---------------------------------------------------- Subject: SMB Digest v08i13 SMB Digest March 31, 2008 Volume 08 Issue 13 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 CfP: Workshop Algorithms in Bioinformatics 08, Sept 15-17, Karlsruhe 5th International Symposium on Networks in Bioinformatics, Amsterdam Workshop: Autonomous Decision Making in Planning and Control ICNC'08-FSKD'08: Extended Deadline 10 April, Jinan, China TOC: Bulletin Of Mathematical Biology, Volume 70 Number 3 PhD Position: Mathematical Biology, University of Strathclyde PhD Position: Reduction ... Models of Biochemical Networks, INRIA PhD Position: Evolutionary Dynamics, Simula Research Laboratory Postdoctoral Position: Computational Physiology, U Kentucky SMBnet Reminders ---------------------------------------------------- From: Patrick De Leenheer Date: Fri, 21 Mar 2008 08:51:36 -0400 (EDT) Subject: Conference: Mathematical Tools for Multi-Scale Biological Processes 2nd 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: Raffaele Giancarlo Date: Mon, 24 Mar 2008 11:23:58 +0100 (CET) Subject: CfP: Workshop Algorithms in Bioinformatics 08, Sept 15-17, Karlsruhe WABI 2008 8th Workshop on Algorithms in Bioinformatics (WABI) September 15-17, 2008 Universität Karlsruhe, Germany IMPORTANT DATES: Submission deadline: May 12, 2008 Notification to authors: June 4, 2008 Final version due: June 18, 2008 Workshop: September 15-17, 2008 RELEVANT URLs: http://www.easychair.org/conferences/?conf=wabi2008 http://algo2008.org/doku.php/wabi ---------------------------------------------------- From: Jaap Kaandorp Date: Wed, 26 Mar 2008 09:50:04 +0100 Subject: 5th International Symposium on Networks in Bioinformatics, Amsterdam 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: Maria Schilstra Date: Thu, 27 Mar 2008 11:36:40 +0000 Subject: Workshop: Autonomous Decision Making in Planning and Control The Lean Engineering Research Group, Centre for Manufacturing at De Montfort University, Leicester, UK, and the Biological and Neural Computation Research Group, Science and Technology Research Institute at the University of Hertfordshire, Hatfield, UK, are planning to hold a workshop on: Autonomous Decision Making in Industrial Operations Planning and Control Date: Thursday, 29 May 2008 Venue: De Montfort University, Leicester, East Midlands, UK The aim of the workshop is to bring together researchers from a range of disciplines and potential users of research outcomes, to discuss the application of biological control processes to facilitate autonomous decision making in operations management. Biological control processes of interest include those that control gene transcription and translation processes, and the sequencing and synchronization required to produce individual organelles. The aim of the discussion is to develop a shared understanding of the problem domain, and defining the scope of research issues involved. For further details contact: Dr Riham Khalil, De Montfort University, Leicester - rkhalil@dmu.ac.uk Dr Maria Schilstra, University of Hertfordshire, Hatfield - m.j.1.schilstra@herts.ac.uk Preliminary programme: 9.30 Professor David Stockton, De Montfort University: Introduction and welcome 9.45 Dr Riham Khalil, De Montfort University and Dr Mark McAuley, University of Hertfordshire: Discrete event simulation of biological control processes, and its application to autonomous decision making in manufacturing systems 10.45 Break 11.00 Professor Herbert Kotzab, Copenhagen Business School: Autonomous cooperating logistic processes 11.40 Professor Edmund Burke, University of Nottingham: Next generation decision support: automating the heuristic design process 12.20 Lunch 13.20 Dr Ken Young, Warwick University: The future of autonomous systems in the UK 14.00 Lieven Demeester, Lieven, INSEAD, France: Organic production systems: what biological cells can teach us about manufacturing 14.40 Break 15.00 Panel discussion session 16.00 Professor David Stockton: Overview and future actions ---------------------------------------------------- From: Mary Qin Date: Fri, 28 Mar 2008 21:26:03 +0800 Subject: ICNC'08-FSKD'08: Extended Deadline 10 April, Jinan, China The 4th International Conference on Natural Computation (ICNC'08) The 5th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'08) 25-27 August 2008, Jinan, China Extended Submission Deadline: 10 April 2008 http://www.icnc-fskd2008.sdu.edu.cn For more information, visit the conference web page. If you have any questions after visiting the conference web page, please email the secretariat at nc2008@sdu.edu.cn ---------------------------------------------------- From: Springer Date: Sun, 23 Mar 2008 08:25:37 -0700 (PDT) Subject: TOC: Bulletin Of Mathematical Biology, Volume 70 Number 3 Volume 70 Number 3 of "Bulletin of Mathematical Biology" is now available on the SpringerLink web site at http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1gRqkl.BwJlVW..T.EroS.2yHU.VAEFBX00 Nucleotide Frequencies in Human Genome and Fibonacci Numbers Author(s): Michel E. Beleza Yamagishi, Alex Itiro Shimabukuro Page: 643 - 653 Continuous Traveling Waves for Prey-Taxis Author(s): J. M. Lee, T. Hillen, M. A. Lewis Page: 654 - 676 A Computational Study of the Development of Epithelial Acini: I. Sufficient Conditions for the Formation of a Hollow Structure Author(s): Katarzyna A. Rejniak, Alexander R. A. Anderson Page: 677 - 712 Some Elementary Properties of SIR Networks or, Can I Get Sick because You Got Vaccinated? Author(s): William Floyd, Leslie Kay, Michael Shapiro Page: 713 - 727 Modeling Imatinib-Treated Chronic Myelogenous Leukemia: Reducing the Complexity of Agent-Based Models Author(s): Peter S. Kim, Peter P. Lee, Doron Levy Page: 728 - 744 Klebsiella pneumoniae Flocculation Dynamics Author(s): D. M. Bortz, T. L. Jackson, K. A. Taylor, A. P. Thompson, J. G. Younger Page: 745 - 768 Modeling Spruce Budworm Population Revisited: Impact of Physiological Structure on Outbreak Control Author(s): Naveen K. Vaidya, Jianhong Wu Page: 769 - 784 Parameter Identifiability and Estimation of HIV/AIDS Dynamic Models Author(s): Hulin Wu, Haihong Zhu, Hongyu Miao, Alan S. Perelson Page: 785 - 799 Two-Fluid Model of Biofilm Disinfection Author(s): N. G. Cogan Page: 800 - 819 Quantifying the Routes of Transmission for Pandemic Influenza Author(s): Michael P. Atkinson, Lawrence M. Wein Page: 820 - 867 Modeling of Branching Patterns in Plants Author(s): N. Bessonov, N. Morozova, V. Volpert Page: 868 - 893 Global Stability of Equilibria in a Two-Sex HPV Vaccination Model Author(s): Elamin H. Elbasha Page: 894 - 909 Mathematical Modeling of Mechanically Modulated Rhythm Disturbances in Homogeneous and Heterogeneous Myocardium with Attenuated Activity of Na+-K+ Pump Author(s): Tatiana Sulman, Leonid B. Katsnelson, Olga Solovyova, Vladimir S. Markhasin Page: 910 - 949 ---------------------------------------------------- From: David Greenhalgh Date: Fri, 21 Mar 2008 16:35:42 +0000 Subject: PhD Position: Mathematical Biology, University of Strathclyde We have been awarded a PhD studentship to study Mathematical Modelling of the spread of Hepatitis C amongst Injecting Drug Users in Scotland. Supervisors: Dr. David Greenhalgh (Department of Statistics and Modelling Science (STAMS), University of Strathclyde, Glasgow, UK) and Dr. Sharon Hutchinson (Health Protection Scotland (HPS)). Project aim: The project aims to develop mathematical models for the spread of hepatitis C virus (HCV) amongst injecting drug users (IDUs). The models will use differential equations in the first instance. Such models have been usefully employed to inform public health policy to control the spread of Human Immunodeficiency Virus (HIV) amongst injecting drug users (IDUs) in the USA and foot-and-mouth disease in the UK. Models for the spread of HIV amongst IDUs will be adapted to HCV. Equilibrium and stability analyses will be performed on the models and key epidemiological parameters calculated such as the basic reproduction number R_0. We will concentrate on designing models to examine the effect of HCV prevention measures, such as the provision of needles/syringes and other injecting equipment, methadone treatment and educational interventions. Heterogeneity in injecting risk behaviours among IDUs will be explored in the model. If time permits we would also explore individual-based stochastic Monte-Carlo simulation models to compare the results with the deterministic models and the effect of friendship networks and geographical dispersion on the spread of HCV. A very important part of this project is the link with HPS and we would use epidemiological data on HCV from HPS to estimate the parameters in our models as well as guidance from HPS staff (particularly Dr. Hutchinson and Professor Goldberg) in the model formulation. We would also aim to link in with the detailed numerical computer simulation models of the spread of HCV used by Dr. Hutchinson and colleagues. Stipend: This studentship is funded by EPSRC/HPS at standard EPSRC rates (£12,923 p.a. for 2008/9), plus home fees. The preferred start date is 1st October 2008, but other start dates may be possible. Eligibility: This studentship is suitable for UK or EU-eligible students (fees and stipend) or other EU students (fees only) with a good or expected good (2i or above or equivalent) Honours degree in Mathematics, Statistics or other numerate subject (Physics, other numerate subjects considered). International students are not eligible. Further Information: For further information about this project and an application form please contact Dr. David Greenhalgh, Department of Statistics and Modelling Science, University of Strathclyde, Livingstone Tower, 26 Richmond Street, Glasgow G1 1XH, Scotland, UK, Tel: +44-141-552-4400 Ext 3653, Fax +44-141-552-2079, email:-david@stams.strath.ac.uk ---------------------------------------------------- From: Hidde de Jong Date: Sat, 29 Mar 2008 14:32:37 +0100 Subject: PhD Position: Reduction ... Models of Biochemical Networks, INRIA INRIA Grenoble-Rhône-Alpes is seeking a PhD student to work on Methods for the reduction of large and complex models of biochemical networks A description of the subject of the PhD project, as well as conditions for applicants, can be found on the INRIA web site: http://www.inrialpes.fr/jsp/fiche_actualite.jsp?CODE=1204618110974&LANGUE=1&STNAV=&RUBNAV=&RH=ACCUEIL The application dead-line is May 15, 2008. All further information can be obtained from Daniel Kahn, INRIA Grenoble-Rhône-Alpes and Laboratory of Biometry and Evolutionary Biology, CNRS/University of Lyon (Daniel.Kahn@inria.fr) or Hidde de Jong, INRIA Grenoble-Rhône-Alpes (Hidde.de-Jong@inria.fr) ---------------------------------------------------- From: Joakim Sundnes Date: Mon, 31 Mar 2008 13:15:34 +0200 Subject: PhD Position: Evolutionary Dynamics, Simula Research Laboratory Simula Research Laboratory conducts basic research in the fields of communication technology, software engineering and scientific computing. The research in the Scientific Computing (SC) department is focused on the development of numerical methods, algorithms and software, and large scale biomedical and systems biology oriented simulation studies applying these methods. In recent years, the main application area for computational research studies has been the simulation of the electrical and mechanical activity of the heart. Currently, we plan to extend our computational research to simulations of the evolutionary dynamics of genetic networks controlling the properties of organisms. The aim of the research project is to study key evolutionary processes such as the adaptation of organisms to their environment, the splitting up of a species into multiple species and the development of multicellular organisms from a single fertilized cells. A key aspect of the research will be to study how the architecture and dynamics of genome organization and gene regulatory network structure influence the properties of organisms and hence how they influence the above mentioned evolutionary processes and how this contrasts with findings from more classical population genetics models. Our understanding of genome organization and gene regulatory networks has changed dramatically over the last decade. A large part of DNA that was previously considered junk turns out the be functional after all, coding for RNAs that are however not translated into proteins. These RNAs in turn are often involved in regulating the expression of genes, which were previously thought to be exclusively regulated by proteins. Incorporating these new insights into our models is another key aspect of the research project. Modeling formalisms used will typically be discrete, individual- based, event-based, and often spatially extended and will involve the explicit modeling of the evolution of genes, genomes and gene regulatory networks determining the properties of simulated agents. The project will be supervised by a new member of our research group, Dr. Kirsten ten Tusscher (http:// www-binf.bio.uu.nl/khwjtuss/). Simula offers excellent opportunities for doing high quality research, generous support for travels and equipment, and competitive salary (around 47.000,- Euro/69.000,- USD for a Ph.D. position) We are looking for candidates who fulfill one or more of the following requirements: a strong interest in evolutionary biological research a University degree in computational biology, systems biology, biomedical engineering, artificial life, artificial intelligence, computer science, physics or applied mathematics experience with computational modeling, simulation and analysis of complex (biological) systems. The position requires excellent English writing skills and high marks from the BSc and MSc degree. Women are encouraged to apply. For more information contact Joakim Sundnes (sundnes@simula.no) or Kirsten ten Tusscher(tentussc@simula.no). To apply, email a short application letter, curriculum vitae, copies of transcripts and grades, and a publication list to jobs@simula.no. The subject of the email must contain 0830 Scientific Computing. Application deadline: May 16, 2008 ---------------------------------------------------- From: "Bruce, Eugene" Date: Fri, 28 Mar 2008 16:01:49 -0400 Subject: Postdoctoral Position: Computational Physiology, U Kentucky A postdoctoral position in computational physiology is available in the Center for Biomedical Engineering at the University of Kentucky. This NIH-funded research project involves: (i) development of signal processing methods to detect arousals and other transient events in EEG signals, and; (ii) mathematical modeling of oxygen delivery to the brain in healthy elderly subjects and in patients with sleep-disordered breathing. Candidates should have training in stochastic signal processing (e. g., spectral analysis, entropy, time-frequency analysis) and experience using simulation software for solving time-dependent differential equations. Basic knowledge of respiratory physiology and neurophysiology is necessary. The ideal candidate will be enthusiastic about participating in both aspects of the project. Additional information about the laboratory may be found at http://www.uky.edu/~ebruce/. Applications may be sent by email to ebruce@uky.edu. Candidates should submit the following (PDF attachments preferred): (1) current C. V.; (2) contact information for 3 references. Eugene N. Bruce, Ph. D. Professor, Center for Biomedical Engineering University of Kentucky, Lexington, KY 40506-0070 ---------------------------------------------------- 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. 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