Scalable Software Services for Life Science
GROMACS is a highly-optimized and one of the fastest packages for Molecular Dynamics simulations. It includes a suite of over 80 analysis tools for raw data post-processing.
Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.
DISCRETE is a package devised to perform Discrete Molecular Dynamics (DMD) simulations. In such simulations the particles are considered to move with constant velocity until a collision occurs thus drastically saving on computation time compared to standard MD protocols.
Ergo is a linear scaling program for Hartree-Fock and Kohn-Sham density functional theory electronic structure calculations using Gaussian basis functions.
MUSIC is a C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.
XMIPP is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.

Applications

ScalaLife Pilot Applications

Development of scalable techniques and provision of expert user support within the ScalaLife project is currently done with three "pilot" applications. The latest versions of the software packages can be obtained directly from the ScalaLife downloads section.

DISCRETE is a new software being developed at IRB. Pilot Beta-versions of the program are distributed in different laboratories. The program will be distributed as free software to the scientific community. We plan to distribute first production versions of DISCRETE with current versions of GROMACS to facilitate its use in the community. Local access to coarse-grained DISCRETE will be provided within the FlexServ utility. DISCRETE use case scenarios.

DALTON is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. DALTON use case scenarios.

GROMACS is a versatile package to perform Molecular Dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS use case scenarios.

ERGO is a quantum chemistry program for large-scale self-consistent field (SCF) calculations using the Hartree-Fock and Kohn-Sham density functional theory methods, with emphasis on linear scaling algorithms.

MUSIC is a C++ library which allows parallel applications, especially neuronal network simulators, to exchange data during run-time. THe librarry allows spike events and continuous time series to be communicated between applications in a cluster computer. The typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.

XMIPP is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.

 

Other Software

In future, the project may include other Life Science software packages for development and user support. As a proponent of open source software and standards, the ScalaLife proejct requires that the core applications adhere to the license requirements.