Software-List

Software that I had installed, maintained, and used in my research and teaching

Cloud Computing:

• AWS

• Google Cloud Platform 

• Azure AI Language Studio

Programming Languages:

• R 

  • RStudio

• SQL 

• Python 

  • Jupyter Notebook and JupyterLab

• Fortran 

• PERL

• COLAB Notebooks (R/Python/GitHub)

Bioinformatics scientific workflow management system:

• Galaxy

• NCBI 

  • software tools (e-direct, SRA toolkits, standalone BLAST etc.)

  • NCBI Genome Data Viewer (GDV)

  • NCBI workbench

  • NCBI Cn3D 

• Ensembl 

  • BioMart

  • Variant Effect Predictor (VEP)

  • BioMart 

• 3D Modeling

  • ITasser

  • SwissModel

  • Phyre2

Scientific Software: 

• R Bioconductor library

• Discovery Studio (now called Biovia Chemoinformatics and visualization software)

• AMBER/AmberTools (Molecular Dynamics Software)

• G03 (Quantum chemistry software)

• Gromacs (MD software)

• VMD (MD and visualization) 

• CSD (Chemoinformatics software)

• EMBOSS (Bioinformatics software)

• DOCK, ZDOCK (protein-protein docking software)

• AutoDock, Vina, AutoDockTools (Protein-ligand docking software)

• OpenEye (Chemoinformatics and molecular modeling software)

• FFTW (Fourier transform software)

• NAMD (MD software)

• LAPACK/BLAS (Linear Algebra libraries)

• MPI Libraries (OpenMPI, LAM-MPI, MPICH)

• Swarm (NIH script that automates serial jobs; suitable for HPC cluster)

• Molekel (Molecular Modeling software)

• FreeMat (Matrix algebra software)