. S2 is the list of all bacterial amino-acid sequences from genbank, joined together. Given threshold D , find all triples(s1,s2,L) of lengths L and subsequences s1 of length L from S1 and subsequences s2 of length L from S2 such that p-value(|s1-s2|) < D . Typically this is done for several Ds simultaneously, basically trying to find the n best subsequences for some given n. Solve that task as quickly as possible. ----------------------------------- algorithm suggestion: ---------------------------------------------------- for all length=(4?) subsequences s1 from S1 make a table T[s1] of addresses where that subsequence occurs in S1 walk through all length=4 subsequences s2 of S2 (load S2 into a cyclic 256 byte-buffer) whenever s2 is marked in T (T[s2]>0), check the extended subsequences x1 bytes forward, x2 bytes backward from s2 , enter it into the best(L) lists for the various lengths L=x1+x2+4. Print those that are CALL FOR PAPERS - INTERNATIONAL JOURNAL OF BIOMETRICS AND BIOINFORMATICS (IJBB) ISSN: 1985-2347 Volume 6, Issue 4 Info. at http://www.cscjournals.org/csc/journals/IJBB/journal_cfp.php?JCode=IJBB Computer Science Journals (CSC Journals) invites researchers, editors, scientists & scholars to publish their scientific research papers in an International Journal of Biometrics and Bioinformatics (IJBB) Volume 6, Issue 4. The International Journal of Biometric and Bioinformatics (IJBB) brings together both of these aspects of biology and creates a platform for exploration and progress of these, relatively new disciplines by facilitating the exchange of information in the fields of computational molecular biology and post-genome bioinformatics and the role of statistics and mathematics in the biological sciences. Bioinformatics and Biometrics are expected to have a substantial impact on the scientific, engineering and economic development of the world. Together they are a comprehensive application of mathematics, statistics, science and computer science with an aim to understand living systems. We invite specialists, researchers and scientists from the fields of biology, computer science, mathematics, statistics, physics and such related sciences to share their understanding and contributions towards scientific applications that set scientific or policy objectives, motivate method development and demonstrate the operation of new methods in the fields of Biometrics and Bioinformatics. CSC Journals anticipate and invite papers on any of the following topics: Bio-grid Data visualization Bio-ontology and data mining DNA assembly, clustering, and mapping Bioinformatics databases E-health Biomedical image processing (fusion) Fuzzy logic, Neural networks Biomedical image processing (registration) Gene expression and microarrays Biomedical image processing (segmentation) Gene identification and annotation Biomedical modeling and computer simulation Genetic algorithms Computational genomics & intelligence Hidden Markov models Computational proteomics High performance computing Computational structural biology Molecular evolution and phylogeny Molecular modeling and simulation Molecular sequence analysis Important Dates - IJBB CFP - Volume 6, Issue 4. Paper Submission: May 31, 2012 Author Notification: July 15, 2012 Issue Publication: August 2012 For complete details about IJBB archives publications, abstracting/indexing, editorial board and other important information, please refer to IJBB homepage. We look forward to receive your valuable papers. If you have further questions please do not hesitate to contact us at cscpress at cscjournals.org. Our team is committed to provide a quick and supportive service throughout the publication process. A complete list of journals can be found at http://www.cscjournals.org/csc/bysubject.php Sincerely, J. Stewart Computer Science Journals (CSC Journals) B-5-8 Plaza Mont Kiara, Mont Kiara 50480, Kuala Lumpur, Malaysia Tel: + 603 6207 1607, + 603 2782 6991 Fax:+ 603 6207 1697 Url: http://www.cscjournals.org From delnitin at gmail.com Sat May 19 10:39:01 2012 From: delnitin at gmail.com (NITIN) Date: Sat, 19 May 2012 20:09:01 +0530 Subject: [BiO BB] IEEE PDGC-2012 CFP In-Reply-To: References: Message-ID: ***Apologies for Multiple and Cross Posting*** Second Call for Paper *PDGC 2012-The Second IEEE International Conference on Parallel, Distributed and Grid Computing* *(http://www.juit.ac.in/pdgc-2012/index1.php)* *December 6-8, 2012 * *Jaypee University of Information Technology, * *P.O. Waknaghat, Solan-173234, Himachal Pradesh, INDIA* The Second IEEE International Conference on Parallel, Distributed and Grid Computing (PDGC-2012) will serve as an international forum for researchers and practitioners interested in recent advances in the areas of parallel, distributed and grid computing. It will provide an opportunity to present and exchange advanced scientific and technological information in hardware, software and theoretical foundation in these areas. The proceedings of PDGC 2012 will appear in the proceedings published by IEEE and fully indexed by IEEE Xplore. The Best 4-6 Selected Papers from PDGC 2012 will be published in the Special Issue of International Journal of Parallel, Emergent and Distributed Systems (IJPEDS- http://www.tandf.co.uk/journals/titles/17445760.asp), Taylor and Francis. Topics of interest include but are not limited to: ? Distributed Systems ? Parallel Computer Systems ? Networks and Interconnection Networks ? Network-based Computing ? Dependable Computing and Systems ? Cluster and Grid Computing ? Cloud Computing ? Multimedia and Service Networking ? Peer-to-Peer Computing ? Security and Privacy ? Petri Nets ? Software Tools and Environments for Parallel and Distributed Platforms ? Related Fields Keynote Speakers: ? Thomas H. Cormen (http://www.cs.dartmouth.edu/~thc/), Darmouth College, USA ? Ivan Stojmenovic, Fellow IEEE (http://www.site.uottawa.ca/~ivan/), SITE, University of Ottawa, CANADA ? Assaf Schuster (http://www.cs.technion.ac.il/~assaf/), Technion - Israel Institute of Technology, Haifa, ISRAEL ? Nikil Dutt, Fellow IEEE and ACM Distinguished Scientist ( http://www.ics.uci.edu/~dutt/), University of California-Irvine, USA ? Eliezer Dekel ( https://researcher.ibm.com/researcher/view.php?person=il-DEKEL), IBM Haifa Research Lab, Haifa, ISRAEL ? Peter Widmayer (http://www.pw.ethz.ch/people/head/widmayer/index), ETH Z?rich, SWITZERLAND ? Sanay Ranka (https://sites.google.com/site/sanjayranka/), University of Florida, USA Paper Submission: Authors are invited to submit full papers in English of not more than 6 pages (including figures, tables & references) in IEEE double-column format. Submissions must present original work that has not been previously published, and is not under submission elsewhere. All articles will be reviewed for scientific quality by the Technical Program Committee and external reviewers. Submissions should use the general IEEE template with the minimum font size of 10 points. All papers must include a title, complete contact information for all authors, and keywords on the cover page. The corresponding author should be identified clearly. Papers must be submitted electronically (in PDF format) via on-line submission using the EDAS system at the following link: http://edas.info/newPaper.php?c=11771. If you encounter problems in submitting the papers through our EDAS conference paper submission system, forward your paper at pdgc2012 at gmail.com Important Dates: Paper Submission: 15 August, 2012 Acceptance Notification: 15 September, 2012 Camera-Ready Manuscript: 15 October, 2012 Conference Registration: 01 October, 2012 General Co-Chairs: Satya Prakash Ghrera ( http://www.juit.ac.in/Department/CSE/faculty_cs&it.php?faculty_id=63), Jaypee University of Information Technology, INDIA & Nitin (http://www.juit.ac.in/Department/CSE/faculty_cs&it.php?faculty_id=79), Jaypee University of Information Technology, INDIA From luca at dmi.units.it Sat May 26 09:44:06 2012 From: luca at dmi.units.it (Luca Bortolussi) Date: Sat, 26 May 2012 15:44:06 +0200 Subject: [BiO BB] HSB 2012 - call for papers Message-ID: <4FC0DE26.2090103@dmi.units.it> [Apologies for multiple copies - changes on topic list and special issue] First International Workshop on Hybrid Systems and Biology Newcasle upon Tyne, UK, September 3, 2012 Colocated with CONCUR 2012 http://hsb2012.units.it/ The goal of systems biology is to provide a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. The intrinsic multi-scale nature of these systems, both in space, in organization levels, and in time, makes extremely difficult to model all of them in a uniform way, e.g. by means of differential equations or discrete stochastic processes. Furthermore such models are often not easily amenable to formal analysis and simulation at the organ or even the cell level is frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale well for both the simulation and formal analysis of biological processes. Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology, and they have been applied to successfully capture the behavior of several biological complex systems, ranging from genetic networks, biochemical reactions, signaling pathways and cardiac tissues electrophysiology. This workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. Topics of interest include, but are not limited to: - Hybrid models of biological systems (case studies of genetic, cellular networks, models of tissues, etc.) - Models of biological systems with hybrid behavior - Computational and mathematical analysis techniques for hybrid systems (i.e. reachability, model checking, abstract interpretation, bifurcation theory for hybrid dynamical systems, stability analysis, etc.), with applications in Systems Biology - Hybrid system identification techniques (learning the model from the experimental data) - Efficient simulation techniques for hybrid systems - Hybrid modeling languages for biological systems - Hybrid systems coping with incomplete and uncertain information - Hierarchical Hybrid Systems for multi scale analysis - Stochastic Hybrid Systems - Hybrid simulation (stochastic/deterministic) methods for biological systems - Abstraction and Approximation techniques - Hybrid Systems modeling for Synthetic Biology - Hybrid Control of biological systems - Sensitivity analysis for hybrid systems - Behaviour-driven parameters identification for hybrid systems - Analysis and simulation tools We solicit the submission of unpublished results that address on both theoretical and applied aspects of hybrid modeling techniques in systems biology. The proceedings will be published in the Electronic Proceedings in Theoretical Computer Science (EPTCS) series. There will be a following special issue on Information and Computation, based on selected papers of the workshop. Paper submission Full papers should be no more than 15 pages long, typesetted in the EPTCS-style. Electronic submissions of abstracts and of full-length papers (in PDF format), can be done through the online submission system: https://www.easychair.org/conferences/?conf=hsb2012 Special Issue There will be a special issue on Information and Computation, based on selected papers of the workshop. Registration The registration can be done via the CONCUR 2012 web site. Important dates June 15, 2012 - Abstract submission deadline June 22, 2012 - Full paper submission deadline July 30, 2012 - Notification of paper acceptance August 7, 2012 - Camera-ready of accepted papers Invited Speaker Radu Grosu, TU Wien, Austria Program co-chairs Ezio Bartocci, TU Wien, Austria Luca Bortolussi, Univerity of Trieste, Italy Program committee Marco Antoniotti, University of Milano Bicocca Gregory Batt, INRIA Paris-Rocquencourt, France Alberto Casagrande, University of Trieste, Italy Edmund Clarke, Carnegie Mellon, USA Thao Dang, VERIMAG Lab, Grenoble, France Alexandre Donz?, UC Berkley, USA James R. Faeder, University of Pittsburgh, USA Jasmin Fisher, Microsoft Research, Cambridge, UK Vashti Galpin, University of Edinburgh, UK Colas Le Guernic, NYU, USA Oded Maler, VERIMAG Lab, Grenoble, France Emanuela Merelli, University of Camerino, Italy Bud Mishra, NYU, USA Carla Piazza, University of Udine, Italy Alberto Policriti, University of Udine, Italy Scott A. Smolka, University of Stony Brook, USA Gouhei Tanaka, University of Tokyo, Japan Verena Wolf, Saarland University, Germany Paolo Zuliani, Carnegie Mellon, USA From paolo.romano at istge.it Tue May 29 03:39:13 2012 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 29 May 2012 09:39:13 +0200 Subject: [BiO BB] NETTAB 2012 Integrated Bio-Search: First Announcement and Call for Abstracts Message-ID: <201205290739.q4T7dXKm025891@clus2.istge.it> Dear all, it's a pleasure to send you a summary of the First Announcement and the First Call for Abstracts for next NETTAB workshop.. For more information, you are welcome to visit the web site of the workshop at http://www.nettab.org/2012/ or to get in touch with the organization by email at nettab2012 at elet.polimi.it . I'm looking forward to see many of you in Como in November. Best regards. Paolo Romano ==== NETTAB 2012 on "Integrated Bio-Search" November 14-16, 2012, Como, Italy http://www.nettab.org/2012/ Focus NETTAB 2012 on "Integrated Bio-Search" will be focused on all technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, knowledge, infrastructures, services and tools that are required to answer complex bio-medical-molecular questions. Keynote talks (confirmed) + Integration and search of heterogeneous data for biomedical knowledge discovery Erik Bongcam-Rudloff, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, and Department of Immunology, Genetics and Pathology, Uppsala University, Sweden. + Semantics based biomedical knowledge search, integration and discovery Barend Mons, Leiden University Medical Center and Netherlands Bioinformatics Center, The Netherlands Deadlines - July 23, 2012: Abstract submission deadline for Oral communications - September 30, 2012: Abstract submission deadline for Posters - October 16, 2012: Early registration deadline Chairs - Marco Masseroli, Polytechnic of Milan, Italy - Paolo Romano, IRCCS San Martino IST, Genoa, Italy - Fr?d?rique Lisacek, Swiss Institute of Bioinformatics, Switzerland Supporting Institutes - Polytechnic of Milan, Milan, Italy - IRCCS San Martino IST, Genoa, Italy - Swiss Institute of Bioinformatics, Switzerland - Flagship INTEROMICS Research Project, CNR, Italy - Interdepartmental BIOINFORMATCS Project, CNR, Italy - Bioinformatics Italian Society, Italy For more information, please refer to the web site at http://www.nettab.org/2012/ or contact the organization by email at nettab2012 at elet.polimi.it . Paolo Romano (paolo.romano at istge.it) Bioinformatics IRCCS San Martino University Hospital - IST National Cancer Research Institute http://www.nettab.org/ NETTAB Workshops. Stay tuned! ======= WARNING. This message and any attachments is intended solely for the use of the intended addressees and is confidential. Any unauthorized review, use, disclosure or distribution is prohibited. If you receive this message in error, please delete it, destroy all copies and immediately notify us. Mail is not a secure protocol, therefore IST will not be liable for interception or amendment of this message. ======= From calendarsites at insticc.org Wed May 30 11:00:09 2012 From: calendarsites at insticc.org (CalendarSites) Date: Wed, 30 May 2012 16:00:09 +0100 Subject: [BiO BB] CFP BIOINFORMATICS 2013 - International Conference on Bioinformatics Models, Methods and Algorithms Message-ID: <013301cd3e74$e9e379a0$bdaa6ce0$@insticc.org> CALL FOR PAPERS International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS 2013 Website: http://www.bioinformatics.biostec.org February 11 - 14, 2013 Barcelona, Spain Important Deadlines: Regular Paper Submission: July 20, 2012 Authors Notification (regular papers): October 23, 2012 Final Regular Paper Submission and Registration: November 13, 2012 In Collaboration with: Universitat de Vic The purpose of the International Conference on Bioinformatics Models, Methods and Algorithms is to bring together researchers and practitioners interested in the application of computational systems and information technologies to the field of molecular biology, including for example the use of statistics and algorithms to understanding biological processes and systems, with a focus on new developments in genome bioinformatics and computational biology. Areas of interest for this community include sequence analysis, biostatistics, image analysis, scientific data management and data mining, machine learning, pattern recognition, computational evolutionary biology, computational genomics and other related fields. BIOINFORMATICS encourages authors to submit papers to one of the main topics indicated below, describing original work, including methods, techniques, advanced prototypes, applications, systems, tools or survey papers, reporting research results and/or indicating future directions. Accepted papers will be presented at the conference by one of the authors and published in the proceedings. Acceptance will be based on quality, relevance and originality. There will be both oral and poster sessions. The proceedings will be indexed by several major international indexers. Special sessions are also welcome. Please contact the secretariat for further information on how to propose a special session. BIOINFORMATICS 2013 is part of the International Joint Conference on Biomedical Engineering Systems and Tecnologies (BIOSTEC 2013) that has 3 more conferences with very strong synergies between them, namely: - BIODEVICES: International Conference on Biomedical Electronics and Devices (http://www.biodevices.biostec.org) - BIOSIGNALS: International Conference on Bio-inspired Systems and Signal Processing (http://www.biosignals.biostec.org/) - HEALTHINF: International Conference on Health Informatics(http://www.healthinf.biostec.org/) These four concurrent conferences are held in parallel and registration to one warrants delegates to attend all four. BIOSTEC Keynote Speakers Pedro G?mez Vilda, Universidad Polit?cnica de Madrid, Spain Christian Jutten, GIPSA-lab, France Adam Kampff, Champalimaud Foundation, Portugal PUBLICATIONS All accepted papers (full, short and posters) will be published in the conference proceedings, under an ISBN reference, on paper and on CD-ROM support. All papers presented at the conference venue will be available at the SciTePress Digital Library (http://www.scitepress.org/DigitalLibrary/). SciTePress is member of CrossRef (http://www.crossref.org/). A short list of presented papers will be selected so that revised and extended versions of these papers will be published by Springer-Verlag in a CCIS Series book. The proceedings will be submitted for indexation by Thomson Reuters Conference Proceedings Citation Index, INSPEC, DBLP and EI. AWARDS Best paper awards will be distributed during the conference closing session. Please check the website for further information (http://www.bioinformatics.biostec.org/best_paper_awards.asp). Conference Co-chairs Jordi Sol?-Casals, University of Vic, Spain Ana Fred, Technical University of Lisbon / IT, Portugal Hugo Gamboa, CEFITEC / FCT - New University of Lisbon, Portugal Conference Topics Simulation Computational Intelligence Genomics and Proteomics Sequence Analysis Structural Bioinformatics Image Analysis Visualization Databases and Data Management Data mining and Machine Learning Biostatistics and Stochastic Models Pharmaceutical Applications Systems Biology Algorithms and Software Tools Web Services in Bioinformatics Computational Molecular Systems Immuno- and chemo-informatics Pattern recognition, clustering and classification Structure prediction Model design and evaluation Transcriptomics Next Generation Sequencing Structural Variations PROGRAM COMMITTEE Tatsuya Akutsu, Kyoto University, Japan Charles Auffray, CNRS Institute of Biological Sciences, France Tim Beissbarth, University of G?ttingen, Germany Inanc Birol, BC Cancer Agency, Canada Carlos Brizuela, Centro de Investigaci?n Cient?fica y de Educaci?n Superior de Ensenada, Baja California, Mexico Chris Bystroff , Rensselaer Polytechnic Institute, United States Kun-Mao Chao, National Taiwan University, Taiwan Antoine Danchin, AMAbiotics SAS, France Thomas Dandekar, University of W?rzburg, Germany Richard Edwards, University of Southampton, United Kingdom George Eleftherakis, CITY College, International Faculty of the University of Sheffield, Greece Peter F. Stadler, Universit?t Leipzig, Germany Elisa Ficarra, Politecnico di Torino, Italy Liliana Florea, Johns Hopkins University, United States Gianluigi Folino , Institute for High Performance Computing and Networking, National Research Council, Italy Andrew French, University of Nottingham, United Kingdom Reinhard Guthke, Hans Knoell Institute, Germany Sion Hannuna, University of Bristol, United Kingdom Liisa Holm, University of Helsinki, Finland Bo Jin, Sigma-aldrich, United States Giuseppe Jurman, Fondazione Bruno Kessler, Italy Jir? Kl?ma, Czech Technical University in Prague, Faculty of Electrical Engineering, Czech Republic Bohumil Kov?r, Institute of Information Theory and Automation of the ASCR, Czech Republic Lukasz Kurgan, University of Alberta, Canada Yinglei Lai, George Washington University, United States Matej Lexa, Masaryk University, Czech Republic Shuangge Ma, Yale University, United States Elena Marchiori, Radboud University, Netherlands Majid Masso, George Mason University, United States Francesco Masulli, University of Genova, Italy Petr Matula, Faculty of Informatics, Masaryk University, Czech Republic Pavel Matula, Faculty of Informatics, Masaryk University, Czech Republic Tommaso Mazza, Casa Sollievo della Sofferenza, Italy Imtraud Meyer, University of British Columbia, Canada Hunter Moseley, University of Louisville, United States Vincent Moulton , University of East Anglia, United Kingdom Chad Myers, University of Minnesota, United States Radhakrishnan Nagarajan, University of Arkansas for Medical Sciences, United States Jean-Christophe Nebel, Kingston University, United Kingdom Jos? Luis Oliveira, Universidade de Aveiro, Portugal Matteo Pellegrini , University of California, Los Angeles, United States Michael R. Peterson , University of Hawaii at Hilo, United States Esa Pitk?nen, University of Helsinki, Finland Marylyn Ritchie, Pennsylvania State University, United States Miguel Rocha, University of Minho, Portugal David Rocke, University of California, Davis, United States Simona E. Rombo, DEIS, Universit? della Calabria, Italy Chiara Romualdi, Universita degli Studi di Padova, Italy Juho Rousu, Aalto University, Finland Thomas Schlitt, King's College London, United Kingdom Reinhard Schneider, University of Luxembourg, Germany Mark Segal, University of California, San Francisco, United States Hamid Reza Shahbazkia, Universidade do Algarve, Portugal Christine Sinoquet, LINA / UMR CNRS 6241, University of Nantes, France Yanni Sun, Michigan State University, United States David Svoboda, Faculty of Informatics, Masaryk University, Czech Republic Sandor Szedmak, University of Innsbruck, Austria Silvio C. E. Tosatto, Universit? di Padova, Italy Jyh-Jong Tsay, National Chung Cheng University, Taiwan Alexander Tsouknidas, Aristoteles University of Thessaloniki, Greece Egon L. van den Broek, Human-Centered Computing Consultancy / University of Twente / Radboud UMC Nijmegen, Netherlands Massimo Vergassola, Physics of Biological Systems, Institut Pasteur, France Dong Xu, University of Missouri, United States Tangsheng Yi, University of California at San Francisco, United States Yanbin Yin, University of Georgia, United States Qingfeng Yu, Stowers Institute for Medical Research, United States Jingkai Yu, Institute of Process Engineering, Chinese Academy of Sciences, China Erliang Zeng, University of Notre Dame, United States Jie Zheng, Nanyang Technological University, Singapore Leming Zhou , University of Pittsburgh, United States (list not yet complete) Please check further details at the conference website (http://www.bioinformatics.biostec.org). From calendarsites at insticc.org Wed May 30 11:02:17 2012 From: calendarsites at insticc.org (CalendarSites) Date: Wed, 30 May 2012 16:02:17 +0100 Subject: [BiO BB] CFP HEALTHINF 2013 - International Conference on Health Informatics Message-ID: <013d01cd3e75$3595fc10$a0c1f430$@insticc.org> CALL FOR PAPERS International Conference on Health Informatics - HEALTHINF 2013 Website: http://www.healthinf.biostec.org February 11 - 14, 2013 Barcelona, Spain Important Deadlines: Regular Paper Submission: July 20, 2012 Authors Notification (regular papers): October 23, 2012 Final Regular Paper Submission and Registration: November 13, 2012 In Collaboration with: Universitat de Vic The purpose of the International Conference on Health Informatics is to bring together researchers and practitioners interested in the application of information and communication technologies (ICT) to healthcare and medicine in general and to the specialized support to persons with special needs in particular. Databases, networking, graphical interfaces, intelligent decision support systems and specialized programming languages are just a few of the technologies currently used in medical informatics. Mobility and ubiquity in healthcare systems, standardization of technologies and procedures, certification, privacy are some of the issues that medical informatics professionals and the ICT industry in general need to address in order to further promote ICT in healthcare. In the case of medical rehabilitation and assistive technology the use of ICT has had important results in the enhancement of the quality of life, contributing to a full integration of all citizens in the societies they are also part of. HEALTHINF is a forum for debating all these aspects. Furthermore, this conference is also a meeting place for those interested in understanding the human and social implications of technology, not only in healthcare systems but in other aspects of human-machine interaction such as accessibility issues. HEALTHINF encourages authors to submit papers to one of the main topics indicated below, describing original work, including methods, techniques, advanced prototypes, applications, systems, tools or survey papers, reporting research results and/or indicating future directions. Accepted papers will be presented at the conference by one of the authors and published in the proceedings. Acceptance will be based on quality, relevance and originality. There will be both oral and poster sessions. The proceedings will be indexed by several major international indexers. Special sessions are also welcome. Please contact the secretariat for further information on how to propose a special session. HEALTHINF 2013 is part of the International Joint Conference on Biomedical Engineering Systems and Tecnologies (BIOSTEC 2013) that has 3 more conferences with very strong synergies between them, namely: - BIODEVICES: International Conference on Biomedical Electronics and Devices (http://www.biodevices.biostec.org) - BIOINFORMATICS: International Conference on Bioinformatics Models, Methods and Algorithms (http://www.bioinformatics.biostec.org) - BIOSIGNALS: International Conference on Bio-inspired Systems and Signal Processing (http://www.biosignals.biostec.org) These four concurrent conferences are held in parallel and registration to one warrants delegates to attend all four. BIOSTEC Keynote Speakers Pedro G?mez Vilda, Universidad Polit?cnica de Madrid, Spain Christian Jutten, GIPSA-lab, France Adam Kampff, Champalimaud Foundation, Portugal PUBLICATIONS All accepted papers (full, short and posters) will be published in the conference proceedings, under an ISBN reference, on paper and on CD-ROM support. All papers presented at the conference venue will be available at the SciTePress Digital Library (http://www.scitepress.org/DigitalLibrary/). SciTePress is member of CrossRef (http://www.crossref.org/). A short list of presented papers will be selected so that revised and extended versions of these papers will be published by Springer-Verlag in a CCIS Series book. The proceedings will be submitted for indexation by Thomson Reuters Conference Proceedings Citation Index, INSPEC, DBLP and EI. AWARDS Best paper awards will be distributed during the conference closing session. Please check the website for further information (http://www.healthinf.biostec.org/best_paper_awards.asp). Conference Co-chairs Jordi Sol?-Casals, University of Vic, Spain Ana Fred, Technical University of Lisbon / IT, Portugal Hugo Gamboa, CEFITEC / FCT - New University of Lisbon, Portugal PROGRAM CHAIR Deborah Stacey, University of Guelph, Canada CONFERENCE TOPICS * e-Health * Telemedicine * Medical and Nursing Informatics * Design and Development Methodologies for Healthcare IT * Interoperability * Semantic Interoperability * Confidentiality and Data Security * Knowledge Management * Databases and Datawarehousing * Datamining * Decision Support Systems * Wearable Health Informatics * Mobile Technologies for Healthcare Applications * Evaluation and Use of Healthcare IT * Physiological Modeling * Cognitive Informatics * Affective Computing * Therapeutic Systems and Technologies * Healthcare Management Systems * Human-Machine Interfaces for Disabled Persons * Development of Assistive Technology * ICT, Ageing and Disability * Practice-based Research Methods for Healthcare IT * Electronic Health Records and Standards * Software Systems in Medicine * Pervasive Health Systems and Services * e-Health for Public Health * Clinical Problems and Applications * Data Visualization * Pattern Recognition and Machine Learning PROGRAM COMMITTEE Sergio Alvarez, Boston College, United States Francois Andry, Optum / UnitedHealth Group Inc., United States Philip Azariadis, University of the Aegean, Greece Adrian Barb, Penn State University, United States R?mi Bastide, Jean-Francois Champollion University, France Bert-Jan van Beijnum, University of Twente, Netherlands Eric Campo, LAAS CNRS , France James Cimino, NIH Clinical Center, United States Miguel Coimbra, Faculdade de Ci?ncias da Universidade do Porto, Portugal Carlos Costa, Universidade de Aveiro, Portugal Ricardo Jo?o Cruz-Correia, Faculdade de Medicina da Universidade do Porto, Portugal Stephan Dreiseitl, Upper Austria University of Applied Sciences at Hagenberg, Austria Ioannis Fudos, University of Ioannina, Greece Alfredo Go?i, University of the Basque Country, Spain David Greenhalgh, University of Strathclyde, United Kingdom Alexander H?rbst, UMIT - Private University for Health Sciences, Medical Informatics and Technology, Austria Chun-Hsi Huang, University of Connecticut, United States Ivan Evgeniev Ivanov, Technical University Sofia, Bulgaria Anastasia Kastania, Athens University of Economics and Business, Greece Andreas Kerren, Linnaeus University, Sweden Georgios Kontaxakis, Universidad Politecnica de Madrid, Spain Baoxin Li, Arizona State University, United States Giuseppe Liotta, University of Perugia, Italy Guillaume Lopez, The University of Tokyo, Japan Martin Lopez-Nores, University of Vigo, Spain Michele Luglio, University of Rome "Tor Vergata", Italy Emilio Luque, University Autonoma of Barcelona (UAB), Spain Christoph M. Friedrich, University of Applied Science and Arts Dortmund, Germany Paloma Mart?nez, Universidad Carlos III de Madrid, Spain Alice Maynard, Future Inclusion, United Kingdom Gerrit Meixner, German Research Center for Artificial Intelligence (DFKI), Germany Mohyuddin Mohyuddin, King Abdullah International Medical Research Center (KAIMRC), Saudi Arabia Sai Moturu , Massachusetts Institute of Technology, United States Radhakrishnan Nagarajan, University of Arkansas for Medical Sciences, United States Goran Nenadic , University of Manchester, United Kingdom Shane O'Hanlon, Graduate Entry Medical School, University of Limerick, Ireland Jos? Luis Oliveira, Universidade de Aveiro, Portugal Rui Pedro Paiva, University of Coimbra, Portugal Chaoyi Pang, The Australian e-Health Research Centre, CSIRO, Australia Danilo Pani, University of Cagliari, Italy Jos? J. Pazos-arias, University of Vigo, Spain Carlos Eduardo Pereira, Federal University of Rio Grande Do Sul - UFRGS, Brazil Rosario Pugliese, Universita' di Firenze, Italy Juha Puustj?rvi, University of Helsinki, Finland Arkalgud Ramaprasad, University of Illinois at Chicago, United States Marcos Rodrigues, Sheffield Hallam University, United Kingdom George Sakellaropoulos, University of Patras, Greece Akio Sashima, AIST, Japan Bettina Schnor, Potsdam University, Germany Kulwinder Singh, University of Calgary, Canada Jan Stage, Aalborg University, Denmark K?re Synnes , Lule? University of Technology, Sweden Francesco Tiezzi, IMT - Institute for Advanced Studies Lucca, Italy Alexey Tsymbal, Siemens AG, Germany Aristides Vagelatos, CTI, Greece Egon L. van den Broek, Human-Centered Computing Consultancy / University of Twente / Radboud UMC Nijmegen, Netherlands Rob van der Mei, CWI Amsterdam, Netherlands Francisco Veredas, Universidad de M?laga, Spain Lixia Yao, GlaxoSmithKline, United States Vera Yashina, Dorodnicyn Computing Centre of the Russian Academy of Sciences, Russian Federation (list not yet complete) Please check further details at the conference website (http://www.healthinf.biostec.org). From luca at dmi.units.it Wed May 30 10:41:28 2012 From: luca at dmi.units.it (Luca Bortolussi) Date: Wed, 30 May 2012 16:41:28 +0200 Subject: [BiO BB] BCI summer school Message-ID: <4FC63198.6090909@dmi.units.it> ************************************************************** Joint Second FVG International Summer School on Bioinformatics Seventh International Summer School on Biology, Computation and Information BCI 2012 ************************************************************** September 10-14, 2012, Udine, Italy ************************************************************** CALL FOR PARTICIPATION ************************************************************** The School of Biology, Computation, and Information (BCI), reaching this year its seventh edition, as a joint event with the second FVG summer school on bioinformatics, aims at bringing together Teachers and Students in Biology, Mathematics, and Computer Science. The main goal of the School is to give an updated overview of interdisciplinary techniques and problems cross-bordering the three fields. This year's edition will be dedicated to the study of interaction networks in biological systems, particularly on genetic regulatory networks and biochemical networks. The topics of the school will cover such issues as production of experimental data, construction of mathematical and computaional models, and statistical validation and fitting of models agaist data. The three distinguished speakers for this year's edition are Bijoern Usadel (Biology), Vincent Danos (Computer Science), and Guido Sanguinetti (Mathematics) and the school will take place during the second week of September (September 10-14, 2012). A workshop will take place during the last day of the summer school, while poster session will be organized throughout the conference. ************************************************************** COURSES Main topic: biological interaction networks ------------------------------------------------------------- Area: Mathematics Lecturer: Dr. Guido Sanguinetti, University of Edinburgh, UK. Bio: Guido Sanguinetti received his degree in Physics from the University of Genova and his DPhil in Mathematics from the University of Oxford. He was a postdoc, then lecturer, in the Department of Computer Science at the University of Sheffield prior to joining the faculty at the School of Informatics, University of Edinburgh, in 2010. His interests focus on mathematical and statistical models of dynamic biological systems. Abstract: Uncertainty is inherent in many aspects of biology, from the intrinsic noise of cellular reactions, to the extrinsic noise due to fluctuating environments, to inevitable experimental noise in the measurement process. Proper handling of uncertainty is essential in many steps of model development. In these lectures, I will review the mathematical foundations of stochastic modelling and introduce some more advanced tools for statistical inference in models of biological systems. I will introduce the basic concepts of probability theory and focus on Bayes' theorem as a tool for calibration and uncertainty quantification. I will explain some concepts of statistical inference such as Markov chain Monte Carlo and variational methods. I will then present some basic time-series models and their use in biology, and conclude discussing more advanced continuous time stochastic models. ------------------------------------------------------------- Area: Computer Science Lecturer: Prof. Vincent Danos, University of Edinburgh, UK. Bio: Vincent Danos graduated in Engineering, obtained a PhD in maths. He has a 20 years academic career in logic and theoretical computer science, with an increasing concern for applications, mostly in formalising, modeling and analysing complex systems?e.g., biomolecular networks. Abstract: We will describe a new methodology to describe, simulate and investigate complex biomolecular networks. This method is called rule-based modelling and has the advantage that it can cope better with combinatorial molecular systems than usual reaction-based methods. The following aspects will be covered: knowledge representation, simulation, causal analysis, model reduction techniques. ------------------------------------------------------------- Area: Biology Lecturer: Prof. Bijoern Usadel RWTH Aachen University, Gernamy Bio: Dr. Bj?rn Usadel studied in Biochemistry in Berlin and New York where he worked in Prof Ulrike Gaul's lab on the development on the visual system of Drosophila. During this time he got interested in Bioinformatics and then went on to Golm where he did his PhD in the group of Dr. Markus Pauly on the identification and characterization of novel cell wall genes. He then worked as a Postdoc in Prof. Mark Stitt's lab on the visualization and evaluation of high throughput data. After having been offered a Lecturership position within the Scottish SULSA initiative he was offered his own group at the Max Planck Institute and since then worked on data visualization, analysis as well as sugar status and cell wall biosynthesis. Since 2011 he is a full pofessor at the RWTH Aachen university and a co-director at the Forschungszentrum J?lich. Abstract: The last decade has seen a massive explosion of omics data becoming available to the individual researcher. Initially, the focus was on individual experiments focusing on the limited study of a certain condition. However, given the massive growth of omics data in public data bases, these data can be holistically integrated and novel inferences made. In the beginning this was e.g. based on large scale approaches using simple correlation and a guilt by association approach, having lead to a massive knowledge gain for experimental biologists. Here we present several different streams of how to combine public (and own) dataset stemming from different disciplines in order to make new inferences about the plant as a whole. Firstly we present a novel normalization method for Affymetrix type microarrays beneficial for correlation analysis. We then show how this normalized transcript data from focused areas can be used to predict plant status which we validate using metabolite data. Based on these models we combined metabolite and transcript data sets to make informed decisions about gene knock-out experiments validating our predictions. We also show that guilt by association approaches can be improved by incorporating novel measures, if a large data set is properly mined using expert rules. These results also imply that the automatic incorporation of additional e.g. sequence information will aid in data interpretation. As a proof of concept we show that integration of sequence with simple microarray derived expression data leads to an improved predictor for plant protein chloroplast import. We finish by showing that next-generation sequencing data is not making matters more complicated but will allow us to get an even deeper understanding of living organisms. ************************************************************** WORKSHOP A workshop, will take place during the last day of the summer school, with title "Networks in Biology". Invited speakers for the workshop are: * Ezio Bartocci (TU Wien) * Francesca Cordero (Universit? di Torino) * Nicola Soranzo (CRS4 Bioinformatica, Pula, CA) Participants of the School may submit an abstract for a presentation during the workshop. Abstracts can be submitted via the online submission system available at the school website, and will be selected/judged by the Scientific Committee. ************************************************************** REGISTRATION Registration deadline: 31 August. We can provide accommodation for 40 participants, assigned on a first-come first-served basis. To apply use the online registration form available at school's website http://www.dmi.units.it/bci2010/ Acceptance of more participants will be evaluated by the organizers. Registration fee: EUR 100 (#) The registration fee covers participation at all lectures, course materials, coffee break, and lunches. Accomodation is not included. Please contact the organization or visit the web site for additional information. (#) The registration is free for students and staff of the University of Udine, University of Trieste, and SISSA. ************************************************************** LOCATION The school will take place in Udine, in Friuli Venezia Giulia, Italy. Lessons will be held at the congress center of ERDISU, in Viale Ungheria, I-33100, Udine The congress center is 15 minutes walking from the train station. ************************************************************** WEBSITE AND CONTACT For all additional information, please visit the website: http://phdsummerschools.uniud.it/bci/second-joint-summer-school-biology-computation-and-information ********************************************************************************* SPONSORS - Regione Autonoma del Friuli Venezia Giulia - University of Trieste. - University of Udine. - SISSA, Trieste. ********************************************************************************* ORGANIZING AND SCIENTIFIC COMMITTEE - Alberto Policriti, University of Udine (school co-director) - Luca Bortolussi, University of Trieste (school co-director) - Claudio Altafini, SISSA, Trieste (school co-director) - Nicola Vitacolonna, University of Udine *********************************************************************************