---------------------------------------------------- Subject: SMB Digest v08i19 SMB Digest May 14, 2008 Volume 08 Issue 19 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: Symposium in Honor of Professor René Thomas, 30-31 May, ULB Workshop: Transmission - from theory to policy, 7-9 July, U Warwick Workshop: Computation of Biochemical Pathways and Genetic Networks Sixth Annual BioMaPS/DIMACS Summer School: Chromatin Structure ... DIMACS Workshop: Models/Methodological Problems of Botanical Epi Last Call: Mathematical Tools for Multi-Scale Biological Processes PhD Studentship: French National Institute for Agricultural Research Postdoc: Ecological Modeling, UC Santa Barbara Biological Modeler: SimBiotic Software SMBnet Reminders ---------------------------------------------------- From: Marcelline Kaufman Date: Thu, 8 May 2008 11:24:52 +0200 Subject: Symposium in Honor of Professor René Thomas, 30-31 May, ULB To honor Professor René Thomas, who will celebrate his 80th birthday in May this year, and to pay tribute on this occasion to his seminal, pioneering work in a rapidly developing field, a Symposium will be held in Brussels at ULB (Universite Libre de Bruxelles), on Friday 30 and Saturday 31 May 2008, on the theme "The logic of gene regulatory networks". The Workshop will be supported by the Solvay Institutes in Physics and Chemistry (with partial support from the BioSim European Network). The poster and further details can be found on the web site of the symposium: http://www.solvayinstitutes.be/Activities/Symposium_ReneThomas/Symposium_ReneThomas.html where the program will be posted. NB: Attendance to the Symposium will be limited and requires on line pre-registration. ---------------------------------------------------- From: Thomas House Date: Fri, 9 May 2008 14:22:18 +0100 (BST) Subject: Workshop: Transmission - from theory to policy, 7-9 July, U Warwick Transmission - from theory to policy A workshop hosted by the University of Warwick 7-9 July 2008. http://www.warwick.ac.uk/go/transmission2008/ Transmission is a workshop on infectious disease epidemiology; it aims to bring together leading researchers and policy-makers, and to consider models from within-host to global scales, and how they may effectively inform public policy. Confirmed speakers include: Angela McLean, University of Oxford; Azra Ghani, Imperial College; Jon Read, University of Liverpool; Mike Boots, University of Sheffield; Graham Medley, University of Warwick; Nick Savill, University of Edinburgh; Christophe Fraser, Imperial College; Mark Woolhouse, University of Edinburgh; Matt Keeling, University of Warwick; John Edmunds, LSHTM; Ian Hall, Health Protection Agency; Neil Ferguson, Imperial College. Registration is now open, and will run throughout May. ---------------------------------------------------- From: Ursula Kummer Date: Wed, 07 May 2008 15:54:21 +0200 Subject: Workshop: Computation of Biochemical Pathways and Genetic Networks We would like to announce the 5th Workshop on Computation of Biochemical Pathways and Genetic Networks in Heidelberg, Germany. It will take place on the 22nd and 23rd of September 2008. Like its predecessors the workshop focuses on recent methodological developments in computational systems biology. This year the sessions will be: - Model merging - Model identification - Analysis of stochastic systems - New methods in nonlinear dynamics Informations are frequently updated on: http://otto.bioquant.uni-heidelberg.de/workshop08 Registration is now open. The number of participants is strictly limited to 60 and is on a first-come, first-serve basis. ---------------------------------------------------- From: Linda Casals Date: Thu, 8 May 2008 11:08:29 -0400 (EDT) Subject: Sixth Annual BioMaPS/DIMACS Summer School: Chromatin Structure ... The Sixth Annual BioMaPS/DIMACS Summer School: Chromatin Structure and Gene Regulation June 9 - 13, 2008 Life Science Auditorium, Life Sciences Building, Busch Campus, Rutgers University http://dimax.rutgers.edu/pipermail/sy-compmolecbio-global/2008-May/000171.html Organizers: Alexandre Morozov, Rutgers University, morozovp at physics.rutgers.edu Vasily Studitsky, UMDNJ, studitvm at umdnj.edu Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology. This special focus is jointly sponsored by the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), and the Biological, Mathematical, and Physical Sciences Interfaces Institute for Quantitative Biology (BioMaPS). The National Institutes of Health provides partial funding of the BioMaPS Summer School through the NIH Roadmap for Medical Research, Grant 5 K07 GM72919. ---------------------------------------------------- From: Linda Casals Date: Tue, 13 May 2008 11:10:58 -0400 (EDT) Subject: DIMACS Workshop: Models/Methodological Problems of Botanical Epi DIMACS Workshop on Models/Methodological Problems of Botanical Epidemiology October 27 - 29, 2008 DIMACS Center, CoRE Building, Rutgers University http://dimacs.rutgers.edu/Workshops/Botanical/ Organizers: Chris Gilligan, Cambridge, cag1@cus.cam.ac.uk Presented under the auspices of the Special Focus on Computational and Mathematical Epidemiology. This workshop will gather experts from the botanical epidemiology and genetics communities together with mathematicians interested in modeling using differential equations, discrete systems, and stochastic processes to investigate modeling and methodological problems of spread of disease in plants. The workshop is motivated by biological questions: How can we model: (1) invasion and persistence of plant disease in spatially-extended and heterogeneous environments, and the consequences for optimizing the spatial and temporal deployment of resistance genes; minimizing the risk of pesticide resistance; prediction of crop loss and yield; (2) the effects of changing agricultural practices (use of GM technology, change of farm, field size and landscape mosaic) and changing climate on host (crop), parasite, vectors and antagonist (biocontrol agents) dynamics; (3) the interplay between population genetics, population dynamics and epidemiology. We will confront a variety of modeling issues, including the need to construct a suite of models for spatially-extended dynamics that: goes across heterogeneous scales (from microscopic behavior in soil (porous medium) or in a plant, through single infected plants to a disease patch, multiple patches, field, region and continental scales); includes periodic forcing (due to seasonal change); involves temporally disturbed environments (with abrupt changes due to sowing, harvest and switching on and off of favorable periods for transmission); and deals with quenched systems (as host susceptibility changes with host age). Other issues include: scaling from individual to population behavior; development and testing of stochastic models for the evolution of probability distributions within and between replicate epidemics with and without; model reduction, including perturbation and asymptotics. The workshop will investigate modeling approaches including ode, pde, individual-based models including percolation, random graph, stochastic, spatially-explicit and spatially-implicit (moment closure and pairwise approximation) and metapopulation models. We will also discuss data and model testing issues, such as parameter estimation for spatially-explicit and spatially-implicit models with and without unobserved compartments; data collection for model testing and parameter estimation from lattice crops, row crops, continuum and mosaics; optimization of experimental design for parameter estimation and model discrimination; and analysis of microcosm data to distinguish demographic and environmental stochasticity. ---------------------------------------------------- From: Patrick De Leenheer Date: Mon, 12 May 2008 11:33:05 -0400 (EDT) Subject: Last Call: Mathematical Tools for Multi-Scale Biological Processes Early registration deadline (May 15) for the International Conference: *Mathematical Tools for Multi-Scale Biological Processes* Venue: Montana State University, Bozeman, MT, June 4 to June 6, 2008. Early registration ($90) and abstract due date: May 15, 2008. There is limited financial support for graduate students and postdoctoral researchers. Preliminary program and more information available at: http://www.math.ufl.edu/~deleenhe/montana/index.html ---------------------------------------------------- From: Juhui WANG Date: Tue, 13 May 2008 10:43:27 +0200 Subject: PhD Studentship: French National Institute for Agricultural Research An innovative and outstanding young scientist training program is available at the French National Institute for Agricultural Research (http://www.international.inra.fr/). The studentship will be founded for 5 years at once. The first three years will be devoted to a PhD training which is supported by three French laboratories: Team BANG contact dirk.drasdo@inria.fr at INRIA, Unit MIA; Computer Science and Applied Mathematics contact: Juhui.Wang@jouy.inra.fr, and Unit BDR (Developmental Biology and Reproduction) contact: Isabelle.Hue@jouy.inra.fr at INRA. The last two years will be devoted to a post-doc training at foreign laboratories outside France. The successful candidate will be expected to work on a funded project developing a computational model of the bovine trophoblast morphogenesis which is capable of explaining the growth and pattern formation observed in the developmental processes. The simulation method will combine individual-cell-based models (for further information on this model see http://ms.izbi.uni-leipzig.de/) with continuum equations for the intracellular regulation to investigate the effects of chemical substance production, transport and consumption on the properties of the cells and the shape of the developing embryo. Image processing is used to analyze the experimentally found development scenario. Basic optimization techniques will be used to identify the most likely out of the possible models and estimate the model parameters, and sensitivity analysis will be considered to analyze the model behavior. Applicants should have a master degree relevant to mathematical, physical, or biomedical modeling. The applicant must be highly motivated. Technical skills in basic applied mathematics and programming (C/C++, if possible: OpenGL) are necessary. The base salary is about 2000 Euros per month for the PhD training period and 2500 Euros per month for the Post-doc training period. Further information including the research context may be obtained from the persons mentioned at the first paragraph. APPLICATIONS WILL PROBABLY CLOSE BEFORE THE END OF MAY. To apply, please contact us immediately. The application might be highly competing. ---------------------------------------------------- From: Cherie Briggs Date: Tue, 13 May 2008 17:43:34 -0700 Subject: Postdoc: Ecological Modeling, UC Santa Barbara Postdoc in Ecological Modeling at UC Santa Barbara: Amphibian/chytrid fungus, host/pathogen dynamics We are searching for a creative postdoctoral researcher with experience in mathematical and/or statistical modeling to work on an NSF-funded Ecology of Infectious Disease Program project entitled: "After the crash: factors allowing host persistence following outbreaks of a highly virulent disease". This project is investigating the impacts of the recently emerged chytrid fungal pathogen, Batrachochytrium dendrobatidis, on amphibian populations. We are primarily concentrating on the Sierra Nevada and southern yellow-legged frogs (Rana muscosa and R. sierrae) in California, for which extensive experimental and long-term population data are available. We are looking for a postdoctoral researcher with strong mathematical or statistical modeling skills to help develop and parameterize models aimed at understanding the impacts of this pathogen, including effects of host diversity, behavior, age, and/or spatial structure. Excellent writing skills are required. The project involves a large interdisciplinary group of researchers, and there will be many opportunities for collaboration, and to become involved in lab and/or field work if desired. The postdoc will be in the Department of Ecology, Evolution, and Marine Biology (http://www.lifesci.ucsb.edu/eemb/) on the beautiful University of California, Santa Barbara campus (http://www.ucsb.edu/). The salary is approximately $41,000. The position is available for a minimum of 2 years, with the possibility of additional years. The start date is flexible (any time from immediately to the beginning of January 2009). Please send a CV and a brief statement of qualifications to Cherie Briggs, briggs@lifesci.ucsb.edu , by Monday, June 9, 2008. ---------------------------------------------------- From: Brynn Laird Date: Wed, 07 May 2008 16:49:36 -0600 Subject: Biological Modeler: SimBiotic Software SimBiotic Software is a leading developer of biology education software. We are looking for a self-motivated individual to program biological simulations within our modeling framework. This individual will work with others in SimBiotic to write a range of biology simulations for use in both education and research. Among the initial projects would be work on salmon response to climate change in the Pacific Northwest, and simulations for teaching ecology. We expect results from some of these models to appear in high-impact, peer-reviewed biology research and education research journals, and the person in this position would receive authorship as appropriate. This job would make a good post-doc or career for a biologist with modeling skills. The job can be based in either Boston, MA, or Missoula, MT. Start date will be in summer, 2008. For more information and to apply, please visit www.simbio.com. Please contact me directly with any questions regarding the posting of this job advertisement. Thank you! Brynn Laird Director of Sales and Production SimBiotic Software, Inc. brynn@simbio.com ---------------------------------------------------- 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. 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