UP Mathematical

1

• 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
• eduardom_at_math.upd.edu.ph
  Eduardo.Mendoza_at_physik.uni-muenchen.de

2
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)

3
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 Mendoza has 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)

4
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

5
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

6
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

7
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

8
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.

9
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-SystemCompartment 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

10
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

11
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)

12
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

13
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