Investigating the speedup of systems biology simulation using the SZTAKI Desktop Grid

Systems biology studies the complex interactions of biological and biochemical systems rather than their individual molecular components. System biology simulations can be embarrassingly parallel jobs that have no dependency among individual simulation instances, and thus lend themselves to parallel execution over distributed resources to reduce their overall execution time. One example of such distributed resources is a Desktop Grid for Volunteer Computing that aims to use vast numbers of computers to support scientific applications. The SZTAKI Desktop Grid (SZDG) uses a modified form of the volunteer computing software BOINC to implement an institution-wide Desktop Grid. This paper reports on experiences of porting the SIMAP systems biology ODE simulator to SZDG. A case study using a simulation of the mammalian ErbB signaling pathway reports on significant speedup.

[1]  Giancarlo Mauri,et al.  Stochastic Simulations on a Grid Framework for Parameter Sweep Applications in Biological Models , 2009, 2009 International Workshop on High Performance Computational Systems Biology.

[2]  Stephen John Turner,et al.  Improving simulation through advanced computing techniques: Grid computing and simulation interoperability , 2010, Proceedings of the 2010 Winter Simulation Conference.

[3]  Suresh Marru,et al.  The LEAD Portal: a TeraGrid gateway and application service architecture , 2007, Concurr. Comput. Pract. Exp..

[4]  Ivan Merelli,et al.  Functional Genomics Applications in GRID , 2009 .

[5]  Diego Scardaci,et al.  The GENIUS Grid Portal: Its Architecture, Improvements of Features, and New Implementations about Authentication and Authorization , 2007, 16th IEEE International Workshops on Enabling Technologies: Infrastructure for Collaborative Enterprises (WETICE 2007).

[6]  M. Swain,et al.  A Parallel Plasma Membrane Simulation , 2009, 2009 International Workshop on High Performance Computational Systems Biology.

[7]  Ian T. Foster,et al.  The anatomy of the grid: enabling scalable virtual organizations , 2001, Proceedings First IEEE/ACM International Symposium on Cluster Computing and the Grid.

[8]  David P. Anderson,et al.  SETI@home: an experiment in public-resource computing , 2002, CACM.

[9]  Peter Graf,et al.  Photons, Photosynthesis, and High-Performance Computing: Challenges, Progress, and Promise of Modeling Metabolism in Green Algae , 2008 .

[10]  Gilles Fedak,et al.  Towards Making BOINC and EGEE Interoperable , 2008, 2008 IEEE Fourth International Conference on eScience.

[11]  F. Al-Shamali,et al.  Author Biographies. , 2015, Journal of social work in disability & rehabilitation.

[12]  Richard O. Sinnott,et al.  BioNessieG - A Grid Enabled Biochemical Networks Simulation Environment , 2008, HealthGrid.

[13]  Nazareno Andrade,et al.  Labs of the World, Unite!!! , 2006, Journal of Grid Computing.

[14]  Douglas Thain,et al.  Building Reliable Clients and Services , 2004, The Grid 2, 2nd Edition.

[15]  David P. Anderson,et al.  BOINC: a system for public-resource computing and storage , 2004, Fifth IEEE/ACM International Workshop on Grid Computing.

[16]  Péter Kacsuk,et al.  GenWrapper: A generic wrapper for running legacy applications on desktop grids , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[17]  Francine Berman,et al.  The Virtual Instrument: Support for Grid-Enabled Mcell Simulations , 2004, Int. J. High Perform. Comput. Appl..

[18]  T. Hunter,et al.  Protein kinases and phosphatases: The Yin and Yang of protein phosphorylation and signaling , 1995, Cell.

[19]  Suresh Marru,et al.  The LEAD Portal: a TeraGrid gateway and application service architecture: Research Articles , 2007 .

[20]  Péter Kacsuk,et al.  SZTAKI Desktop Grid (SZDG): A Flexible and Scalable Desktop Grid System , 2009, Journal of Grid Computing.

[21]  A. D. Meglio,et al.  Programming the Grid with gLite , 2006 .

[22]  M. Peitsch,et al.  The application of systems biology to drug discovery. , 2006, Current opinion in chemical biology.

[23]  Monika Heiner,et al.  An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways , 2008, Workshop on Membrane Computing.

[24]  Ian T. Foster,et al.  Globus Toolkit Version 4: Software for Service-Oriented Systems , 2005, Journal of Computer Science and Technology.

[25]  H. Wiley,et al.  An integrated model of epidermal growth factor receptor trafficking and signal transduction. , 2003, Biophysical journal.

[26]  Jarek Nabrzyski,et al.  The Vine Toolkit: A Java Framework for Developing Grid Applications , 2007, PPAM.

[27]  S.J.E. Taylor,et al.  Integrating BOINC with Microsoft Excel: A Case Study , 2007, 2007 29th International Conference on Information Technology Interfaces.

[28]  Andrew A. Chien,et al.  Entropia: architecture and performance of an enterprise desktop grid system , 2003, J. Parallel Distributed Comput..

[29]  Simon J. E. Taylor,et al.  Grid-enabled SIMAP utility: Motivation, integration technology and performance results , 2009 .

[30]  Mark H. Ellisman,et al.  Case Studies on the Use of Workflow Technologies for Scientific Analysis: The Biomedical Informatics Research Network and the Telescience Project , 2007, Workflows for e-Science, Scientific Workflows for Grids.

[31]  D. Lauffenburger,et al.  Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data , 2009, Molecular systems biology.

[32]  R. Barbera.  The GENIUS Grid Portal , 2003 .

[33]  Giancarlo Mauri,et al.  Tau Leaping Stochastic Simulation Method in P Systems , 2006, Workshop on Membrane Computing.

[34]  Oliver E. Sturm,et al.  Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. , 2005, The Biochemical journal.

[35]  Péter Kacsuk,et al.  P‐GRADE portal family for grid infrastructures , 2011, Concurr. Comput. Pract. Exp..

[36]  Kwang-Hyun Cho,et al.  Modelling the dynamics of signalling pathways. , 2008, Essays in biochemistry.

[37]  Gilles Fedak,et al.  EDGeS: Bridging EGEE to BOINC and XtremWeb , 2009, Journal of Grid Computing.