---------------------------------------------------- Subject: SMB Digest v08i04 SMB Digest January 30, 2008 Volume 08 Issue 4 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: New REU in Biomathematics, Virginia Tech Matlab / R Reference Short Course: Modeling Applications in Cardiovascular and ... 1st UCIrvine Symposium on Mathematical Systems Biology, Feb 28-29 Call for Special Session: Computational Biology, CMMSE 2008 Early Registration: Thematic Research School, Deadline 15 Feb CfP: 3rd Int'l Workshop on Hybrid Artificial Intelligence Systems 6th International Summer School in Formal Languages & Applications Postdoctoral Fellowship: Modeling of Viral Transcriptional Circuitry Biomathematical Modeling, BWH & Harvard Medical School Postdoc Position: Biocomplexity Institute, Indiana University SMBnet Reminders ---------------------------------------------------- From: Reinhard Laubenbacher Date: Wed, 23 Jan 2008 07:45:57 -0500 Subject: New REU in Biomathematics, Virginia Tech A new Research Experiences for Undergraduates (REU) site, supported by the National Science Foundation, and focused on "Modeling and Simulation in Systems Biology (MSSB)" will begin this summer. The program is a partnership between the Virginia Bioinformatics Institute and the Interdisciplinary Center for Applied Mathematics, both on the campus of Virginia Tech. Targeted students are sophomores and juniors in mathematics and other quantitative sciences. Program dates are May 25 to August 1, 2008, with an application deadline of February 24, 2008. More details are available at http://biomath.vbi.vt.edu Information about other summer undergraduate research opportunities related to mathematical biology, systems biology, and bioengineering is available at https://www.vbi.vt.edu/education_and_outreach/educational_programs/undergraduate ---------------------------------------------------- From: David Hiebeler Date: Mon, 28 Jan 2008 10:33:33 -0500 Subject: Matlab / R Reference I've put together a Matlab/R Reference document that SMB folks may find useful. It's something I (as a long-time Matlab user) started writing last year, as I learned R while teaching a course on Modeling and Simulation. I was happy to find that R could do pretty much everything I needed for the types of spatial simulations I taught in my course. The document is particularly handy as a translation tool for people familiar with one package and learning the other, but can also serve as a brief stand-alone reference for either package. Since most people may think "statistics" upon hearing the name R, I should point out that I do very little statistics, so that's not what the reference is about. But it covers basics of (scalar and vector/matrix) computation, programming, random variables and probability distributions, numerically solving ODEs, a fair bit of graphics, etc. The reference is available at http://www.math.umaine.edu/faculty/hiebeler/comp/matlabR.html and it is still evolving, so if you find it useful you may want to check back occasionally for updates. ---------------------------------------------------- From: Tarynn M Witten/FS/VCU Date: Wed, 23 Jan 2008 11:28:57 -0500 Subject: Short Course: Modeling Applications in Cardiovascular and ... VCU is one of three US universities to be awarded funds to develop an NIH/NHLBI Short Course on Computational Modeling Applications in Cardiovascular and Cardiopulmonary Dynamics. The course will be held 23 February - 1 March 2008 at Virginia Commonwealth University, Richmond, VA. This course is designed to introduce clinician and biomedical scientists to the application of appropriate theoretical and computational, tools, models and simulation methods to problems arising in cardiopulmonary and cardiovascular dynamics. These problems range from biomolecular and cellular scale topics such as calcium transport and cell cycle dynamics to larger scale problems such as mechanical biophysics and fluid dynamics. The short course offers intensive modeling and simulation mentoring allowing participants to interact directly with seasoned researchers in their respective fields and thereby creating an environment for the development of longer term collaborative interaction. Readings, lecture notes and other course materials are supplied via the website and in lectures. Registration, scholarship, travel and related information can be found at the course website http://www.vcu.edu/csbc/nhlbi. This activity is approved for AMA PRA credit. CEU credit is available for non-physicians. For further information, visit the website or contact Tarynn M. Witten, PhD, MSW, FGSA PI and Course Director CSBC Director of Research & Development Associate Professor, Biological Complexity, Emergency Medicine Phone: (804) 827-7371 Fax: (804) 828-1961 Email: tmwitten@vcu.edu ---------------------------------------------------- From: Qing Nie Date: Wed, 23 Jan 2008 11:03:13 -0800 (PST) Subject: 1st UCIrvine Symposium on Mathematical Systems Biology, Feb 28-29 1st UCIrvine Symposium on Mathematical Systems Biology, February 28-29, 2008 The 1st UCIrvine Symposium on Mathematical Systems Biology - "Spatial Dynamics of Growth and Signaling", will be held at UC Irvine on February 28-29, 2008. The speakers for the symposium are Alexander Anderson (Dundee) Mark Chaplain (Dundee) Olivier Cinquin (Wisconsin) Vittorio Cristini (U. of Texas, Houston) Timothy Elston(UNC) Avner Friedman (MBI, Ohio State) Boris Kholodenko (Thomas Jefferson) Wallace Marshall (UCSF) Steven McDougall(Heriot-Watt) Hans Othmer (Minnesota) Ertugrul Ozbudak (Stowers Institute) Vito Quaranta (Vanderbilt) Christopher Rao (UIUC) Kristin Swanson (Washington) David Umulis (Minnesota) Jin Wang (Stony Brook) More information for the symposium can be found at the symposium website: http://cmcb.math.uci.edu/Symposium/ ---------------------------------------------------- From: Jesus Vigo-Aguiar Date: Fri, 25 Jan 2008 13:51:30 +0100 Subject: Call for Special Session: Computational Biology, CMMSE 2008 CALL FOR SPECIAL on COMPUTATIONAL BIOLOGY Conference Name: 8th Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE--2008) Location: Hotel Melia Galua, Manga del Mar Menor, Murcia, Spain. (Two seas one coastline- the Mediterranean and the mar menor, in the south of Spain) Dates: June 13-16, 2008 Web page: www.usal.es/~CMMSE Expected special issues at: Int. J. of Computer Mathematics, J. Mathematical Chemistry Registration is Now Available. For additional information please contact cmmse@usal.es or jvigo@usal.es ---------------------------------------------------- From: François Képès Date: Fri, 25 Jan 2008 13:01:39 +0100 Subject: Early Registration: Thematic Research School, Deadline 15 Feb http://epigenomique.free.fr/en/ Thematic Research School on "Modeling Complex Biological Systems in the Context of Genomics" LILLE (F) April 7-11, 2008 [See also http://smb.org/publications/SMBnet/digest/v07i40 .] ---------------------------------------------------- From: Dacheng Tao Date: Wed, 30 Jan 2008 12:02:19 +0800 Subject: CfP: 3rd Int'l Workshop on Hybrid Artificial Intelligence Systems 1st CFP. HAIS'08 3rd International Workshop on Hybrid Artificial Intelligence Systems (HAIS'08) 24th-26th September, 2008.- Burgos, Spain http://www2.ubu.es/hais2008/home.shtml ---------------------------------------------------- From: carlos.martin@urv.cat Date: Sat, 26 Jan 2008 19:48:38 GMT Subject: 6th International Summer School in Formal Languages & Applications 6th INTERNATIONAL SUMMER SCHOOL IN FORMAL LANGUAGES AND APPLICATIONS (formerly International PhD School in Formal Languages and Applications) Tarragona, Spain, July 21 - August 2, 2008 Organized by: Research Group on Mathematical Linguistics Rovira i Virgili University http://www.grlmc.com ADDRESSED TO: Graduate students from around the world. Most appropriate degrees include: Computer Science and Mathematics. Other graduate students (for instance, from Linguistics, Electrical Engineering, Molecular Biology or Logic) as well undergraduate students can attend too provided they have a good background in discrete mathematics. All courses will be compatible in terms of the schedule. (There will be no courses in parallel.) COURSES AND PROFESSORS JULY 21-26: Martyn Amos (Manchester), Synthetic Biology: Biological Engineering [6 hours] Erzsebet Csuhaj-Varju (Budapest), Language Theoretic Models of Multi-Agent Systems [14 hours] Zoltan Esik (Tarragona), An Axiomatic Theory of Automata [6 hours] Rusins Freivalds (Riga), Elliptic Curves [6 hours] Max Garzon (Memphis), Biomolecular Nanotechnology [6 hours] Masami Ito (Kyoto), Regular Grammars [6 hours] Martin Kutrib (Giessen), Cellular Automata [6 hours] Claudio Moraga (Mieres), Fuzzy Formal Languages [6 hours] Kenichi Morita (Hiroshima), Two-Dimensional Languages [6 hours] Mitsunori Ogihara (Rochester), Computational Complexity and Molecular Computation Models [6 hours] Friedrich Otto (Kassel), Restarting Automata [6 hours] COURSES AND PROFESSORS JULY 28 - AUGUST 2: Francine Blanchet-Sadri (Greensboro), Partial Words [6 hours] Henning Bordihn (Potsdam), Mildly Context-Sensitive Grammars [8 hours] Wojciech Buszkowski (Poznan), Type Logics and Grammars [8 hours] Manfred Droste (Leipzig), Weighted Automata [8 hours] Joerg Flum (Freiburg, Germany), Parameterized Complexity [6 hours] Tom Head (Binghamton), Computing with Light Using Transparency and Opacity [6 hours] Satoshi Kobayashi (Tokyo), Grammatical Models and Algorithms for Biological Sequence Analysis [6 hours] Mark-Jan Nederhof (St.-Andrews), Probabilistic Parsing [6 hours] Alexander Okhotin (Turku), Language Equations [6 hours] Detlef Wotschke (Frankfurt), Descriptional Complexity of Automata and Grammars [12 hours] Sheng Yu (London, Canada), Finite Automata [16 hours] REGISTRATION: It has to be done on line at: http://www.grlmc.com FEES: They are variable for each student, depending on the number of courses each one takes. The rule is: 1 hour = - 10 euros (for payments until March 24, 2008), - 12 euros (for payments after March 24, 2008). The fees must be paid to the School's bank account: IBAN code: ES13 0073 0100 5104 0350 6598 Please mention SSFLA'08 and your full name in the subject. An invoice will be provided on site. To check the eligibility for early registration, what counts is the date of the bank order for payment (not the date when the registration form was filled in). People registering on site at the beginning of the School must pay in cash. ACCOMMODATION: Information about accommodation will be provided through the website of the School in due time. IMPORTANT DATES: Announcement of the programme: January 26, 2008 Starting of the registration: February 4, 2008 Early registration deadline: March 24, 2008 Starting of the School: July 21, 2008 End of the School: August 2, 2008 QUESTIONS AND FURTHER INFORMATION: Carlos Martin-Vide: carlos.martin@urv.cat WEBSITE: http://www.grlmc.com POSTAL ADDRESS: SSFLA'08 Research Group on Mathematical Linguistics Rovira i Virgili University Plaza Imperial Tarraco, 1 43005 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-559597 ---------------------------------------------------- From: Leor Weinberger Date: Wed, 23 Jan 2008 11:13:09 -0800 Subject: Postdoctoral Fellowship: Modeling of Viral Transcriptional Circuitry Postdoctoral Fellowship: Mathematical Modeling of Viral Transcriptional Circuitry, U of California, San Diego Dr. Leor S Weinberger's laboratory (recently moved from Princeton) seeks applicants for a postdoctoral fellowship (2-3 years) exploring HIV and viral transcriptional regulation. The specific research project is flexible and can be tailored to the interests of the individual, but should fall under the broad fields of transcriptional regulation and circuitry. Our lab is a joint theoretical and experimental lab ( http://chem-faculty.ucsd.edu/weinberger) that stresses close interaction between theorists and experimentalists and houses all the computational resources and the wet-lab experimental infrastructure (including several confocal microscopes for live single-cell time-lapse imaging) required for joint theoretical/experimental projects. Applicants will be considered from a diverse spectrum of backgrounds (including PhDs in mathematics, statistics, physics, biology or related areas) but preference will be for highly motivated applicants with excellent communication skills. The ideal candidate should also have good interaction capability with experimentalists and a proven record of independent research. The postdoctoral fellowship provides a competitive annual stipend plus benefits and health insurance. Start date and term are negotiable. Applications are welcome from candidates of any nationality, and will be reviewed on a rolling basis. UCSD offers an outstanding intellectual environmental with many top-five ranked scientific departments (including Biochemistry and Bioengineering), a highly regarded medical school, a Center for Theoretical Biological Physics (CTBP), and close proximity to the Salk and Scripps Institutes. Highly motivated applicants are encouraged to email a statement of research interests, CV, and contact details for three references to lsw (at) ucsd.edu. Informal inquiries are also welcome. ---------------------------------------------------- From: Elizabeth Klerman Date: Wed, 30 Jan 2008 18:57:12 -0500 Subject: Postdoc: Biomathematical Modeling, BWH & Harvard Medical School POSTDOC OPPORTUNITY (1 opening) in BIOMATHEMATICAL MODELING with Elizabeth Klerman, Division of Sleep Medicine, Brigham and Women's Hospital and Harvard Medical School Projects cover a range of topics in dynamics of circadian rhythms and sleep at the network level, utilizing physiologically-based models, in deterministic and stochastic frameworks. Projects typically involve close collaboration with experimentalists, both analyzing and modeling data as well as designing experiments. The Division of Sleep Medicine is interdisciplinary, with members from backgrounds in applied mathematics, computer science, statistics, physiology, psychology and medicine. The rich environments of the Division of Sleep Medicine (http://sleep.med.harvard.edu) and the Harvard Medical School (www.hms.harvard.edu) offer many opportunities for career development through seminars, lab meetings, formal courses and interaction with other groups. Currently seeking applicant for: Modeling of dynamical circadian rhythms and sleep processes. Potential projects involve multi-dimensional data sets of human circadian rhythms, sleep, neurobehavioral performance and alertness. We are interested in quantifying inter-individual differences and using these to predict performance and sleep. Current funding for this work is from NSBRI (NASA), AFOSR and NIH. A desirable candidate will have skills and knowledge in applied mathematics and statistics. Applicants with additional background and experience with engineering, signal processing, dynamical systems, simulation, and/or computational modeling are especially encouraged to apply. Knowledge of MatLab is appreciated. A course in circadian rhythms and sleep will be offered in fall 2008 that the candidate will be expected to attend. The initial appointment is for 2 years, renewable annually thereafter. Interested candidates should send a letter of interest, curriculum vitae, and contact information for three references to: Elizabeth B Klerman MD PhD Division of Sleep Medicine Brigham and Women's Hospital 221 Longwood Ave Boston MA 02115 Email: Ebklerman@hms.harvard.edu Harvard Medical School and Brigham and Women's Hospital are Affirmative Action/Equal Opportunity Employers. We strongly encourage applications from women and minority candidates. ---------------------------------------------------- From: Randy Heiland Date: Wed, 23 Jan 2008 10:31:19 -0500 Subject: Postdoc Position: Biocomplexity Institute, Indiana University Software Developer/Research Associate/Post Doctoral Fellow The Indiana University Biocomplexity Institute seeks a Research Associate or Post Doctoral Fellow to participate in research on the development and improvement of the Tissue Simulation Environment (compucell3d.org). Rank is commensurate with experience. There is a possibility that two positions will be filled. Preferred skills and abilities include extensive experience in C++, Python, user interface design and implementation. Candidate should be able to interact with users and help prepare training workshops, and should be able to work in a small team environment with limited supervision. Position will offer opportunities to collaborate on new research projects and participate in publications with Biocomplexity Institute scientists. Areas of interest include Monte Carlo methods, statistical mechanics, fluid dynamics, partial differential equations, mathematical modeling of biological systems, computer graphics visualization, and scientific software development. Skills in numerical modeling, graphics and visualization, or parallel programming are a plus, as is having a strong (Masters or Ph.D.) scientific background. Technical writing and documentation experience also preferred. Review of applicants will begin immediately and continue until position is filled. Initial appointment will begin as early as January 7, 2008, and is expected to last one year with extension possible, subject to satisfactory performance. Please send a CV to Randy Heiland (heiland@indiana.edu). Indiana University is an equal opportunity / affirmative action employer. ---------------------------------------------------- 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 use e-mail, send mail to LISTSERV@listserv.biu.ac.il with "subscribe SMBnet Your Name" in the body of the mail (omit the quotes). 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. 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