From dan.bolser at gmail.com Mon Oct 3 15:09:27 2011 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 3 Oct 2011 20:09:27 +0100 Subject: [BiO BB] Fwd: Virus Discovery in the Clinical Setting 2012: Open for applications In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Wellcome Trust Advanced Courses < mail.uhmaxgpbsecdpzl at advanced-courses-wellcome.msgfocus.com> Date: 3 October 2011 13:53 Subject: Virus Discovery in the Clinical Setting 2012: Open for applications To: dan.bolser at gmail.com Having problems reading this? See a web version. [image: Wellcome Trust | Celebrating 75 Extraordinary Years] Virus Discovery in the Clinical Setting 13-18 May 2012 *Open for applications > * Applications are now invited for this popular Wellcome Trust Advanced Course. Full course and application details are on our website. The application deadline is *3 February 2012*. The course focuses on how to investigate an evolving outbreak of an infectious disease. Theoretical and practical sessions are integrated around a theme of using modern laboratory and epidemiological methods to identify the source of an outbreak. There will be daily morning update sessions analysing the results from the previous day and exploring the next steps in both investigating the cause and managing the clinical situation. It will provide training for specialty trainees in virology, medical microbiology and infectious diseases, veterinary sciences and healthcare scientists in the application of current molecular and serological techniques in identifying and characterising a novel virus in a clinical setting. *Programme* - Identification of emerging infectious agents ? pathogen discovery - Virus isolation, immunofluorescence and electron microscopy - Nucleic acid extraction, real-time PCR assays and primer and probe design - PCR product identification and cloning - Sequencing and bioinformatics - Practical aspects of proteomics - Practical aspects of ELISA design - Theoretical aspects of microarrays - Epidemiological and public health investigations in an outbreak situation *Course instructors* Dr Kevin Brown (Health Protection Agency) Dr Mark Zuckerman (Health Protection Agency and King?s College Hospital) * Guest speakers* Dr David Brown (Virus Reference Department, Health Protection Agency) Dr Oliver Pybus (Department of Zoology, University of Oxford) Dr Mary Ramsey (Immunisation Division, Health Protection Agency) Dr Richard Madeley (Professor of Clinical Virology, Newcastle University [now retired]) Professor Haroun Shah (Centre for Infections, Health Protection Agency) *CPD accreditation* CPD accreditation will be sought from the Royal College of Pathologists and the Institute of Biomedical Science. *Bursaries* Limited bursaries are available to cover up to 50% of the course fee. These are subject to open competition and are awarded on merit. [image: Contact us] Please do not reply to this email. For further information please contact advancedcourses at hinxton.wellcome.ac.uk [image: Keep in touch with the Trust] [image: Twitter] [image: Facebook] [image: RSS] [image: Blog] [image: YouTube] [image: Subscription Info] To unsubscribe from future Advanced Courses, please emailus with the subject line 'Unsubscribe'. To unsubscribe from all Wellcome Trust communications, click here . The Wellcome Trustis a charity registered in England and Wales, no. 210183. Its sole trustee is The Wellcome Trust Limited, a company registered in England and Wales, no. 2711000 (whose registered office is at 215 Euston Road, London NW1 2BE, UK) From jeff at bioinformatics.org Thu Oct 13 16:28:25 2011 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 13 Oct 2011 16:28:25 -0400 Subject: [BiO BB] Course on Perl for Biologists Message-ID: <4E9749E9.4090203@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CS101A Perl for Biologists, Level 1 Oct. 24-28, 2011 Online at Bioinformatics.Org http://www.bioinformatics.org/wiki/CS101A -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: Taught in the context of biological research, this course helps biologists learn how to use the scripting language Perl to automate certain tasks. Armed with some knowledge and hands-on experience with a programming or scripting language, scientists taking a CS101 course at the Bioinformatics Organization will be able to perform basic software development tasks and phrase research questions in the context of the language. As a result, they will be able to appreciate and use computers better in their organization and communicate better with their IT group. INSTRUCTOR: Shailender Nagpal, M.Sc. is a data analysis consultant in the biotechnology and pharmaceutical industries and specializes in the interpretation of data generated from various platforms in drug discovery, such as genomics and proteomics. CV: http://www.bioinformatics.org/wiki/Shailender_Nagpal SYLLABUS: Session 1 - Installing Perl, Perl basics . storing and displaying data with variables, getting user input Session 2 - File I/O, flow control statements, string and array operations Session 3 - Hash arrays, functions Session 4 - Regular Expressions, Perl packages, BioPerl PREREQUISITES: No experience is required, although prior experience with any other programming language will be helpful. Math skills will also be useful. TUITION: For-profit & government: $500 USD Non-profit & self-pay: $300 USD Additional discounts are available as follows: * Professional members: 20% discount (please inquire) * Limited scholarships may also be available for those in low-income economies (please inquire). REGISTRATION: Please visit: http://www.bioinformatics.org/edu/ACCG FOR MORE INFORMATION: For more information, please visit: http://www.bioinformatics.org/wiki/CS101A or contact edu at bioinformatics.org. From Phoebe.Chen at latrobe.edu.au Fri Oct 14 19:56:41 2011 From: Phoebe.Chen at latrobe.edu.au (Phoebe Chen) Date: Sat, 15 Oct 2011 10:56:41 +1100 Subject: [BiO BB] APBC2012 Call for Posters Message-ID: Dear Colleagues, We apologize if you receive multiple copies of this call for posters. Please distribute it to your colleagues. Regards, Organizing Committee of APBC2012 ------------ CALL FOR POSTERS (APBC 2012) The Tenth Asia Pacific Bioinformatics Conference (APBC2012) 17-19 Jan, 2012, Melbourne, Australia http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/ Please consider submitting a poster to the conference. The deadline for Posters submission is 25th Oct 2011. The details of the call for posters can be found here: http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/ and click 'Call for Posters' We are looking forward to meeting you in Melbourne . Organizing Committee of APBC2012 Conference program chairs Peer Bork, EMBL Heidelberg, Germany Phoebe Chen, La Trobe University, Australia From sandra.gesing at uni-tuebingen.de Tue Oct 18 04:52:31 2011 From: sandra.gesing at uni-tuebingen.de (Sandra Gesing) Date: Tue, 18 Oct 2011 10:52:31 +0200 Subject: [BiO BB] IWSG-Life 2012 - Call For Papers Message-ID: <20111018105231.42300xpxy5wvfcy7@webmail.uni-tuebingen.de> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx IWSG-Life 2012 (4th International Workshop on Science Gateways for Life Sciences) Workshop Website: http://iwsg-life.org/2012 Date: 23-25 May 2012 Place: Amsterdam, The Netherlands Important dates: The deadline for paper/abstract submission: 16 January 2012 Notification of acceptance: 14 February 2012 Submission of camera ready papers: 19 March 2012 The workshop will take place in conjunction with the Healthgrid Conference 2012 (http://amsterdam2012.healthgrid.org/) and featuring EGI.eu. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Scope: IWSG-Life'12 will bring together scientists from the field of life sciences, bioinformatics and computer science. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of Science Gateways. We invite the submission of papers related to various aspects of molecular and systems biology and Science Gateways/Portals. Suggested topics include, but are not limited to: * Management of biological high-throughput data * Modeling protein-carbohydrate recognition * Machine learning for computational immunomics * Molecular simulations for drug discovery * Portal technology and portal construction methods * Usage models and gateway tools for life sciences * Security aspects of Science Gateways for life sciences * Usability studies of life sciences portals/gateways * Workflows and service composition for life sciences * Service discovery and ontologies for life sciences * Tools for managing grid and cloud portability * Integration of life sciences with e-infrastructures * Demonstrations/ success stories Call for papers There are three alternatives for researchers to present their work: talks, lightning talks, and demonstration sessions. Submission of a full paper may result in a talk, submission of an abstract may result in an lightning talk or a demonstration. Additionally, attendees are invited to participate in a structured discussion facilitated by EGI.eu and an open discussion at the end of the workshop. *Accepted full papers will be published in PubMed-listed proceedings together with the proceedings of the Healthgrid Conference 2012.* Full papers All full papers will be double-blind peer reviewed and evaluated on quality and relevance. All submissions are held in confidentiality prior to publication in the proceedings. Presenters will be given a 20-minute time slot (plus 5 minutes for questions) to provide a summary and update to their work. Papers will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site at https://www.easychair.org/conferences/?conf=hgiwsg2012. They have to be formatted according to the layout style required by the IOSPress. Formatting requirements can be found at: http://www.iospress.nl/authco/instruction_crc.html. The paper length must not exceed ten pages and the papers must be written in clear and readable English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. Abstracts Abstracts can be submitted for the lightning talk or for the demonstration sessions. Authors must indicate clearly which presentation format they are aiming for. All abstracts will be double-blind peer reviewed and evaluated on quality and relevance. Accepted lightning talk submissions will be given a 10-minute time slot (plus 5 minutes for questions) in an lightning talk session. Accepted demonstration submissions will be given a 10-minute time slot (plus 5 minutes for questions) in a demonstration session. Demonstrations will be given live to the workshop audience. Abstracts will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site at https://www.easychair.org/conferences/?conf=hgiwsg2012. The abstract length must not exceed 200 words and the abstracts must be written in clear and readably English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. From iccabs-l at dna.engr.uconn.edu Tue Oct 18 22:55:45 2011 From: iccabs-l at dna.engr.uconn.edu (ICCABS Mailing List) Date: Tue, 18 Oct 2011 22:55:45 -0400 Subject: [BiO BB] ICCABS'12 1st CFP Message-ID: CALL FOR PAPERS 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) Feb. 23-25, 2012, Las Vegas, Nevada http://www.iccabs.org/ Advances in high-throughput technologies such as DNA sequencing and mass spectrometry are profoundly transforming life sciences, resulting in the collection of unprecedented amounts of biological and medical data. Using this data to advance our knowledge about fundamental biological processes and improve human health requires novel computational models and advanced analysis algorithms. IEEE ICCABS aims to bring together leading academic and industry researchers to discuss the latest advances in computational methods for bio and medical sciences. SCOPE Topics of interest include but are not limited to: * Biological modeling and simulation: Molecular and cellular modeling, stochastic and rule-based modeling, modeling languages and systems * Biomedical image processing: Image segmentation and classification, visualization, functional and molecular imaging * Biomedical data and literature mining: Data integration, knowledge discovery from electronic medical records and scientific literature * Computational genetic epidemiology: Linkage and association analysis, gene-gene and gene-environment interaction modeling, genetic risk analysis * Computational metabolomics: Metabolomics databases, metabolite identification, spectral analysis, metabolic network modeling * Computational proteomics: Peptide identification and quantification, post-translational modifications, protein-protein interactions * Databases and ontologies: Biomedical data warehouses, database integration, biomedical ontologies and semantic web services * Gene regulation: Regulatory motifs and modules, post-transcriptional regulation, regulatory networks * Genome analysis: Genome assembly, genome annotation, comparative genomics, metagenomics * Health Informatics: Medical data management and privacy, medical recommender systems, therapy optimization * High-performance bio-computing: Cloud and grid computing, advanced multi-core, GPU, and FPGA biomedical applications * Immunoinformatics: Epitope prediction, vaccine design, immune system simulators * Molecular evolution: Models of evolution, reconstruction of phylogenetic trees and networks, comparative genomics * Population genomics: Haplotype and recombination analysis, structural genomic variation, signatures of natural selection * Sequence analysis: Multiple sequence alignment, motif discovery, sequence search and clustering * Structural bioinformatics: RNA and protein structure prediction and classification, molecular docking, RNA and protein design * Systems biology: Systems approaches to molecular biology, multi-scale modeling, biological networks, synthetic biology * Transcriptomics: Microarray and sequencing-based transcriptome profiling, novel transcript discovery, alternative splicing, non-coding RNA analysis SUBMISSION INSTRUCTIONS Authors are invited to electronically submit extended abstracts in PDF format by following the instructions at http://www.easychair.org/conferences/?conf=iccabs12. Submissions should be prepared using IEEE Computer Society's Word/LaTeX templates available at http://www2.computer.org/portal/web/cscps/formatting and should not exceed 6 pages in length. Accepted abstracts will be published in the IEEE Xplore Digital Library. Special issues of journals on selected extended abstracts are under negotiation. A limited number of student travel awards will be made (conditional upon NSF support). KEY DATES Abstract submission: Dec. 22, 2011 Notification of acceptance: Jan. 25, 2012 Camera-ready version and author registration: Feb. 2, 2012 STEERING COMMITTEE Srinivas Aluru (Iowa State U.) Reda A. Ammar (U. of Connecticut) Tao Jiang (U.C. Riverside) Vipin Kumar (U. of Minnesota) Ming Li (U. of Waterloo) S. Rajasekaran (U. of Connecticut), Chair John Reif (Duke University) Sartaj Sahni (U. of Florida) GENERAL CHAIRS Sorin Istrail (Brown University) S. Rajasekaran (U. of Connecticut) PROGRAM CHAIRS Ion Mandoiu (U. of Connecticut) Mihai Pop (U. of Maryland) John Spouge (NCBI/NIH) FINANCE CHAIR Reda A. Ammar (U. of Connecticut) LOCAL ARRANGEMENTS CHAIR Martin Schiller (U. of Nevada LV) A pdf version of this CFP is available at http://iccabs.org/files/ICCABS-CFP.pdf _______________________________________________ To modify subscription preferences or unsubscribe from the ICCABS-L mailing list visit http://dna.engr.uconn.edu/cgi-bin/mailman/listinfo/iccabs-l From jeff at bioinformatics.org Thu Oct 20 13:50:35 2011 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 20 Oct 2011 13:50:35 -0400 Subject: [BiO BB] Free online conference on systems biology Message-ID: <4EA05F6B.1050700@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Bioinformatics to Systems Biology 2011 Oct. 28, 2011 Online at Bioinformatics.Org http://www.bioinformatics.org/edu/BSB11 (log in as guest) -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- The BSB series is aimed at students and those in the research community who fall under broader disciplines of bioinformatics and systems biology. The BSB ?11 conference will include invited keynote talks within sub-disciplines of these two exciting fields. Ample time will be set aside for discussion during the presentation of participants. SCHEDULE: 11:00-11:30 GMT Kanagasabai Rajaraman, A-STAR, Singapore Semantic Technologies for Life Sciences 11:40-12:10 GMT Sundararajan VS, Nanyang Technological University, Singapore Bioinformatics and Cloud Computing: Challenges 12:20-12:50 GMT Sivaramaiah Nallapeta, Bruker Daltonics, Bangalore, India Recent Trends and Applications of Mass Spectrometry in Life Sciences: A Bioinformatical Perspective 13:00-13:45 GMT Alfredo Benso, Politecnico Di Torino, Italy A Chaotic Model for the Simulation of Biological Systems 13:55-14:40 GMT Richard Wintle, The Hospital for Sick Children, Canada TBA FOR MORE INFORMATION: Please contact edu at bioinformatics.org. -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 621 8258 -- From andreavasquez.c at gmail.com Thu Oct 20 22:24:19 2011 From: andreavasquez.c at gmail.com (Andrea Vasquez) Date: Thu, 20 Oct 2011 21:24:19 -0500 Subject: [BiO BB] Question about bioinformatic tool for SSR Message-ID: what's the best program for finding SSRs?? i'd tried MISA which i find good but there are many in literature what do you recomend?? -- Andrea Vasquez From jprudhomme at healthtech.com Fri Oct 21 07:15:29 2011 From: jprudhomme at healthtech.com (James Prudhomme) Date: Fri, 21 Oct 2011 07:15:29 -0400 Subject: [BiO BB] Integrated R&D Informatics & Knowledge Management Message-ID: <001501cc8fe2$bde23080$39a69180$@com> CONFERENCE ANNOUNCEMENT - Please distribute this message to your colleagues. Thank you. CHI's Fourth Annual Integrated R&D Informatics & Knowledge Management (part of the Molecular Medicine Tri-Conference) February 21-23, 2011 Moscone North Convention Center, San Francisco, CA http://www.triconference.com.com/ird About the event: In the Pharmaceutical industry today, it is now critical to enable researchers to better predict outcomes and make good decisions. Developing integrated informatics systems and intelligent interfaces to support drug discovery and translational research continues to play a pivot role. Our fourth annual Integrated R&D Informatics & Knowledge Management will bring together thought leaders from across the life sciences to share their experiences dealing with moving large and complex data sets through public and private networks, the integration of disperse data streams and the correlation between pre-clinical observations and clinical outcomes. The integration of clinical and discovery data is key to translational research strategies in all major Pharma companies. We will present case studies on how to build an infrastructure to support translational research and medicine, dealing with complex clinical and translational data sets while allowing end users to ask complex questions. We will showcase innovative data analysis, visualization and informatics platforms and systems to support discovery, clinical and translational research. Examples of how to support secure collaboration between Pharma and academia to foster innovation will be presented, and informatics solutions to workflow management will also be featured. Conference topics: Integration of Internal & External Data Ontologies Integrating & Accessing Non-Standard Public Data to Drive R&D Workflow Project Meeting the Informatics Needs to Support Biologics Development Informatics for Translational Science Download a PDF brochure at http://www.triconference.com/mmtc_content.aspx?ekfrm=109217 Early registration discounts are available. Register at https://chidb.com/register/2012/mmtc/reg.asp or call 781-972-5400. I hope to see you in San Francisco this coming February. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme at healthtech.com From jprudhomme at healthtech.com Wed Oct 26 14:12:04 2011 From: jprudhomme at healthtech.com (James Prudhomme) Date: Wed, 26 Oct 2011 14:12:04 -0400 Subject: [BiO BB] Integrated R&D Informatics & Knowledge Management Message-ID: <000f01cc940a$c432f740$4c98e5c0$@com> CONFERENCE ANNOUNCEMENT - Please distribute this message to your colleagues. Thank you. CHI's Fourth Annual Integrated R&D Informatics & Knowledge Management (part of the Molecular Medicine Tri-Conference) February 21-23, 2012 Moscone North Convention Center, San Francisco, CA http://www.triconference.com.com/ird About the event: In the Pharmaceutical industry today, it is now critical to enable researchers to better predict outcomes and make good decisions. Developing integrated informatics systems and intelligent interfaces to support drug discovery and translational research continues to play a pivot role. Our fourth annual Integrated R&D Informatics & Knowledge Management will bring together thought leaders from across the life sciences to share their experiences dealing with moving large and complex data sets through public and private networks, the integration of disperse data streams and the correlation between pre-clinical observations and clinical outcomes. The integration of clinical and discovery data is key to translational research strategies in all major Pharma companies. We will present case studies on how to build an infrastructure to support translational research and medicine, dealing with complex clinical and translational data sets while allowing end users to ask complex questions. We will showcase innovative data analysis, visualization and informatics platforms and systems to support discovery, clinical and translational research. Examples of how to support secure collaboration between Pharma and academia to foster innovation will be presented, and informatics solutions to workflow management will also be featured. Conference topics: Integration of Internal & External Data Ontologies Integrating & Accessing Non-Standard Public Data to Drive R&D Workflow Project Meeting the Informatics Needs to Support Biologics Development Informatics for Translational Science Download a PDF brochure at http://www.triconference.com/mmtc_content.aspx?ekfrm=109217 Early registration discounts are available. Register at https://chidb.com/register/2012/mmtc/reg.asp or call 781-972-5400. I hope to see you in San Francisco this coming February. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme at healthtech.com