A collection of software written by researchers at the Division of Scientific Computing

• BENCHOP - The BENCHmarking project in Option Pricing. Six benchmark problems in computational finance and a collection of solution codes employing various numerical methods.
• Chunks and Tasks. Open source library for the parallelization of dynamic, hierarchical algorithms
• cnF2freq. Codebase for computing genotype and haplotype probabilities given a pedigree and (possibly incomplete) genotypes based on an interatively optimized Hidden Markov Model.
• Cogito: Software framework for parallel numerical PDE solvers on composite grids. An object-based code framework for the construction of parallel numerical solvers for PDEs on block-structured grids
• Ergo. An open source (GPL) program for large-scale electronic structure calculations
• GenFoo. A general Fokker-Planck solver
• Mesh Refinement Routines. Matlab code for refinement of grids composed of triangles/tetrahedra and quadrilaterals/bricks
• MOLNs. Create and manage a cloud computing platform for scalable, distributed experiments in computational systems biology using Ipython Parallel/Notebook. Also provides FEniCS/Dolfin as a service.
• PyURDME. Python modeling and simulation API for stochastic reaction-diffusion problems
• Radial Basis Function Interpolation: RBF-QR. A Matlab implementation of the RBF-QR method for radial basis function interpolation
• siminf. An R-package with the ability to simulate arbitrary models of epidemics using temporal contact data
• stenglib. A collection of Matlab packages for daily use
• StochSS. Stochastic Simulation as a service, in collaboration with the Petzold Lab at UCSB. Modeling and simulation of biochemical networks on multiple modeling levels from ODEs to spatial stochastic solvers.
• SuperGlue. A library for data-dependency driven task parallelism
• URDME. Stochastic simulation of spatial mesoscopic models of reaction-diffusion systems on unstructured meshes
• Wave propagation tools
• Various tools

For employees: short overview of open source code licenses