Algorithm 755: ADOL-C: a package for the automatic differentiation of algorithms written in C/C++
ACM Transactions on Mathematical Software (TOMS)
Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by homotopy continuation
ACM Transactions on Mathematical Software (TOMS)
Scatter Search: Methodology and Implementations in C
Scatter Search: Methodology and Implementations in C
Parallel coordinates: a tool for visualizing multi-dimensional geometry
VIS '90 Proceedings of the 1st conference on Visualization '90
Kepler: An Extensible System for Design and Execution of Scientific Workflows
SSDBM '04 Proceedings of the 16th International Conference on Scientific and Statistical Database Management
SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers
ACM Transactions on Mathematical Software (TOMS) - Special issue on the Advanced CompuTational Software (ACTS) Collection
Completely Derandomized Self-Adaptation in Evolution Strategies
Evolutionary Computation
The dispersion metric and the CMA evolution strategy
Proceedings of the 8th annual conference on Genetic and evolutionary computation
OPT++: An object-oriented toolkit for nonlinear optimization
ACM Transactions on Mathematical Software (TOMS)
Bioinformatics
Distributed cell biology simulations with e-cell system
LSGRID'04 Proceedings of the First international conference on Life Science Grid
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The High Performance Systems Biology Toolkit (HiPer SBTK) is a collection of simulation and optimization components for metabolic modeling and the means to assemble these components into large parallel processing hierarchies suiting a particular simulation and optimization need. The components come in a variety of different categories: model translation, model simulation, parameter sampling, sensitivity analysis, parameter estimation, and optimization. They can be configured at runtime into hierarchically parallel arrangements to perform nested combinations of simulation characterization tasks with excellent parallel scaling to thousands of processors. We describe the observations that led to the system, the components, and how one can arrange them. We show nearly 90% efficient scaling to over 13,000 processors, and we demonstrate three complex yet typical examples that have run on $\sim$1000 processors and accomplished billions of stiff ordinary differential equation simulations. This work opens the door for the systems biology metabolic modeling community to take effective advantage of large scale high performance computing resources for the first time.