joint with
2nd International Workshop on High Performance Computational
Systems Biology (HiBi 2010)
September 30 - October 1, 2010, Twente, The Netherlands
Co-locating with
5th International Conference on Graph Transformation (ICGT 2010)
, 29 September - 1 October, 2010
17th Annual workshop on Software Model Checking (SPIN 2010),
27 September - 29 September, 2010
9:15 - 9:30 Workshop opening INVITED TALK 9:30 - 10:30 Parallel SAT Solving
Youssef Hamadi (Microsoft Research Cambridge)
10:30 - 11:00 Coffee Break SHARED-MEMORY PARALLEL MODEL CHECKING 11:00 - 11:30 DiVinE: Parallel Distributed Model Checker (Tool paper)
11:30 - 12:00 A General Lock-Free Algorithm for Parallel State Space Construction
12:00 - 12:30 GPU-PRISM: An Extension of PRISM for General Purpose
Graphics Processing Units (Tool paper)
12:30 - 13:30 Lunch PARALLEL COMPUTING IN SYSTEMS BIOLOGY (1) 13:30 - 14:00 Enhancing the Scalability of Simulations by Embracing Multiple
Levels of Parallelization
14:00 - 14:30 Fast Parallel Markov Clustering in Bioinformatics using Massively
Parallel Graphics Processing Unit Computing
14:30 - 15:00 HMMlib: A C++ Library for General Hidden Markov Models
Exploiting Modern CPUs
15:00 - 15:30 Coffee Break DISTRIBUTED VERIFICATION METHODS 15:30 - 16:00 Industrial Strength Distributed Explicit State Model Checking
16:00 - 16:30 A BSP Algorithm for the State Space Construction of Security Protocols
16:30 - 17:00 Three High Performance Architectures in the Parallel Approximate Probabilistic Model Checking Boat
INVITED TALK 9:30 - 10:30 Problem Solving by Inverse Methods in Systems Biology
Peter Schuster (Institute for Theoretical Chemistry)
10:30 - 11:00 Coffee Break PARAMETER-DEPENDENT ANALYSIS 11:00 - 11:30 Parallel computing algorithms for reverse-engineering and analysis
of genome-wide gene regulatory networks from
gene expression profiles
11:30 - 12:00 Parameter Scanning by Parallel Model Checking with Applications
to Systems and Synthetic Biology
12:00 - 12:30 Predicting the effects of parameters changes in stochastic models
through parallel synthetic experiments and multivariate analysis
12:30 - 13:30 Lunch PARALLEL COMPUTING IN SYSTEMS BIOLOGY (2) 13:30 - 14:00 Parallel particle-based reaction diffusion: a GPU implementation
14:00 - 14:30 Using the GPU and Multi-Core CPU to Generate a 3D Oviduct Through
Feature Extraction from Histology Slides
14:30 - 15:00 Implementation of Smith-Waterman algorithm in OpenCL for GPUs
15:00 - 15:10 Workshop Closing