---------------------------------------------------- Subject: SMB Digest v08i06 SMB Digest February 11, 2008 Volume 08 Issue 6 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: PIMS Course: Mathematical Biology, May 11-June 11, UBC, Vancouver Undergraduate Biomathematics Day, April 18-19, Niagara Falls Workshop: Mathematical Perspective on Cancer Immunology, May 5-7 Workshop: MPDE-08, March 12, University of Leicester 5th Int'l Symposium on Networks in Bioinformatics, 21-22 April Training Workshop: CompuCell3D, June 16-20, Indiana University Summer School: NN2008, July 7-11, Porto, Portugal Modelling Cancer Invasion: 'Let's Stick Together' Scientific Programmer: Mathematical Biology, University of Helsinki Postdoc Position: ISTM, Keele Postdoc / Research Assistant: Cambridge Systems Biology Centre Software Developer/Research Associate/Post Doctoral Fellow, Indiana U 5 Tenure Faculty Positions: Biological Sciences, Royal Holloway Nine Research Scientist Positions, Fisheries and Oceans Canada SMBnet Reminders ---------------------------------------------------- From: Leah Keshet Date: Wed, 6 Feb 2008 18:15:08 -0800 (PST) Subject: PIMS Course: Mathematical Biology, May 11-June 11, UBC, Vancouver Announcing: The Pacific Institute for Mathematical Sciences (PIMS) is sponsoring its first International Graduate Training Center (IGTC) Graduate Summer School in Mathematical Biology May 11 - June 11, 2008 at the University of British Columbia Campus in Vancouver, BC Canada Applications are welcomed from graduate students interested in Mathematical Biology: A description of the course, and registration form are available at: http://www.pims.math.ca/science/2008/08ssigtcmb/ Eligible students accepted into this program may have part of their local costs covered by PIMS: Limited on-campus accommodations are being held for this course, and will be partly subsidized by PIMS. Sincerely, Leah Edelstein-Keshet We are also receiving support for this summer school from MITACS. ---------------------------------------------------- From: Gregg Hartvigsen Date: Thu, 07 Feb 2008 14:14:34 -0500 Subject: Undergraduate Biomathematics Day, April 18-19, Niagara Falls UNDERGRADUATE BIOMATHEMATICS DAY BUFFALO AND GENESEO SUNY COLLEGES APRIL 18-19 2008 http://www.Buffalo-biomath.info Buffalo and Geneseo SUNY Colleges are pleased to host Undergraduate Biomathematics Day. This two day event will feature presentations and poster sessions by undergraduate students and their faculty mentors whose research topics are at the intersection of biology and mathematics. The goal of the conference is to offer students and their faculty mentors the opportunity to share their research and to meet fellow student researchers and faculty in the rapidly growing field of mathematical biology. FUNDING AND REGISTRATION: For registration and/or talk/poster submission, please send an e-mail to Joaquin Carbonara (carbonjo@buffalostate.edu). Please be clear on whether you would like to present or just participate and, if presenting, whether you want give a poster or a talk. The NSF-UMB Program at SUNY Geneseo has funding available for potentially all student participants and their faculty mentors. However, space is limited. Preference for student funding will first be given to student presenters. Funding for talks will be given preference over posters. The remaining funds will be distributed on a first come basis. Students will share a room with one other student. All registrants will automatically be considered for meal and housing support. In some cases, additional travel support can be requested. Please contact Tony Macula (macula@geneseo.edu) with requests and questions regarding additional travel support. TARGET DATES: Registration: March 22, 2008 (to ensure accommodations, but late registrations can be considered) Abstracts: April 4, 2008 ---------------------------------------------------- From: Fred Adler Date: Mon, 4 Feb 2008 16:42:57 -0700 (MST) Subject: Workshop: Mathematical Perspective on Cancer Immunology, May 5-7 Mathematical Perspective on Cancer Immunology Salt Lake City, Utah May 5-7, 2008 Hosted by the Research Training Group in Mathematical Biology University of Utah The workshop will bring together a broad range of mathematical biology trainees and researchers, with interests ranging from immunology, physiology, biophysics and evolutionary biology to develop a framework for synthetic research on cancer immunology. The principle speakers are: Dominik Wodarz, University of California at Irvine Baltazar Aguda, Boston University Peter Lee, Stanford University Although diverse in the balance of mathematics and biology, the speakers are united by common questions. Participants will read and discuss recommended papers in advance, and the workshop will mix formal lectures with paper discussions and question sessions. Support for travel and lodging is available. Please apply through the web site at http://www.math.utah.edu/research/mathbio/rtg/ciw/ Please contact Kathleen Moore (kerr@math.utah.edu) with any questions about travel, lodging, registration or any special circumstances, and Fred Adler (adler@math.utah.edu) with questions about the workshop content or format. ---------------------------------------------------- From: "Petrovskiy, Dr S." Date: Tue, 5 Feb 2008 09:54:05 -0000 Subject: Workshop: MPDE-08, March 12, University of Leicester A one-day international workshop "2nd Leicester Colloquium on Models of Population Dynamics and Evolution (MPDE-08)" will be held on March 12, 2008, in the University of Leicester. The final program and the abstracts of the talks are now available at the workshop website: http://www.math.le.ac.uk/PEOPLE/sp237/workshop2/mpde08.htm We encourage a wide participation in this meeting. Attendance is free; there is no any registration fee. However, we may have some restrictions in terms of space availability; therefore, those who are wishing to attend are advised to pre-register by sending an email to Dr. Sergei Petrovskii as soon as possible. ---------------------------------------------------- From: Jaap Kaandorp Date: Sat, 9 Feb 2008 09:34:59 +0100 Subject: 5th Int'l Symposium on Networks in Bioinformatics, 21-22 April ISNB 2008 THE 5th INTERNATIONAL SYMPOSIUM ON NETWORKS IN BIOINFORMATICS 21-22 April, 2008 Science Park Amsterdam Amsterdam, The Netherlands For details about registration, paper submission etc see http://isnb.amc.uva.nl/isnb2008/ ABSTRACT The 5th International Symposium on Networks in Bioinformatics (ISNB 2008) is scheduled on 21 and 22 April 2008 and is likely to continue its success from previous years in bringing different disciplines together to discuss ongoing research in bioinformatics and biology of networks. The focus of 5th International Symposium on Networks in Bioinformatics will be on biological networks such as metabolic networks, signal transduction pathways and genetic regulatory networks. This year we also aim to include topics like modeling of cells, tissues and gene regulation. We also want to invite researchers working on gene networks in plants (e.g. Arabidopsis), model organisms such as Drosophila and organisms with a relatively simple and basal body plan such as sponges and scleractinian corals. Understanding of these networks is crucial for understanding molecular and cellular processes in the organism or system under study. This field is subject of lively research and both experimental and computational approaches are used to elucidate the biological networks. The bioinformatics of biological networks involves a broad range of research and approaches. Research includes the identification of regulatory elements in DNA, developmental biology, genome context analysis, modelling and simulation of pathways, reconstruction of pathways from experimental data, visualization of pathways, and the representation of pathways in database, graphs and mark-up languages. ---------------------------------------------------- From: James Glazier Date: Wed, 06 Feb 2008 12:33:26 -0500 Subject: Training Workshop: CompuCell3D, June 16-20, Indiana University Training Workshop Developing Multi-Cell Developmental and Biomedical Simulations with CompuCell3D June 16th-20th 2008 Indiana University, Biocomplexity Institute, Bloomington, IN 47405-7105 USA http://www.compucell3d.org/Workshop08/ [Additional details at http://lists.siam.org/pipermail/siam-ls/2008-February.txt] For More Information, Please Contact: Maciej Swat (mswat@indiana.edu). Or visit: http://www.compucell3d.org/ ---------------------------------------------------- From: alexandra Date: Thu, 7 Feb 2008 10:57:50 -0000 Subject: Summer School: NN2008, July 7-11, Porto, Portugal SUMMER SCHOOL NN2008 NEURAL NETWORKS in CLASSIFICATION, REGRESSION and DATA MINING July 7-11, 2008, Porto, Portugal http://www.nn.isep.ipp.pt email: nn-2008@isep.ipp.pt ---------------------------------------------------- From: Rebecca Martin Date: Fri, 08 Feb 2008 11:41:24 -0500 Subject: Modelling Cancer Invasion: 'Let's Stick Together' Modelling Cancer Invasion: 'Let's Stick Together' Nugget submitted by Mark Chaplain In vivo cancer growth is a complicated 'multi-scale' phenomenon involving many inter-related biochemical and cellular processes at many different spatial and temporal scales. Although there are many different types of cancers (e.g. carcinoma, sarcoma, melanoma, leukaemia, glioma), solid tumours (carcinoma, sarcoma) make up a large fraction of all clinically observed cancers. The growth of solid tumours occurs in two distinct phases: the initial growth being referred to as the relatively harmless avascular phase and the later growth as the vascular phase. During the early avascular stage of solid tumour growth there may be an immune response to the cancer from the host, with cells of the immune system, most notably T-lymphocytes, responding to and attacking the cancer cells. However, unfortunately solid tumours do not always remain avascular and localised. The transition from avascular growth to vascular growth depends upon the crucial process of angiogenesis which is necessary for the tumour to attain nutrients and dispose of waste products. To achieve vascularization, tumour cells secrete a diffusible substance known as tumour angiogenesis factor (TAF) into the surrounding tissue. This has the effect of stimulating nearby capillary blood vessels to grow towards and penetrate the tumour, re-supplying the tumour with vital nutrient. Invasion and metastasis can now take place. Indeed, invasion, the ability of cancer cells to break out of tissue compartments and spread locally, is one of the hallmarks of cancer and gives solid tumours a defining deadly characteristic. Cancer cells achieve this through the secretion of matrix degrading enzymes, cell proliferation, loss of cell-cell adhesion, enhanced cell-matrix adhesion and active migration. Invasion of tissue by the cancer cells is one of the key components in the metastatic cascade, whereby cancer cells spread to distant parts of the host and initiate the growth of secondary tumours (metastases). Recent new work by A. Gerisch and M.A.J. Chaplain (Mathematical modelling of cancer cell invasion of tissue: Local and non-local models and the effect of adhesion. J. Theor. Biol. 250, 684-704) formulates a novel continuum model of cancer cell invasion of tissue which explicitly incorporates the important biological processes of cell-cell and cell-matrix adhesion. This is achieved using non-local (integral) terms in a system of partial differential equations where the cells use a so-called 'sensing radius' R to detect their environment. A numerical exploration of this model using computational simulations shows that for certain parameter sets, the cancer cells 'split' into two sub-populations, with one sub-population actively invading the tissue, the other sub-population remaining close to the initial spatial location. The computational results of the model provide experimentally testable hypotheses regarding the relative strengths of cell-cell and cell-matrix adhesion i.e. how well cancer cells 'stick together'. One may draw the general conclusion that the tumour microenvironment i.e. the oxygen/nutrient supply to the tumour, the biomechanical properties of the matrix and cell-cell and cell-matrix adhesion, has a major impact on invasion. This novel approach complements existing previous work in the area going back to the seminal paper of Greenspan (1976} and developed theoretically and analytically by Byrne and Chaplain (1996, 1997) and computationally by Lowengrub and co-workers (2003, 2007). Unravelling and better understanding the complex processes involved in cancer invasion may ultimately lead to treatments being developed which can localise cancer and prevent metastasis. ---------------------------------------------------- From: Otso Ovaskainen Date: Tue, 5 Feb 2008 16:21:50 +0200 Subject: Scientific Programmer: Mathematical Biology, University of Helsinki The Mathematical Biology Group at the Department of Biological and Environmental Sciences, University of Helsinki, Finland (leader Dr. Otso Ovaskainen) is seeking an outstanding, highly motivated Scientific Programmer. The position is available for 2 years, with the possibility of a 3-year extension. The candidate is required to have a MS degree (PhD degree being counted as an advantage) in computer science, computational biology, bioinformatics, statistics, engineering, math, or a related field. The main selection criterion is the applicant's ability and experience in scientific computing with both functional languages (Mathematica) and object-oriented languages such as C# (Microsoft Visual Studio), Object Pascal (CodeGear Delphi), or C++ (CodeGear C++ Builder). In particular, expertise with advanced matrix operations (e.g. sparse matrix algebra), MCMC computations (e.g. adaptive Bayesian methods), and spatial statistics is appreciated. The successful candidate will be responsible for developing and maintaining algorithms used in research projects at the interface between mathematics and ecology and evolutionary biology. The main emphasis is on developing efficient algorithms for computationally heavy problems, but the work involves also development and documentation of user-friendly interfaces. The Mathematical Biology group is part of the Metapopulation Research Group (leader prof. Ilkka Hanski), which is a Centre of Excellence in Research supported by the Academy of Finland. We offer an international research environment with excellent possibilities to cooperate with experts in mathematics, statistics, population biology, and evolutionary ecology. Salary and social benefits according to the University of Helsinki Salary system, depending on the experience and performance of the employee (2,300 - 3,500 Euro / month). Applications including a short CV (max 3 pages) and the e-mail addresses of two researchers willing to write a letter of reference should be sent to otso.ovaskainen@helsinki.fi with cc to tuuli.ojala@helsinki.fi; write "scientific programmer" on the subject line. For more details on our research projects and on the application procedure, see http://www.helsinki.fi/science/metapop/MBG/positions/index.htm Deadline for applications 14th March 2008, starting date 1st May 2008 (negotiable). ---------------------------------------------------- From: Jan-Herman Kuiper Date: Fri, 8 Feb 2008 10:59:36 -0000 (UTC) Subject: Postdoc Position: ISTM, Keele POSTDOCTORAL RESEARCH ASSISTANT MATHEMATICAL SIMULATION OF ARTICULAR JOINT FORMATION (2 YEAR FIXED TERM) Starting Salary: Grade 7 £27,466 The Institute of Science and Technology in Medicine (ISTM) at Keele University (www.keele.ac.uk/research/istm) is seeking to appoint a Postdoctoral Research Assistant in the area of biomechanics and mechanobiology. The work forms part of the MyJoint project (www.myjoint.org). MyJoint is an EU-funded multi-disciplinary project combining ten partners and aims to grow biological replacement joints within the patients that will use them. You will work under the guidance of Dr. Jan Herman Kuiper, Prof. Alicia el Haj and Prof. James Richardson. Your work will aim to further our understanding of the interaction between mechanical conditions and articular joint formation and you will collaborate with engineers, biologists and clinicians. You will develop novel computer models to simulate the relation between skeletal cells, physical environment, geometry, and material properties in joint formation. You will use computer models to find the effects of variations in parameters describing cells, environment and geometry on joint formation and tissue quality. You will also assist in assessing mechanical quality of tissue from and around joints produced under experimental conditions. You will compare the findings of the computer model to experimental results, and adjust the model if required. You will have a PhD degree, with a background in the physical, mathematical or engineering sciences. You should have experience in the execution of a researched project involving mathematical or computational simulation, ideally of biological processes. You should be familiar with the use of Finite Element simulation tools or alternative multi-physics tools to simulate biological processes. Experience in mechanical testing procedures of biological tissues would be an advantage. ISTM is a 5* highly rated (5A or 5* over the last three RAEs), interdisciplinary Institute housing biological and physical scientists, clinicians and engineers. You will be based at our site at the Robert Jones and Agnes Hunt Orthopaedic Hospital in Oswestry, a renowned Orthopaedic Hospital with several active clinical and research programs in orthopaedic cell therapy (www.oscell.enta.net). Informal enquiries may be directed to Dr. Jan Herman Kuiper (j.h.kuiper@keele.ac.uk) Full job packs are available from the Human Resources Department, Keele University, Keele, Staffordshire, ST5 5BG. Fax: 01782 583471 or e-mail vacancies@keele.ac.uk or www.keele.ac.uk/depts/uso/hr/cwisvacs.htm Please quote post reference: RE08/05INT Closing date for applications: 25 February 2008 ---------------------------------------------------- From: Karen Lipkow Date: Tue, 5 Feb 2008 16:59:01 +0000 Subject: Postdoc / Research Assistant: Cambridge Systems Biology Centre Research Assistant / Associate In Cellular Systems Biology, University of Cambridge Salary: £21,682-£24,403 pa or £25,134-£32,796 pa Applications are invited for the position of a postgraduate or postdoctorate researcher in the group of Dr. Karen Lipkow in the Cambridge Systems Biology Centre. The person appointed will utilise a large computer grid to study the interplay of signalling and cellular architecture through detailed simulations. The project is funded by the EU-IndiaGrid and involves collaboration with the National Centre for Biological Sciences in Bangalore, India. The ideal candidate has good programming skills (especially C/C++), experience with Grid Computing and an interest in computational cell biology. However, suitable training will be given where required. The post is for 6-8 months in the first instance, with a possibility of extension subject to the availability of funds. The position is available immediately. Applications should include a covering letter describing relevant research experience to date, a CV, completed PD18 form (Part 1 and 3) and the names and addresses of two referees. These should be sent quoting the reference by email by 29th February 2008 to jobs@bioc.cam.ac.uk or post to The Principal Assistant, Department of Biochemistry, Building O, Downing Site, Tennis Court Road, Cambridge, UK, CB2 1QW.Informal enquiries can be directed to K. Lipkow: KL280@cam.ac.uk. Quote Reference: PH02992 Closing Date: 29 February 2008 ---------------------------------------------------- From: James Glazier Date: Wed, 06 Feb 2008 12:31:18 -0500 Subject: Software Developer/Research Associate/Post Doctoral Fellow, Indiana U The Indiana University Biocomplexity Institute seeks a Research Assistant, 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. 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 Review of applicants will begin immediately and continue until position is filled. [Initial appointment will begin March 1'st , 2008 (precise starting date negotiable)] and is expected to last one year with extension possible, subject to satisfactory performance. Please send a CV and arrange to have 3 letters of recommendation sent to glazier@indiana.edu or by mail to Prof. James Glazier, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, U.S.A. Indiana University is an equal opportunity / affirmative action employer. ---------------------------------------------------- From: Jansen Vincent Date: Tue, 5 Feb 2008 16:54:15 -0000 Subject: 5 Tenure Faculty Positions: Biological Sciences, Royal Holloway Royal Holloway is seeking to fill five permanent positions in Biology in various areas. For those with a modelling background the senior lecturer/reader position in biological sciences (equivalent to associate professor) is probably most relevant. We are seeking to employ in someone in the area of organismal biology/plant biology area, and in are particularly in interested in the areas highlighted. Feel free to contact me if you need further information on this position Vincent Jansen (vincent.jansen@rhul.ac.uk) ROYAL HOLLOWAY SCHOOL OF BIOLOGICAL SCIENCES The School of Biological Sciences constitutes 3 highly-integrated and dynamic research centres: Biomedical Sciences, Plant Molecular Sciences; and Ecology, Evolution & Behaviour. In addition, staff are associated with Faculty-based inter-departmental research centres in Computational Biology, Neuroscience and Nanobiotechnology. The School holds grade 5 research assessment (2001 RAE) status, and a maximum grade 24 teaching quality assessment (QAA) rating. Research and teaching activities are underpinned by technologies spanning functional genomics, metabolomics, molecular genetics, microbiology, gene therapeutics, computational & systems biology, advanced cell biology, model organism analysis, population studies, ecology, evolutionary biology, mathematical biology and advanced microscopy facilities. Applications are invited for five academic posts in the School. Lecturers (2) in Biomedical Sciences (Ref KB/4926) Applications in the fields of neurosciences, cell signalling, molecular microbiology/parasitology, infection and immunity or epidemiology are especially welcome. Lecturer in Chemical Biology (Ref KB/4927) Candidates should have a strong background in chemistry to contribute to bioscience chemistry teaching and research experience especially in the fields of medicinal chemistry, nutraceuticals, natural product chemistry or cell signalling. Professor/Reader in Neuroscience (Ref KB/381 ) Applicants should have expertise in molecular and cellular neuroscience or neurophysiology. Senior Lecturer/Reader in Biological Sciences (Ref KB/4928) Applicants with particular interest in the areas of behaviour/behaviour ecology, modelling or ecological genomics are especially welcome. Informal enquiries are welcome to the Head of School, Professor Peter Bramley (tel. +44 (0)1784 443555; email: p.bramley@rhul.ac.uk) Salaries in the range of: Lecturer £36,927 - £43,073 p.a., Senior Lecturer £44,925 - £51,017 p.a. Professorial salaries are negotiable starting at £53,229 p.a. All salaries are inclusive of London Allowance. All posts are tenable from 1 September 2008 unless otherwise stated in the further details. The closing date for all posts is 27 February 2008. Further details and a copy of the application form are available at www.rhul.ac.uk/Personnel/JobVacancies.htm We positively welcome applications from all sections of the community. ---------------------------------------------------- From: "Edwards, Andrew" Date: Tue, 5 Feb 2008 21:31:59 -0800 Subject: Nine Research Scientist Positions, Fisheries and Oceans Canada Please see the link below for information on applying for a Research Scientist position with Fisheries and Oceans Canada. It is expected that nine positions will be filled across the country, in the areas of modelling, stock assessment and benthic ecology. Closing date is 2nd March. https://psjobs-emploisfp.psc-cfp.gc.ca/psr/applicant/applicant.jobOppSearchResult;jsessionid=NrTxHjLTQ9QxwQJ8bMn4Kh2QgwxQPLnBt5TKsJ58p1snfnnNrxKf!1695550467?togleLanguage=en&psrsMode=1&poster=30917&noBackBtn=true ---------------------------------------------------- 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 **************************************************** ----------------------------------------------------