---------------------------------------------------- Subject: SMB Digest v08i07 SMB Digest February 18, 2008 Volume 08 Issue 7 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: Conference: Mathematical Tools for Multi-Scale Biological Processes Call for Applicants: Summer School for Computational Immunology Okinawa Computational Neuroscience Course 2008, Deadline Approaching Conference on Systems Biology of Mammalian Cells 2008, May 22-24 CfP: Special Issue on Recent Advances ... Biomedical Imaging NIH Requirements for Public Access to Journal Articles Graduate Position: Math or EES, University of Maine PhD-student Positions: Biomedical Data Processing, Leuven Systems Biology Posts: Aberdeen and CISBIC Postdoctoral Positions: Warwick Systems Biology Centre Lectureship: Biomathematics, Imperial College London SMBnet Reminders ---------------------------------------------------- From: Patrick De Leenheer Date: Feb 11, 2008 1:30 PM Subject: Conference: Mathematical Tools for Multi-Scale Biological Processes Call for abstracts for the International Conference: Mathematical Tools for Multi-Scale Biological Processes Venue: Montana State University, Bozeman, MT, June 4 to June 6, 2008. Early registration ($90) and abstract due date: May 15, 2008. There is limited financial support for graduate students and postdoctoral researchers. For more information, see: http://www.math.ufl.edu/~deleenhe/montana/index.html ---------------------------------------------------- From: Uri Hershberg Date: Wed, 13 Feb 2008 10:05:00 -0500 Subject: Call for Applicants: Summer School for Computational Immunology First call for applications: 3RD ANNUAL SUMMER SCHOOL FOR COMPUTATIONAL IMMUNOLOGY Venue: Yale University School of Medicine, New Haven, CT Dates: August 11-15, 2008 Organized by PRiME: Program for Research on Immune Modeling and Experimentation Summary: Like all biological systems, the immune system acts across multiple scales involving complex interactions and feedback, from the molecular interaction of receptors and ligands to the systemic inflammatory reaction to disease. Computational modeling provides a framework to integrate observational data collected from multiple modes of experimentation and provide insights the immune response in health and disease. This summer school will introduce graduate students, post doctoral fellows, and faculty to computational modeling of immunity. Who should attend? The summer school is intended for early computational biology graduate students, and experimental biologists at all levels who desire an introduction to computational modeling techniques and their applications to problems in immunology. Four broad topics will be covered by faculty who are experts in the area: · Gene expression analysis and data mining · Deterministic modeling (including ordinary differential equations) · Stochastic and agent based modeling · Model fitting and parameter estimation Each of the modules above will combine lectures and hand on labs, and will be motivated by a group project to be developed throughout the course. The final day of the summer school will include a symposium on 'Systems Biology of Innate Immunity'. What is the application process? Participation in the summer school is by competitive application. There is no tuition for those accepted, and scholarships are available to cover travel, room and board. Applications for the summer school and scholarships are due by April 15, 2008. Details can be found at: http://tsb.mssm.edu/prime/summer2008 Further questions should be addressed to Uri Hershberg (uri.hershberg@yale.edu). A poster advertising the school can be found at http://tsb.mssm.edu/prime/files/Summer2008_Immunology.pdf ---------------------------------------------------- From: Erik De Schutter Date: Tue, 12 Feb 2008 21:30:01 +0900 Subject: Okinawa Computational Neuroscience Course 2008, Deadline Approaching OKINAWA COMPUTATIONAL NEUROSCIENCE COURSE 2008 Methods, Neurons, Networks and Behaviors June 15 - July 4, 2008. Okinawa, Japan http://www.irp.oist.jp/ocnc/2008 The aim of the Okinawa Computational Neuroscience Course is to provide opportunities for young researchers with theoretical backgrounds to learn the latest advances in neuroscience, and for those with experimental backgrounds to have hands-on experience in computational modeling. We invite graduate students and postgraduate researchers to participate in the course, held from June 15th through July 4th, 2008 at an oceanfront seminar house of the Okinawa Institute of Science and Technology. Interested students can now apply through the course web page at http://www.irp.oist.jp/ocnc/2008 Applications will close February 17th, Applicants will receive confirmation of acceptance in the 3rd week of March. Like last year, OCNC will be a comprehensive three-week course covering single neurons, networks, and behaviors with ample time for student projects. The first week will focus exclusively on methods with hands-on tutorials during the afternoons, while the second and third weeks will have lectures by international experts. We invite those who are interested in integrating experimental and computational approaches at each level, as well as in bridging different levels of complexity. The sponsor will provide lodging and meals during the course and support travel for those without funding. We hope that this course will be a good opportunity for theoretical and experimental neuroscientists to meet each other and to explore the attractive nature and culture of Okinawa, the southernmost island prefecture of Japan. ---------------------------------------------------- From: SBMC 2008 Date: Tue, 12 Feb 2008 13:24:23 +0100 Subject: Conference on Systems Biology of Mammalian Cells 2008, May 22-24 May 22 to May 24, 2008 in Dresden, Germany Under the auspices of Dr. Annette Schavan, Federal Minister of Education and Research Call for talks, posters and bursary application We are pleased to invite you to enter a poster abstract for the SBMC 2008, taking place on May 22 to May 24, 2008. Abstracts must be submitted for review by February 29, 2008. For more information, please see www.sbmc08.de/08/submission.html. For the first time there is the additional possibility to apply for the Systems Biology Award, to get a nominee talk on the second day of the conference. Applications for the award must be submitted until February 18, 2008. For more details on the application please visit www.fz-juelich.de/ptj/systembiologie. The SBMC 2008 offers a 3-day program of 5 academic sessions covering the issues; New theoretical approaches and cutting edge technologies; Signaling Networks; Self-organization and collective phenomena; Developmental Pattern Formation; and Biomedicine. The conference holds an extraordinary list of speakers with session talks by internationally renowned speakers (www.sbmc08.de/08/speakers.html). Poster presentation spaces will only be authorized to registered delegates, so don't miss your chance to register now and take advantage of the Early Bird discount. ---------------------------------------------------- From: Weihua Geng Date: Fri, 15 Feb 2008 11:27:02 -0500 Subject: CfP: Special Issue on Recent Advances ... Biomedical Imaging Call for Papers "Special Issue on Recent Advances in Computational Techniques for Biomedical Imaging" Communications in Numerical Methods in Engineering will publish a special issue on Recent Advances in Computational Techniques for Biomedical Imaging. The Guest Editors for this issue will be Professor Guo-Wei Wei, Department of Mathematics and Department of Electrical and Computer Engineering, Michigan State University and Professor Ge Wang, Director of Biomedical Imaging Division, Virginia Polytechnic Institute and State University. Recent advances in biomedical imaging have revolutionized diagnosis, therapy and discovery in both clinical and pre-clinical settings. While traditional tomographic and post-processing methods become increasingly sophisticated, emerging new modalities play more and more critical roles in anatomical, functional, cellular and molecular imaging. Mathematical and computational techniques have been instrumental to these developments and their momentum. We invite the original papers and high-quality overviews on all the relevant topics including but not limited to: Algorithms for biomedical image reconstruction Techniques for biomedical image analysis and visualization Forward models and inverse solutions Interface problems in biomedical imaging Multi-modal imaging Evaluation and comparison of biomedical imaging modalities Paper Submission Details Completed papers should conform to the journal's style and according to the instructions for authors which can be found on the journal's homepage, under For Authors. Papers have to be submitted online via the journal's homepage to http://www3.interscience.wiley.com/cgi-bin/jabout/5902/ForAuthors.html under Online Submission. Authors must select Guo-Wei Wei or Ge Wang as Editor. Each submission must be clearly identified as a submission for this special issue, and the special issue code, RACTI, must be entered in the Special Issue Title field, when requested. Publication will take place according to the following schedule: Manuscript due: 1 April 2008 First review completion: Mid 2008 Anticipated publication date: End of 2008 ---------------------------------------------------- From: Springer Date: Tue, 12 Feb 2008 05:48:26 -0800 (PST) Subject: NIH Requirements for Public Access to Journal Articles News for Journal Authors, February 2008. Visit us at springer.com Do you receive research funding from the National Institutes of Health (NIH)? If so, as from April 2008 you will be required to deposit the final manuscript of your journal articles in PubMed Central and ensure free availability (open access) within 12 months of publication. You will be pleased to hear that Springer journals are fully geared up for that requirement. All you have to do is opt for open access publication of your article through Springer's Open Choice - you will be given that option as soon as your article has been accepted for publication after peer review - and we will handle the administrative process. Springer will take care of the immediate deposit in PubMed Central and what's more, not of the manuscript, but of the final, published article. And it will also be available with open access right away, and not just after 12 months. The cost of Open Choice is - as stated on the NIH web site - a permissible cost in your grant so please take care to budget for it. Publishing with open access in Springer journals completely takes away any worries you might have about complying with the new NIH rules for grantees when it comes to publishing your research results. We look forward to the submission of your next paper. ---------------------------------------------------- From: dhjm5@sunhou.com Date: Tue, 12 Feb 2008 16:22:54 -0500 Subject: Graduate Position: Math or EES, University of Maine The University of Maine in Orono currently has a two-year graduate assistantship position available for qualified applicants seeking graduate training leading to a master's degree (either an M.A. in Mathematics, or an M.S. in Ecology and Environmental Science), beginning in Fall 2008. The relevant area of research for the position is spatial population modeling in spatiotemporally structured heterogeneous environments. This includes mathematical and computational models of populations in dynamic heterogeneous habitats. Collaboration with faculty in the School of Biology and Ecology would also be a likely part of the position, as the models will be applied to the spread of agricultural crop pests and invasive species, such as maggot flies in commercial blueberry fields and invading Asian woodwasps. The position is part of the Spatial Population Ecological and Epidemiological Dynamics Lab group (SPEED Lab) of Dr. David Hiebeler (http://www.math.umaine.edu/faculty/hiebeler/speedlab.html). Potential applicants are strongly encouraged to contact Dr. Hiebeler prior to their application. Application materials should be submitted through the University's Graduate School (see http://www2.umaine.edu/graduate/article.php?id=63), and should indicate in the application that they wish to be considered for Dr. Hiebeler's SPEED Lab position. Applicants will be considered until the position is filled. This position is restricted to U.S. citizens and permanent residents. The University of Maine is an Equal Opportunity/Affirmative Action Employer. ---------------------------------------------------- From: Diana Sima Date: Fri, 15 Feb 2008 10:01:25 +0100 Subject: PhD-student Positions: Biomedical Data Processing, Leuven PhD-student Positions in Biomedical Data Processing at Katholieke Universiteit Leuven, Belgium Location: Department of Electrical Engineering, Division ESAT-SCD, research group BioMed, Katholieke Universiteit Leuven, Leuven, Belgium (http://www.esat.kuleuven.be/sista/members/biomed/) Research group. The BIOMED team within the ESAT-SCD division consists of 2 staff members, 3 postdocs, 17 PhD students. Research ^ fundamental/theoretical as well as application oriented -- is performed in the domain of (multi)linear algebra, (non)linear signal analysis, classification and system identification with special focus to the development of numerically reliable and robust algorithms for the extraction of clinically, biochemically or pharmaceutically relevant information (e.g. metabolite concentrations in the brain) out of low-quality multi-channel measurements in order to enable an improved medical diagnosis. In this domain the group has built up an international reputation. Applications under study are: quantification of metabolite concentrations using in-vivo Magnetic Resonance Spectroscopic (MRS) data and images, quantification of brain oxygenation and autoregulation in neonates using (functional) Near-Infrared Spectroscopy, quantification of cardiovascular dynamics and heart-rate variability analysis, event-related potential analysis using EEG, stress monitoring using EMG, detection and localization of epileptic seizures based on scalp-EEG monitoring, and preoperative classification and prognosis of (brain, ovarian, prostate) tumours. Three PhD positions. We seek one of more outstanding graduate students for the following multidisciplinary research projects: 1. EEG signal processing for non-invasive Brain-Computer interaction, possibly combined with multimodal registration of other relevant information (EMG/ECG/) and signal interpretation for motor recovery; 2. Descriptive and predictive models and advanced Statistical analysis for computer-aided diagnosis and prognosis of cancer and autism; 3. Integration of EEG and functional MR Imaging with applications in monitoring cognitive disorders in patients with MS and ADHD. The research is done in a multidisciplinary environment in strong collaboration with the appropriate divisions in the University Hospitals K.U.Leuven. All positions are immediately vacant. The PhD work will be supervised by Prof. Sabine Van Huffel. Profile: We are particularly seeking candidates with a Master-of-Science degree in biomedical, electrical, computer science or mathematical engineering, in bioengineering or in mathematics, and with strong interests in optimization, signal processing, statistics, numerical computations, and biomedical applications. The ability to become acquainted with new methods within short time and good familiarity with scientific tools like MATLAB programming and statistical analysis are appreciated. The chosen candidate will be an enthusiastic person and initiator with good communication skills and a good knowledge of English. Application: To apply, please send a CV and a cover letter before April 15, 2008 to Prof. Sabine Van Huffel (sabine.vanhuffel@esat.kuleuven.be) Information: The salary will be assigned according to the Belgian university salary system. The PhD-student appointment is for the duration of four years. ---------------------------------------------------- From: J. Stark Date: Fri, 15 Feb 2008 16:46:02 +0000 Subject: Systems Biology Posts: Aberdeen and CISBIC Systems Biology Posts at Aberdeen and CISBIC We are currently recruiting to the large interdisciplinary Combinatorial Responses In Stress Pathways (CRISP) team which will be jointly based at the University of Aberdeen and at CISBIC, Imperial College London. are seeking ambitious and committed scientists to join the CRISP team. This team will include four experimental biologists, four applied mathematicians, six PhD students supervised by the ten group leaders. The project will study the Systems Biology of stress responses in the medically important fungi Candida albicans and Candida glabrata. We will combine advanced modelling techniques with state-of-the-art genomics, molecular biology, biochemistry and cell biology in these pathogens. This project is funded by the BBSRC under the SABR initiative for up to five years. A PDF summary of the available posts can be found at http://www.ma.ic.ac.uk/~jstark/PDF/SABR%20Advert%20Final.pdf ---------------------------------------------------- From: David Rand Date: Tue, 12 Feb 2008 08:56:04 +0000 Subject: Postdoctoral Positions: Warwick Systems Biology Centre The Warwick Systems Biology Centre (WSB) has recently received three large grants from the SABR (Systems Approaches to Biological Research) initiative funded by BBSRC and EPSRC. These are to study (i) the dynamics and function of the NF-kB signaling system (with Prof. M White, Liverpool). (ii) the robustness of plant signaling systems to temperature changes (led by Dr K Halliday, Edinburgh), and (iii) the mechanisms determining the switching between different stress responses in plants. As a results we have available a number of postdoctoral posts for people with a strong mathematical, statistical or computational background. The people appointed to these will be involved in modeling, analysis of cutting-edge biological data and experimental design and will be involved in all aspects of the biological projects. There is also a post for a bioinformatics technician. Anyone interested in any of these posts should contact Professor David Rand (d.a.rand@warwick.ac.uk) as soon as possible for further details. Please reply to d.a.rand@warwick.ac.uk * Professor David Rand * Warwick Systems Biology & Mathematics Institute, * EPSRC Senior Research Fellow, * Co-director, Warwick Systems Biology, * Address: Warwick Systems Biology, Coventry House, University of Warwick, Coventry CV4 7AL, UK * tel: +44 (0)24 7652 3599 fax: +44 (0)24 7652 4182 * email: dar@maths.warwick.ac.uk * secretary/PA: J.A.Maynard@warwick.ac.uk, tel: +44 (0)24 7652 8321 * web: http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/rand/ ---------------------------------------------------- From: J. Stark Date: Fri, 15 Feb 2008 16:58:56 +0000 Subject: Lectureship: Biomathematics, Imperial College London Imperial College London Department of Mathematics Lectureship in Biomathematics Applications are invited for a Lectureship in Biomathematics within the Department of Mathematics at Imperial College London, starting 1 October 2008 or as soon as possible thereafter. Collaboration be-tween biomedicine and the mathematical sciences is a very high priority throughout the whole of Imperial College London. Within the Department of Mathematics, this has been reflected by the recent appointments of a chair and a lectureship in this field and the establishment of the Biomathematical Sciences research group. Members of this group have a very broad range of research interests, including cellular decision making, gene and protein networks, pattern formation, DNA topology and models of evolution. Many have close links with experimental biologists in the Faculties of Life Sciences and Medicine. Further details can be found at http://www.ma.imperial.ac.uk/ammp/bms/index.php The Department of Mathematics also plays a significant role in the BBSRC/EPSRC Centre for Integrative Systems Biology at Imperial College (CISBIC). This 7.5m interdisciplinary research initiative brings together experimentalists, modellers and computational scientists in the general area of host-pathogen interactions. CISBIC is currently directed by Prof J. Stark, a member of the Department of Mathematics. In addition the newly established Institute for Mathematical Sciences has several biologically oriented research programmes. Candidates for this lectureship should possess a PhD in the Mathematical Sciences or closely related discipline. They would be expected to demonstrate an outstanding record of research in any area of biomathematics, systems biology, biophysics or similar field. The successful applicant should have experience of collaboration with experimental biologists. This is a permanent appointment and salary will be in the range £40,050 to £44,730 per annum, de-pending on experience. An application form and further particulars can be obtained from http://www.imperial.ac.uk/employment/academic/index.htm. Alternatively please contact Mr Kalra Taylor, email: k.taylor@imperial.ac.uk tel: +44 (0)20 7594 8483.To apply, please post five copies of your application form together with a single copy of your CV, list of publications and names of three referees to Mr Kalra Taylor, Department of Mathematics, Exhibition Road, Imperial College London SW7 2AZ, UK. Closing date: 7th March 2008 Valuing diversity and committed to equality of opportunity ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------