Software

Package Version Application Area Official Website
abyss 1.5.1 Bioinformatics http://www.bcgsc.ca/platform/bioingo/software/abyss 
abyss 1.5.2 Bioinformatics http://www.bcgsc.ca/platform/bioingo/software/abyss
anuga 1.3.0-beta Hydrological modelling https://anuga.anu.edu.au
arpack-ng 3.1.5 Linear Algebra http://forge.scilab.org/index.php/p/arpack-ng
atlas 3.10.1 Linear Algebra http://math-atlas.sourceforge.net 
blas 1 Linear Algebra http://www.netlib.org/blas
boost 1.55 C++ library http://www.boost.org/users/download
cuda 5.5 / 6.5 / 7.0 GPU Computing https://developer.nvidia.com/category/zone/cuda-zone
fftw 3.3.4 Fourier Transform http://www.fftw.org
gcc 4.8.2 Compiler Suite http://gcc.gnu.org
glpk 4.54 Linear Programming http://www.gnu.org/software/glpk/
gnuplot 4.6.5 Graphic Utility http://www.gnuplot.info
grads 2.1.a2 Visuzalization earth science data http://cola.gmu.edu/grads
gromacs 5.0.2 Molecular dynamic http://www.gromacs.org
hdf5 1.8.12 Portable data format http://www.hdfgroup.org/HDF5
lapack 3.5.0 Linear Algebra http://www.netlib.org/lapack
mpc 1.0.2 Multi Precision C http://www.multiprecision.org/
meme 3.5.4 bioinformatics http://meme-suite.org
namd

2.10b1-multicore-cuda
2.10-multicore-cuda
2.10-tcp

Molecular dynamic http://ks.uiuc.edu/research/namd
netcdf

4.3.2
fortran-4.2

Machine-independent Data Format http://www.unidata.ucar.edu/software/netcdf/
octave 3.8.1 Data analysis and visualization http://www.gnu.org/software/octave
openmpi 1.6.5 MPI http://www.open-mpi.org
openmpi 1.7.5 MPI http://www.open-mpi.org
phase0

2014.01
2014.03

Material simulation https://azuma.nims.go.jp/software/phase
pcre 8.35 Regular Expression http://www.pcre.org
python 2.7.6 General purpose programming language http://www.python.org
qhull 2012.1 Computational geometry http://www.qhull.org
qrupdate 1.1.2 Linear Algebra http://qrupdate.sourceforge.net
quantum espresso 5.1 Quantum material simulation http://www.quantum-espresso.org
R 3.1.0 Statistical computing language http://www.r-project.org
Ray 2.3.1 Bioinformatics http://www.sourceforge.net/denovoassembler
RegCM 4.0 Climate Modelling http://gforge.ictp.it/gf/project/regcm
SOAPdenovo 2.04 Bioinformatics http://soap.genomics.org.cn/soapdenovo.html
SuiteSparse 4.2.1 Suite Sparce Matrix Softw http://www.cise.ufl.edu/research/sparse/SuiteSparse/
Velvet 1.2.10 Bioinformatics http://www.ebi.ac.uk/~zerbino/velvet