UP Mathematical

1

• UP Mathematical
• Life Sciences
• Initiative (UP-MLSI)
• May 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

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Introduction

• Based on the feedback to last months inquiry, we
  have renamed the initiative as UP Mathematical
  Life Sciences Initiative to emphasize the
  coverage of the biological, ecological and
  environmental sciences. At the same time, weve
  dropped computational to reduce redundancy (the
  use of computers in modeling/simulation work is
  self-evident).
• Topics to be covered
• Status of local joint projects
• Status of foreign joint projects
• Related developments, news
• Status of action items

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Local Joint Projects
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LP1 PAH Pollution Modeling

• Investigators E. Santiago (NSRI), C. Epes, A.
  Hermosilla, E. Baja (Math)
• Activities/Results
• SAS Analysis of the NSRI data sets done
• Draft outline of joint paper proposed by A.
  Hermosilla
• Issues
• Follow-up meetings (originally planned in
  April/May) not yet executed ? tight schedule to
  get paper done for submission to 1st National
  Conference on Environmental Science (Oct 03)
• Next Steps
• Presentation/discussion on prelim analyses
  planned (at NSRI)
• Agree on further collaboration schedule
• Submit abstract of joint paper to 1st Nat Conf
  organizers

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LP2 Coral Reef Modeling

• Investigators H. Yap, R. Dizon, A. Reyes (MSI),
  E. Mendoza, J. Pasia, R. Del Rosario, E. Victoria
  (Math)
• Activities/Results
• A position paper Coral Reefs as Complex Systems
  by R. Dizon and H. Yap has been drafted, R. Dizon
  plans to do PhD research in this area
• Email discussions on complex network aspects of
  coral reefs ongoing (R. Dizon, H. Yap, E.
  Mendoza)
• Further potential coop (in addition to Sole Lab
  in Barcelona) with LMU GeoBioCenter
  (http//www.geobio-center.de/ ) under
  consideration
• PhD Math student could focus on a modeling
  problem here
• Issues
• Need focus on this as modeling of marine
  ecosystems (incl. coral reefs) as complex
  networks is starting to attract various research
  groups
• Next Steps
• Define focus for next phase June October
  (possibly 2 subgroups)
• Clarify involvement of C. Ejes, A. Hermosilla, J.
  Pasia, E. Victoria in next project phase (as they
  are heavily involved in other projects)

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LP3 Math Immuno- Oncology

• Investigators G. Concepcion, D. de Guzman
  (MSI), E. Jacinto, E. Mendoza, E. Tan, E.
  Victoria (Math)
• Activities/Results
• Immuno-Onco Study Group has met regularly in the
  summer break (thursdays, 15-16 at Math)
• Intensive discussions on modeling cell cycle,
  particular pathways in apoptosis were conducted
• Issues
• Problem to focus on needs to be defined (after
  the summer learning phase)
• Next Steps
• Refinement of investigation focus for next phase
  (June-Oct)

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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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Foreign Joint Projects
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FP1 Modeling eukaryotic chemotaxis

• Investigators S. Thunnessen (LMU), T.
  Bretschneider (MPI Biochemistry), E. Mendoza
  (Math), P. Naval (CompSci)
• Activities/Results
• Proposal made by Pros Naval on research topics
  second topic is promising but will need other
  experimental partner (large-scale data)
• Progress on BST approach potential
  software-related research topics identified (s.
  Minutes for details)
• Issues
• Experimental data not yet available
• Identfication of resources (students) to work on
  software-related topics
• Next Steps
• Follow up on ETH Zürich opportunity (E. Mendoza)
  for Pros2nd proposal
• Identify resources for BST software-related
  topics (E. Mendoza, P. Naval)

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FP2 Math Bio-Character Theory

• Investigators P. Stadler (U Leipzig), A.
  Balbuena, E. Jacinto, E. Mendoza (Math), A. Lao
  (DLSU Math)
• Activities/Results
• A. Balbuena, A. Lao have started to work on their
  theses (including regular meetings of AB with E.
  Jacinto, meetings of AL with D. Diesto planned)
• First (monthly) progress reports on theses
  submitted to E. Mendoza
• Email discussion between P. Stadler and E.
  Mendoza on refining the research focus
• Issues
• A. Balbuena might need more topology-oriented
  local advisor (L. Torrechante?)
• Next Steps
• Continue monthly progress reports and remote
  research management
• 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
• Issues
• Not clear which NIP resources will be involved
• Next Steps
• Obtain further details on Harder Lab work (E.
  Mendoza)
• Clarify whether/which resources will be available
  (C. Saloma)

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FP4 Math of RNA Structures

• Investigators P. Stadler (U Leipzig), H.
  Adorna, E. Jacinto, E. Mendoza (Math)
• Activities/Results
• SIG (Special Interest Group) on Parsing RNA
  Sequences in the summer break (H. Adorna, A.
  Balbuena, E. Jacinto)
• Talk on Parsing RNA Sequences at Math Society
  of the Philippines Annual Convention (May 24-25)
  by H. Adorna
• Issues
• P. Stadler is not focussed on formal language
  approaches to RNA ? might need further foreign
  collaborators (Japan, U Bielefeld)
• Next Steps
• H. Adorna will include some topics from this area
  in his course Mathematics of Computation
• Initiate contacts to other potential foreign
  collaborators

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MLSI-relevant developments, news

• Chris Monterola (NIP) will start his postdoc
  (July 03) at the Max-Planck Institute for Physics
  of Complex Systems in Dresden, Germany. Initial
  focus is modeling of the olfactory system
  (Zapotocki Lab, Biological Physics Department)
• Marla Endriga (IB) started in Apr 03 her Masters
  in Bioinformatics at Cologne University
• MSI Biological Structures Course will take
  place Mo, Th 4-530 pm, MSI Rm 107, first session
  on June 16 this is meant to provide (non-bio)
  science and engineering graduate students and
  faculty an overview of interesting life sciences
  research areas

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Sustain Nurture Activities May status

• Execute on identified projects (true for most of
  the MLSI projects)
• Establish Immuno-Onco Summer Study Group (Lead
  G. Concepcion/Dennis de Guzman) Thursdays 3 - 4
  pm at Math
• MSI Biological Structures Course (First Sem 03
  - 04) will take place
• Identify future funding needs and secure
• Strengthen Bioinformatics/Computational Biology
  network (? Computer Science has decided to make
  Bioinformatics a focus program starting this
  academic year)

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Feedback/action items May Status

• DONE Find better name for Initiative than MCBI
  (as Ecological and Environmental Sciences are
  also affected) ? UP-MLSI (UP Mathematical Life
  Sciences Initiative)
• 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
• Question should this be a topic of proposed
  review session too?
• DONE Identify Post-doc to focus on Biomath
  (several post-docs from Math are intensively
  involved in different MLSI projects, need to do
  systematic planning for 2nd sem

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Feedback/action items May status

• DONE Address authors directly for papers rather
  than increase subscriptionsoften faster, more
  focussed and establishes links
• DONE EM to conduct Project Mgmt WS in Aug/Sep (2
  half-day sessions planned)
• DONE Request from MSI to create graduate courses
  on modeling for non-Math majors (synch with Math
  undergraduate courses)
• Graph Theory and Complex Networks course offered
  in First Sem