ICMSB 2008: 10th International Conference on Molecular Systems Biology (Program of Activities)

ICMSB 2008
10th International Conference on Molecular Systems Biology
25 - 28 February 2008
University of the Philippines-Diliman
Quezon City, Philippines
Website: http://www.icmsb08.org/


PROGRAM OF ACTIVITIES

February 25 (Monday)
Pre-Conference Tutorials
Venue: UP National Institute for Science and Mathematics Education Development
(UP NISMED)

8:00-8:30am Registration
8:30-8:45am Welcome Remarks
8:45-10:15am [T1] Modeling Biochemical Networks
Eberhard Voit (Georgia Tech, USA)
10:15-10:30am Coffee Break
10:30-12:00nn [T2] Efficient Inferring Method of Genetic Interactions Based on Time Series Gene Expression Profiles: Application of Conceptual Modeling by S-System Formalism
Masahiro Okamoto (Kyushu U, Japan)
12:00-1:30pm Lunch Break
1:30-2:45pm [T3] Parameter Estimation Methods in Biochemical Systems Theory: Classical and Evolutionary Approaches
Ricardo del Rosario (UPD, Philippines and MPI Biochem, Germany) and Prospero Naval, Jr (UPD, Philippines)
2:45-3:00pm Coffee Break
3:00-4:00pm [T4] Extracting Network Models from Pathway Databases
Baltazar Aguda (Ohio State U, USA)
4:00-5:00pm [T5] Digital Libraries and Workflow Processes for Systems Biology
Su-Shing Chen (PICB Shanghai, China)
6:00pm onwards Welcome Dinner



February 26 (Tuesday)
Conference Day 1
(Morning Session)

Venue: UP NISMED

8:00-8:25am Registration
8:25-8:40am Welcome Remarks
8:40-9:10am Keynote [K1]: Systems Biology with SMILES
Eduardo Mendoza (LMU Munich, Germany and UPD, Philippines)
Session Theme: Biological Network Reconstruction
Session Chair: TBA (to be announced)
9:10-9:15am Session Introduction
9:15-9:45am [P1] Computational Identification of Dynamic Biological Networks:
Inverse Modeling Approach and Parameter Estimation Strategies
I-C Chou, M. Vilela, J.S. Almeida, and E.O. Voit
9:45-10:15am [P2] MADMan: A Benchmarking Framework for Parameter
Estimation in Biochemical Systems Theory Models
R. del Rosario, M.T. Echavez, M.T. de Paz, P.C. Zuniga,
M.C.R. Bargo, C.O. Talaue, C. Arellano, J.M. Pasia,
P.C. Naval, E.O. Voit, and E. Mendoza
10:15-10:30am Coffee Break
10:30-11:00am [P3] Approximate Kinetic Formalisms for Modeling Metabolic Networks: Does Anything Work?
A. Sorribas, E. Villaprinyo, and R. Alves
11:00-11:30am [P4] Determination of Bottleneck Enzymes in a Metabolic
Reaction System by Dynamic Sensitivity Analysis
F. Shiraishi and Y. Suzuki
11:30-12:00nn [P5] Semi-Automated Reconstruction of Biological Circuits
R. Alves, E. Villaprinyo, and A. Sorribas
12:00-1:00pm Lunch/Transfer to Ateneo de Manila
February 26 (Tuesday)


Conference Day 1: February 26, 2008

(Afternoon Session)

“TOWARDS SYSTEMS BIOLOGY OF RICE” WORKSHOP
Venue: Ateneo de Manila University
Workshop Chair: Rafael Saldaña (Ateneo de Manila U, Philippines)

1:00-1:30pm Registration/Setting up of Posters
1:30-1:45pm Welcome Remarks
1:45-2:30pm [K2] Klaus Gerwert (Ruhr U Bochum, Germany)
2:30-3:15pm [W1] Biological Systems Analysis: Crop and Individual Plant
Properties in the Context of Engineering C4 Rice
John Sheehy A. B. Ferrer, K.G. Tan, and F. Danila (IRRI, Phil.)
3:15-3:3pm Coffee Break
3:30-4:15pm [W2] Rice Genetic Modification for Improved Nutrient Content
Rhodora Almedita (PhilRice, Philippines)
4:15-5:00pm [W3] The GCP Information System
Richard Bruskiewich (IRRI, Philippines)
5:00-6:30pm Poster Session 1 (Posters N1 to N9)
6:30pm onwards Cocktails


February 27 (Wednesday)

Conference Day 2
(Morning Session)
Venue: UP NISMED
8:00-8:20am Registration
8:20am Start of Morning Session
8:25-9:10am [K3] Dynamic Modeling of Cell Signaling Systems
Olaf Wolkenhauer (U of Rostock, Germany)
Session Theme: Information Infrastructures for Systems Biology
Session Chair: TBA
9:10-9:15am Session Introduction
9:15-9:45am [P6] EUCLIS: Towards a Digital Library-Based Common
Information Space for Chronobiologists
R. Santos and E. Mendoza
9:45-10:15am [P7] Programming Language Support in Simulating Semantic Multimodal Network Models
A. Sioson and L. Heath
10:15-10:30am Coffee Break
10:30-11:00am [P8] Design of a Homogeneous Ensemble for Splice-Site
Identification in Human Sequences
J. Pabico, E. Mojica, and J.R. Micor
11:00-11:30am [P9] Patent Prosecution in Systems Biology Software
M-F Lee and D. Fernandez
11:30-12:00nn [P10] Global Nonlinear Root-Finding Using the Canonical
S-System Form
R. Fasani and M. Savageau
12:00-1:15pm Lunch


February 27 (Wednesday)
Conference Day 2
(Afternoon Session)


Venue: UP NISMED
1:20pm Start of Afternoon Session
1:25-2:10pm [K4]: Metabolomics and Its Applications to Integrative
Systems Biology
Masaru Tomita (Keio U, Japan)
Session Theme: Metabolic Networks
Session Chair: TBA
2:10-2:15pm Session Introduction
2:15-2:45pm [P11] A Mathematical Model of Light-Induced ATP Synthesis
in the Archaea Halobacterium Salinarum
S. Veflingstad, D. Oesterheld, E.O. Voit
2:45-3:15pm [P12] Model-Driven Optimization Based on Standard Formalisms
A. Marin-Sanguino, N.V. Torres-Darias, E. Mendoza, and
D. Oesterhelt
3:15-3:30pm Coffee Break
3:30-4:00pm [P13] A Computational Model of Dopamine Metabolism and
Parkinson's Disease
Z. Qi, G.W. Miller, and E.O. Voit
4:00-4:30pm [P14] Global Tolerance of Biochemical Systems and the
Design of Moiety-Transfer Cycles
P. Coelho, A. Salvador, M. Savageau
4:30-5:00pm [P15] Growth and Ligninolytic System Production Dynamics of the
Phanerochaete chrysosporium Fungus: A Modeling and Optimization Approach
J. Hormiga, J. Vera, I. Frias O. Wolkenhauer, and N.V. Torres-Darias
5:30-7:00pm Poster Session 2 (Posters N10 to N18)
Venue: UPD Department of Computer Science Lobby

February 28 (Thursday)

Conference Day 3

(Morning Session)
Venue: UP NISMED

8:00-8:20am Registration
8:20am Start of Morning Session
8:25-9:10am [K5]: Multiscale Models of Tumors
Avner Friedman (Ohio State U, USA)
Session Theme: Signal Transduction Networks
Session Chair: TBA
9:10-9:15am Session Introduction
9:15-9:45am [P16] Inferring the Mechanistic Basis for the Dynamic Response
of the MyD88-dependent and -independent Pathways
K. Selvarajoo, M. Helmy, M. Tomita, and M. Tsuchiya
9:45-10:15am [P17] Cephalostatin 1-Induced Apoptosis in Leukemic Cells:
From Petri Net Model to Kinetic Model
E. Rodriguez, R. del Rosario, A. Rudy, A. Vollmar, E. Mendoza
10:15-10:45am Coffee Break
10:30-11:00am [P18] Noisy: Identification of Problematic Columns in Multiple
Sequence Alignments
A.W.M. Dress, C. Flamm, G. Fritzsch, S. Grunewald, M. Kruspe,
S.J. Prohaska and P.F. Stadler
11:00-11:30am [P19] Implementing Brane Calculus
M.P. David, A. Phillips, E. Mendoza, and L. Cardelli
11:30-12:00nn [P20] On the Structural Complexity of DNA Templates and
Some Wider Implications
G. Yagil

February 28 (Thursday)
Conference Day 3
(Afternoon Session)
Venue: UP NISMED
1:20pm Start of Afternoon Session
1:25-2:10pm [K6] Modeling Concept Maps with BST
Eberhard Voit (Georgia Tech, USA)
Session Theme: Gene Regulatory Networks
Session Chair: TBA
2:10-2:15pm Session Introduction
2:15-2:45pm [P21] Energetic Constraints in Adaptive Gene Expression
Responses of Yeast Under Environmental Changes
E. Villaprinyo, A. Salvador, R. Alves, A. Sorribas
2:45-3:15pm [P22] Variability Dynamics of Protein Levels in Human Cells
A. Sigal, R. Milo, A. Cohen, and U. Alon
3:15-3:30pm Coffee Break
3:30-4:00pm [P23] Gene Expression Levels in Saccharomyces cerevisiae
Strongly Reflect Energetic Cost Rates of Gene Products
E. Villaprinyo, R. Alves, A. Sorribas, and A. Salvador
4:00-4:30pm [P24] Multi-Objective Evolutionary Optimization for Inferring
S-System Models of Biological Networks
P-K Liu and F-S Wang
4:30-4:45pm Conference Close (Co-Chairs)
5:00-7:00pm Post-ICMSB “Beer and Pizza” Session on BST Tools and
Platforms, UPD Computer Science




ACCEPTED POSTERS

Poster Session 1

Venue: Ateneo de Manila University

Poster N1: Regulation of the FNR System (D. Tolla and M. Savageau)

Poster N2: Avoiding Catabolite Repression Using Systems Biology (A. Sevilla, M. Canovas, C. Gonzalez-Alcon, N.V. Torres-Darias, and J.L. Iborra)

Poster N3: Mathematical Analysis of the Dynamics of a Single-Strain HIV Model with Multiple Endemic States (L.K. Faina, L. Almocera, and P. Sy)

Poster N4: Exploring Characteristics of Metabolic Networks Lactococcus lactis IL1403 (I-F Chung, S-Y Yang, S-Y Huang, and F-S Wang)

Poster N5: Halobacterium salinarum R-1 Metabolism: Reconstruction, Modeling & Analysis (O. Gonzalez, S. Gronau, M. Falb, F. Pfeiffer, E. Mendoza)

Poster N6: Location of Malaria Infection in Cells Through Grammatical Evolution of Image Processing Techniques (MICE)
(C. Clarin and P. C. Naval)

Poster N7: In Silico Dynamical Analysis of Cellular Systems: A Molecular Perturbation Approach (T.M. Perumal, W. Yan, and R. Gunawan)

Poster N8: Identification of the Biochemical Response Variables to Glycerol Pulse in E. coli by a Multivariate Approach
(D.V. Guebel, M. Canovas, N.V. Torres-Darias)

Poster N9: Agent-Based Models for Biochemical Systems (T-Y. Wang, K-C. Chen, D.F. Hsu, C-Y Kao)

POSTER SESSION 2

Venue: UP Department of Computer Science Lobby

Poster N10: Extending Biochemical System Theory to Hybrid Modeling by Means of Functional Petri Nets (J. Wu and E.O. Voit)

Poster N11: 13C-NMR to Monitor Online the Kinetics of Intracellular Metabolite Pools in Response to Heat Stress: Input Data for Modeling the Trehalose Cycle in Saccharomyces cerevisiae
(L. Fonseca, C. Sanchez, J. Wu, H. Santos, and E.O. Voit)

Poster N12: EUCLIS — Towards an Information Infrastructure for the Chronobiology Community (E. Mendoza, R. Santos, R.T. Batista, M.C. del Rosario, M.P. David, C. Clarin, A. Lao, and R. Bernardo)

Poster N13: In Silico Simulation of the Terpenoid Metabolic Network (A.H Hawari, Z.A.M. Hussein, and N.M. Nor)

Poster N14: Heptylprodigiosin Induces Apoptosis in Various Carcinoma Cell Lines and Triggers Death Receptor Pathway in Jurkat T-Cell Leukemia (G. Ranches, A. Rudy, G. Concepcion, and A. Vollmar)

Poster N15: Comparisons of the Performances of Three Methods for Dynamic Sensitivity Computation (F. Shiraishi, K. Hattori, and H. Hirayama)

Poster N16: Parameter Estimation in S-Systems Using the Newton Flow (M. de Paz. R. del Rosario, and E. Mendoza)

Poster N17: An Ant Colony Optimization Algorithm for Parameter Estimation and Network Inference Problems in S-System Models
(P. Zuniga, J. Pasia, H. Adorna, R. del Rosario, and P.C. Naval)

Poster N18: A Biochemical Systems Theory Model of Oxidative Phosphorylation in Halobacterium salinarum (C. Talaue, R. del Rosario, E. Mendoza, D. Oesterhelt)


SPEAKERS

Baltazar Aguda (Ohio State U, USA)
Rhodora Aldemita (PhilRice, Philippines)
Richard Bruskiewich (IRRI, Philippines)
Su-Shing Chen (CAS-MPG Partner Institute of Computational Biology, China)
Ricardo del Rosario (UP Diliman, Philippines and MPI Biochemistry, Germany)
Avner Friedman (Ohio State U, USA)
Eduardo Mendoza (LMU Munich, Germany)
Prospero Naval Jr. (UP Diliman, Philippines)
Dieter Oesterhelt (MPI Biochemistry, Munich)
Masahiro Okamoto (Kyushu U, Japan)
Michael Purugganan (New York University, USA)
Michael Savageau (UC Davis, USA)
John Sheehy (IRRI, Philippines)
Eberhard Voit (Georgia Tech, USA)



ACCEPTED PAPERS


AUTHORS

TITLE

R. Alves, E. Villaprinyo, and A. Sorribas
Semi-Automated Reconstruction of Biological Circuits

I-C Chou, M. Vilela, J.S. Almeida, and E.O. Voit
Computational Identification of Dynamic Biological Networks: Inverse Modeling Approach and
Parameter Estimation Strategies

P. Coelho, A. Salvador, M. Savageau
Global Tolerance of Biochemical Systems and the Design of Moiety-Transfer Cycles

M.P. David, A. Phillips, E. Mendoza, and L. Cardelli
Implementing Brane Calculus

A.W.M. Dress, C. Flamm, G. Fritzsch, S. Grunewald, M. Kruspe, S.J. Prohaska and P.F. Stadler
Noisy: Identification of Problematic Columns in Multiple Sequence Alignments

R. Fasani and M. Savageau
Global Nonlinear Root-Finding Using the Canonical S-system Form

J. Hormiga, J. Vera, I. Frias O. Wolkenhauer, and N.V. Torres-Darias
Growth and Ligninolytic System Production Dynamics of the Phanerochaete chrysosporium Fungus: A Modelling and Optimization Approach

M-F Lee and D. Fernandez
Patent Prosecution in Systems Biology Software

P-K Liu and F-S Wang
Multi-Objective Evolutionary Optimization for Inferring S-System Models of Biological Networks

A. Marin-Sanguino, N.V. Torres, E. Mendoza, and D. Oesterhelt
Model-Driven Optimization Based on Standard Formalisms

J. Pabico, E. Mojica, and J.R. Micor
Design of a Homogeneous Ensemble for Splice-Site Identification in Human Sequences

Z. Qi, G.W. Miller, and E.O. Voit
A Computational Model of Dopamine Metabolism and Parkinson's Disease

E. Rodriguez, R. del Rosario, A. Rudy, A. Vollmar, E. Mendoza
Cephalostatin 1-Induced Apoptosis in Leukemic Cells: From Petri Net Model to Kinetic Model

R. del Rosario, M.T. Echavez, M.T. de Paz, P.C. Zuniga, M.C.R. Bargo, C.O. Talaue, C. Arellano, J.M. Pasia, P.C. Naval, E.O. Voit, E. Mendoza
MADMan: A Benchmarking Framework for Parameter Estimation in Biochemical Systems Theory Models

R. Santos and E. Mendoza
EUCLIS: Towards a Digital Library–Based Common Information Space for Chronobiologists
K. Selvarajoo, M. Helmy, M. Tomita, and M. Tsuchiya
Inferring the Mechanistic Basis for the Dynamic Response of the MyD88-Dependent and –Independent Pathways

A. Sigal, R. Milo, A. Cohen, and U. Alon
Variability Dynamics of Protein Levels in Human Cells
F. Shiraishi and Y. Suzuki
Determination of Bottleneck Enzymes in a Metabolic Reaction System by Dynamic Sensitivity Analysis

A. Sioson and L. Heath
Programming Language Support in Simulating Semantic Multimodal Network Models
A. Sorribas, E. Villaprinyo, and R. Alves
Approximate Kinetic Formalisms for Modeling Metabolic Networks: Does Anything Work?

S. Veflingstad, D. Oesterheld, E.O. Voit
A Mathematical Model of Light-Induced ATP Synthesis in the Archaea Halobacterium salinarum

E. Villaprinyo, R. Alves, A. Sorribas, and A. Salvador
Gene Expression Levels in Saccharomyces cerevisiae Strongly Reflect Energetic Cost Rates of Gene Products

E. Villaprinyo, A. Salvador, R. Alves, A. Sorribas
Energetic Constraints in Adaptive Gene Expression Responses of Yeast Under Environmental Changes

G. Yagil
On the Structural Complexity of DNA Templates and Some Wider Implications


HISTORY

Systems biology has become a buzzword in recent years. Apparently out of nothing, a new field emerged, and within a few short years, many researchers from biology, physics, computer science and other fields of endeavor declared themselves systems biologists. Articles appeared, books were written, educational programs were created. Fueled by the scientific community and the lay media alike, the expectations for systems biology grew sky high. Are they based on fact or fiction? Is systems biology all hype, or are the enormous expectations and predictions warranted?

To get a glimpse of the future, it is useful to look into trends of the past. There we quickly find that the term system biology may be new, but that its roots can easily be traced back to earlier times. As a case in point, the Austrian scientist Karl Ludwig von Bertalanffy must be recognized as a pioneering, visionary systems biologist, as his work from the 1920s to the 1960s contains uncounted discussions of systems in biology that even today are still modern, relevant and interesting. Beginning in the 1980s, easier access to computers empowered growing numbers of researchers to explore systems in biology than ever before and small communities of like-minded systems biologists started to assemble. In 1989 one such group organized the first conference in a series of which the upcoming ICMSB 2008 meeting is the tenth. This inaugural conference in Charleston (U.S.A.) honored the 20th anniversary of Biochemical Systems Theory, one of the first mathematical and computational forays into representing and modeling biological systems in a suitable and general fashion. Reviewing the series of subsequent conferences demonstrates in a nutshell how ideas for analyzing complex systems began to blossom, and we are beginning to fathom how powerful close collaborations between biologists, mathematicians and computer scientists can be and what they may accomplish in the future. The complexity of systems that can be modeled today is easily a magnitude higher than at the first conference, and the speed with which our methods improve suggests that we may soon be able to analyze biological systems with hundreds of components and processes.

So, is systems biology all hype? Certainly not. Systems biology will not solve all biological problems in a few years, and patience an persistence are of the essence. But deep thinkers of the past century have paved the way, giving us the opportunity to explore an uncharted and exciting territory that promises us solutions to some of mankind’s grand challenge problems in biology, medicine, and sustainable stewardship of the environment.

— Eberhard Voit



ADVISORY COMMITTEE

Baltazar Aguda (Ohio State U, USA)
Andreas Dress (PCIB Shanghai, China)
Avner Friedman (Ohio State U, USA)
Michael Savageau (UC Davis, USA)
Masaru Tomita (Keio U, Japan)
Eberhard Voit (Georgia Tech, USA)
Momiao Xiong (Fudan U, China and U Texas, Houston)


PROGRAM COMMITTEE

Program Co-Chairs:
Prospero Naval Jr. (UPD, Philippines) and Li Jin (PICB Shanghai, China)
Program Committee:

Richard Bruskiewich (IRRI, Philippines) Su-Shing Chen (U Florida Gainesville, USA and PICB Shanghai, China) Kwang-Hyun Cho (SNU, Korea) Vincent Daria (UPD, Philippines)
Rudiyanto Gunawan (NUS, Singapore) Lenwood Heath (Virginia Tech, USA) Yongwimon Lenbury (Mahidol U, Thailand) Eduardo Mendoza (UPD, Philippines and LMU Munich, Germany) Christopher Monterola (UPD, Philippines) Felix Muga (ADMU, Philippines) Normah Mohd Noor (UKM, Malaysia)
Masahiro Okamoto (Kyushu U, Japan)
Michael Purugganan (NYU, USA) Ricardo del Rosario (UPD, Philippines and MPI Biochem, Munich)
Rafael Saldaña (AdMU, Philippines) Armindo Salvador (U Coimbra, Portugal) John Sheehy (IRRI, Philippines) Allan Sioson (ADNU, Philippines) Luis Sison (UPD, Philippines) Albert Sorribas (U Lleida, Spain)
Nestor Torres ( U la Laguna, Spain)
Feng-Sheng Wang (National Chung Cheng U, Taiwan)
Louxin Zhang (NUS, Singapore)





ORGANIZING COMMITTEE

Organizing Co-Chairs:

Henry Adorna (UPD, Philippines)
Jimmy Caro (UPD and UP Information Technology Training Center, Philippines)

Organizing Committee:
Caslon Chua (DLSU, Philippines)
Rommel Feria (UPD, Philippines)
Rafael Saldaña (AdMU, Philippines)
Polly Sy (UPD, Philippines)

Organizational Support Group:

Riza Theresa Batista (UPD, Philippines)
Angel Calayag (UPD, Philippines)
Christine Clarin (UPD, Philippines)
Ma. Pamela David (UPD, Philippines)
Michael Echavez (UPD, Philippines)
Eduardo Mendoza (UPD, Philippines and LMU Physics, Germany)
Prospero Naval Jr. (UPD, Philippines)
Ricardo del Rosario (UPD, Philippines and MPI Biochemistry, Germany)
Jan Michael Yap (UPD, Philippines)