---------------------------------------------------- Subject: SMB Digest v09i41 SMB Digest October 18, 2009 Volume 09 Issue 41 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: UCI Symposium on Mathematical Systems Biology, January 11-12, Irvine News: National Institute for Mathematical & Biological Synthesis Call for Submissions: Academics on Zombies Informational NSF Webcast: Building Engineered Complex Systems PhD Position: Mathematical Biology, Institute for Animal Health, UK PhD Position: Molecular Based Mathematical Biology, MSU PhD Student: Computational Biology of Cnidarians, U Amsterdam PhD Students, Postdocs, Senior, Associate Researchers: BCAM, Bilbao PhD Fellowships: Mathematical-Biology Group, São Paulo, Brazil Postdoc or PhD Student: Computational Biology of Calcification ... Postdoc or PhD Student: Computational Biology, Visual Analysis ... Postdoc: Developmental Biology & Calcification in Embryogenesis ... Postdoc Fellowships: Model in Ecology & Epidemiology, São Paulo SMBnet Reminders ---------------------------------------------------- From: Qing Nie Date: Thu, Oct 15, 2009 at 12:47 PM Subject: UCI Symposium on Mathematical Systems Biology, January 11-12, Irvine 2nd UCI Symposium on Mathematical Systems Biology "Collective Dynamics in Biological Systems" Dates: January 11 -12, 2010 Beckman Center of the National Academies of Sciences and Engineering Organizing Committee: Simon Levin, Qing Nie, and John Wooley Please visit the conference website for more information: http://cmcb.math.uci.edu/Symposium2/ Confirmed speakers: Frank Doyle (UCSB) Wayne Getz (UCB) Alan Hastings (UC Davis) Michael Holst (UCSD) Terence Hwa (UCSD) Arthur Lander (UC Irvine) James Lloyd-Smith (UCLA) Marc Mangel (UC Santa Cruz) George Oster (UCB) Charles Stevens (Salk/UCSD) Leor Weinberger (UCSD) ---------------------------------------------------- From: NIMBioS Date: Tue, Oct 13, 2009 at 1:26 PM Subject: News: National Institute for Mathematical & Biological Synthesis NIMBioS News Bi-Monthly News from the National Institute for Mathematical and Biological Synthesis September/October  2009 - Vol 1, Issue 3 http://archive.constantcontact.com/fs032/1102610363105/archive/1102740061160.html ---------------------------------------------------- From: Robert Smith? Date: Wed, Oct 14, 2009 at 6:10 PM Subject: Call for Submissions: Academics on Zombies Call for submissions: Academics on Zombies The recent publicity over the academic work "When Zombies Attack!: Mathematical modelling of an outbreak of zombie infection": http://www.mathstat.uottawa.ca/~rsmith/Zombies.pdf illustrated the power that bridging popular culture and academia can have. As a result, the authors of that paper are putting together an edited collection, provisionally titled "Academics on Zombies". The aim is to do for your discipline what the Zombie-outbreak paper did for the field of mathematical modelling of infectious diseases: illustrate key concepts in a friendly and accessible way. Reports from readers of the modelling paper were that a) high school students were interested in mathematics for the first time ever, b) people who found the idea of equations horrendous nevertheless read the paper and c) people unaware that there even was such a field as mathematical modelling of infectious diseases were fascinated to learn of its existence and potential. The aim of the book is to treat zombies as real and apply techniques to understand them, or to intervene. Aside from that, the specifics are up to you. Possible topics might include: -A history of zombie outbreaks -Steps to contain an outbreak from a public-health point of view -Medical examination of zombie infection -Gender and race-based examination of zombies as othered -Zombies and the law Please submit a pitch to Robert Smith? with the words "Zombie Pitch" in the title of the email. This pitch should describe, in some detail, your idea and your qualifications. Deadline: November 15. The aim is to have some fun with this, but also to showcase your academic field. Please pass this on to anyone who might be interested, especially anyone who's in a field different to yours. - Robert Smith? ---------------------------------------------------- From: Warchall, Henry A. Date: Sat, Oct 17, 2009 at 12:04 AM Subject: Informational NSF Webcast: Building Engineered Complex Systems "Building Engineered Complex Systems (BECS)" Informational Webcast Date: Wednesday, October 21st, 2009, 1 - 3 PM EDT Solicitation: 09-610 (http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503431) The Directorate for Engineering (ENG) and the Division of Mathematical Sciences (DMS) in the Directorate for Mathematical and Physical Sciences (MPS) at the National Science Foundation (NSF) are collaborating in this solicitation to provide "seed funding" for small teams of innovative engineers and mathematical scientists (mathematicians or statisticians) to seek and develop a theoretical basis of complex systems, with the aim of developing formal methods for the design of engineered complex systems. ENG and DMS will hold an information webcast on October 21st, 2009, at 1 p.m. (Eastern Time) to describe this program and answer any questions. Details about the BECS webcast are posted on the BECS website (www.nsf.gov/eng/efri/becs.jsp). Registration for the webcast can be made at ---------------------------------------------------- From: david schley (IAH-P) Date: Tue, Oct 13, 2009 at 3:57 AM Subject: PhD Position: Mathematical Biology, Institute for Animal Health, UK Fully Funded 4 year PhD Studentship in Integrative Systems Biology Mathematical Biology Group & Pathogenesis of Vesicular Disease Group, Institute for Animal Health, UK in collaboration with the Department of Mathematical Sciences, Loughborough University, UK. Project Systems biology applying mathematical modelling to biomedical research is a fast growing area of science. This exciting project will focus on modelling foot-and-mouth virus within bovine epithelial cells to help identify important factors in the dynamics and control of the disease. Theoretical results will motivate and help direct laboratory experiments studying virus replication and cell-death. The student will undertake advanced mathematical modelling, analysis and simulation as well as experimental work in the laboratory. Applicant Suitable candidates for this project will have a strong background in applied mathematics (including differential equation modelling) and a keen interest in undertaking inter-disciplinary work. Computational skills and experience of project or research work would also be advantageous. Students with laboratory experience, knowledge of biology or a strong interest in experimental work are encouraged to apply, although all appropriate training will be provided as part of the studentship. Training Students will receive significant support and training throughout their four year programme. This will include supplementary mathematical, statistical and computational training, especially in Matlab, and training in relevant biological techniques including cell culture, PCR methods, bioimaging and immunology. Qualification Students will be registered for their PhD at Loughborough University (Times University of the Year 2008), firmly established as one of the leading research-led universities in the UK. Funding £17,490 stipend p.a. for four years (plus all fees). Start date Available immediately, preferably by 5th January 2010. Eligibility Open to students world-wide. Applicants should possess, or expect to obtain, either an Upper Second Class honours (2:1) in an appropriate subject or an MSc in appropriate subjects. Location The student will be based at the Institute for Animal Health in Pirbright near Woking, Surrey, part of the largest research institute in the United Kingdom dedicated to the study of infectious animal diseases. IAH is one of five research institutes sponsored by the Biotechnology and Biological Sciences Research Council. Student accommodation is usually available. Application Closing date 31st October. For further information about the project and an application form email studentship.iah@bbsrc.ac.uk. Potential candidates are welcome to contact the supervisors informally: please email Dr David Schley (David.Schley@bbsrc.ac.uk) or Dr John Ward (John.Ward@lboro.ac.uk) ---------------------------------------------------- From: Wei, Guowei Date: Tue, Oct 13, 2009 at 10:18 AM Subject: PhD Position: Molecular Based Mathematical Biology, MSU Department of Mathematics at Michigan State University invites outstanding students for PhD degrees in Molecular Based Mathematical Biology. A major feature of 21st-century's biological science is its transition from phenomenological and descriptive science to quantitative science. Revolutionary opportunities have emerged for mathematically driven advances in biological and life sciences. Currently, almost all funded research in experimental biology is based on molecular level understandings. However, most research work in mathematical biology nowadays is not based on molecular level understandings. We envision a dramatic and historic transition from the traditional mathematical biology to molecular based mathematical biology in the next decade. The department of Mathematics at Michigan State University has ongoing research projects that span a wide spectrum of topics in new emerging areas in molecular based mathematical biology. Our mathematical biology research activities concern biological frontiers, including ion channels, biomolecular solvation, protein folding, protein-protein interaction, protein-DNA binding, signal transduction, gene regulation, molecular motors, ATP synthase motors, drug design and discovery. We make use of a wide range of mathematical theories, methods and techniques, such as differential geometry, partial differential equations, topology, linear algebra, functional analysis, etc. We are interested in developing new mathematical models, theoretical approaches, analytical algorithms, and computational methods for problems in the general context of molecular based biology. We are seeking outstanding students who are interested in working at the interface of mathematics and molecular biology. Our goal is to train next generation researchers in molecular based mathematical biology. Ideal students should possess MSc or BS degrees in mathematics or other disciplines that have a strong background in mathematics. Most  importantly, an ideal student should have a strong desire to engage in interdisciplinary research in molecular based mathematical biology. Interested students should contact Prof. Guowei Wei via e-mail wei@math.msu.edu ---------------------------------------------------- From: Jaap Kaandorp Date: Mon, Oct 12, 2009 at 3:51 PM Subject: PhD Student: Computational Biology of Cnidarians, U Amsterdam PhD student in Computational Biology of cnidarians at the University of Amsterdam 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: Philipp Getto Date: Wed, Oct 14, 2009 at 9:13 AM Subject: PhD Students, Postdocs, Senior, Associate Researchers: BCAM, Bilbao Call for researchers at all levels in Applied Mathematics, including Mathematical Biology, at BCAM Basque Center for Applied Mathematics Bilbao, SPAIN The Basque Center for Applied Mathematics (BCAM) has opened an international call for researchers, including Senior and Associate Researchers, Postdoctoral Fellows and PhD Students. All topics of Applied Mathematics will be considered, with special emphasis on existing research lines, one of which is Mathematical Biology. Applicants should visit the website http://www.bcamath.org/joboffers, must complete the application form and upload the required documentation (cover letter, curriculum vitae, a list of publications, a statement describing current and planned research) and provide the name and e-mail address of two referees (the system will automatically ask for these reference letters). Referees who are unable to submit their letters electronically may mail them to the following address: join_us@bcamath.org, indicating the name of the candidate they are supporting. You can find further details of our center and activities at our website: http://www.bcamath.org BCAM supports and signs the European Charter for Researchers (http://ec.europa.eu/euraxess/index_en.cfm?l1=31&CFID=306654&CFTOKEN=59f5e54d627aac17-14D6EB5A-BE88-7BB1-47C3013FE33E0081) and encourages applications from women, minorities and outstanding researchers from developing countries. ---------------------------------------------------- From: Roberto André Kraenkel Date: 2009/10/17 Subject: PhD Fellowships: Mathematical-Biology Group, São Paulo, Brazil PhD Fellowships in São Paulo, Brazil The Mathematical-Biology Group at the Institute for Theoretical Physics in São Paulo ( Brazil) ( http://www.ift.unesp.br/users/kraenkel ) welcomes applications for post-doctoral fellowships beginning March or August 2010. The main interests of the group are connected to mathematical models in ecology and epidemiology. Research is focused on real-world applications. Candidates should possess a recent Bachelor degree in Physics. Fellowships are for either three or four years, depending on the funding agency. Presently, the amount is R$ 1800,00 per month, corresponding to approximately US$ 1000,00 per month. Prospective candidates should establish a first contact e-mailing Roberto Kraenkel at kraenkel@ift.unesp.br sending him a CV and stating their interests. ---------------------------------------------------- From: Jaap Kaandorp Date: Mon, Oct 12, 2009 at 3:49 PM Subject: Postdoc or PhD Student: Computational Biology of Calcification ... Postdoc or PhD student in Computational Biology of calcification of scleractinian coral The Section computational Science (University of Amsterdam) has a vacancy for a PhD Student or postdoc for the project "multi-scale modelling of calcification in scleractinian corals" This project is financed by the Netherlands Organisation for Scientific Research (NWO) as part of its Computational Life Sciences research programme. The project is a collaboration with the research groups headed by Prof. R.P.M. Bak (Netherlands Institute for Sea Research (NIOZ) and Prof. D.J. Miller (James Cook University, Australia). The appointee will collaborate extensively with molecular developmental biologists. The central research aim of this project is to characterize the genes that control the differences in coral morphology for related coral species. We will do this by making a quantitative comparison of gene expression patterns, with a special focus on genes that are involved in the process of calcification. To test the hypothesis that these genes can explain the differences in morphology, we plan to use the estimated quantities in a simulated network controlling calcification. We intend to study the emergence of the micro-morphology structure and link gene expression patterns to the corallite structure. This polyp (corallite) based model will be coupled with a macroscopic growth form model describing Ca2+ and HCO3- fluxes from the environment. A better understanding of calcification in corals is of fundamental importance in research on the potentially detrimental impact of increasing atmospheric carbon dioxide concentrations, decreasing ocean pH and carbonate ion concentrations on the calcification process in corals and other calcifying organisms. Requirements The position is open to candidates at both the PhD and the postdoc level. All candidates should hold a Master's degree (or equivalent) in scientific computing or computational science, computational physics, computational chemistry or a comparable field. Candidates must have expertise in modelling and scientific programming, an active interest in life science applications and the ability to work in an international research team. Candidates who wish to apply for the postdoc position should also have a strong research record (as evidenced by a PhD thesis and papers published in peer-reviewed journals), be fluent in both oral and written English, and be prepared to travel to a another country and integrate efficiently into a new research team. Further information Further information can be obtained from Dr J. A. Kaandorp, Section Computational Science, University of Amsterdam, Kruislaan 403, 1098 SJ, Amsterdam, The Netherlands; tel: +31 20 525 7539; email: J.A.Kaandorp@uva.nl.  More information (application procedure, deadlines etc.) is available on the website http://www.uva.nl/vacatures ---------------------------------------------------- From: Jaap Kaandorp Date: Mon, Oct 12, 2009 at 3:50 PM Subject: Postdoc or PhD Student: Computational Biology, Visual Analysis ... Postdoc or PhD Student Computational Biology, visual analysis of Computer Tomography Scans of scleractinian corals The research group of Prof. R. van Liere, Centre for Mathematics and Computer Science Amsterdam has a vacancy for a PhD Student or postdoc for the project "A Visual Exploration environment for Analyzing gene Regulation in Developmental processes" The project is financed by the Netherlands Organisation for Scientific Research, NWO, research program Visual Interactive Effective Worlds (VIEW). The project is a collaboration with the research group from Dr. J.A. Kaandorp (Section Computational Science, University of Amsterdam). In this project we propose to develop visualization techniques for quantitative research on complex shaped and variable biological and simulated objects and techniques for the visualization of abstract n-dimensional parameter spaces in models of gene regulatory networks. The project aims to develop methods and tools to extract and present geometrical information from spatial measurements and simulation, to develop visualization methods to compare simulation models and measured data, and techniques for the navigation of morphometric parameter spaces (morphospaces) and model parameter spaces.  In this part of the project we will focus on the analysis of calcification in  3D images (Computer Tomography Scans) of scleractinian corals. A better understanding of calcification in corals is of fundamental importance in research on the potentially detrimental impact of increasing atmospheric carbon dioxide concentrations, reducing ocean pH and carbonate ion concentrations on the calcification process in corals.  The candidate is expected to collaborate extensively with  biologists. Requirements The position is open for candidates at both the PhD or postdoc level. Candidates should have a master's degree (or equivalent) in computer science, mathematics, physics or a comparable expertise. Candidates are expected to have expertise in 3D image processing and computational geometry and have an active interest in life science applications. The candidate should be able to work in an international research team. In the case of candidates applying for a postdoc position: a strong research record, evidenced by a PhD thesis and papers published in peer-reviewed journals. 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 : Prof. R. van Liere, Centre for Mathematics and Computer Science, Robert.van.Liere@cwi.nl; Dr J. A. Kaandorp, Section Computational Science, University of Amsterdam; e-mail: J.A.Kaandorp@uva.nl Appointment PhD level: This is a full-time appointment (38 hours a week) for a total of four years Postdoc level: This will be a full-time appointment (38 hours per week) for a period of three years. Job application Applications should include a letter of motivation, pdfs of most relevant publications and a curriculum vitae. Please include the names and contact information of two references. Applications should be sent by e-mail to Robert.van.Liere@cwi.nl The application period will remain open until the position is filled; however, review of applications will commence on November, 2009, with the intent of filling the position as quickly as possible. ---------------------------------------------------- From: Jaap Kaandorp Date: Mon, Oct 12, 2009 at 3:48 PM Subject: Postdoc: Developmental Biology & Calcification in Embryogenesis ... Postdoc Developmental biology and calcification in embryogenesis of scleractinian corals at the NIOZ Royal Netherlands Institute for Sea Research The NIOZ Royal Netherlands Institute for Sea Research has a vacancy for a postdoc for the project "Developmental biology and calcification in embryogenesis of scleractinian corals" (full-time appointment for a maximum period of three years). The project Developmental biology and calcification in embryogenesis of scleractinian corals is financed by the Netherlands Organisation for Scientific Research, NWO, research program Computational Life Sciences. The project is a collaboration with the research groups from Prof. R.P.M. Bak & Dr. J. van Bleijswijk (Netherlands Institute for Sea Research (NIOZ), Dr. J.A. Kaandorp (Section Computational Science, University of Amsterdam) and Prof. D.J. Miller (James Cook University, Australia). The candidate is expected to collaborate extensively with molecular developmental biologists and computational biologists. The central research question we propose to investigate in this project is to characterize the genes that control the differences in coral morphology for related coral species. We do this by a quantitative comparison of gene expression patterns. We especially focus on genes involved in the process of calcification. As a start, we will study the developmental process in Acropora millepora larvae, in collaboration with Prof. D.J. Miller (James Cook University). We aim to collect and analyze spatio-temporal gene expression patterns of genes involved in the calcification process for different developmental stages. A better understanding of calcification in corals is of fundamental importance in research on the potentially detrimental impact of increasing atmospheric carbon dioxide concentrations, reducing ocean pH and carbonate ion concentrations on the calcification process in corals and other calcifying organisms. In collaboration with Dr. J.A. Kaandorp (University of Amsterdam) a computational model of calcification in corals will be developed. Requirements Candidates should have a PhD degree in molecular developmental biology with preferably an expertise in cnidarians.  The Postdoc is expected to collaborate with computational biologists. The Postdoc should be able to work in an international research team. A strong research record, evidenced by a PhD thesis and papers published in peer-reviewed journals is required. Fluency in oral and written English is required. Motivation to travel to different countries  and integrate efficiently in a new research team is fundamental. Further information Further information on the project can be obtained from : Dr. J. van Bleijswijk, Molecular Biology Laboratory, Royal NIOZ, The Netherlands, tel +31 222 369521, e-mail: Judith.van.Bleijswijk@nioz.nl or Dr J. A. Kaandorp, Section Computational Science, University of Amsterdam, Amsterdam, The Netherlands; tel. +31 20 525 7539; e-mail: J.A.Kaandorp@uva.nl or otherwise from Jolanda Evers, Human Resources (Email: Jolanda.evers@nioz.nl, phone +31-222-369371) More information on the application procedure, deadlines etc., research and our institute see: www.nioz.nl ---------------------------------------------------- From: Roberto André Kraenkel Date: 2009/10/17 Subject: Postdoc Fellowships: Model in Ecology & Epidemiology, São Paulo Post-Doctoral Fellowships in São Paulo, Brazil The Mathematical-Biology Group at the Institute for Theoretical Physics in São Paulo ( Brazil) ( http://www.ift.unesp.br/users/kraenkel ) welcomes applications for post-doctoral fellowships beginning March 2010 or later. The main interests of the group are connected to mathematical models in ecology and epidemiology. Research is focused on real-world applications. Background of candidates should either be on physics or applied mathematics. Fellowships are for one year, renewable twice, depending on achievements. Presently, the amount is R$ 4500,00 per month, corresponding to approximately US$ 2500,00 per month. Prospective candidates should establish a first contact e-mailing Roberto Kraenkel at kraenkel@ift.unesp.br sending him a CV and stating their interests. ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------