---------------------------------------------------- Subject: SMB Digest v10i25 SMB Digest June 24, 2010 Volume 10 Issue 25 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: Colloquium: Life Sciences in Society, Sept 28, Collège de France, Paris Distance Courses in Computational Biology, University of Manchester Register Now: Microscopy, Modeling and Biophysical Methods HiBi 2010, Deadline Extension to July 1 CfP: STCAN 2010, December 1-3, Boston PhD Position: Systems Biology, Edinburgh Postdoc: Computational Systems Biology, Rice University Postdoc: Mathematical Modeling of Biological Systems, Texas A&M U Postdoc: Dynamic Medical Image Modeling & Analysis, URMC SMBnet Reminders ---------------------------------------------------- From: Date: Wed, Jun 2, 2010 at 3:25 PM Subject: Colloquium: Life Sciences in Society, Sept 28, Collège de France, Paris Registration Open - Early Registration before July 30th Ever since Paul Berg's call in the early 1970s for contemporary debates on stem cells or synthetic biology and more recent controversies concerning GMOs, the life sciences and technologies have been at the heart of the relationship between science and society. What types of regulations and controls should be placed on scientific research? Is regulation of the applications of research enough, or should research itself be regulated? Where does research freedom stop and at what point should a researcher's sense of responsibility start to intervene? Should the public be informed? How can public debates on these issues be organized? The objective of this joint Genopole®-IFRIS initiative is to revisit these questions by organizing a dialogue between life science and the human & social sciences. We intend to use what has been learned over the last four decades to clarify the most contemporary issues. The goal is to (i) avoid a position which would create a head-to-head conflict between rational scientists and a society prey to its emotions and fears and (ii) understand how science and society co-evolve. The five-year cycle of one-day annual meetings organized by Genopole® and the IFRIS intend to deal seriously with the question of science/society co-evolution by inviting a few of the world's leading specialists in the field of science, technology and society to debate on the last decade's developments with politicians, journalists, associations and research managers as well as life scientists. Although public opinion now appears to have a major influence on science policies, there is no obvious reason why this should necessarily be the case. The idea behind this first colloquium organized on the 28th of September at the College de France in Paris, is to work on the notion of "public opinion" by using illustrative case studies: the public opinion that comes out of opinion polls, public opinion in the blogosphere, concerned groups, militant groups, etc. Presentation will be given in English or French depending on the speakers but a simultaneous interpreting service will be provided in both languages. Program, information and registration : http://www.genopole.fr/Home,4211.html Mail : communication@genopole.fr ---------------------------------------------------- From: Heather Vincent Date: Thu, Jun 17, 2010 at 3:27 PM Subject: Distance Courses in Computational Biology, University of Manchester At the University of Manchester, UK, we have over 10 years experience in teaching a range of online courses in computational biology. These courses are designed to enable those with a background in the life sciences, computer science, mathematics or related disciplines to update their skills, while remaining in the workplace. The courses are also very suitable for home study, helping you to keep in touch with a research environment while taking a career break. The modules running next semester, from October 2010, include : Introduction to software development in Java Bioinformatics for Systems Biology Biocomputing Computational Systems Biology These modules can be studied individually, or you can choose to register for a formal qualification. Those wishing to progress to the MSc will complete a supported research project. Examples of projects that have been published in a range of journals are listed here : http://octette.cs.man.ac.uk/bioinformatics/research/index.html For further information, please visit our programme website : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or would like advice on the options, please contact Heather.Vincent@manchester.ac.uk ---------------------------------------------------- From: EMBL Courses Date: Thu, Jun 24, 2010 at 12:29 PM Subject: Register Now: Microscopy, Modeling and Biophysical Methods Dear colleagues, The registration closes on 12 July 2010 for the EMBL Practical Course Microscopy, Modeling and Biophysical Methods 20 Sep - 2 Oct 2010 which will take place in Heidelberg, Germany at the Advanced Training Centre on EMBL Campus. Please check the website for the programme and more information: www.embl.de/events/2010/MSY10 There is a limited number of fellowships available, you will find more information on the website. The objective of this course is to introduce effective methods for doing research in the field of systems biology. This course is aimed at PhD students and postdoctoral fellows interested in quantitative approaches in cell biology. We wish to attract practicing experimentalists as well as researchers from other disciplines (physics, engineering, computer science, etc.) interested in biology. We will teach modern light microscopy, focusing in particular on the acquisition and processing of digital time-lapse movies. The participants will write matlab programs in order to analyze their images. The third foundation of the course is mathematical modeling. The objective of this course is to introduce effective methods for doing research in the field of systems biology. Registration deadline: 12 July 2010 ---------------------------------------------------- From: Davide Prandi Date: Fri, 18 Jun 2010 11:48:22 +0200 Subject: HiBi 2010, Deadline Extension to July 1 In response to the large number of requests from the community, the organizing committee of HiBi 2010 extend the deadline for paper and abstract submission from Monday June 21 to Thursday July 1, 2010. http://www.cosbi.eu/hibi2010/ IMPORTANT DATES: * Abstract submission: July 1, 2010 * Paper submission: July 1, 2010 AIM AND SCOPE: The HiBi workshop establishes a forum to link researchers in the areas  of parallel computing and computational systems biology. One of the main limitations in managing models of biological systems comes from the fundamental difference between the high parallelism evident in biochemical reactions and the sequential environments employed for the analysis of these reactions. Such limitations affect all varieties of continuous, deterministic, discrete and stochastic models; undermining the applicability of simulation techniques and analysis of biological models. The goal of HiBi is therefore to bring together researchers in the fields of high performance computing and computational systems biology. Experts from around the world will present their current work, discuss profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology. ---------------------------------------------------- From: Hiroki Sayama Date: Fri, Jun 18, 2010 at 4:27 PM Subject: CfP: STCAN 2010, December 1-3, Boston CALL FOR PAPERS STCAN 2010: Special Track on State-Topology Coevolution in Adaptive Networks In BIONETICS 2010 December 1-3, 2010, Boston, Massachusetts, USA http://www.bionetics.org/sp/stcan.shtml ---------------------------------------------------- From: Peter Swain Date: Thu, Jun 17, 2010 at 10:41 AM Subject: PhD Position: Systems Biology, Edinburgh PhD Position: Systems Biology, Edinburgh Gene expression is fundamental to life, but only recently have we appreciated how stochastic, or "noisy", this process is, with the numbers of proteins and mRNAs changing substantially over time in any particular cell. Such fluctuations are important: sometimes allowing one cell to survive environmental stress while its genetically identical neighbour does not. The Scottish Universities Life Sciences Alliance (SULSA) is funding a Ph.D. studentship to experimentally investigate and model stochastic gene expression in budding yeast. Although there is a consensus on how gene expression should be modelled in bacteria, there are several different ad hoc approaches for eukaryotes. Working with Peter Swain (Edinburgh) and Ian Stansfield (Aberdeen), the SULSA student will experimentally examine the key factors generating stochasticity using a combination of systems and synthetic biology. The aim is to establish a standard for other models in yeast and higher eukaryotes. By constructing synthetic transcriptional and translational control loops in a simple biochemical network, the student will test both the model and the efficiency of the two types of control for damping or amplifying stochastic fluctuations. Applicants should be a graduate from a U.K. or E.U. university with a 2.1 or 1st class degree, or an equivalent qualification, in either the physical sciences or the biological sciences, but with significant mathematical training. The student will be based in Edinburgh at the Centre for Systems Biology at Edinburgh in a new, purpose-built building, but will also take advantage of the expertise and facilities of the Institute of Medical Sciences in Aberdeen, where Dr. Stansfield is based. All tuition and living expenses of £13,000 per year will be provided by SULSA and the School of Biological Sciences of the University of Edinburgh. Interested candidates should contact either Peter Swain (peter.swain@ed.ac.uk) or Ian Stansfield (i.stansfield@abdn.ac.uk). http://swainlab.bio.ed.ac.uk http://www.abdn.ac.uk/stansfield http://csbe.bio.ed.ac.uk http://www.sulsa.ac.uk http://www.lonelyplanet.com/scotland/edinburgh The expected start date is Autumn 2010. Applications will be accepted until the position is filled. ---------------------------------------------------- From: Oleg Igoshin Date: Thu, Jun 17, 2010 at 2:00 PM Subject: Postdoc: Computational Systems Biology, Rice University 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 statistical image analysis and quantification of the dynamic biofilms formed by Myxobacteria. PROJECT BACKGROUND: In recent years the ubiquity of microbial communities in nature has become apparent: for instance, most bacteria related to human diseases are associated with biofilms. However, it is still not clear how individual cells self-organize in these communities and how community as a whole responds to environmental cues. This project aims to discover the mechanisms of self-organization in dynamic single-species biofilms (swarms). In these swarms, bacteria display collective surface motility, cooperatively sense the environment, execute collective developmental programs and often differentiate into distinct cell types performing specialized functions. This research focuses on self-organization in spreading or aggregating biofilms formed by Myxococcus xanthus - an important model organism for studying microbial cooperation, development, and collective motility. The main project for this position would be to determine quantitative pattern descriptions (features) that describe biofilm phenotypes and distinguish mutant strains from wild-type strains. We will analyze the spreading and aggregation phenotype of biofilms formed by various mutant strains. Subsequently, we will use the information to find a set of quantitative features (pattern descriptions, order parameters) that comprehensively characterize given biofilm phenotypes. RESPONSIBILITIES: The postdoctoral fellow will be responsible for the image quantification and data analysis based on available biological data of our collaborators. Statistical quantification and processing of experimental data (time-lapse microscopy images) will be primary computational techniques. Furthermore, statistical analysis techniques like clustering, factor analysis, wavelet transform and PCA would be used to quantify the distinction between the mutant strains. The 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. QUALIFICATIONS: PhD in science or engineering is required for this position. Candidates are required to have experience in mathematical and computational modeling or statistical analysis of biological images as well as some knowledge of basic biology. Candidates with publications in the field of mathematical/computational biology are strongly preferred. Previous experience in statistics, image processing computational biophysics, mathematical biology, 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 August 1, 2010 until filled. The initial appointment is for 1 year with possible continuation for the second year upon satisfactory performance. Please visit http://igoshin.rice.edu/ or contact Prof. Igoshin for more information. Applicants should submit their resume and letter stating their research interests to igoshin@rice.edu ---------------------------------------------------- From: Paul Lindahl Date: Fri, Jun 18, 2010 at 2:33 PM Subject: Postdoc: Mathematical Modeling of Biological Systems, Texas A&M U Post-Doctoral Position Available Mathematical Modeling of Biological Systems The Chemistry department at Texas A&M University invites applications for a postdoctoral position starting immediately. The position requires a Ph.D. in applied mathematics, physical chemistry, or a closely related discipline. A background in kinetic modeling of complex chemical systems would be advantageous, as would be a general understanding of molecular cell biology. The applicant should have computational skills and an ability to read the molecular cellular biology research literature. The successful applicant will work on an NSF-supported multidisciplinary project involving a biophysical chemist (Dr. Lindahl) and a biomathematician (Dr. Wolfgang Angerer) at Texas A&M University. We collaborate extensively with two mathematicians (Drs. Jeffrey Morgan and Zhigang Zhang) at the University of Houston. We are modeling the dynamics of biochemical processes involved in cellular self-replication, and are integrating those processes within a whole-cell modeling framework (see references below). Current efforts involve modeling the assembly, contraction and centering of contractile rings which are involved in cytokinesis, and in modeling a cell-size checkpoint as found in fission yeast. The expected term of appointment is two years. Salaries are competitive and commensurate with experience. The position includes full health and retirement benefits. To apply, send a cover letter, curriculum vitae and two letters of recommendation to Lindahl@chem.tamu.edu. Texas A&M University is an equal opportunity employer committed to excellence through diversity. Relevant Literature "Mathematical modeling of a minimal protocell with coordinated growth and division" Ivan V. Surovtsev, Zhigang Zhang, Paul A. Lindahl, and Jeffrey J. Morgan Journal of Theoretical Biology 2009, 260, 422-429. "Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis" Ivan V. Surovtsev, Jeffrey J. Morgan, Paul A. Lindahl Plos Computational Biology, 2008, 4, 1-19. "Whole-cell modeling framework in which biochemical dynamics impact aspects of cellular geometry" Ivan V Surovtsev, Jeffrey J Morgan and Paul A Lindahl Journal of Theoretical Biology, 2007, 244, 154-166. ---------------------------------------------------- From: "Miao, Hongyu" Date: Sun, 20 Jun 2010 14:30:58 -0400 Subject: Postdoc: Dynamic Medical Image Modeling & Analysis, URMC Postdoctoral Research Associate in Dynamic Medical Image Modeling and Analysis A postdoctoral position is immediately available at the Department of Biostatistics & Computational Biology, University of Rochester School of Medicine and Dentistry in Rochester, NY. The successful candidates will perform mathematical modeling and statistical analysis of dynamic images generated using multi-photon equipments. The ideal candidate should have a doctoral degree in biomedical engineering, computer science, biostatistics, mathematics, biophysics or related fields. Strong programming skills (e.g., c++, JAVA, python, or MATLAB) and experience in population tracking and lineage construction are required. Candidates with strong communication skills and previous publications in related fields are highly desirable. The position is initially available for two years. Interested individuals should send a CV and a brief statement of research goals via email to Dr. Hulin Wu, C/O: Ms. Debra Perno (Job Code: Image) Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY 14642. Debra_Perno@URMC.Rochester.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 . 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 **************************************************** ----------------------------------------------------