---------------------------------------------------- Subject: SMB Digest v09i36 SMB Digest September 15, 2009 Volume 09 Issue 36 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: Networks: Dynamics and Flows, 28 Sept - 2 Oct, U Warwick Workshop: Health and Complex Systems, 30/11 and 01/12, Lyon Highlights from COPUS, Year of Science 2009 & Understanding Science New Book: Computational Intelligence, Springer DOTcvpSB, Matlab Toolbox for Dynamic Optimization in Systems Biology PhD Student: Computational Biology, University of Amsterdam PhD Position: Spatial Population Dynamics, Atlantic Sea Turtles ... Postdoc: Theoretical and Computational Biology, UTK Postdoc & Senior Research Positions: Computational Cell Biology, UCD Assistant Professor: Quantitative Biology, Oakland University SMBnet Reminders ---------------------------------------------------- From: "François Képès" Date: Mon, 14 Sep 2009 16:49:46 +0200 Subject: Networks: Dynamics and Flows, 28 Sept - 2 Oct, U Warwick Networks: Dynamics and Flows, 28 September - 2 October 2009, University of Warwick, Warwick Mathematics Institute. More information available on http://www2.warwick.ac.uk/fac/sci/maths/research/events/2009-2010/symposium/netwks/ A more detailed programme covering all aspects of network research can be found at http://www2.warwick.ac.uk/fac/sci/maths/research/events/2009-2010/symposium/netwks/programme/ This workshop is part of the EPSRC Symposium on the Mathematics of Complexity Science and Systems Biology http://www2.warwick.ac.uk/fac/sci/maths/research/events/2009-2010/symposium/ We have divided the workshop into several topics related to (biological) networks, see http://www2.warwick.ac.uk/fac/sci/maths/research/events/2009-2010/symposium/netwks/programme/ All travel and accommodation expenses will be covered by the workshop organisers for accepted participants. In case you can accept this invitation please contact Markus Kirkilionis mak@maths.warwick.ac.uk For booking purposes you should also register at https://www.warwick.ac.uk/mrc/register.php?event=89&linked=no&PHPSESSID=129638680a1bc19f3d1d690ac6568025 The workshop will take place a week after the European Conference on Complex Systems (ECCS'09), see http://eccs09.info ---------------------------------------------------- From: Stephane Genieys Date: Tue, 15 Sep 2009 13:45:22 +0200 Subject: Workshop: Health and Complex Systems, 30/11 and 01/12, Lyon In the framework of the 22nd "Entretiens du centre Jacques Cartier", the Complex Systems Institute of Lyon organizes the workshop "Health and Complex Systems" in Lyon, November 30 and December 1st 2009. Topics will include among others modelling of hematopoiesis, chronotherapy, diabetes treatment, HIV treatment, prion diseases, modelling in pharmacology, in infectiology, computer assisted surgery,... Speakers: Michael MACKEY, Jorge PACHECO, Samuel BERNARD, Fabien CRAUSTE, Jean CLAIRAMBAULT, Hulin WU, Carolyn CHO, Frédérique FENNETEAU, Vincent LEMAIRE, Sandy PANG, Jean-Pierre LIAUTARD, Laurent PUJO-MENJOUET, Vincent CALVEZ, John MILTON, Julien ARINO, Pierre MAGAL, Philippe CINQUIN. Organizers: France : Stéphane GENIEYS, Pablo JENSEN Québec : Jacques BELAIR, Fahima NEKKA Complete program: http://www.ixxi.fr/cartier.php ---------------------------------------------------- From: COPUS / Year of Science 2009 Date: Wed, 9 Sep 2009 16:55:17 -0400 Subject: Highlights from COPUS, Year of Science 2009 & Understanding Science Highlights from the Coalition on the Public Understanding of Science (COPUS), Year of Science 2009, and Understanding Science initiatives: 1. INTEGRATE SCIENCE AND ART - SUBMIT YOUR ZINE! Summer has come and gone and we are revving up for the Year of Science Zine-a-thon contest! These mini - magazines that pack science in the palm of your hands are a great way to have fun communicating your science through art! Don't forget that there will be fabulous prizes for winning submissions and there is still plenty of time to perfect your idea, as the deadline has been extended to November 15. http://www.yearofscience2009.org/about/zine-contest.html Be sure to share this information with your local schools! 2. This month, Year of Science participants are celebrating Biodiversity and Conservation! http://www.yearofscience2009.org/themes_biodiversity_conservation/celebrate/ 3. Featured Program from the COPUS Clarion: The Encyclopedia of Life http://www.yearofscience2009.org/about/COPUS-Clarion-September2009.pdf 4. More cool stuff: - The American Journal of Botany released three new articles this month about "How to Advance Scientific Literacy." All three are available for free viewing through October 3, 2009 on the journal Web site. For the direct links to the articles, visit the press release at: http://www.yearofscience2009.org/blog/2009/09/how-to-advance-scientific-literacy.html - Hooray for the Understanding Science Flowchart!! Because of the amazing number of requests we had for the flowchart poster last month we were inspired to create this one page handout that will be useful for sharing the resource. One side has the flowchart; the other side an article by blogger Carl Zimmer (Discover magazine) sharing his thoughts as we launched the Year of Science 2009. http://www.yearofscience2009.org/about/YoS09-CarlZimmerUndSci.pdf. - Now available: the one-page handout highlighting the Biodiversity and Conservation theme of the Year of Science, which can be used in your business, classroom, library, museum, facility. One side is blank for your own organizational YoS message! http://www.yearofscience2009.org/themes_biodiversity_conservation/YoS09SeptemberOnePage.pdf - Understanding Science Flow Chart as an 18" x 24" poster. http://undsci.berkeley.edu/lessons/pdfs/complex_flow_posterv.pdf ---------------------------------------------------- From: "Leszek Rutkowski (kik.pcz.pl)" Date: Thu, 10 Sep 2009 09:09:04 +0200 Subject: New Book: Computational Intelligence, Springer COMPUTATIONAL INTELLIGENCE Methods and Techniques Rutkowski, Leszek Original Polish edition published by Polish Scientific Publishers PWN, 2005 2008, XIV, 514 p. 242 illus., Hardcover ISBN: 978-3-540-76287-4 Online version available Online orders shipping within 2-3 days. http://www.springer.com/engineering/book/978-3-540-76287-4 ---------------------------------------------------- From: Julio R. Banga Date: Tue, 15 Sep 2009 16:39:43 +0200 Subject: DOTcvpSB, Matlab Toolbox for Dynamic Optimization in Systems Biology We are pleased to announce DOTcvpSB, a Matlab toolbox for advanced dynamic optimization in systems biology. Software and documentation are available at: http://www.iim.csic.es/~dotcvpsb/ DOTcvpSB facilitates the statement and solution of dynamic optimization (optimal control) problems related with biological systems, modelled with ODEs (although arbitrary black-box models can be handled as well). The toolbox can import SBML models for the dynamics via the SBML toolbox. Examples of problems provided with the toolbox: - optimal drug infusion to a patient - minimization of intracellular oscillations - bioreactor optimization DOTcvpSB is described in the following paper: Hirmajer, T., E. Balsa-Canto and J. R. Banga (2009) DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinformatics 2009, 10:199. http://www.biomedcentral.com/1471-2105/10/199/abstract/ More details, documentation and examples available at: http://www.iim.csic.es/~dotcvpsb/ ---------------------------------------------------- From: Jaap Kaandorp Date: Wed, 9 Sep 2009 14:48:29 +0200 Subject: PhD Student: Computational Biology, University of Amsterdam PhD student in Computational Biology for the project: "Genetic and Cellular Mechanisms for Controlled Growth" The Section computational Science (University of Amsterdam) has a vacancy for a PhD Student for the project "Genetic and Cellular Mechanisms for Controlled Growth" (38 hours per week). The project is funded by the Honda Research Institute Europe. In this project the candidate will collaborate with researchers from the Honda Research Institute Europe and should be willing to spend 1-2 months each year at this institute in Offenbach (Germany). The candidate is expected to collaborate extensively with molecular developmental biologists. The main target of the project is to develop computational models for cellular development to achieve a controlled growth. By controlled growth, we mean three mutually related properties. First, the morphological growth should stop within a limited time. This does not necessarily mean that cells should stop dividing, rather, a balance between cell proliferation and cell death should be achieved. Second, it should achieve a desired shape with a sufficient complexity. Third, it should show a certain capability of self-repairing, i.e., when a small number of the cells are destroyed, the balanced cell growth process should be able to re-generate these cells at the right place. Cellular interaction mechanisms that facilitate a structured growth will be studied. Second, evidence indicating mechanisms for controlled growth found in biology, such as the role of negative and positive feedback loops in gene regulatory networks, will be evaluated and related to those network motifs found in the computational model. Based on the understanding of the structure, dynamics and cellular behaviour of the gene regulatory network model, we will perform a case study of a GRN model for the development of cnidarians Nematostella vectensis and Acropora millepora using biological data, including spatio-temporal gene expression data (in situ hybridisations) and morphological data. Requirements Candidates should have a master's degree (or equivalent) in scientific computing or computational science, (computational) physics, (computational) chemistry or a comparable expertise. Candidates are expected to have expertise in modelling and scientific programming and an active interest in life science applications. Candidate should be able to work in an international research team. Fluency in oral and written English is required. Motivation to travel to a different country and integrate efficiently in a new research team is fundamental. More information Further information can be obtained from Dr J. A. Kaandorp, Section Computational Science, University of Amsterdam, Kruislaan 403, 1098 SJ, Amsterdam, The Netherlands, +31 20 525 7539, J.A.Kaandorp@uva.nl and Dr Y. Jin, Honda Research Institute Europe, Germany, yaochu.jin@honda-ri.de. More information (application procedure, deadlines etc.) is available on the website http://www.uva.nl/vacatures ---------------------------------------------------- From: Jean-Yves Georges Date: Fri, 11 Sep 2009 16:04:40 +0200 Subject: PhD Position: Spatial Population Dynamics, Atlantic Sea Turtles ... Announcement of a PhD position, sept 2009 *Title* Spatial population dynamics of Atlantic sea turtles in relation to oceanographic conditions and high-sea fisheries : modelling, prediction, and conservation *Host institutions* Institut Pluridisciplinaire Hubert Curien, IPHC, UMR 7178 CNRS/Université de Strasbourg, Département Ecologie, Physiologie, Ethologie; 23 rue Becquerel, 67087 Strasbourg Jean-Yves Georges, jean-yves.georges@c-strasbourg.fr Collecte Localisation Satellite, Modélisation des Ecosystèmes Marins et Monitoring par Satellites, Division océanographie spatiale; 8-10 rue Hermès, 31520 Ramonville St Agne Patrick Lehodey, plehodey@cls.fr *Project summary* Marine ecosystems are amongst the most productive, yet their inappropriate management witnesses a lack of knowledge on their functioning. Today, there is an increasing institutional concern for integrating sustainable management of exploited species in an ecosystemic approach taking into account the ecosystem dynamics in its whole, particularly for ensuring biodiversity conservation and integrating the impacts of global changes, being they either natural and/or human induced. As such the increasing fishing pressure induces risks of overexploitation of both targeted species, but also untargeted species such as endangered sea turtles. An ecostystemic approach requires new modelling tools. Recent spatial ecosystem and population dynamics models allow developing sustainable management and conservation strategies for the ecosystems and their biodiversity. Here, we propose to model the spatial population dynamics of species indicator and emblematic of marine biodiversity: the leatherback turtle Dermochelys coriacea and the olive Ridley turtle Lepidochelys olivacea, being representative of the diversity of the life history traits and of the ecology of the large populations of sea turtles in the Atlantic ocean. By doing so, we aim at predict population trends both through time and space, in relation to global change and fisheries intensification. This multidisciplinary project based on oceanography, behavioural ecology and modelling aims at: - precising the critical habitat of the two study species based on existing telemetry data gathered by IPHC-Strasbourg in order to identify the oceanographic characteristics (bathymetry, sea surface temperature, oceanographic discontinuity, surface chlorophyll, micronekton distribution) of areas exploited by sea turtles and potential overlaps with high sea fisheries; - developing, from the existing SEAPODYM ecosystemic model initially based for tunas by CLS-Toulouse, a module specific to turtles whose physiology and ecology (ectothermy, pluriannual life cycle, transoceanic migrations, deep diving performances) allow a realistic adjustment of the initial model - developing predictions on the spatial dynamics of sea turtles populations and of the natural resources they exploit by integrating available global change scenarios (IPCC) with physics-biochemical forcing based on coupled models (PISCES and IPSL-CM4). Similar studies en route presently done on tune show the relevance of such approach for assessing the complex responses of populations to multiple changes of the oceans (being they physical and/or biochemical) predicted by the increasing atmospheric CO2 levels. A preliminary simulation run recently showed strong similarities between model outputs (CLS) and field data (IPHC), indicating that the model is realistic and that the project is feasible. The project thus will permit exploring the mechanisms involved in turtle/fisheries interactions, considered as the major cause of the worldwide decline of sea turtles populations, and will provide a new management tool for concerned agencies. This project will be integrated in two projects recently funded by the ANR. *Required skills* - an academic background in oceanography with good understanding of the relationships between physical, biochemical and biological compartments in marine ecosystems, and in behavioural ecology in marine vertebrates - skills in mathematics applied to animal behaviour, data analysis, numerical modelling, with an concrete experience with modelling tools (e.g. MATLAB, R) - some field experience with marine vertebrates, ideally sea turtles *Expertise that will be acquired during the project* -in field studies, by participating to field work on sea turtles in French Guyana within the MIRETTE project http://projetmirette.fr - in behavioural ecology and spatial oceanography, from data acquisition, analysis and interpretation in specific scientific environments at IPHC-Strasbourg and CLS-Toulouse - in numerical modelling applied to spatial dynamics of ecosystems and populations *Project schedule* The position will start by 1st October 2009 for three years. Candidates should apply before 20th September for permitting final selection by the 25th September. The position will be mostly held at CLS, Toulouse, France. *Salary* Based on the national grid for PhD studentships, the net salary will be between 1000 and 1200 euros. *How to apply* Candidates can apply by sending an updated cv before the 20th September to JYGeorges jean-yves.georges@c-strasbourg.fr and PLehodey plehodey@cls.fr ---------------------------------------------------- From: Jaewook Joo Date: Wed, 09 Sep 2009 15:13:56 -0400 Subject: Postdoc: Theoretical and Computational Biology, UTK Postdoctoral Position in Theoretical and Computational Biology A postdoctoral position in quantitative biology is immediately available in the Department of Physics and National Institute for Mathematical and Biological Synthesis at University of Tennessee at Knoxville. The successful candidate will develop and analyze predictive stochastic models for cell signaling networks that play a role in immunity and will interact with experimental collaborators. The applicant is expected to meet several of the following criteria: (1) Ph.D. degree in computational biology, physical/mathematical sciences, or engineering, (2) Experience with computational simulation and analysis, (3) Solid background in at least one of statistical physics, nonlinear dynamics, and stochastic processes, and (4) Excellent collaboration and communication skills. However, a strong desire of understanding biological phenomena using quantitative methods values more than a particular set of skills. The initial appointment will be for a period of one year and renewable upon mutual agreement. Applicants should directly send a cover letter with a possible starting date, CV, publication list, and names and contact information of three references to Prof. Jaewook Joo by email (stochasticdynamics at gmail dot com). ---------------------------------------------------- From: Mary Kavanagh Date: Mon, 14 Sep 2009 14:18:52 +0100 Subject: Postdoc & Senior Research Positions: Computational Cell Biology, UCD Postdoctoral and senior research positions in COMPUTATIONAL CELL BIOLOGY Systems Biology Ireland, UCD, Dublin. We seek outstanding candidates on junior and senior levels to work on computational modeling of signaling and gene networks in mammalian cells at Systems Biology Ireland, University College Dublin. Ongoing projects include the temporal and spatial dynamics of receptor tyrosine kinase signaling and transcriptional networks that govern cell proliferation, differentiation and motility (supported by a multi-PI grant to Profs. Boris Kholodenko, Walter Kolch and Zoltan Neufeld). The successful applicant will work closely with experimentalists at the interface between mathematics, engineering and biology in a multi disciplinary research community at Systems Biology Ireland. This presents a unique opportunity for creative individuals who want to work at the cutting-edge of systems biology. You will be a part of an interdisciplinary team with national and international collaborations in the field of systems biology. The following skills and qualifications are required: 1) PhD in Biophysics, Chemical Engineering, Mathematics, or Biochemistry and evidence of practical work experience in the systems biology of signal transduction; 2) knowledge and experience of advanced mathematical modelling, including non-linear systems and non-linear dynamics, and 3) basic knowledge of cell/molecular biology. Understanding of probability theory and statistics is a plus. The complexity of the relevant problems requires at least a two years initial commitment. Benefits and salary commensurate with experience. Individuals with an interest in Systems Biology are encouraged to apply. Salary Scale: Euro 40,000 - 50,000; for experienced researcher up to Euro 76,000. Informal enquiries are welcome, please send them to systemsbiology@ucd.ie. For formal applications, please visit our website http://www.ucd.ie/hr/jobvacancies/ Closing date: 23.30hrs on Wednesday, 14th October 2009 NOTE: Applications must be submitted by the closing date and time specified. UCD are unable to accept late applications Please note at this time UCD do not require assistance from Recruitment Agencies - Any CV's submitted by Recruitment Agencies will be returned. All current recruitment which is taking place within UCD is dependent on non-Exchequer, external and self-funding sources of finance. UCD is an equal opportunities employer ---------------------------------------------------- From: Brad Roth Date: Mon, 14 Sep 2009 15:15:16 -0400 Subject: Assistant Professor: Quantitative Biology, Oakland University Assistant Professor in Quantitative Biology Oakland University is seeking an outstanding researcher in Quantitative Biology, starting January 1, 2010. Applicants from a wide variety of disciplines are welcome, including bioinformatics, mathematical modeling, biostatistics, and bioengineering. Applicants should possess a PhD in mathematics, biology, engineering, or a closely related field to the area of Quantitative Biology, and preferably additional postdoc experience. Teaching experience at the college level, or the potential to be an outstanding teacher, and extensive research experience in the area of Quantitative Biology is required. The faculty member will be hired into a department that best fits the background of the applicant, such as mathematics and statistics, biological sciences, or electrical & computer engineering. Candidates for this position must engage in interdisciplinary research that crosses department boundaries, and must use mathematical or numerical methods to solve important biomedical problems. The applicant will initially focus on developing a world-class, externally funded research program. In the long term, the applicant should have the potential to become a researcher/educator who can help establish and lead a planned Quantitative Biology PhD program. The ideal candidate should fit well with several of the established strengths at Oakland University, and should be able to contribute to biomedical research at the new Oakland University William Beaumont School of Medicine. Applicants should submit a curriculum vitae, a description of research interests, and arrange for three letters of reference to be sent to: Dr. Brad Roth, Quantitative Biology Search Committee, Dept. Physics, Oakland University, Rochester, MI 48309, or by email to roth@oakland.edu. To receive full consideration, applications should be received by October 15. Oakland University is an Equal Opportunity Employer. Women and Minorities are encouraged to apply. ---------------------------------------------------- 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 . The SMB Digest is also available on the SMB Home Page at http://smb.org/publications/SMBnet/digest/ The contents of this publication may be reproduced in whole or in part with attribution. End of SMB Digest **************************************************** ----------------------------------------------------