Provided Applications
The following table lists the third-party software which we have installed on our systems. Additional software may be available on request. Please contact Selim Kalayci if you are interested in the availability of software not shown in this list.
Knightrider
| Software | Version | Area | License Type | Software Homepage |
|---|---|---|---|---|
| Gromacs | 4.0.7 | Molecular Dynamics | Free software | Gromacs webpage |
| Mpi4py | 1.3 | MPI bindings for Python | BSD - free | Mpi4py reference |
| Scipy | 0.10.1 |
Scientific Computing extensions for Python |
Open-source | Scipy webpage |
| Numpy | 1.6.1 |
Scientific Computing extensions for Python |
Open-source | Numpy webpage |
| ORCA | 2.9.1 | Quantum Chemistry | Academic License | ORCA webpage |
| NWChem | 6.1 | Quantum Chemistry | Open-source (ECL) | NWchem webpage |
| VASP |
4.6, 5.2 |
Quantum Physics | Licensed | VASP webpage |
| OpenMPI (GNU) | 1.4.3 | MPI development/runtime | Open-source | OpenMPI webpage |
| OpenMPI (Intel) | 1.4.5 | MPI development/runtime | Open-source | OpenMPI webpage |
| gcc,gfortran | 4.1.2 | GNU C/Fortran Compilers | Open-source | GNU Compilers |
| icc, ifort | 12.1.3 | Intel C/Fortran Compilers | Non-commercial v. | Intel Parallel Studio XE 2011 |
| Python | 2.4.3 | Python development env. | PSFL - free | Python official webpage |
| Java | 1.6 | Java development/runtime | Open-source | Oracle Java |
| Torque | 2.5.9 | Resource Manager | Open-source | Torque webpage |
| Moab | 6.0.4 | Batch Scheduler | Commercial | Moab HPC Suite |
Blackpearl
| Software | Version | Area | License Type | Software Homepage |
|---|---|---|---|---|
| MATLAB | 2010b |
Comprehensive package for numerical computation, visualization and programming |
Licensed | Matlab |
| AutoDock | 4.2.3 |
Automated Docking tools |
open-source | Autodock |
| AutoDock Vina | 1.1.2 |
Drug Design, molecular docking |
open-source | Autodock Vina |
| Autogrow | 2.0.4 |
Drug Design |
open-source | Autogrow |
| PyRx | 0.7 |
Virtual Screening software for Computational Drug Discovery |
open-source | PyRx |
| I-TASSER | 2.0 |
Protein Structure and Function Prediction Application Suite |
Free for non-commercial | I-TASSER |
| PyMOL | 1.1 |
Molecular Visualization |
open-source | PyMol |
| R | 2.15.1 |
Statistical Computing and Graphics |
GNU GPL-2 | R Project |
| Bioconductor | 2.10 | Genomic Data Analysis | Open-source | Bioconductor webpage |
| Mpi4py | 1.3 | MPI bindings for Python | BSD - free | Mpi4py reference |
| Scipy | 0.10.1 |
Scientific Computing extensions for Python |
Open-source | Scipy webpage |
| Numpy | 1.6.1 |
Scientific Computing extensions for Python |
Open-source | Numpy webpage |
| VASP | 5.2 | Quantum Physics | Licensed | VASP webpage |
| OpenMPI (GNU) | 1.3.3 | MPI development/runtime | Open-source | OpenMPI webpage |
| OpenMPI (Intel) | 1.4.5 | MPI development/runtime | Open-source | OpenMPI webpage |
| gcc,gfortran | 4.1.2 | GNU C/Fortran Compilers | Open-source | GNU Compilers |
| icc, ifort | 12.1.3 | Intel C/Fortran Compilers | Non-commercial v. | Intel Parallel Studio XE 2011 |
| Python |
2.7.3,
2.4.3(default) |
Python development env | PSFL - free | Python official webpage |
| Java | 1.6 | Java development/runtime | Open-source | Oracle Java |
| Torque | 2.4.5 | Resource Manager | Open-source | Torque Web Site |
| Moab | 5.3.6 | Batch Scheduler | Commercial | Moab HPC Suite |