From dan.bolser at gmail.com Thu Jul 1 09:31:48 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 1 Jul 2010 09:31:48 +0100 Subject: [Sbforum-general] BioWikis - NETTAB 2010 Call for Contributions Message-ID: Blatantly not sorry for cross-posting, Dan. ---------- Forwarded message ---------- From: Date: 30 June 2010 17:15 Subject: [Nettab-Announce] NETTAB 2010 Call for Contributions To: nettab-announce at istge.it NETTAB 2010 on "Biological Wikis" November 29 - December 1, 2010, Naples, Italy http://www.nettab.org/ CALL FOR PAPERS See below for Topics, Contributions sought, Deadlines, Instructions and Committees. RATIONALE It is now clear that wiki systems offer a variety of advantages for the management of biological data and information. Some of the specific aims of wikis for biology (bio-wikis) include: ? ?* Collaborative development and sharing of knowledge ? ?* Collaborative annotation of database contents ? ?* Collaborative creation of database contents The collaborative development and sharing of documentation and knowledge allows communities to promote, exploit, discuss and reach consensus on procedures, data, experiences, news, and other varied information. Indeed valuable expertise and interests in special topics are usually distributed, and are rarely concentrated in a unique site or research group. The collaborative annotation of biological databases is increasingly under consideration because extended and accurate curation of an ever increasing volume of data is extremely costly and time consuming. Such distributed networks can help to improve and extend databases curation beyond that which is possible with, typically, limited numbers of curation staff. It allows users to contribute their expertise and observations ?independently of database central organizations. Although the contents of the database are collaboratively annotated, the underlying databases themselves are left unchanged. Furthermore, collaborative creation of community databases can capture emerging structure in rapidly developing fields. These database-wikis are indexes of biologically relevant data that emerge from focused and rapidly developing communities. They form a stopgap between unstructured discussion in fora and on mailing lists and the 'mature' databases that emerge subsequently. Hence they can be useful for discerning trends and promoting best practices, as well as ?collect unique and timely information. In the future, collaborative 'wiki' updates of almost all database contents can be envisaged. However several important issues need to be addressed: ? ?* How reliable are user contributions? ? ?* What format should annotations take? ? ?* How is this information feed back into 'authoritative' databases? Procedures should be implemented to support assessment of users' contributions, extraction of structured data from annotations, uptake of original data into reference databases. The authoritativeness of contributions is essential: how can quality be assessed? How do we deal with contributions from casual end users, since these are usually not considered adequate when compared with professional annotation at service centers. Can the open edition model of many wiki systems, e.g. Wikipedia, be as successful in life sciences? ?Alternatively, should the usual criteria for assessing quality of research be applied, including peer-evaluation of contributions and identification of users? Crediting users for their contributions (e.g. authorship assignment) may be necessary to stimulate ?the broadest possible participation. ?Which further benefits may be imagined to acknowledge user investment (subscriptions to services, journals, ...)? Special features may be required to cater for the specificity of biological data: textual information is only a small part of biological data, how can the numerous and heterogeneous biological data types be catered for, e.g. ?images, plots, diagrams? An adaptation of current wiki systems is needed. A survey of existing systems as well as current development efforts will be useful, so that possible synergies can be identified and supported, as well as ensure a coherent set of interoperable biological wikis. TOPICS The following list is not meant to be exclusive of any further topics as stated above. Submitted contributions should address one or more of the following topics: ? ?* Wiki development tools ? ? ? ? ?o Wikimedia ? ? ? ? ?o Wikimedia extensions ? ? ? ? ?o Semantic Wikis ? ? ? ? ?o Wiki-coupled CMSs ? ? ? ? ?o Other wikis ? ?* Arising issues for the biomedical domain: ? ? ? ? ?o Authoritativeness of contributions and sites ? ? ? ? ?o Quality assessment ? ? ? ? ?o Users acknowledgement ? ? ? ? ?o Stimulatation of quality contributions ? ? ? ? ?o Authorships management and reward ? ? ? ? ?o 'Scientific production' value for contributions ? ? ? ? ?o Management of bioinformatics data types ? ?* Wikis and collaborative systems for: ? ? ? ? ?o Genomics, proteomics, metabolomics, any -omics ? ? ? ? ?o Proteins analysis and visualization ? ? ? ? ?o gene and proteins interactions ? ? ? ? ?o metabolic pathways ? ? ? ? ?o oncology research ? ?* Issues to be tackled by wiki and collaborative research for: ? ? ? ? ?o Genomics, proteomics, metabolomics, any -omics ? ? ? ? ?o Proteins analysis and visualization ? ? ? ? ?o gene and proteins interactions ? ? ? ? ?o metabolic pathways ? ? ? ? ?o oncology research TYPE OF CONTRIBUTIONS The following possible contributions are sought: ? ?* Oral communications ? ?* Posters ? ?* Software demos All accepted contributions will be published in the proceedings of the workshop. DEADLINES * ?September 24, 2010: Oral communications submission ? ? ? ? ?o Decisions announced: October 24, 2010 * October 17, 2010: Posters submission ? ? ? ? ?o Decisions announced: October 24, 2010 * October 29, 2010: Early registration ends * November 29 - December 1, 2010: Workshop and Tutorials INSTRUCTIONS Kindly follow the instructions carefully when preparing your contribution and submit your contribution through the EasyChair system at http://www.easychair.org/conferences/?conf=nettab2010. All contributions should follow the same format, as specified here: font type: Times New Roman, font size: 12 pti, page size: A4, left and right margins: 2.0 cm, upper margin: 2.5 cm, lower margin: 2.0 cm. The lenght of contributions for oral communications should be between 3 and 5 pages, including tables and figures. They should include: Abstract, Introduction, Methods, Results and Discussion, References. All contributions for oral communications will be evaluated by at least three referees. The length of contributions for posters should be no more then 3 pages, including tables and figures. They should include: Introduction, Methods, Results, References. All posters will be evaluated on the basis of their relevance fot the workshop's topics only. For any further information or clarification, please contact the organization by email at info at nettab.org. ORGANIZATION Co-chairs ? ?* Angelo Facchiano, CNR-ISA, Avellino, Italy ? ?* Paolo Romano, National Cancer Research Institute, Genoa, Italy Scientific Committee ? ?* Claudia Angelini, IAC, National Research Council, Napoli, Italy ? ?* Roland Barriot, Universit? Paul Sabatier - CNRS, Toulouse, France ? ?* Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, United Kingdom ? ?* Dan Bolser, University of Dundee, Scotland, United kingdom ? ?* Philip E. Bourne, University of California, San Diego UCSD, La Jolla, USA ? ?* Mike Carasio, Keygene N.V., Wageningen, The Netherlands ? ?* Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, Italy ? ?* Italia De Feis, IAC, National Research Council, Napoli, Italy ? ?* Angelo Facchiano, ISA, National Research Council, Avellino, Italy ? ?* Carl Herrmann, Universit? de la M?diterran?e, Marseille, France ? ?* Pascal Hingamp, Universit? de la M?diterran?e, Marseille, France ? ?* Eran Hodis, Weizmann Institute of Science, Rehovot, Israel ? ?* Robert Hoffmann, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, USA ? ?* Thomas Kelder, BiGCaT Bioinformatics, University of Maastricht, The Netherlands ? ?* Alexander Pico, The Gladstone Institutes, University of California, San Francisco, USA ? ?* Jaime Prilusky, Bioinformatics, Weizmann Institute of Science, Rehovot, Israel ? ?* Paolo Romano, Bioinformatics, National Cancer Research Institute, Italy ? ?* Andrew Su, Bioinformatics, Genomics Institute of the Novartis Research Foundation, San Diego, USA ? ?* Joel Sussman, Weizmann Institute of Science, Rehovot, Israel ? ?* Tim Vickers, Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, USA ? ?* Wyeth Wasserman, Department of Medical Genetics, University of British Columbia, Vancouver, Canada ? ?* and further members yet to be confirmed Organizing Committee ? ?* Claudia Angelini, IAC, National Research Council, Napoli, Italy ? ?* Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, Italy ? ?* Italia De Feis, IAC, National Research Council, Napoli, Italy ? ?* Angelo Facchiano, ISA, National Research Council, Avellino, Italy ? ?* Paolo Romano, Bioinformatics, National Cancer Research Institute, Genoa, Italy Supporting Institutes, Scientific Societies and Projects This list is still under definition. ? * National Research Council (CNR), Italy ? * National Cancer Research Institute (IST), Genoa, Italy ? * Italian Network for Oncology Bioinformatics (RNBIO) Sponsors Sponsorships are still under definition. You are welcome to email us for further information if you are interested in sponsoring this workshop. We look forward to meeting you in Naples! Paolo Romano and Angelo Facchiano ?on behalf of the Scientific Committee Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 ?Fax: +39-010-5737-295 ?Skype: p.romano Web: http://www.nettab.org/promano/ _______________________________________________ Nettab-Announce mailing list Nettab-Announce at istge.it http://webmail.istge.it/mailman/listinfo/nettab-announce From anne.smith at st-andrews.ac.uk Fri Jul 9 08:42:52 2010 From: anne.smith at st-andrews.ac.uk (V. Anne Smith) Date: Fri, 9 Jul 2010 08:42:52 +0100 Subject: [Sbforum-general] Job vacancy: Postdoc in Cancer Systems Biology/Bioinformatics/Machine Learning Message-ID: Postdoc in Cancer Systems Biology/Bioinformatics/Machine Learning A 3-year postdoctoral position is available in the laboratory of Dr V Anne Smith to perform systems biology research aiming to improve predictive patient selection for ovarian cancer. The project is part of a collaborative effort with researchers at the Edinburgh Cancer Research Centre under the auspices of Centre for Research in Informatics and Systems Pathology (CRISP). You will work with gene and protein data collected by our Edinburgh colleagues from xenograft and clinical samples; you will apply Bayesian network inference algorithms to identify biomarker pathways predicting patient response to therapy. You should have a PhD in Systems or Computational Biology, a Computational Science, or related field, strong computer programming skills, and a desire to perform clinically relevant systems biology research. Informal enquiries to Dr V Anne Smith, email: anne.smith at st-andrews.ac.uk and for further information about the lab please visit http://biology.st-andrews.ac.uk/vannesmithlab/. Please make formal applications through University of St Andrews HR via: https://www.vacancies.st-andrews.ac.uk/ -- Dr V Anne Smith School of Biology Sir Harold Mitchell Building University of St Andrews St Andrews, Fife KY16 9TH United Kingdom +44 (0)1334-463368 anne.smith at st-andrews.ac.uk biology.st-andrews.ac.uk/vannesmithlab/ The University of St Andrews is a charity registered in Scotland : No SC013532? From sandra.borthwick at sbforum.org Wed Jul 28 16:08:33 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Wed, 28 Jul 2010 16:08:33 +0100 Subject: [Sbforum-general] SBF/S3 - Storing, Accessing and Sharing Data: Addressing the Challenges and Solutions Message-ID: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Storing, Accessing and Sharing Data: Addressing the Challenges and Solutions Date: 9th September 2010 Location: Royal Society of Edinburgh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The event will showcase how technology can underpin the requirements for biomedical and life science research data management and sharing in Universities and other research organisations. Addressed will be the feasibility of achieving data storage, access, and sharing from a technological perspective. The areas that will be addressed/considered are: o Cost effectively storing Data o Data Mobility/ Accessibility/ Transfer of data o Meta Data ? best ways to store the data and also how to make sure the right people can access the material and the wrong people can?t! o Effectively managing different data types e.g from millions of small files to lots of large image files o Indexing the data and being able to recover the right information o Data sustainability and Durability (is it appropriate to move data to tape and if so when and how do you futureproof this?) o Tiering of Data to help reduce cost (and the automation of this) o Scalability o Building a resilient infrastructure For more information and registration details please see: http://www.sbforum.org/events.php?e_id=95 *** Programme and to follow shortly *** Thank you for your time, we look forward to seeing you on 9th September. -- Sandra Borthwick, Executive Assistant Scottish Bioinformatics Forum The Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel:? +44 (0)131 240 2783 Fax: +44 (0)131 240 2786 email: sandra.borthwick at sbforum.org www.sbforum.org 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ The SBF is a project of the RSE Scotland Foundation, Scottish Charity No. SC024636 The information contained in this e-mail is confidential, intended for the above named individual/s and may be legally privileged. This message may contain personal views which are not the views of the Foundation/Forum, unless specifically stated www.rsescotlandfoundation.org.uk? www.sbforum.org