---------------------------------------------------- Subject: SMB Digest v08i14 SMB Digest April 8, 2008 Volume 08 Issue 14 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: AIBS Annual Meeting, 12 -13 May, Arlington, VA Summer School: Ecological Networks Summer School, 16-20 June, Parma Summer School: Cardiovascular Mathematics, Aug 16-31, Cortona DIMACS/DyDAn Workshop on Disease Clusters, May 6-8, Rutgers CfP: NETTAB 2008, Bioinformatics Methods for ... Complex Systems DIMACS Workshop on Computational Issues in Genetic Epidemiology 2008 MBI Workshop for Young Researchers in Mathematical Biology Inverse Problems Editorial Board Highlights of 2007 MSc/PhD/Post-Doctoral Trainees: Computational Immunology, Bar-Ilan Postdoctoral Position: Mathematical Biology, UBC Research Fellowship: Mathematical / Computational Ecology, Belfast Group Leader: Biomodeling & Biosystems Analysis, NISB, Amsterdam SMBnet Reminders ---------------------------------------------------- From: "Richard O'Grady" Date: Mon, 31 Mar 2008 09:40:32 -0400 Subject: AIBS Annual Meeting, 12 -13 May, Arlington, VA Register now for the ANNUAL MEETING of the American Institute of Biological Sciences Climate, Environment, and Infectious Diseases 12 - 13 May 2008 Westin Arlington Gateway Hotel, 801 North Glebe Road, Arlington, Virginia Registration, program, posters, exhibits / sponsorships online at: http://www.aibs.org/annual-meeting/annual_meeting_2008.html ---------------------------------------------------- From: FoodWeb School Date: Mon, 7 Apr 2008 15:41:38 +0200 Subject: Summer School: Ecological Networks Summer School, 16-20 June, Parma Dear colleagues, this is to inform you that we will be hosting an international summer school at the University of Parma (Italy) from the 16-20 June 2008. The aim is to introduce ecological network analysis to graduate students and early postdocs: from data collection to theoretical analysis, using a wide array of network types (food webs, ecosystem models, plants-pollinators networks, etc.) and mathematical and statistical tools. Please find a more detailed description and how to apply in the attached file or visit our web-site: www.dsa.unipr.it/foodwebschool/ Best regards Stefano Allesina Antonio Bodini Giulio De Leo ---------------------------------------------------- From: Fabio Nobile Date: Tue, 8 Apr 2008 10:37:19 +0200 Subject: Summer School: Cardiovascular Mathematics, Aug 16-31, Cortona EMS-SMI Cortona Summer School on Mathematical and Numerical Models for the Cardiovascular System Main lecturers: Dominique Chapelle, Piero Colli-Franzone, Alfio Quarteroni Cortona (Italy), August 16-31, 2008 http://mox.polimi.it/cortona08 The European Mathematical Society (EMS) in collaboration with Scuola Matematica Interuniversitaria (SMI) of Florence, Italy, organises a summer school in Cortona, Italy. The school aims at addressing in a unified framework several aspects of the mathematical modelling and numerical simulation of the circulatory physiology. In particular we will address the electrical excitation of the heart, the related mechanical contraction, models for blood flow circulation and the transport of biochemicals. Emphasis will be put on modelling aspects, the analysis of coupled system of PDEs, numerical approximation and algorithmic issues. In particular, we will address efficient methods for the incompressible Navier-Stokes equations, Arbitrary Eulerian Lagrangian formulation, numerical techniques for the dynamics of biological structures, coupling strategies for fluid structure interaction schemes, numerical schemes for the non linear reaction diffusion system governing the cardiac bio-electrical activity and domain decomposition techniques for their parallel implementation. Beside traditional lectures, the school includes practical sessions, organised with the aid of scientific software. The course is addressed to researchers and graduate students in applied mathematics, as well as bioengineers and medical researchers interested in the numerical simulation aspects. A limited number of scholarships are available. Scholarships cover accommodation, living expenses and part of travel expenses according to budget availability. Applications deadline is May 30th 2008. Preference will be given to nationals of EU and associated states, yet applications from motivated students of other nationalities will be considered as well. Further information about eligibility criteria may be found on the EMS web site http://www.emis.de/etc/ems-summer-schools.html More details and contact information may be found on the web page of the school. ---------------------------------------------------- From: Linda Casals Date: Tue, 1 Apr 2008 09:48:08 -0400 (EDT) Subject: DIMACS/DyDAn Workshop on Disease Clusters, May 6-8, Rutgers DIMACS/DyDAn Workshop on Disease Clusters May 6 - 8, 2008 DIMACS/DyDAn Center, CoRE Building, Rutgers University Organizers: Andrew Lawson, University of South Carolina, alawson at gwm.sc.edu Daniel Wartenberg, Robert Wood Johnson Medical School, dew at eohsi.rutgers.edu Presented under the auspices of the Special Focus on Computational and Mathematical Epidemiology and the Center for Dynamic Data Analysis (DyDAn). Disease clusters, defined as local excesses of disease in space, time or space and time, represent an important but vexing problem in public health. Clusters are usually identified by community residents who believe that some unusual circumstance leading to unexpected illness has befallen their families, friends or neighbors. Clusters of leukemia are reported most often, although clusters of other cancers, birth defects and other adverse health outcomes are also reported. While there are many protocols to assess whether a given cluster is etiologic, i.e., due to an identifiable cause, there is no clear consensus about how best to conduct an investigation and reach a scientifically valid conclusion. A variety of statistical issues confront investigators of clusters. For example, since cluster reports typically are based on a handful of cases, it is possible that the observed excess is simply due to random variation, particularly if the investigator fails to adjust for multiple comparisons. On the other hand, the statistical power of traditional cluster analysis methods is fairly low, likely resulting in many false negatives which might cause investigators to miss true, etiologic clusters. In addition, assumptions are made about the amount of disease expected because large data sets are generally not available at a scale that would enable investigators to determine background rates of disease, such as at the census block, census tract or zip code. Some recent methods have begun to look at approaches for conducting prospective surveillance by analyzing data collected for each time unit (e.g., year) it is collected. These methods offer the opportunity the overcome some of the statistical limitations of traditional cluster analyses and provide a more appropriate perspective for health officials to use in responding to community concerns. The workshop will bring together mathematicians, biostatisticians, epidemiologists and public health officials to develop an approach that, while statistically rigorous, is able to address the concerns of the public. Registration: For details and to register see: http://dimacs.rutgers.edu/Workshops/Clusters/ ---------------------------------------------------- From: Paolo Romano Date: Wed, 02 Apr 2008 15:01:38 +0200 Subject: CfP: NETTAB 2008, Bioinformatics Methods for ... Complex Systems Call for Papers for NETTAB 2008 workshop NETTAB 2008 Bioinformatics Methods for Biomedical Complex System Applications 19-21 May 2008, Villa Monastero, Varenna, Lake Como, Italy http://www.nettab.org/2008/ The NETTAB 2008 workshop will focus on all aspects needed to provide the framework for understanding multi-scale, complex biological systems, from the single bio-molecule to the cell, across a wide range of clinical information. A special emphasis will be given to combine theory, experiments, software, and technologies for an integrative systems approach to biological research, which is becoming increasingly multi-disciplinary, multi-dimensional, information driven. Sessions Bioinformatics Methods for Complex Systems Gene networking applications Mathematical Methods for System Biology Oncology Bioinformatics Tutorials Systems Biology Tools Systems Biology Standards Important dates 10 April 2008: Paper submission 21 April 2008: Communication of acceptance 22 April 2008: Registration starts 19 May 2008: Tutorials 19-21 May 2008: Workshop Abstracts' submission Submit an extended abstract (max 3 pages) within next 10 April 2008. Guidelines and instructions for submission are available at: http://www.nettab.org/call.html . A MS Word template is available at: http://www.nettab.org/2008/abstract.doc . Registration Registration opens on 22 April 2008. Register for the NETTAB 2008 workshop: http://www.nettab.org/2008/rform.html For all information, please email to nettab2008@itb.cnr.it . ---------------------------------------------------- From: Linda Casals Date: Thu, 3 Apr 2008 09:28:43 -0400 (EDT) Subject: DIMACS Workshop on Computational Issues in Genetic Epidemiology DIMACS Workshop on Computational Issues in Genetic Epidemiology August 21 - 22, 2008 DIMACS Center, CoRE Building, Rutgers University http://dimacs.rutgers.edu/Workshops/ComputationalIssues/ Organizers: Andrew Scott Allen, Duke University, andrew.s.allen at duke.edu Ion Mandoiu, University of Connecticut, ion at engr.uconn.edu Dan Nicolae, University of Chicago, nicolae at galton.uchicago.edu Yi Pan, Georgia State University, pan at cs.gsu.edu Alex Zelikovsky, Georgia State University, alexz at cs.gsu.edu Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology. Workshop Announcement: There is strong evidence that genes play a major role in susceptibility to all common human diseases. While linkage analysis has been very successful in finding the genes involved in Mendelian diseases such as Huntington disease, early onset Alzheimer's disease and cystic fibrosis, current interest has shifted towards mapping genes involved in diseases with complex etiologies such as diabetes and cancer, for which association studies have been shown to be more powerful. The workshop will bring together computer scientists, geneticists, and statisticians aiming to address current computational challenges in gene mapping, which include dealing with complex missing data patterns, multiple hypotheses testing, population substructure, gene-gene and gene-environment interactions. New directions of research, such as capturing the effects of structural genomic variation and using biological networks in whole-genome studies, will also be investigated. Call for Participation: Speakers are by invitation only. Registration is open to all. Registration: Pre-registration deadline: August 14, 2008 Please see website for additional registration information. ---------------------------------------------------- From: jday@mbi.ohio-state.edu Date: Mon, 7 Apr 2008 12:22:17 -0400 (EDT) Subject: 2008 MBI Workshop for Young Researchers in Mathematical Biology The application deadline for the 2008 MBI Workshop for Young Researchers in Mathematical Biology (WYRMB) is now APRIL 17, 2008. Please apply at: http://www.mbi.ohio-state.edu/forms/wyrmbapplyworkshop.html September 2-4, 2008 Mathematical Biosciences Institute, The Ohio State University Columbus OH, USA This workshop is intended to broaden the scientific perspective of young researchers in mathematical biology and to encourage interactions with other scientists. Workshop activities include plenary talks and poster sessions, as well as group discussions on issues relevant to mathematical biologists. We cordially invite young mathematical biologists to participate. The MBI will plan to cover local expenses for all invitees, but travel expenses may only be available on a competitive basis. Accepted Plenary Speakers: - Sally Blower, Disease Modeling Group, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles - Carson Chow, Department of Mathematics, University of Pittsburgh and Laboratory of Biological Modeling, NIDDK, NIH - Stephen Coombes, School of Mathematical Sciences, University of Nottingham - Jun Liu, Department of Statistics, Harvard University - Markus Owen, Division of Applied Mathematics, School of Mathematical Sciences, University of Nottingham - John White, Department of Bioengineering, University of Utah Further Details can be found at: http://www.mbi.ohio-state.edu/postdocworkshop/wyrmb2008.html Questions? Email Rebecca Martin at rebecca@mbi.osu.edu ---------------------------------------------------- From: Zoe Crossman Date: Mon, 31 Mar 2008 15:08:21 +0100 Subject: Inverse Problems Editorial Board Highlights of 2007 The Inverse Problems Editorial Board Highlights of 2007 are now online and free to read until 31 December 2008: http://herald.iop.org/IPHighlights2007SMB/m103/cid//link/1477 This selection of articles chosen by the Inverse Problems Editorial Board highlights the breadth and quality of the research published in Inverse Problems in 2007. It comprises regular papers of particular interest on topics regularly covered by the journal, such as medical imaging, as well as an article from the highly downloaded special section on photo- and thermo-acoustic imaging, published in December 2007. This is intended not as a list of the 'best' articles, but as an interesting and stimulating reading list. Articles were selected for many reasons, some contain outstanding research and breakthroughs, some may have an especially clear exposition and are beautifully presented, others are instructive, containing results and tools useful to many readers. We hope you enjoy reading these articles as much as we have. Kate Watt Publisher, Inverse Problems ip@iop.org ---------------------------------------------------- From: Ramit Mehr Date: Mon, 7 Apr 2008 09:31:15 +0200 Subject: MSc/PhD/Post-Doctoral Trainees: Computational Immunology, Bar-Ilan The Computational Immunology Lab of Prof. Ramit Mehr Bar-Ilan University, Israel (http://repertoire.os.biu.ac.il/) needs Research Students (for the MSc or PhD degrees) and Post-Doctoral Trainees for several fascinating projects More info: http://repertoire.os.biu.ac.il/Info-4-candidates.htm If you are interested: Please send email to mehrra@mail.biu.ac.il, stating the position you are interested in, and attach: * Your CV, * Any publications or reports you have from your previous research projects, * Your grades in your previous studies (full lists), * A statement of your research interests, career goals and plans, * Names of people who will be willing to recommend you . e.g., advisors from previous studies, projects or jobs (please give names + phone numbers and/or email addresses of these persons). ---------------------------------------------------- From: Leah Keshet Date: Thu, 3 Apr 2008 10:57:03 -0700 (PDT) Subject: Postdoctoral Position: Mathematical Biology, UBC Postdoctoral position for 2008-09 http://www.math.ubc.ca/~keshet/MathBioAd.html Modelling actin-based cell motility and its biochemical regulation Vancouver, British Columbia A PDF position has reopened in the Mathematical Biology group at UBC. We are still seeking an excellent candidate for this job. Job description (1) Modelling the cytoskeleton, cell motility, and signal transduction: The research focuses on the regulation of the actin cytoskeleton and implications for cell polarity and motility. Incoming post-doctoral fellows are sought from either experimental cell biology background (with strong interest in quantitative methods and modelling) or mathematical/biophysics background. Applications are also welcomed from candidates with strong computational skills (e.g. finite element, immersed boundary) wishing to enter this area. Setting The Math-Biology group at UBC presents many opportunities to work on a variety of exciting research (including, but not limited to theoretical immunology, neurophysiology, epidemiology, ecology and evolution) and to collaborate with other researchers. PDFs are encouraged to explore a variety of interests within this setting. In future, teaching in the Dept of Mathematics could be arranged, subject to interest and approval by the Department. Preference will be given to candidates with track record in quantitative research with good communication skills, and with ability to work well both independently and in a team. Please send the following material: (1) CV including a list of publications, preprints, reprints (2) statement of research interests (3) names, addresses, email addresses, of three people who could provide letters of reference on your behalf L. Edelstein-Keshet, Dept of Mathematics, UBC, keshet@math.ubc.ca ---------------------------------------------------- From: Keith Farnsworth Date: Wed, 2 Apr 2008 13:16:09 +0100 Subject: Research Fellowship: Mathematical / Computational Ecology, Belfast Beaufort Marine Research Fellowship. Applications are invited for this prestigious 7-year Fellowship in mathematical / computational ecology in support of the Ecosystem Approach to Fisheries Management. Based in Belfast, the position will be instrumental in building and evaluating multi-species size-spectrum models of specific sea areas. Much of the planned work will be highly innovative and often mathematically or computationally challenging. The Research Fellow will work closely with colleagues and research students in the Danish (see http://www.dfu.dtu.dk/English/Commercial_fisheries/Marine_ecosystems.aspx) and Irish (see http://www.marine.ie/home/services/operational/fishstock/Ecosystems.htm) Marine Institutes (some time may be spent in those countries). The project is led by Dr Keith Farnsworth (see http://www.qub.ac.uk/schools/SchoolofBiologicalSciences/Staff/DrKDFarnsworth/) at Queen's University Belfast. We are looking for someone with at least 3 years recent relevant research experience and competence with systems of PDEs and stochastic differential equations; expertise in at least one of: Mathematica, Matlab, or R (or one of its relatives) and experience with Unix. Experience of grid or parallel computing will be an advantage as well. Further information can be obtained from the School of Biological Sciences, Queen's University Belfast (sobb.office@qub.ac.uk). For application and further particulars see http://www.qub.ac.uk/sites/QUBJobVacancies/ResearchJobs/ . Salary Scale: £27,466 - £35837 (including contribution points) Closing Date: 4.00 pm on Friday 25th April 2008. It is anticipated that interviews for the position will be held on 15th May 2008. Beaufort Marine Research Awards grant-aided by the Irish Government under the National Development Plan 2007-2013 (NDP). ---------------------------------------------------- From: Nada Mitrovic Date: Tue, 08 Apr 2008 10:55:21 +0200 Subject: Group Leader: Biomodeling & Biosystems Analysis, NISB, Amsterdam Job Opening Group leader biomodeling and biosystems analysis Netherlands Institute for Systems Biology (NISB, www.sysbio.nl) Amsterdam, The Netherlands The Netherlands Institute for Systems Biology (NISB, www.sysbio.nl) is a joint venture of the two Amsterdam universities (the Vrije Universiteit and the University of Amsterdam) and two national research institutes in Amsterdam (the CWI (Netherlands research institute for mathematics and computer science) and AMOLF (FOM Institute for Atomic and Molecular Physics)). The Netherlands Genomics Initiative (NGI, www.genomics.nl) has recently initiated the Netherlands Consortium for Systems Biology (NCSB), a 15 million Euro national research program to implement systems biology in ongoing research lines of seven high ranking Dutch research groups in the fields of biomedical and biotechnological research. As part of this investment a Biomodeling and Biosystems Analysis Group will be set up in the Netherlands Institute for Systems Biology (NISB) in Amsterdam. The task of the Biomodeling and Biosystems Analysis Group is to develop generic as well as specific tools and approaches for modeling and analysis of complex biological systems, specifically those that are addressed in the context of the NCSB program. The group will be housed in Amsterdam in the premises of one of the four parties that constitute the NISB (two universities and two national research institutes in Amsterdam). The group leader has a budget of 1.5 million Euro for a period of five years. A tenure position can be negotiated for this function. In addition to the postdocs, PhD students and other personnel in the group, the group leader will be responsible for the modeling and system analysis activities of about twelve investigators (postdocs and PhD students) that are positioned in the different biomedical and biotechnological research groups that participate in the NCSB program. In this, the Biomodeling and Biosystems Analysis Group plays a central role in the NCSB program. Candidates should fulfill the following criteria. - Strong track record in modeling and analysis of complex biological systems based on experimental data sets. - Able to build bridges between mathematicians/physicists/informaticians and experimental biologists. - Proven leadership. - Able to communicate with researchers in the fields of biomedical and biotechnological research. Application should be send to the director of the Netherlands Institute for Systems Biology (NISB): prof. Dr Roel van Driel, c/o University of Amsterdam, Kruislaan 318, 1098SM Amsterdam, the Netherlands. Information can be obtained from the same person (office: +31 (0)20 525 5150; home: +31 (0)251 657 356; mail: van.driel@science.uva.nl). Deadline May 1st, 2008. ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------