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UP Mathematical Life Sciences Initiative (UP-MLSI) June 2003 Report Dr. Eduardo Mendoza Mathematics Department Physics Department University of the Philippines Ludwig-Maximilians-University Diliman Munich, Germany

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UP Mathematical

Life Sciences

Initiative (UP-MLSI)

June 2003 Report

Dr. Eduardo Mendoza

Mathematics Department Physics Department

University of the Philippines Ludwig-Maximilians-University

Diliman Munich, Germany

[email protected]@physik.uni-muenchen.de

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June MLSI Project Highlights

  • First MLSI-inspired paper(R. Dizon,H.Yap „Coral Reefs As Complex Systems“)submitted for publication; two publications on modelling PAH pollution (E. Santiago, C.Ejes, A. Hermosilla) are being prepared

  • Immuno-Onco Group has progressed their research focus on apoptotic pathways and is currently refining their methodical approach

  • UP Computer Science team focussed on S-Systems modeling now has 2 members: P. Naval, O. Gonzalez (MS candidate)

  • New coop opportunities with

    • E. Zitzler group (ETH Zürich, Switzerland)

    • R. Laubenbacher group (Viriginia Bioinformatics Institute, USA) and B. Pareigis (LMU Math, Germany)

    • W. Gabriel Lab (LMU Ecology, Germany)

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MLSI-related news & developments

  • May Lim (NIP)is a participant (first ever from the Philippines) of the renowned Santa Fe Institute Summer School on Complex Systems (June 8-July 5) – this course has a strong focus on biosystems modeling

  • A National Initiative in Bioinformatics (NIMBUS),has been initiated by DOST, contact with MLSI has started and potential coop targeted

  • Eddie Mendozahas been elected(per July 1) a member of the Center for NanoScience (www.cens.de ) at LMU

  • In addition to the MSI „Biological Structures“ course, the Math Dept is offering a further MLSI-related course „Graph Theory and Complex Networks“ (instructors: E. Tan/E. Mendoza)

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MLSI Action Items - status

  • Invite DOST representatives to future events to familiarize them with Initiative

    Proposal: organize a half-day review session of MLSI projects during 1st week of September, invite DOST representatives

  • Organize sharing of MSI experience regarding research funding acquisition

    Proposal: workshop end August / early September

  • Identify future funding needs and secure

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LP1: PAH Pollution Modeling

  • Investigators: E. Santiago (NSRI), C. Epes, A. Hermosilla (Math)

  • Activities/Results:

    • Several working meetings have resulted in the ff:

      • A first draft of a paper by E.Santiago, C. Ejes on „Fingerprinting of Primary Sources of Polycyclic Aromatic Hydrocarbons in Greater Manila „ will be ready by end of July. This paper covers only the soot types

      • A second paper by E. Santiago, C.Ejes & A. Hermosilla (proposed title: „Some Classificatory Structures on PAH Particulates and Sediments in Manila Bay“) is under preparation

  • Issues:

    • 1st National Conference on Environmental Science (orginally planned for Oct 03) is indefinitely postponed  new venue for results presentation to be sought

  • Next Steps:

    • Progress first paper writing to achieve draft by end of July (ES,CE)

    • Determine title and scope of second paper at follow-up meeting (ES,AH)

    • Survey further channels for presentation of results

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LP2: Coral Reef Modeling

  • Investigators: H. Yap, R. Dizon (MSI), E. Mendoza, R. Del Rosario,(Math)

  • Activities/Results:

    • The paper „Coral Reefs as Complex Systems“ by R. Dizon and H. Yap has been submitted to „Marine Pollution Bulletin“(Elsevier)

    • W. Gabriel Ecology Lab (LMU) is interested in cooperating in this project

  • Issues

    • Need more full-time resources (graduate students) to focus on this as modeling of marine ecosystems (incl. coral reefs) as complex networks is starting to attract various research groups

  • Next Steps

    • Meeting on July 21 to define focus for next phase July – October

    • Clarify further involvement of other Math Faculty (as they are heavily involved in other projects)

    • Identify graduate students to focus on modeling activities

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LP3: Math Immuno- & Oncology

  • Investigators: G. Concepcion, D. de Guzman, J. Madrazo (MSI), E. Jacinto, R. del Rosario, P. Sy, E. Tan, E. Victoria (Math)

  • Activities/Results:

    • Tutorials for Math people on concepts/principles underlying biochemical signalling pathways

    • Discussion of experimental work by G. Concepcion Lab on apoptotic pathways

  • Issues:

    • Need to check if pathway crosstalk has to be considered in model

    • Selection of appropriate modeling and parameter estimation methods for apoptotic pathway (S-System approach proposed by E. Mendoza)

  • Next Steps:

    • Evaluate S-System approach for modeling (all)

    • Data mining of literature on pathway kinetic parameters (Dennis)

    • Identify MS student(s) to do the data mining, apoptotic modeling and experiments

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LP4: Modeling medical data

  • Investigators: F. Natividad, R. Matias (St. Lukes Med Center), R. Del Rosario, E. Jacinto (Math)

  • Activities/Results:

    • Draft MOA sent to Director of the Office of Coordination and Extension (this office will incorporate necessary UP provisions (R. Del Rosario)

  • Issues/Questions

    • Identify Math Department faculty or graduate students who can work on problems posed by St. Lukes (there is a PhD Math student who could focus on this)

  • Next Steps:

    • Send draft MOA to St. Lukes after Office of Coordination and Extension has edited it.

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FP1: Modeling eucaryotic chemotaxis

  • Investigators: S. Thunnessen (LMU), T. Bretschneider (MPI Biochemistry), E. Mendoza (Math), O. Gonzalez, P. Naval (CompSci)

  • Activities/Results:

    • Progress on modeling gradient sensing via simpler S-System+Compartment approach (T. Bretschneider / E. Mendoza)

    • Orland Gonzalez (MS candidate) has started his thesis work in this area

  • Issues:

    • Delay in P. Naval work due to teaching load and PhD EE course requirements

  • Next Steps:

    • Report on next project jour-fixe (Munich, July 22)

    • Determine the final MS thesis topic for O. Gonzalez (E. Mendoza / P. Naval) by end of July

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FP2: Math Bio-Character Theory

  • Investigators: P. Stadler (U Leipzig), A. Balbuena, E. Jacinto, E. Mendoza (Math), D. Diesto, A. Lao (DLSU Math)

  • Activities/Results:

    • A. Balbuena, A. Lao are progressing their theses (including regular meetings of AB with E. Jacinto, meetings of AL with D. Diesto planned)

    • First chapter on basic concepts and terminology drafted by A. Lao is a good common basis for both theses  proposal b y E. Mendoza for both theses to use this document as starting point

    • A. Balbuena to focus his BS Senior thesis on applying the general Stadler-Wagner results to RNA shape space (in comparison to Cupal et al paper)

  • Issues:

    • How to implement closer communication & coop between A. Balbuena and A. Lao

  • Next Steps:

    • Proposal for closer coop between both thesis students (E. Mendoza)

    • Meeting with P. Stadler and G. Wagner (Yale) planned during week of Aug 11-15 in Leipzig

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FP3: Modeling LAT complexes in T-cells

  • Investigators: Harder Lab (Oxford U), NIP Instrumentation Physics Group, E. Mendoza (Math)

  • Activities/Results:

    • no activities in May and June

  • Issues:

    • Currently no UP resources available

  • Next Steps:

    • Obtain further details on Harder Lab work (E. Mendoza)

    • Clarify whether/which resources from NIP or Immuno-Onco Group will be available (C. Saloma/E. Mendoza)

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PPx: Potential Projects List (1)

  • Formal Languages and RNA Structures

    • Foreign Partner: to be determined

    • UP Investigator: H. Adorna (Math)

    • Next Steps:

      • H. Adorna will include some topics from this area in his course „Mathematics of Computation“

      • Initiate contacts to other potential foreign collaborators

  • Reverse Engineering of Genetic Networks

    • Foreign Partner: ETH Zürich (Swiss Federal Institute of Technology, Zürich), Zitzler Group

    • UP Investigator: Pros Naval (CS)

    • Coop areas: Evolutionary Computation, Statistical Methods – opportunity for PhD students

    • Next planning session end of October

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PPx: Potential Projects List (2)

3.Mathematics of Discrete Simulation

  • Foreign Partners:

    • Virginia Bioinformatics Institute/Virginia Tech: Laubenbacher Group

    • LMU Math Department: Prof. B. Pareigis

  • UP Investigator: Eddie Mendoza (Math)

  • Coop areas: Polynomial models for biochemical networks, Mathematical Theory of Simulation – opportunity for PhD students

  • At meetings with Prof. Laubenbacher (June 27) and Prof. Pareigis (July 9), both expressed strong interest in research coop as well as being involved in „sandwich“ PhD programs

  • Further follow-up in August (post-vacation time)

  • „Local“ Math Dept investigator needed (preferrably from Algebra & Number Theory Research Group