UP Numerical Life Sciences Activity (UP-MLSI) June 2003 Report Dr. Eduardo Mendoza Arithmetic Office Material science Of.

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UP Numerical Life Sciences Activity (UP-MLSI) June 2003 Report Dr. Eduardo Mendoza Science Division Material science Office College of the Philippines Ludwig-Maximilians-College 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 eduardom@math.upd.edu.ph Eduardo.Mendoza@physik.uni-muenchen.de

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June MLSI Project Highlights First MLSI-propelled paper (R. Dizon,H.Yap „Coral Reefs As Complex Systems“) submitted for production; two distributions on demonstrating PAH contamination (E. Santiago, C.Ejes, A. Hermosilla) are being readied Immuno-Onco Group has advanced their exploration concentrate on apoptotic pathways and is as of now refining their systematic methodology UP Computer Science group focussed on S-Systems displaying now has 2 individuals: P. Maritime, O. Gonzalez (MS hopeful) New coop opportunities with E. Zitzler bunch (ETH Zã¼rich, Switzerland) R. Laubenbacher gathering (Viriginia Bioinformatics Institute, USA) and B. Pareigis (LMU Math, Germany) W. Gabriel Lab (LMU Ecology, Germany)

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MLSI-related news & improvements May Lim (NIP) is a member (first ever from the Philippines) of the prestigious Santa Fe Institute Summer School on Complex Systems (June 8-July 5) – this course has an in number spotlight on biosystems demonstrating A National Initiative in Bioinformatics ( NIMBUS ), has been started by DOST, contact with MLSI has begun and potential coop focused on Eddie Mendoza has been chosen (per July 1) an individual from the Center for NanoScience ( www.cens.de ) at LMU notwithstanding the MSI „ Biological Structures “ course, the Math Dept is putting forth a further MLSI-related course „ Graph Theory and Complex Networks “ (teachers: E. Tan/E. Mendoza)

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MLSI Action Items - status Invite DOST agents to future occasions to acquaint them with Initiative Proposal: sort out a half-day audit session of MLSI undertakings amid first week of September, welcome DOST delegates Organize sharing of MSI experience in regards to research subsidizing obtaining Proposal: workshop end August/early September Identify future financing needs and secure

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LP1: PAH Pollution Modeling Investigators: E. Santiago (NSRI), C. Epes, A. Hermosilla (Math) Activities/Results: Several working gatherings have brought about 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 prepared by end of July. This paper covers just the residue sorts 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 arrangement Issues: first National Conference on Environmental Science (orginally got ready for Oct 03) is uncertainly put off  new venue for results presentation to be looked for Next Steps: Progress first paper composing to accomplish draft by end of July (ES,CE) Determine title and extent of second paper at subsequent meeting (ES,AH) Survey further stations 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 keen on coordinating in this task Issues Need all the more full-time assets (graduate understudies) to concentrate on this as demonstrating of marine biological systems (incl. coral reefs) as mind boggling systems is beginning to draw in different exploration bunches Next Steps Meeting on July 21 to characterize center for next stage July – October Clarify further inclusion of other Math Faculty (as they are intensely included in different ventures) Identify graduate understudies to concentrate on displaying exercises

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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 individuals on ideas/standards fundamental biochemical flagging pathways Discussion of test work by G. Concepcion Lab on apoptotic pathways Issues: Need to check if pathway crosstalk must be considered in model Selection of fitting demonstrating and parameter estimation techniques for apoptotic pathway (S-System methodology proposed by E. Mendoza) Next Steps: Evaluate S-System approach for displaying (all) Data mining of writing on pathway active parameters (Dennis) Identify MS student(s) to do the information mining, apoptotic demonstrating and trials

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LP4: Modeling medicinal information 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 consolidate essential UP procurements (R. Del Rosario) Issues/Questions Identify Math Department workforce or graduate understudies who can take a shot at issues postured by St. Lukes (there is a PhD Math understudy who could concentrate on this) Next Steps: Send draft MOA to St. Lukes after Office of Coordination and Extension has altered it.

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FP1: Modeling eucaryotic chemotaxis Investigators: S. Thunnessen (LMU), T. Bretschneider (MPI Biochemistry), E. Mendoza (Math), O. Gonzalez, P. Maritime (CompSci) Activities/Results: Progress on demonstrating slope detecting by means of less difficult S-System+Compartment approach (T. Bretschneider/E. Mendoza) Orland Gonzalez (MS applicant) has begun his theory work around there Issues: Delay in P. Maritime work because of showing burden and PhD EE course prerequisites Next Steps: Report on next venture jour-fixe (Munich, July 22) Determine the last MS proposal point for O. Gonzalez (E. Mendoza/P. Maritime) 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 advancing their proposals (counting customary gatherings of AB with E. Jacinto, gatherings of AL with D. Diesto arranged) First part on fundamental ideas and wording drafted by A. Lao is a decent basic premise for both theories  proposition b y E. Mendoza for both postulations to utilize this archive as beginning stage A. Balbuena to center his BS Senior postulation on applying the general Stadler-Wagner results to RNA shape space (in examination to Cupal et al paper) Issues: How to actualize closer correspondence & coop between A. Balbuena and A. Lao Next Steps: Proposal for closer coop between both theory understudies (E. Mendoza) Meeting with P. Stadler and G. Wagner (Yale) arranged amid week of Aug 11-15 in Leipzig

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FP3: Modeling LAT edifices in T-cells Investigators: Harder Lab (Oxford U), NIP Instrumentation Physics Group, E. Mendoza (Math) Activities/Results: no exercises in May and June Issues: Currently no UP assets accessible Next Steps: Obtain further points of interest on Harder Lab work (E. Mendoza) Clarify whether/which assets from NIP or Immuno-Onco Group will be accessible (C. Saloma/E. Mendoza)

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PPx: Potential Projects List (1) Formal Languages and RNA Structures Foreign Partner: to be resolved UP Investigator: H. Adorna (Math) Next Steps: H. Adorna will incorporate a few themes from this region in his course „Mathematics of Computation“ Initiate contacts to other potential remote colleagues Reverse Engineering of Genetic Networks Foreign Partner: ETH Zã¼rich (Swiss Federal Institute of Technology, Zã¼rich), Zitzler Group UP Investigator: Pros Naval (CS) Coop regions: Evolutionary Computation, Statistical Methods – open door for PhD understudies Next arranging session end of October

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PPx: Potential Projects List (2) 3. Science of Discrete Simulation Foreign Partners: Virginia Bioinformatics Institute/Virginia Tech: Laubenbacher Group LMU Math Department: Prof. B. Pareigis UP Investigator: Eddie Mendoza (Math) Coop ranges: Polynomial models for biochemical systems, Mathematical Theory of Simulation – open door for PhD understudies At gatherings with Prof. Laubenbacher (June 27) and Prof. Pareigis (July 9), both communicated solid enthusiasm for exploration coop and also being included in „sandwich“ PhD projects Further catch up in August (post-excursion time) „Local“ Math Dept agent required (pre

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