1 / 13

UP Mathematical Life Sciences Initiative (UP-MLSI) June 2003 Report Dr. Eduardo Mendoza Mathematics Department

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

paul2
Download Presentation

UP Mathematical Life Sciences Initiative (UP-MLSI) June 2003 Report Dr. Eduardo Mendoza Mathematics Department

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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@math.upd.edu.phEduardo.Mendoza@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 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)

  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-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

  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

More Related