November 2010 - BBClist - maillist.psb.ugent.be

CFP: ECAL 2011 in Paris
by Tom Lenaerts 30 Nov '10

30 Nov '10

==================== C A L L F O R P A P E R S : E C A L 2 0 1 1 << Back to the origins of Alife >> ECAL 2011, European Conference on Artificial Life, an international conference on the simulation and synthesis of living systems 8-12 August 2011, Paris, France www.ecal11.org ==================== Artificial Life is an interdisciplinary undertaking that investigates the fundamental properties of living systems through the simulation and synthesis of biological entities and processes. It also attempts to design and build artificial systems that display properties of organisms, or societies of organisms, out of abiotic or virtual parts. ECAL, the European Conference on Artificial Life, is a biennial event that alternates with the US-based Alife conference series. In the early 1990's, the first two ECAL conferences in Paris and Brussels were mainly centered on theoretical biology and the physics of complex systems. Today, we feel that Alife can look back on these origins and take more inspiration from new developments at the intersection between computer science and theoretical biology — thus it is our wish to refocus the conference on complex biological systems. Closing a loop, this ECAL will mark the 20th anniversary of the 1st ECAL and will be framed as a tribute to the late Francisco Varela, co-organizer in 1991 with two of this year's committee members (Paul Bourgine and Hugues Bersini). You are invited to submit papers to this exciting event! (Please forward this call responsibly.) IMPORTANT DATES --------------------- o Paper and abstract submission: 6 April 2011 o Paper and abstract notification: 10 June 2011 o Camera ready papers: 1 July 2011 o Early registration: 10 June 2011 o End of registration: 31 July 2011 THEMES --------------------- A new body of disciplines: Over the past two decades, biological knowledge has grown at an unprecedented rate, giving rise to new disciplines such as systems biology —- testimony of the striking progress of modeling and quantitative methods across the field. During the same period, highly speculative ideas have matured, and entire conferences and journals are now devoted to them. Synthesizing artificial cells, simulating large-scale biological networks, storing and making intelligent use of an exponentially growing amount of data (e.g., microarrays), exploiting biological substrates for computation and control, and deploying bio-inspired engineering are all cutting-edge topics today. ECAL 2011 will leverage the remarkable development of biological modeling and extend the topics of Artificial Life to the fundamental properties of living organisms: their multiscale pattern-forming morphodynamics, their autopoiesis, robustness, capacity to self-repair, cognitive capacities, and co-adaptation at all levels, including ecological ones. ECAL 2011 will bring together a large interdisciplinary community of biologists, computer scientists, physicists, and mathematicians. It will invite them to reflect on how traditional boundaries between disciplines have become blurred, and to revisit in depth what constitutes “life”. Papers are welcome in all areas of the field, including: - Artificial Chemistries - Biological & Chemical Information Processing and Production - Complex Networks - Emergent Engineering - Evolutionary and Learning Dynamics - Minimal Cognition and Physical Intelligence - Minimal (Bottom up) Synthetic Cells - Mixed Living (Technology) Systems - Modular Robotics - Multilevel Ecologies - Organizations & Collective Intelligence - Origins of Life - Protocellular Energetics & Metabolic Networks - Philosophy of Artificial Life & Living Technology - Robotic Energy Autonomy - Robotic Self-Assembly - (Chemical) Self-Assembly & Complexity - Socio-Technical Systems - Systems Biology - Swarm Intelligence - Theoretical and Computational Frameworks - Top Down Artificial Cells All authors are encouraged to explain how their work sheds light on the fundamental properties of living systems and makes progress on the important open questions identified during previous meetings. PAPER/ABSTRACT FORMAT --------------------- There are two options for submission: either full paper format or abstract format. 1. Full papers have an 8-page maximum length, which should report on new, unpublished work 2. Abstracts are limited to 2 pages and should discuss work previously published in a journal. It is therefore essential that a reference to the previously published article is cited. All submissions will be subject to peer review, and all accepted submissions will be allocated either an oral presentation slot or a poster slot with no distinction being made between the two submission formats. All formatting guidelines (including Word and LaTeX style files) and submission instructions will be available on the conference website within the next few weeks athttp://www.ecal11.org/call-for-papers PUBLICATION --------------------- Every accepted full-paper and abstract submission will be published by MIT Press in a single online open-access proceedings volume. The top 10 accepted publications will have the opportunity to publish a revised and expanded version of their conference paper in the Artificial Life journal. LOCATION --------------------- The conference will be held at the Cité Internationale Universitaire de Paris (CIUP), located on a wooded park at the southern edge of the French capital. See more information at http://www.ecal11.org/venue Registration information will be posted soon at http://www.ecal11.org/registration ORGANIZATION --------------------- * René Doursat, Chair * Hugues Bersini * Paul Bourgine * Mario Giacobini & Tom Lenaerts, Program Chairs * Marco Dorigo CONTACT --------------------- For further information about the conference program and travel arrangements, please see the website, http://www.ecal11.org. For questions about the submission, reviewing process and other issues, email to: contact(a)ecal11.org.

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Systems Biology Symposium, Amsterdam
by Lodewyk Wessels 28 Nov '10

28 Nov '10

The NWO-ZonMW Centers for Systems Biology Research and the NCSB invite you to the following one-day symposium: 'Cancer Systems Biology' 4 February 2011 NH Barbizon Palace, Amsterdam Speakers: Ursula Klingmuller | DKFZ, Heidelberg, Germany Tomer Shlomi | Israel Institute of Technology, Haifa, Israel Rene Bernards |The Netherlands Cancer Institute, Amsterdam, The Netherlands Mike White | University of Liverpool, Liverpool, UK Stephen Friend | Sage Bionetworks, Seattle, USA Douglas Lauffenburger | MIT, Cambridge, MA, USA Registration: Attendance is free of charge but registration required Please register before 10 December 2010 Registration and program: csbc.nki.nl Organizers | Lodewyk Wessels, Jan Smeitink, Barbara Bakker, Frank Bruggeman

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Systems Biology position at Janssen in Beerse
by Van Vlijmen, Herman [TIBBE] 23 Nov '10

23 Nov '10

Scientist Systems Biology Background : In several of the strategic disease areas where the company is active, it is now believed that drug discovery will provide more robust and safe therapeutics by moving from a reductionist, single target view to an integrative pathway/networks approach. Recent advances have shown the predictive value of probabilistic network control models that integrate experimental data and biological and disease knowledge. Combined with interpretational skills based on cellular, molecular and disease biology knowledge, clear gains can be expected from such systems biology approaches in several components of the discovery chain: at its onset, for the identification of therapeutically relevant cellular processes and molecular readouts; after compound selection for the identification of its mechanisms of action and non-pharmacological side effects; and for the early articulation of the benefits of polypharmacology. The Role To bridge the gaps between experimental evidence, especially from high-dimensional platforms (-omics), actual scientific knowledge, and objectives of the compound discovery teams, the company wishes to recruit in the Research Informatics & Integrated Genomics group a scientist with skills that combine state-of-the-art computational biology modeling with solidly reasoned interpretation of experimental results in discovery models. Qualifications * PhD or MD/PhD in Molecular or Cell Biology or related field. * A proven track record in experimental disease models is an advantage. * Experience in the pharma/life science industry is desirable. * Solid experience and strong understanding of probabilistic computing modeling of (heterogeneous) genome-scale data and biological (pathway) information using, among others, bayesian network methodologies. * Proficiency in the use of computational and visualization tools for the analysis of high-dimensional data. * Experience with analysis of biology of the diseased state with the clear ability, while liaising with discovery biologist team members, to identify testable hypotheses to corroborate the proposed biological control system, in a relevant fashion for the therapeutic area goals. * Excellent interpersonal, networking and communication skills - the ability to operate in a team setting within a complex, matrix, multicultural environment and to interact with people at all levels within the organization and externally * Excellent command of English, spoken and written. Contact: hvvlijme at its.jnj.com

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Topical Day on Bioinformatics (Friday 19/11/2010 in Mol)
by Janssen Paul 08 Nov '10

08 Nov '10

=============================================== Topical Day on Bioinformatics: From Base to Byte and back =============================================== A few places are still available. http://www.sckcen.be/en/Events/TD_BIOINFO Deadline of registration is 10 November Best Regards, Paul Janssen Dr. Ir. Paul J.D. Janssen Molecular and Cellular Biology - Unit of Microbiology Institute for Environment, Health and Safety (EHS) Belgian Nuclear Research Centre SCK/CEN Boeretang 200, B-2400-MOL, Belgium Tel: +32-(0)14-332129 Mobile: +32-(0)486-571043 http://www.sckcen.be/mcb/ SCK�CEN Disclaimer: www.sckcen.be/en/Legal-aspects/E-mail-disclaimer

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Post doc Job Anouncement - at SYSTMOD - Univeristy of Liège
by Louis Wehenkel 05 Nov '10

05 Nov '10

Dear Colleagues, We open a post-doc position in machine learning at the University of Liège, Department of Electrical Engineering and Computer Science. The candidate will work in the context of large scale machine learning and data mining, within the research unit of Systems and Modeling (see http://www.montefiore.ulg.ac.be/services/stochastic/new/doku.php) and in collaboration with PEPITe SA (see http://www.pepite.be/) in order to create innovative solutions for extracting predictive models from very high dimensional data in the form of time-series collected from complex dynamical processes. The initial contract should start early January 2011, and will be of one year. The ideal candidate should have a PhD in Machine Learning or Data Mining, and be interested by challenging real world applications. To apply, please send your CV and motivation letter to Prof. Louis Wehenkel (L.Wehenkel(a)ulg.ac.be) Best regards, Louis Wehenkel

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Integrative Bioinformatics Conference (IB2011): call for abstracts
by Jack Leunissen 04 Nov '10

04 Nov '10

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The conference website is open for registration and abstract submission now, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in Wageningen in March! On behalf of the organising committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologise if you receive this mail more than once. Prof dr JAM Leunissen Lab of Bioinformatics Wageningen University

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Bioinformatics vacancies Leiden University Medical Centre, NL (closes November 8)
by Marco Roos 04 Nov '10

04 Nov '10

L.S. The Human Genetics department of the Leiden University Medical Centre has three vacancies in its Biosemantics and Bioinformatics groups. If you are motivated by solving biological problems using statistical methods or by using emerging 'e-Science' approaches coming from the domain of computer science, then please follow one of the links below and apply BEFORE NOVEMBER 8 (apologies for the short notice). For those who do not know Leiden: Leiden is a beautiful small city in the Netherlands, about 40 minutes away from Amsterdam and accommodating the country's oldest university. The Human Genetics department is internationally highly acclaimed and engages in many international collaborations, including with e-Science institutes in the UK. Links to job advertisement: Academic Transfer <http://www.academictransfer.com/6755> Leiden University Medical Centre <http://www.lumc.nl/home/0004/23583/80611011354221/1010140108085720?setlangu…> Also see Job openings <http://www.biosemantics.org/index.php?page=jobs> on BioSemantics.org <http://BioSemantics.org> Feel free to forward this message to those who you think could be interested. Kind regards, Marco Roos Coordinator BioSemantics Group Leiden, Dept. of Human and Clinical Genetics, LUMC Many thanks, Marco -- Marco Roos (PhD) <http://home.medewerker.uva.nl/m.roos1> *BioSemantics group* <http://www.biosemantics.nl>, Human Genetics department <http://www.humgen.nl>, Leiden University Medical Centre <http://www.lumc.nl> Albinusdreef 2 2333 ZA Leiden Tel. +31 (0) 71 526 8642 Visiting address: Einthovenweg 20, Building 2, room S3-46 ** <http://adaptivedisclosure.org/>*Communities:* LinkedIn <http://www.linkedin.com/in/marcoroos>, myExperiment <http://www.myexperiment.org/users/18>

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