Software

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
Bowtie 1.0.1 short DNA sequences aligner Free software Bowtie
Bowtie2 2.2.2 Sequence read aligner Free software Bowtie2
Trinity 2014-04-23 De novo reconstruction of transcriptomes Free software Trinity
SAMtools 0.1.19 Sequence Alignment/Map Free software SAMtools
VarScan 2.3.6 Variant detection in sequencing data Free software VarScan
RSEM 1.2.12 RNA-Seq by Expectation-Maximization Free software RSEM
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