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Sciences and Physics (IMSP). It is spearheaded by a group of mathematics educators, researchers and students who work with people from other fields of study such as biology, biophysics, computer science, statistics, chemistry, environmental science and management, agriculture and forestry. This Initiative was started to serve the mandate of IMSP as a National Center of Excellence (NCOE) in the Basic Sciences, which is “to help advance science and technology in the country, and specifically, to strengthen and broaden the national capability to train scientific leaders and conduct research in the basic sciences”. The Initiative supports the distinctive excellence thrusts of UPLB in agriculture, natural resources and the environment. Mission Vision We see the UPLB BioMathematics Initiative as the medium that bridges the life sciences and mathematics. We envision the Initiative to be transformed into a strong research program and a model for interdisciplinary research collaboration. Our goal is to help solve emerging problems in biology and related fields by providing quantitative solutions and analysis. We aim to understand biological phenomena by translating biological ideas into the language of mathematics.
Strategies 1. Enhance knowledge base, and train new breed of instructors and researchers in biomathematics a. Conduct campus-wide seminar series and workshops b. Invite local and international experts in biomathematics from other schools or research centers c. Involve experts in other fields of mathematics such as graph theory, combinatorics, operations research, numerical analysis, differential and difference equations, and probability theory among others 2. Present and publish research papers a. Continuously collaborate with other units in the university, e.g. UPLB Bee Program, Institute of Biological Sciences, School of Environmental Science and Management, College of Agriculture, College of Forestry and Natural Resources, Institute of Computer Science, Institute of Chemistry, Institute of Statistics, National Institute of Molecular Biology and Biotechnology and Department of Social Sciences b. Collaborate with experts or groups outside the university c. Conduct research workshops d. Join societies related to biomathematics, and attend various seminars, workshops and summer schools Members From the IMSP-Mathematics Division Dr. Editha C. Jose (IMSP BioMathematics Coordinator) Mr. Jomar F. Rabajante Mr. Allen L. Nazareno Mr. Mark Jayson V. Cortez Ms. Dianne Carmeliza N. Cuaresma
From the left: Mark Jayson, Editha, Allen and Jomar Advisers Collaborators UPLB Bee Program and the Institute of Biological Sciences, with contact persons: Dr. Cleofas R. Cervancia, Mr. Alejandro C. Fajardo and Mr. Andrew D. Montecillo. http://beeprogram.uplb.edu.ph and http://ibs.uplb.edu.ph Institute of Computer Science, with contact persons: Prof. Jaime M. Samaniego and Prof. Arian J. Jacildo. http://www.ics.uplb.edu.ph Operations Research Cluster, Mathematics Division, with contact person: Prof. Jerrold M. Tubay Dynamical Systems Cluster, Mathematics Division, with contact person: Dr. Editha C. Jose Numerical Mathematics (NuMath) Training and Research Team, with contact person: Mr. Jomar F. Rabajante Dr. Baltazar D. Aguda (the UPLB BioMath Initiative lead consultant). http://people.mbi.ohio-state.edu/baguda/AgudaLab Dr. Virgilio P. Sison, IMSP Director Prof. Alleli C. Domingo, College of Arts and Sciences OIC Dean
Current Research Themes Modeling the behavior of certain species, e.g. foraging behavior of bees Modeling the interaction among biotic and abiotic factors in the environment
Systems dynamics and evolutionary games Propagation of infectious objects Optimization in biosystems, e.g. optimizing beekeeping practices Analysis of biological networks Cellular Differentiation
Simulation of Foraging Behavior of Bees using Netlogo
ABOUT BIOMATHEMATICS What is Biomathematics? Biomathematics is a field of mathematics that focuses on the application of mathematics in biology, specifically to theoretical biology and systems biology. The field of Biomathematics, sometimes called Mathematical Biology, largely intersects with Computational Biology and Bioinformatics, and partly intersects with Biophysics and Biostatistics. Biomathematics aims to develop, analyze and apply mathematical models to biology, biotechnology, environmental science and biomedical sciences. Most of the models formulated by biomathematicians are subject to experimental validation. Currently, Biomathematics is in its renaissance stage. The word “biomathematics” was coined by Dr. William Moses Feldman in 1923. Biomath majors
are seen to enjoy plenty of opportunities for graduate studies, and research jobs in pharmaceutical, industrial and government laboratories.
Links to Societies
The Society for Mathematical Biology (SMB): The Society for Mathematical
Biology is an international society which exists to promote and foster interactions between the mathematical and biological sciences communities through membership, journal publications, travel support and conferences. http://www.smb.org
European Society for Mathematical and Theoretical Biology (ESMTB): The
European Society for Mathematical and Theoretical Biology was founded in 1991 during the first European Conference on "Mathematics Applied to Biology and Medicine" in l`Alpes d`Huez. ESMTB is a nonprofit organization. The purpose of the society is to promote theoretical approaches and mathematical tools in biology and medicine in a European and wider context. This goal is pursued by the organization of summer schools and conferences, by the European Communications (the former Newsletter) and the information on its web-site. ESMTB honors the best thesis (showing the most impressive modeling ideas and useful innovative methods) with the Reinhart Heinrich Doctoral Thesis Award. http://www.esmtb.org
The International Society for Computational Biology (ISCB): The International
Society for Computational Biology serves over 2500 members from nearly 70 countries around the world by addressing scientific policies, providing access to
high quality publications, organizing meetings, and serving as a portal to information about training, education, employment and news from related fields. ISCB hosts annual meetings, including the International Conference on Intelligent Systems for Molecular Biology (ISMB), the world's longest running and largest bioinformatics conference (held jointly with ECCB every other year in Europe). It has two official journals of the highest impact factors in the Mathematical & Computational Biology category, and has affiliations in place with several other publications for the benefit of its members. http://www.iscb.org
International Mathematical Union (IMU): IMU is an international nongovernmental and non-profit scientific organization, with the purpose of promoting international cooperation in mathematics. http://www.mathunion.org
The Society for Industrial and Applied Mathematics (SIAM): SIAM exists to
ensure the strongest interactions between mathematics and other scientific and technological communities through membership activities, publication of journals and books, and conferences. http://www.siam.org
International Council for Industrial and Applied Mathematics (ICIAM): ICIAM is a
worldwide organisation for professional applied mathematics societies, and for other societies with a significant interest in industrial or applied mathematics. http://www.iciam.org
International Center for Pure and Applied Mathematics: CIMPA is an international
organisation whose aim is to promote mathematics in developing countries. CIMPA is sponsored by UNESCO and supported by the French Ministry of Higher Education and Research (MESR), the University of Nice-Sophia Antipolis (UNS), the Spanish Ministry for Science and Innovation (MICINN) and the French National Centre for Scientific Research (CNRS). http://www.cimpa-icpam.org
Southeast Asian Mathematical Society (SEAMS): SEAMS seeks to promote the
advancement of mathematics and facilitate exchange and collaboration between mathematicians in the Southeast Asian region, and Asia in general. It is composed of the members of mathematical societies in Southeast Asia. http://www.seams-math.org
The Philippine Society for the Study of Nature (PSSN): Its primary objectives are
to provide and develop strategies towards wise and sustainable use of nature and to ensure a faithful representation of responsible thinking and sentiment regarding issues about nature. It also seeks to establish partnership and/or collaboration with local government units and other institutions that are involved in the development, conservation, and management of natural resources. Its various activities serve as a channel for the exchange of information, sharing of professional expertise, networking, and strengthening of camaraderie and
cooperation among members and partner institutions. PSSN, Inc. was organized as a non-profit, non-stock, non-partisan organization of professionals, researchers, administrators, policymakers, practitioners, students, and institutions involved in nature studies and its related activities. http://pssn.bahaykuboresearch.net
The Mathematical Society of the Philippines (MSP): This society is an academic,
non-stock, non-profit, non-sectarian and a non-partisan organization, and carries out activities in the pursuit of the following objectives: a) to promote interest in and awareness of mathematics and its applications, b) to propagate knowledge in mathematics and mathematics education, and c) to promote mathematical research. http://www.mathsocietyphil.org
Links to Journals
Journal of Mathematical Biology: The Journal of Mathematical Biology fosters the
contribution of mathematical modeling and reasoning to the understanding of biological systems and the explanation of biological phenomena. The journal also serves as a forum for the presentation of biologically inspired problems of a mathematical nature. Published papers provide biological insight as a result of mathematical analysis or identify and open up challenging new types of mathematical problems derived from biological knowledge. Areas of biology covered include, biofluids, cell biology, physiology, neurobiology and behaviour, development, ecology, population biology, genetics and evolution, epidemiology, immunology, molecular biology, DNA and protein structure and function, and more. http://www.springer.com/mathematics/biology/journal/285
Bulletin of Mathematical Biology: A Journal devoted to research at the junction
of Computational, Theoretical and Experimental Biology. Official Journal of The Society for Mathematical Biology. http://www.springer.com/mathematics/biology/journal/11538
Mathematical Medicine and Biology: A Journal of the IMA: Mathematical Medicine
and Biology publishes original articles with a significant mathematical content addressing topics in medicine and biology. Papers exploiting modern developments in applied mathematics are particularly welcome. The biomedical relevance of mathematical models should be demonstrated clearly and validation by comparison against experiment is strongly encouraged. http://imammb.oxfordjournals.org
Computational Biology and Chemistry: Computational Biology and
Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions in the areas of nucleic acid and protein sequence research, molecular evolution, molecular
genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, cybernetics, ecology, environmental sciences, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered. www.elsevier.com/locate/compchem
IEEE/ACM Transactions on Computational Biology and Bioinformatics: TCBB is a
quarterly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. http://www.computer.org/portal/web/tcbb
PLoS Computational Biology: PLoS Computational Biology is a peer-reviewed,
open-access journal featuring works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods. It is an official journal of the International Society for Computational Biology. http://www.ploscompbiol.org/home.action
Journal of Computational Biology: Journal of Computational Biology is the leading
journal covering the analysis, management, and visualization of cellular information at the molecular level. The Journal publishes peer-reviewed papers focusing on novel, cutting-edge methods in computational biology and bioinformatics. http://www.liebertpub.com/products/product.aspx?pid=31
International Journal of Biomathematics (IJB): The goal of this journal is to
present the latest achievements in biomathematics, facilitate international academic exchanges and promote the development of biomathematics. Its research fields include mathematical ecology, infectious disease dynamical system, biostatistics and bioinformatics. The International Journal of Biomathematics is published quarterly. http://www.worldscinet.com/ijb/ijb.shtml
International Journal for Biomathematics and Biostatistics: In recent years
mathematical and statistical methods become more and more important for study complex biological phenomena. The policy of the "„International Journal of Biomathematics and Biostatistics"‟ is to offer of forum high quality research papers in this field. Topics of interests include but are not limited to dynamical systems models, numerical methods, stochastic models and statistics with applications in population dynamics, ecology, epidemiology, physiology, biotechnology and bioengineering, etc. Papers focusing on new mathematical and statistical methods for applications in biology and papers describing new findings in biology based on advanced mathematical and statistical methods will
be equally considered. http://www.serialspublications.com/journals1.asp?jid=577&jtype=1
Mathematical Biosciences: This leading international journal publishes research
and expository papers on the formulation, analysis and solution of mathematical models in the biosciences. The journal serves both mathematicians involved in solving model equations or in reaching conclusions that are testable in the real world, and biologists who are interested in forming mathematical models of biological processes and systems. http://www.elsevier.com/locate/mbs
International Journal on Ecological Modelling and Systems Ecology: The journal
is concerned with the use of mathematical models and systems analysis for the description of ecological processes and for the sustainable management of resources. Human activity and well-being are dependent on and integrated with the functioning of ecosystems and the services they provide. We aim to understand these basic ecosystem functions using mathematical and conceptual modelling, systems analysis, thermodynamics, computer simulations, and ecological theory. This leads to a preference for process-based models embedded in theory with explicit causative agents as opposed to strictly statistical or correlative descriptions. These modelling methods can be applied to a wide spectrum of issues ranging from basic ecology to human ecology to socioecological systems. The journal welcomes research articles, short communications, review articles, letters to the editor, book reviews, and other communications. The journal also supports the activities of the International Society of Ecological Modelling (ISEM). www.elsevier.com/locate/ecolmodel
Mathematical Biosciences and Engineering (MBE) Journal: MBE is
quarterly, focusing on new developments in the fast-growing fields of mathematical biosciences and bioengineering. MBE will be online only, starting 2010. Authors will be granted full access to all MBE publications for one year. Areas covered include general mathematical methods and their applications in biology, medical sciences and bioengineering with an emphasis on work related to mathematical modeling, nonlinear and stochastic dynamics. The editorial board of MBE is strongly committed to promoting cutting-edge integrative and interdisciplinary research bridging mathematics, life sciences and engineering. http://aimsciences.org/journals/mbe/index.htm
Directory of Open Access Journals: http://www.doaj.org Open J-gate: http://www.openj-gate.com
Other Links Institute for Medical BioMathematics (IMBM): http://www.imbm.org
The BioMathematics Laboratory (BioMatLab) at CNR IASI "A. Ruberti", Institute for Systems Analysis and Informatics (IASI), Italian National Research Council (CNR): http://www.biomatematica.it Mathematical Sciences Research Institute (MSRI), Berkeley, California: http://www.msri.org Program in Biostatistics and Biomathematics Fred Hutchinson Cancer Research Center: http://www.fhcrc.org/science/phs/biostats Institute of Biomathematics and Biometry, Helmholtz Zentrum München: http://www.helmholtz-muenchen.de/en/ibb Mathematical Biosciences Institute, Ohio State University: http://mbi.osu.edu PIMS International Graduate Training Centre (IGTC) in Mathematical Biology: http://www.pims.math.ca/scientific/graduate-training-igtc/mathematical-biology Computational Biology Center, IBM: https://researcher.ibm.com/researcher/view_project.php?id=1080 Abdus Salam International Centre for Theoretical Physics (ICTP): http://www.ictp.it International Max Planck Research School for Computational Biology and Scientific Computing: http://www.imprs-cbsc.mpg.de National Institute for Mathematical and Biological Synthesis (NIMBios): http://www.nimbios.org Biomathematics and Statistics Scotland (BioSS): http://www.bioss.ac.uk Computational Systems Biology, Institute of Mathematics, University of the Philippines Diliman: http://math.upd.edu.ph/images/pdf/systems_biology_group_description_101116. pdf
RESOURCES Some Books and Notes for New Biomathematicians Mathematical Biology I & II by J.D. Murray. Springer, 2002.
Mathematical Physiology by J. Keener and J. Sneyd. Springer, 1998. Mathematical Biology: An Introduction with Maple and Matlab by R.W. Shonkwiler and J. Herod. Springer, 2000. Analysis of Evolutionary Processes: The Adaptive Dynamics Approach and Its Applications by F. Dercole and S. Rinaldi. Princeton University Press, 2008. Foundations of Systems Biology edited by H. Kitano. MIT Press, 2001. An Introduction to Mathematical Models in Ecology and Evolution: Time and Space by M. Gillman. Wiley-Blackwell, 2009. Biodynamics by B.J. West and L.A. Griffin. Wiley-Liss, 2004. Dynamic Models and Control of Biological Systems by Vadrevu Sree Hari Rao and Ponnada Raja Sekhara Rao. Springer, 2009. Foraging: Behavior and Ecology edited by D.W. Stephens, J.S. Brown and R.C. Ydenberg. The University of Chicago Press, 2007. Biomathematics: Modeling and Simulation edited by J.C. Misra. World Scientific, 2006. Optimization in Food Engineering edited by F. Erdogdu. CRC Press, 2008. Simulation: A Modeler‟s Approach by J.R. Thompson. Wiley-Interscience, 2000. Mathematics for Life Science and Medicine edited by Y. Takeuchi, Y. Iwasa and K. Sato. Springer, 2007. Structured Population Models in Biology and Epidemiology edited by P. Magal and S. Ruan. Springer, 2008. Analysis of Biological Networks edited by B.H. Junker and F. Schreiber. WileyInterscience, 2008. Biomolecular Networks: Methods and Applications in Systems Biology by L. Chen, R-S. Wang, X-S. Zhang. Wiley, 2009. Introduction to Systems Biology edited by S. Choi. Humana Press, 2007. Nanomedicine: A Systems Engineering Approach edited by M. Zhang and N. Xi. Pan Stanford Publishing, 2009.
Computational Systems Biology edited by A. Kriete and R. Eils. Elsevier, 2006. Protein Networks and Pathway Analysis edited by Y. Nikolsky and J. Bryant. Humana Press, 2009. Systems Biology in Practice: Concepts, Implementation and Application by E. Klipp, R. Herwig, A. Kowald, C. Wierling and H. Lehrach. Wiley-VCH, 2005. Systems Biomedicine: Concepts and Perspectives edited by E.T. Liu and D.A. Lauffenburger. Academic Press, 2010. Bioinformatics and Functional Genomics by J. Pevsner. Wiley-Blackwell, 2009. Chemical Biophysics: Quantitative Analysis of Cellular Systems by D.A. Beard and H. Qian. Cambridge University Press, 2008. Ecological Modeling: A common-sense approach to theory and practice by W.E. Grant and T.M. Swannack. Blackwell Publishing, 2008. Quantitative Fish Dynamics by T.J. Quinn II and R.B. Deriso. Oxford University Press, 1999. Reconstructing Evolution: New Mathematical and Computational Advances edited by O. Gascuel and M. Steel. Oxford University Press, 2007. Protein Interaction Networks: Computational Analysis by A. Zhang. Cambridge University Press, 2009. Spatial Ecology edited by S. Cantrell, C. Cosner and S. Ruan. CRC Press, 2010. Handbook of Computational Molecular Biology edited by S. Aluru. Chapman & Hall/CRC, 2006. Structural Bioinformatics edited by P.E. Bourne and H. Weissig. Wiley-Liss, 2003. Control Theory and Systems Biology edited by P.A. Iglesias and B.P. Ingalls. MIT Press, 2010. Modelling, Analysis and Optimization of Biosystems by W. Krabs and S.W. Pickl. Springer, 2007. Analysis of Phylogenetics and Evolution with R by E. Paradis. Springer, 2006.
Differential Equations and Mathematical Biology by D.S. Jones and B.D. Sleeman. Chapman & Hall/CRC, 2003. Systems Biology in Psychiatric Research: From High-Throughput Data to Mathematical Modeling edited by F. Tretter, P.J. Gebicke-Haerter, E.R. Mendoza and G. Winterer. Wiley-Blackwell, 2010. An Introduction to Systems Biology: Design Principles of Biological Circuits by U. Alon. Chapman & Hall/CRC, 2007. Mathematical Models in Biology: An Introduction by E.S. Allman and J.A. Rhodes. Cambridge University Press, 2003. Modern Infectious Disease Epidemiology: Concepts, Methods, Mathematical Models, and Public Health edited by A. Krämer, M. Kretzschmar and K. Krickeberg. Springer, 2010. Cell Mechanics: From Singe Scale-Based Models to Multiscale Modeling edited by A. Chauviere, L. Preziosi and C. Verdier. Chapman & Hall/CRC, 2010. Mathematical Models in Biology by L. Edelstein-Keshet. SIAM's Classics in Applied Mathematics series, 2005. Nonequilibrium Ecology by K. Rohde. Cambridge University Press, 2005. Systems Biology and Synthetic Biology edited by P. Fu and S. Panke. Wiley, 2009. Cardiovascular Mathematics: Modeling and Simulation of the Circulatory System edited by L. Formaggia, A. Quarteroni and A. Veneziani. Springer, 2009. Mathematical Modeling of Complex Biological Systems: A Kinetic Theory Approach by A. Bellouquid and M. Delitala. Birkhauser, 2006. Models of Cellular Regulation by B. Aguda and A. Friedman. Oxford University Press, 2008.
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