---------------------------------------------------- Subject: SMB Digest v08i18 SMB Digest May 6, 2008 Volume 08 Issue 18 ISSN 1086-6566 Editor: Ray Mejía ray(at)smb(dot)org Note: Information about the Society for Mathematical Biology, including an application for membership, may be found in the SMB Home Page, http://www.smb.org/ . Access the Bulletin of Mathematical Biology, the official journal of SMB, at http://www.springer.com/11538 . Inquiries about membership or BMB fulfillment should be sent to membership(at)smb(dot)org . Issue's Topics: Workshop: Adaptive Dynamics, June 4-6, Biological Station, Paimpont Symposium: Image Processing and Analysis, ICCES'09 Thailand 2nd Announcement: NN2008, July 7-11, Porto CfP: 2nd KDD Workshop: Mining Multiple Information Sources Special Track: Computational Bioimaging and Visualization, ISVC08 BioNumbers - the database of useful biological numbers Request for input for NIH Roadmap Programs Free Sample Online Access to Bioinformatics Journals from Oxford Postdoctoral Position: Computational Systems Biology, Rice U SMBnet Reminders ---------------------------------------------------- From: Joan Van Baaren Date: Thu, 01 May 2008 21:51:12 +0200 Subject: Workshop: Adaptive Dynamics, June 4-6, Biological Station, Paimpont Workshop Adaptive Dynamics of Parasitoids Invitation for contributed speakers Where : Biological Station at Paimpont When : 4-6 juin 2008 Organised by: Jacques van Alphen and Joan van Baaren (UMR CNRS 6553 ECOBIO), Université de Rennes 1, as part of the project COMPAREVOL (http://comparevol.univ-rennes1.fr/) Funded by : BEPAR (ESF), Université de Rennes 1, Agrocampus Rennes, CNRS, Rennes métropole Description of the workshop: The workshop is an initiative of the ESF Network BEPAR (http://bepar.sophia.inra.fr/). The workshop will bring together leading scientists in the field of adaptive dynamics with experts on parasitoid behavioural ecology, in the aim to advance our understanding of the evolution of parasitoid diversity by adaptive speciation by host and habitat shifts. It second aim is to study how behavioural ecological theory can be merged with adaptive dynamics to study host shifts in parasitoids in adaptive dynamics models rich in behavioural details. (i) scientific summary Much of the theory developed for understanding and predicting the evolution of behavioural and life-history traits of parasitoids is based on simplified optimization approaches, which are applicable only if selection is frequency-independent. In contrast, empirical ecological research reveals the ubiquity of frequency-dependent selection pressures on almost all life history traits of interest. Such frequency dependence occurs whenever selection depends on the phenotypic composition of a population, which is the rule in natural systems Even, when frequency dependent selection is taken into account for by using a game theoretical approach, the environment is generally considered to be static. Adaptive dynamics theory can resolve this mismatch between theory and the real world. Adaptive dynamics is a recent body of theory, which is quite successful in modelling evolutionary processes that are difficult to analyze with classical game theoretical models or population genetic models. The method takes into account that an evolutionary change in an organism causes also a change in the way the organism experiences its environment. This allows an evolving population to escape from a fitness valley and reach a new fitness maximum. The method is particularly successful in explaining evolutionary branching and hence in modelling speciation events. Hymenopteran insect parasitoids are disputably the second most species-rich group of insects after the coleopterans, with an estimated number of species well in excess of 200,000. The presence of species rich genera with sympatric species specialized in exploiting different but related host species, host plants or different habitats, suggest that ecological speciation by host or habitat shifts plays an important role in evolutionary radiation and speciation of parasitoids. A key to understanding host and habitat shifts in parasitoids is the foraging behaviour of female parasitoids. Parasitoid foraging behaviour is under strong natural selection because each step in a sequence of behavioural decisions has consequences for the number of offspring produced during adult lifespan. Parasitoids must first find the habitat of its host, often by attraction to olfactory cues, next they must search the host habitat to find a host. After encountering a host the parasitoid must decide if she accepts or rejects the host, and if a host is accepted how many eggs should be laid and which sex the offspring should have. Finally, parasitoids must decide how long to continue searching in a particular host habitat. A rich literature of deductive behavioural ecological models predicts the optimal decisions for each of these steps in a particular environment and there is ample empirical evidence showing that parasitoid foraging behaviour is often close to the predicted optimum for that environment. Moreover, comparative studies based on independent contrasts between phylogenetically close species have provided further evidence that parasitoid foraging behaviour is adaptive. Behavioural ecological evidence, thus, suggests that a parasitoid female choosing a different habitat to search for hosts, or accepting a new host species, would have a high probability decreasing her fitness and hence that host and habitat shifts would be difficult. In contrast, adaptive dynamics theory shows how selection originating from local ecological interactions may drive surprisingly rapid adaptive radiations. However, adaptive dynamics models so far lack the behavioural details of interest to behavioural ecologists. The evolutionary dynamics of parasitoid biodiversity, in particular ecological speciation by host or habitat shifts has so far received little attention. By combining the expertise of parasitoid behavioural ecologists with that of adaptive dynamics theorists, the ecological, evolutionary, and environmental factors that cause the formation, maintenance, and loss of parasitoid species could be characterised. Such an endeavour could provide an explanation for the exceptional biodiversity of parasitoids. Adaptive dynamics theory studies the process of adaptation by implicitly considering the population dynamics of the populations under selection. It would, therefore, also provide a theoretical basis for understanding and predicting the changes in biodiversity in relation to massive changes in land use and progressive changes in climate. The latter is urgent, as insect parasitoids play a key role in the natural and biological control of herbivorous insects, and loss of parasitoid biodiversity could result in insect pest outbreaks and economic losses. It is, thus, timely to bring together parasitoid behavioural ecologists and theoreticians working on adaptive dynamics to study how adaptive speciation by host and habitat shifts could result in radiation and explain the enormous diversity in the parasitic hymenoptera or how evolutionary dynamics may result is species extinctions. The Workshop will be held at the University of Rennes? field station in the Forêt de Paimpont. http://ecobio.univ-rennes1.fr/files/downloads/adaptive_dynamics_of_parasitoids.pdf Six half-day sessions have been programmed: Session 1: Recent advances in evolutionary ecology of parasitoids Session 2: Recent advances in adaptive dynamics Session 3: Adaptive radiations and dynamic games Session 4: Life history trade-offs and the dynamics of parasitoid-host systems Session 5: Adaptive dynamics of parasitic host systems Session 6: Round table and general discussion ---------------------------------------------------- From: João Manuel R. S. Tavares Date: Fri, 2 May 2008 14:51:56 +0100 Subject: Symposium: Image Processing and Analysis, ICCES'09 Thailand Symposium "Image Processing and Analysis" International Conference on Computational & Experimental Engineering and Sciences 2009 (ICCES'09) Phuket, Thailand, 8-13 April 2009 http://icces.org/cgi-bin/ices09/pages/index Dear Colleague, Within the International Conference on Computational & Experimental Engineering and Sciences 2009 (ICCES'09), to be held in Phuket, Thailand, in 8-13 April 2009, we are organizing the Symposium "Image Processing and Analysis". Examples of some topics that will be considered in that symposium are: Image restoring, Description, Compression, Segmentation and Description; Objects tracking, Matching, Reconstruction and Registration; Visualization Enhance; Simulation and Animation; Software Development for Image Processing and Analysis; Grid Computing in Image Processing and Analysis; Applications of Image Processing and Analysis. Due to your research activities in those fields, we would like to invite you to submit your work and participate in the Symposium "Image Processing and Analysis". For instructions and submission, please access to the conference website at: http://icces.org/cgi-bin/ices09/pages/index. Please note, when submitting your work you should choose the Symposium "Image Processing and Analysis". Important dates and Instructions: - 15 Oct 2008: Start abstract submission; - 1 Jan 2009: Deadline for abstract submission; - 10 Jan 2009: End of abstract selection. If you intend to submit your work please notify as soon as possible the main organizer of your intention (tavares@fe.up.pt); Instructions for authors are available at: http://icces.org/cgi-bin/ices09/pages/guide. ---------------------------------------------------- From: alexandra Date: Tue, 6 May 2008 15:49:59 +0100 Subject: 2nd Announcement: NN2008, July 7-11, Porto SUMMER SCHOOL NN2008 NEURAL NETWORKS in CLASSIFICATION, REGRESSION and DATA MINING July 7-11, 2008, Porto, Portugal http://www.nn.isep.ipp.pt email: nn-2008@isep.ipp.pt GENERAL INFORMATION The Summer School will be held at Porto, Portugal, jointly organized by the Polytechnic School of Engineering of Porto (ISEP) and the Faculty of Engineering, Porto University (FEUP). IMPORTANT DEADLINES Early Registration: 18 May 2008 Poster Submission: 15 June 2008 Hotel booking : 15 June 2008 Summer School: 7-11 July 2008 All participants are required to register prior to the start of the School - until the June 15 - even if you choose to pay the late registration fee at the registration desk. Please note that only a LIMITED number of participants can be accepted. ---------------------------------------------------- From: Xingquan Zhu Date: Tue, 06 May 2008 12:09:14 -0400 Subject: CfP: 2nd KDD Workshop: Mining Multiple Information Sources The 2nd ACM KDD Workshop on Mining Multiple Information Sources (MMIS-08) In conjunction with ACM SIGKDD-08, August 24, 2008 http://www.cse.fau.edu/~xqzhu/mmis/kdd08_mmis.html Deadline of Paper Submission: May 30, 2008 Acceptance Notification: June 15, 2008 Camera-ready Paper Submission: June 20, 2008 ---------------------------------------------------- From: João Manuel R. S. Tavares Date: Tue, 6 May 2008 17:29:57 +0100 Subject: Special Track: Computational Bioimaging and Visualization, ISVC08 Special Track "Computational Bioimaging and Visualization" International Symposium on Visual Computing (ISVC08) Las Vegas, Nevada, USA, December 1-3, 2008 http://www.isvc.net Dear Colleague, Within the ISVC08 - International Symposium on Visual Computing (http://www.isvc.net), to be held in Las Vegas, Nevada, USA, in December 1-3, 2008, we are organizing the Special Track "Computational Bioimaging and Visualization". The main goal of the Special Track "Computational Bioimaging and Visualization" is to bring together researchers involved in the related fields (Image Acquisition, Image Segmentation, Objects Tracking, Objects Matching, Shape Reconstruction, Motion and Deformation Analysis, Medical Imaging, Scientific Visualization, Software Development, Grid Computing, etc.), in order to set the major lines of development for the near future. Therefore, this Special Track will bring researchers representing various fields related to Computational Vision, Computer Graphics, Computational Mechanics, Scientific Visualization, Mathematics, Statistics, Medical Imaging, etc. Thus, it will endeavor to contribute to obtain better solutions for more realistic computational "living" models from images, and attempts to establish a bridge between the researchers from these diverse fields. ---------------------------------------------------- From: "Milo, Ron" Date: Mon, 5 May 2008 09:42:03 -0400 Subject: BioNumbers - the database of useful biological numbers BioNumbers (http://bionumbers.hms.harvard.edu/) is a wiki like community effort started at Harvard Systems Biology department to build a database of useful biological numbers. It will enable you to find in one minute any common biological number that can be important for your research, such as the rate of translation of the ribosome, concentrations of metabolites or the number of bacteria in your gut. You will find full reference, comments and related numbers that are useful. Check it out at www.bioNumbers.org. ---------------------------------------------------- From: "Murcia, Ellie (NIH/OD) [E]" Date: Wed, 30 Apr 2008 14:57:45 -0400 Subject: Request for input for NIH Roadmap Programs Dear Colleague: I invite you to participate in a process designed to identify major, cross-cutting challenges to health research and to articulate solutions to these challenges. The NIH Roadmap for Medical Research, funded via the NIH Common Fund, is a series of programs that collectively seek to transform the way health research is conducted so that treatment, diagnosis, prevention, and/or understanding of human disease may be accelerated. Roadmap programs are intended to be stimulatory and are therefore supported by the Common Fund for a maximum of 10 years. These programs accept a high degree of risk to approach complex problems in new ways, to develop transformative tools and technologies, and/or to address fundamental knowledge gaps that impede progress in many disease areas. Each Roadmap program cuts across the missions of NIH Institutes and Centers as well across diseases and is expected to accelerate research on many diseases and conditions. On April 22, 2008, NIH released a Request for Information (RFI) http://grants.nih.gov/grants/guide/notice-files/NOT-RM-08-014.html inviting input and ideas from the scientific community, health professionals, patient advocates, and the general public about major cross-cutting challenges and possible solutions. Collecting these ideas is an initial step in the process of identifying a new cohort of Common Fund / Roadmap programs for Fiscal Year 2011. This RFI provides an opportunity for respondents to submit their own ideas. The NIH expects to spend $30 - 50 million per year from within the currently projected Roadmap budget for new 5-year initiatives. More information on this request can be found at: http://nihroadmap.nih.gov/ I appreciate your time and look forward to your participation in this process. Sincerely, Alan M. Krensky, M.D. Director Office of Portfolio Analysis and Strategic Initiatives (OPASI) National Institutes of Health ---------------------------------------------------- From: "Rawling, Michelle" Date: Fri, 2 May 2008 13:56:03 -0400 Subject: Free Sample Online Access to Bioinformatics Journals from Oxford Free online access to highly ranked bioinformatics journals from Oxford Journals Oxford Journals publishes Bioinformatics, Briefings in Bioinformatics, and Briefings in Functional Genomics and Proteomics, a trio of top bioinformatics journals. Briefings in Bioinformatics received a stunning 24.370 for its first impact factor in the 2006 ISI Journal Citation Reports. Meanwhile, Bioinformatics was ranked 1/87 in Computer Science, Interdisciplinary Applications, and 1/83 in Statistics and Probability with an impact factor of 4.894. Oxford Journals would like to offer you the exciting opportunity to access these three bioinformatics journals with a free online trial subscription. You can access all online articles, from past issues to current, until 15 August 2008, with no obligation to purchase in the future. Visit http://www.oxfordjournals.org/page/3218/3 for instructions on how to activate your trial. ---------------------------------------------------- From: Oleg Igoshin Date: Thu, 1 May 2008 17:01:36 -0500 Subject: Postdoctoral Position: Computational Systems Biology, Rice U Postdoctoral Position in Computational Systems Biology and Bioengineering is available in the laboratory of Prof. Igoshin in the Dept of Bioengineering at Rice University. In our research we use computational and theoretical tools of engineering to study microbiological systems. We are recruiting one postdoctoral researcher to work on integrative modeling of master-level regulation circuits in bacteria with particular focus on bacterial stress response and bacterial development (sporulation). RESPONSIBILITIES: The postdoctoral fellow will be responsible for the construction of mathematical models of the gene networks regulating bacterial sporulation based on available biological data of our collaborators. Numerical solution and analysis of deterministic and stochastic ordinary differential equations, partial differential equations are the essential computational techniques of our research. In addition statistical quantification and processing of experimental data (time-lapse microscopy images) will be required. Proposed research will be conducted in tight collaboration with experimental colleagues and the main results are at least partially expected to be published in biological journals. Interested researchers will have an option to design and perform experimental work in the lab of collaborators. QUALIFICATIONS: PhD in science or engineering is required for this position. Candidates are required to have experience in mathematical and computational modeling of biochemical networks as well as some knowledge of microbial physiology and molecular biology. Candidates with publications in the field of mathematical/computational biology are strongly preferred. Previous experience in computational biophysics, mathematical biology, statistics, image processing or bioinformatics is a plus. Strong interest in interdisciplinary collaboration and English proficiency are also expected. ABOUT RICE AND HOUSTON: Rice is consistently ranked as one of the nation&'s best teaching and research universities. It is a member institution of the world largest Medical Center (TMC). The Department of Bioengineering is consistently ranked among the nation's top 10 bioengineering graduate programs. Rice is situated in the Museum district of Houston, TX; forth largest city in the US. CONDITIONS: Rice University is committed to affirmative action and equal opportunity employer and offers competitive postdoctoral salary and benefits. The position is open from July 1, 2008 until filled. The initial appointment is for 1 year with possible continuation depending on secured funding. Please visit http://www.owlnet.rice.edu/~oi1/ or contact Prof. Igoshin for more information. Applicants should submit their resume and letter stating their research interests to igoshin@rice.edu ---------------------------------------------------- Subject: SMBnet Reminders To subscribe to the SMB Digest please point your browser at http://list.auckland.ac.nz/mailman/listinfo/math-smbnet and complete the subscription information. Alternatively, if you prefer to simply receive notice when the next issue is available, send mail to LISTSERV@listserv.biu.ac.il with "subscribe SMBnet Your Name" in the body of the mail (omit the quotes and include your name). After you subscribe, you will receive a greeting with additional information. Submissions to appear in the SMB Digest may be sent to SMBnet(at)smb(dot)org Items of interest to the mathematical biology community may be submitted for inclusion in the SMBnet archive. See instructions at: http://smb.org/publications/SMBnet/pubs/fyi . 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