---------------------------------------------------- Subject: SMB Digest v10i22 SMB Digest June 3, 2010 Volume 10 Issue 22 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: Summer 2010 Thematic Program: Mathematics of Drug Resistance ... OCCAM Mathematical Neuroscience Workshop, Sept 13-15, Oxford Multi-scale Modelling of Biological Systems, 5-6 July, U Stirling EMBL Vision 2020: The Biology of Gene Regulation by miRNAs, 15 June EMBL Courses & Conferences Newsletter, May 2010 PhD Position: Modeling and Optimization of Motions in Orthopedics Postdoc: Theoretical Epidemiology, Rothamsted Research Two Postdocs: Computational Disease Biologist, Disease Modeling ... Postdoc: Tissue Mechanics Modeling, NYU-Poly / NYU Staff Position: Education and Outreach Coordinator, NIMBioS SMBnet Reminders ---------------------------------------------------- From: Shigui Ruan Date: Mon, May 31, 2010 at 10:06 AM Subject: Summer 2010 Thematic Program: Mathematics of Drug Resistance ... The two-month Summer 2010 Thematic Program on the Mathematics of Drug Resistance in Infectious Diseases at the Fields Institute will take place from July 5 to August 27. It will focus on Emergence and Spread of Drug Resistance, Mathematical Immunology, and Transmission Heterogeneity, and will bring together leading researchers in mathematical epidemiology/immunology from around the world in order to stimulate major progress in this area of applied mathematics. The program will provide a unique opportunity for graduate students, postdoctoral fellows and junior faculty to interact with these researchers in a productive and sustained way over this two-month duration. The National Science Foundation (NSF) has generously awarded us a grant to support U.S. based junior faculty, post doctoral fellows, and graduate students to participate in this program, which include both lodging and travel. If you are interested in participate in the program (whole or any duration) and would like to be considered for financial support, please register at the Theme Program website http://www.fields.utoronto.ca/programs/scientific/10-11/drugresistance/ and send your application email message with the supporting documents to the address below: Dr. Shigui Ruan Department of Mathematics University of Miami Coral Gables, FL 33124-4250 USA E-mail: ruan@math.miami.edu. The supporting documents include a CV, and for graduate students a reference letter from your supervisor. Qualified participants are encouraged to apply. ---------------------------------------------------- From: bressloff Date: Sun, May 30, 2010 at 7:00 AM Subject: OCCAM Mathematical Neuroscience Workshop, Sept 13-15, Oxford OCCAM Mathematical Neuroscience Workshop: Future Challenges in Mathematical and Computational Neuroscience St Anne's College, Oxford. Monday September 13th - Wednesday 15th September 2010 Registration is now open http://www.maths.ox.ac.uk/groups/occam/occam-computational-neuroscience-workshop The aim of this meeting is to bring together world leaders in mathematical and computational neuroscience to identify major future challenges and opportunities in modeling brain function. Over the past 25 years there have been huge advances in experimental techniques within neuroscience: imaging specific regions of the brain at ever increasing spatial and temporal resolutions, recording electrical signals from many neurons simultaneously using multi-electrode arrays, tracking individual proteins using quantum dots, and manipulating genes. Mathematical and computational modeling are needed to handle the vast amounts of data being collected, to develop predictive models of the complex dynamical processes occurring on many different levels of organization - from molecules to single cells to networks ? to understand neural computation and information processing, and to characterize the nature and causes of dysfunctional brain states and behaviour. Organisers: Paul C Bressloff (OCCAM) and Peter Dayan (Gatsby and UCL) Session chairs: Jack Cowan (Chicago) and David Willshaw (Edinburgh) Confirmed Speakers: Peter Bossaerts, (CalTech) Nicolas Brunel, (Paris) Steve Coombes, (Nottingham) Alain Destexhe, (Paris) Bard Ermentrout, (Pittsburgh) Olivier Faugeras, (Sophia-Antipolis) Wulfram Gerstner, (Lausanne) Zhaoping Li, (UCL) Stefano Panzeri, (Genova) Mark van Rossum, (Edin) David Terman, (Ohio) Daniel Wolpert, (Camb) ---------------------------------------------------- From: Rachel Norman Date: Fri, May 28, 2010 at 5:55 AM Subject: Multi-scale Modelling of Biological Systems, 5-6 July, U Stirling Second Call for Participation (note extended deadline for abstracts below) MULTI_SCALE MODELLING OF BIOLOGICAL SYSTEMS 5-6th July 2010 University of Stirling Sponsored by EPSRC IMPORTANT DATES Abstract submission deadline: 5 June, 2010 Notification of programme: 7 June, 2010 Registration deadline 5 June, 2010 Computational and mathematical modelling of biological systems is now commonplace and indeed essential to many projects. A particular problem faced by modellers is that of choosing the most appropriate scale, or level of abstraction, for their model, especially given that there may be different important features at each scale. For example, in an epidemiological model, we might wish to describe the way in which individuals interact. Alternatively, we might be more interested in the analysis of population level features, making ordinary differential equations more appropriate. The aim of the workshop is to bring together researchers working on techniques which allow exploration of models spanning a range of scales, especially those in which the different scales are rigorously related. At Stirling, we are interested in modelling techniques such as Process Algebra that allow large scale properties to emerge from small scale behaviour. We would welcome contributions using other techniques. We also particularly welcome biologists interested in how this sort of modelling across scales can help them understand their system. CONFIRMED INVITED SPEAKERS Modelling and analysis of biological systems using process calculi Federica Ciochetta (The Microsoft Research - University of Trento Center for Computational and Systems Biology) Data Driven Network Modelling for Epidemiology Eiko Yoneki (Computer Laboratory, University of Cambridge) LOCATION The workshop will be held at the Stirling Management Centre, in central Scotland. The Centre is part of the University of Stirling campus, and is easy to reach from most places in the UK. International connections are available via nearby Glasgow and Edinburgh airports. http://www.smc.stir.ac.uk/ REGISTRATION Registration is now open via Eventbrite: http://mmbs2010.eventbrite.com The password for the event is "models". Workshop Fees (including lunch both days, and dinner on the 5th) Early Bird: (first 40) free! Standard (non-student): £100 Standard (student): £80 Research students: There are 10 bursaries to support attendance, covering conference fee, travel and accommodation costs. These will be allocated on a first come, first served basis. ---------------------------------------------------- From: EMBL Seminar Date: Wed, Jun 2, 2010 at 8:11 PM Subject: EMBL Vision 2020: The Biology of Gene Regulation by miRNAs, 15 June Dear Colleague, To celebrate the inaugural year of the EMBL Advanced Training Centre and to set the stage for what we hope will be decades of exceptional scientific presentations, the European Molecular Biology Laboratory is hosting a unique series of forward-looking scientific lectures by world leaders in their fields, called "Vision 2020" www.embl.de/vision2020. Nobel laureates have been invited to share their vision of the future of their field with an audience of scientists from different areas of the life sciences and interested members of the public. They will share their thoughts on where their field currently stands and which exciting new developments and possible breakthroughs they see shaping this field within the next 10 years. Prof. Phillip A. Sharp, Nobel laureate in Physiology or Medicine in 1993, Massachusetts Institute of Technology will give the second lecture in the series on Tuesday, 15 June 2010 at 16:00 at the EMBL Advanced Training Centre: The Biology of Gene Regulation by miRNAs Following his lecture the audience is invited to a wine and cheese reception with Phillip A. Sharp in the foyer. On Tuesday 15 June at 16:10 there will be free bus with 50 seats marked with a Vision 2020 poster to transport interested listeners from the bus stop behind the Hotel Crowne Plaza in Heidelberg to EMBL. The bus will leave EMBL at 18:20 to travel back to the bus stop behind the Hotel Crowne Plaza in Heidelberg. The new EMBL Advanced Training Centre www.embl.de/atc, opened in March 2010, is a unique venue promoting advanced scientific training and education in Europe. Inspired by the double helical shape of DNA, the Advanced Training Centre hosts state-of-the-art conferences and training facilities setting a platform for a new era of scientific conferences. We kindly ask you to circulate this announcement to interested members and groups within your institute. With many thanks in advance, we look forward to welcoming you at the EMBL. There is no entrance fee for this event. Iain W. Mattaj, FRS Director General Matthias W. Hentze, M.D. Associate Director ---------------------------------------------------- From: European Molecular Biology Laboratory Date: Fri, May 28, 2010 at 5:13 AM Subject: EMBL Courses & Conferences Newsletter, May 2010 Online-Version of this E-Mail www.embl.de/events/newsletter ---------------------------------------------------- From: Katja Mombaur Date: Tue, Jun 1, 2010 at 2:01 AM Subject: PhD Position: Modeling and Optimization of Motions in Orthopedics PhD Position on Modeling and Optimization of Motions in Orthopedics The Optimization in Robotics & Biomechanics group at the Interdisciplinary Center for Scientific Computing (IWR) at the University of Heidelberg, Germany is seeking a PhD candidate for a research project on Modeling and Optimization of Motions in Orthopedics with a focus on either - Stability and balance control of human walking   or - Prosthesis modeling. The thesis will be performed in cooperation with Dr. Sebastian Wolf of the division Movement Analytics at the Orthopedic University Hospital Heidelberg. Requirements: - diploma or masters degree in engineering, mathematics, physics, computer science, biomechanics or biology - ideally experience in numerical mathematics, in particular in optimization and optimal control, mechanical modeling / multibody dynamics, and programming skills - motivation to work in an interdisciplinary project The successful applicant will be financed by a scholarship of the Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp) which is funded s funded by the Deutsche Forschungsgemeinschaft (DFG) within the Excellence Initiative. The scholarship is 1436 Euro per month (tax free; duration 36 months). All doctoral students are integrated into the education program of the Graduate School. Please send your application, including a statement of motivation, curriculum vitae, copies of university certificates, list of attended classes and grades, and names and addresses of two references to: Prof. Dr. Katja Mombaur IWR , Universitaet Heidelberg Im Neuenheimer Feld 368 69120 Heidelberg Germany kmombaur at uni-hd.de ---------------------------------------------------- From: stephen parnell (RRes-Roth) Date: Tue, Jun 1, 2010 at 5:14 AM Subject: Postdoc: Theoretical Epidemiology, Rothamsted Research Postdoctoral Research Scientist in Theoretical Epidemiology Biomathematics and Bioinformatics Dept, Rothamsted Research, UK. Applications are invited from suitably qualified ecologists/biologists with a strong background in mathematical modelling for a postdoctoral position to work on fundamental and applied aspects of models for detection and control of invasive plant diseases. These models will specifically be applied to the current invasion of Phytophthora ramorum and P. kernoviae in the UK with the aim to guide the DEFRA funded "Phytophthora ramorum and Phytophthora kernoviae Disease Management Programme." The candidate will develop generic models for the epidemiology of invasive plant diseases as well as methods to detect and control the pathogen at an early stage in the invasion. Specifically, the models will help the detection and control of the pathogens in heathland vegetations, mixed woodlands and heritage gardens. Results of the work will be published in internationally refereed journals. The post will be located in the Biomathematics and Bioinformatics Department under the supervision of Dr Frank van den Bosch (01582 763133 x2372) with close interactions with internal and external collaborators. The successful applicant will have a background in ecology/plant pathology, or mathematical biology. Knowledge of methods used in spatial ecology would be an advantage. Programming experience is essential. This appointment is full time and within Band D-PD with a starting salary normally in the region of £26,610 to £29,566 per annum. Apply by application form only, available with further particulars from www.rothamsted.ac.uk or from the HR Group, Rothamsted Research, Harpenden, Herts, AL5 2JQ, rres.hr@bbsrc.ac.uk. Please quote reference 1134. Closing date: 24 June 2010 ---------------------------------------------------- From: Wojcik, Monika Date: 2010/6/1 Subject: Two Postdocs: Computational Disease Biologist, Disease Modeling ... SCIENTIST - COMPUTATIONAL DISEASE BIOLOGIST YOU are highly motivated and always committed to deliver the best quality. You encourage collaboration and enjoy working in a team. You are passionate individual who likes creative and international work environments. THE OPPORTUNITY The successful candidate will join the Computational Science & Bioinformatics (CS&B) team of Philip Morris Products S.A. in Neuchâtel, Switzerland and will play a major role in the analysis of large scale data sets from various post-genomic technologies and their applications in biomarker discovery. Using newly developed software tools the candidate will interrogate systems biology datasets to discover biological networks differentiating normal and diseased states. His/Her scientific background and ability to critically review biological facts will be essential to developing a coherent synthesis of the biology being modeled. Specifically, you will: * Be responsible for mapping disease progression onto biological pathways * Provide analysis of large scale array-based data (genomics, transcriptomics, protemics) to support the Computational Disease Biology team * Apply advanced technologies in the area of network biology and pathway mining * Have a strong interest in collaborating with experimental biologists and computational scientists to interrogate systems biology datasets to discover biological networks differentiating normal and diseased states * Have scientific writing and critical review skills essential for the production of concise, detailed project reports which represent a coherent synthesis of the biology of the experimental system QUALIFICATIONS * PhD in bioinformatics, computational biology, biological sciences or a related field * Previous experience in disease pathways and network biology as well as experience in inflammation and cancer biology * Broad expertise in computational biology with particular strength in .omics data analysis * Demonstrated ability to manage and interpret large biological data sets * Fluency in English is a must WHAT WE OFFER You will be part of the PMI Research & Development Department, whose primary mission is to research and develop new products which may have the potential to reduce the risks of tobacco related diseases. You will benefit from our dynamic team of professionals, working in a multicultural environment. We offer an excellent salary and benefits package as well as relocation allowance (where appropriate). WHO WE ARE Philip Morris International Inc. (PMI) is the leading international tobacco company, with seven of the world.s top 15 brands, including the number one cigarette brand worldwide. PMI has more than 77,000 employees and its products are sold in approximately 160 countries. In 2009, the company held an estimated 15.4% share of the total international cigarette market outside of the U.S., or 26.0% excluding the People.s Republic of China and the U.S. PMI is an Equal Opportunity Employer. For more information, see www.pmi.com. Want to discover your potential? Come join our team! If you match our profile and you are interested in joining our dynamic team of professionals, please reply online. A valid Swiss work permit or Swiss or EU citizenship is required for this position. SCIENTIST, DISEASE MODELING & SIMULATION YOU are a detail-oriented figure with a passion for problem solving. You encourage collaboration and you enjoy working in a team. You have strong communication skills. You have academic or industrial experience in simulations and modeling of complex and real world problems. THE OPPORTUNITY The successful candidate will join the Computational Science & Bioinformatics (CS&B) team of Philip Morris Products S.A. in Neuchâtel, Switzerland. Computer modeling and simulation are central to the highly multidisciplinary effort at the PMI R&D Center. As a Scientist in Disease Modeling and Simulation, you will develop computational models of biological networks and disease mechanisms, and play a major role in the analysis and interpretation of complex datasets in the context of disease pathways. You will provide general mathematical expertise and create computational and statistical tools to advance the research of the greater team. In addition you will have the opportunity to test model-driven hypotheses by interfacing with clinical and experimental scientists. Specifically, you will: * Develop mathematical and computational models of disease mechanisms using multiple approaches and leveraging PMI's collaboration partners. * Develop hypotheses for disease mechanisms based on the analysis of experimental data in the context of current scientific knowledge * Use state of the art software tools to model the causal relationship between individual components within the whole biological system * Function as a member of a multidisciplinary team which executes scientifically challenging projects * Have a strong interest in collaboration with biologists for the elucidation of biological mechanisms QUALIFICATIONS * You have a Ph.D. in Applied Mathematics, Bioengineering, Computational Biology, Physics, or other closely related field with a strong background in nonlinear dynamics, ODEs, and statistics * You have demonstrated interest and experience in applying your technical knowledge to solve problems in biology and/or medicine * Preferably, you also have domain knowledge in inflammation, cardiovascular disease and/or cancer * You are able to communicate with scientists in biology and mathematics * You are familiar with scripting languages * Fluency in English is a must. WHAT WE OFFER You will be part of the PMI Research & Development Department, whose primary mission is to research and develop new products which may have the potential to reduce the risk of tobacco related diseases. You will benefit from our dynamic team of professionals, working in a multicultural environment. We offer an excellent salary and benefits package as well as relocation allowance (where appropriate). If you match our profile and you are interested in joining our dynamic team of professionals, please reply online. A valid Swiss work permit or Swiss or EU citizenship is required for this position. ---------------------------------------------------- From: Remi Dingreville Date: Wed, Jun 2, 2010 at 3:18 PM Subject: Postdoc: Tissue Mechanics Modeling, NYU-Poly / NYU Postdoctoral research fellow in tissue mechanics modeling at NYU-Poly / NYU Applications are invited for a postdoctoral research position which will be joint between the Computational Mechanics Laboratory within the Department of Mechanical and Aerospace Engineering at NYU-Poly and the Division of Cardiology at NYU School of Medicine. The selected postdoctoral fellow will participate in a vibrant interdisciplinary research group and will be involved in a research effort which aims to construct multiscale models of the mechano-fluidic behavior of the aortic heart valve. This research involves collaborations between basic science researchers and clinical investigators. Requirements: 1. Ph.D. in bioengineering, biomedical engineering, mechanical engineering, computational biology, computational materials science or a related field. 2. Experience in at least two of the following areas: finite element modeling, computational fluid dynamics, tissue engineering, or molecular mechanics modeling. 3. Experience in scientific computing (Fortran, C, or C++ programming, parallel computing, and Unix/Linux computing environments). 4. Strong verbal and written communication skills. 5.Demonstrated ability to work independently in a multidisciplinary research environment. Note: The initial appointment will be for one year, with a possibility of renewal contingent upon the availability of continuing funding and satisfactory performance. How To Apply: Please submit by email a single attachment that includes your CV, a brief statement of your research interests, and the contact information for two references to: Prof. Rémi Dingreville (rdingre@poly.edu) Department of Mechanical and Aerospace Engineering NYU-Poly 6 MetroTech Center Brooklyn, NY 11201 Phone: 718-260-3461 Fax: 718-260-3532 ---------------------------------------------------- From: Catherine Crawley Date: Tue, 01 Jun 2010 13:51:03 -0400 Subject: Staff Position: Education and Outreach Coordinator, NIMBioS Staff Position - Education and Outreach Coordinator - National Institute for Mathematical and Biological Synthesis (NIMBioS) This full-time position is responsible for coordinating all outreach and education research activities of NIMBioS in collaboration with the Director and the Associate Director for Education, Outreach and Diversity. This position develops the array of outreach activities of NIMBioS including activities with the general public, K-12 programs at schools, collaboration networks for high school teachers, coordination of summer undergraduate research programs, mentoring networks for undergraduates, coordination of outreach-linked-to-research with the staff of Great Smoky Mountains National Park, and organization of workshops and conferences related to education and outreach. A MS in a quantitative scientific field (e.g., Mathematics, Statistics or Computer Science) or an area of the Life Sciences or equivalent experience is required; a PhD is a plus. Applicants should also have experience working in collaboration with researchers with BS, MS and PhD degrees to meet project tasks and the ability to communicate scientific topics to diverse audiences. Position Title: Research Associate II. Pay Grade 41. To apply, submit a CV with cover letter and names of two references to: Dr. Chris Welsh via email to cwelsh@utk.edu. The University of Tennessee is an EEO/AA/Title VI/Title IX/Section 504/ADA/ADEA institution in the provision of its education and employment programs and services. All qualified applicants will receive equal consideration for employment without regard to race, color, national origin, religion, sex, pregnancy, marital status, sexual orientation, gender identity, age, physical or mental disability, or covered veteran status. ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------