Engineering
| Software | Open Source? (or Licensed) | Description |
| ANSYS (2023-R2) | No Other License: Student License | Industry-standard multiphysics simulation suite for structural, thermal, and fluid analyses. |
| ANSYS Electronics Desktop(2023 [includes ansys HFSS]) | No Other License: Student License | Electromagnetic field simulation platform (HFSS, Maxwell, etc.) used for antenna, RF, and PCB design. |
| Comsol Multiphysics (ver. 5.3a) | No | Comprehensive finite-element analysis (FEA) and multiphysics modeling software. |
| FreeFEM (ver. 4.10) | Yes | Open-source partial differential equation (PDE) solver using the finite element method (FEM). |
| Gmsh (ver. 4.11) | Yes | 3D finite element mesh generator with built-in CAD and post-processing tools. |
| MathWorks MATLAB (ver. R2018b) | No Other License: Student License | High-level technical computing language and environment for numerical analysis and data visualization. |
| Network-simulator NS-2 (ver. 2.34) | Yes | Discrete event network simulator widely used for academic research in network protocols and systems. |
| OpenFoam (ver. 2.4, 5.0) | Yes | C++ toolbox for computational fluid dynamics (CFD) and continuum mechanics simulations. |
| Peridigm (ver. 1.5) | Yes | Open-source code for peridynamic solid mechanics modeling (nonlocal fracture and damage simulation). |
| SalomeMeca (ver. 2015) | Yes | Open-source platform for pre/post-processing and coupling of numerical solvers (based on SALOME + Code_Aster). |
| Scilab (ver. 5.4) | Yes | Open-source numerical computation software similar to MATLAB, for mathematics and engineering applications. |
Computational Chemistry
| Software | Open Source? (or Licensed) | Description |
| CP2K (ver. 6.1) | Yes | Quantum chemistry and solid-state simulation package supporting DFT, MD, and hybrid QM/MM methods. |
| Crystal explorer (ver. 21.3) | Yes | Tool for visualizing and analyzing intermolecular interactions and crystal packing in molecular crystals. |
| CSDS (ver.2022) | No | Cambridge Structural Database System — database and tools for crystallographic structure data analysis. |
| Gaussian (ver. g09_d01) | No | Widely used ab initio and DFT electronic structure program for molecular systems. |
| GROMACS (ver. 2018-2, 2021, 2022.3) | Yes | High-performance molecular dynamics (MD) package for biomolecular and materials simulation. |
| Gulp (ver.6.0, 6.1.2) | Yes | General Utility Lattice Program — atomistic simulations for solids, surfaces, and defects. |
| Jmol (ver.14.30.2) | Yes | Open-source Java viewer for chemical structures in 3D, used in research and teaching. |
| Mopac (ver.2016) | Yes | Semi-empirical quantum chemistry program for molecular orbital calculations. |
| NAMD (ver.2.14-multicore-cuda) | Yes | Parallel molecular dynamics engine optimized for large biomolecular systems. |
| NWChem(ver. 7.0.2-conda) | Yes | Open-source computational chemistry package supporting quantum and molecular dynamics methods. |
| ORCA (ver.4.2.1, 5.0.1) | No | Quantum chemistry software with DFT, MP2, and coupled-cluster methods; widely used in spectroscopy. |
| Plumed (ver. 2.5.0, 2.7.2) | Yes | Open-source plugin for enhanced sampling, free-energy calculations, and analysis in MD simulations. |
| Pycharm(ver. 2020.2.3) | Free for basic/ Pro features are paid subscription Other License: Student License | Python IDE (not chemistry software itself, but used for scripting scientific workflows). |
| Pymol (ver. 2.3.0, 2.5.0) | Mixed, Paid subscription license | Molecular visualization and analysis tool for structural biology and computational chemistry. |
| Schrodinger (ver.2018-4, 2022-1, 2022-4, 2023-2) | No | Comprehensive molecular modeling, docking, and quantum chemistry software package. |
| VMD (ver.1.9.3 ) | Yes | Visualization and analysis tool for molecular dynamics simulations, often paired with NAMD and GROMACS. |
Bioinformatics/Genomics
| Software | Open Source? (or Licensed) | Description |
| Bcftools (ver. 1.10.2) | Yes | Utilities for manipulating variant-calls in VCF/BCF formats (filtering, indexing, merging) |
| Bcl2fastq (ver. 1.8.4, 2.20.0) | Yes | Tool converting Illumina base-call files (BCL) to FASTQ format |
| Bedops (ver. 2.4.39) | Yes | High-performance command-line utilities for set operations on genomic interval files |
| Bedtools (ver. 2.29.2) | Yes | Suite for “genome arithmetic”: intersecting, merging, subtracting genomic interval files (BED/VCF etc) |
| Bowtie2 (ver. 2.4.1, 2.4.2) | Yes | Ultrafast and memory-efficient aligner of sequencing reads (supports gaps, local/paired-end) |
| Bracken (ver. 2.5) | Yes | Bayesian re‐estimation of species abundances from Kraken-classified reads |
| Chopper (ver. 0.3.0) | Yes | Long-read quality trimming / filtering tool for genome sequencing |
| Cutadapt (ver. 3.5) | Yes | Tool to remove adapter sequences and perform trimming/filtering on reads |
| DeepVariant (ver. 1.0.0) | Yes | Deep-learning based variant caller, uses TensorFlow models for calling SNPs/indels |
| Diamond (ver. 2.0.3) | Yes | Fast sequence aligner (protein/translated search) optimized for large-scale shotgun/metagenomic data |
| Dorado (ver. 0.1.1) | Yes | – |
| Drop (ver. 1.1.4) | – | – |
| Fastp (ver. 0.21.0) | Yes | Ultra-fast all-in-one FASTQ preprocessor: quality filtering, trimming, adapter removal |
| Fastqc (ver. 0.11.9) | Yes | Quality-control tool for high-throughput sequencing data (FASTQ/BAM) generating QC reports |
| GATK4 (ver. 4.1.8.1) | Yes | Toolkit for variant discovery/processing (SNPs, indels) and sequence-data pre-/post-processing |
| HTseq (ver. 0.11.3) | Yes | Python library and tools for processing high-throughput sequencing data (counting, expression analysis) |
| HTSlib (ver. 1.11) | Yes | C library for reading/writing high-throughput sequencing alignment formats (SAM/BAM/CRAM) |
| Humann2 (ver. 2.81) | Yes | Pipeline for functional profiling of microbial communities from metagenomic shotgun data (gene families/pathways) |
| Kraken2 (ver. 2.0.9-beta) | Yes | Ultra‐fast taxonomic classifier for metagenomic reads using k-mer/LCA methods |
| Lofreq (ver. 2.1.5) | Yes | Ultra-sensitive variant caller for low-frequency variants in viral/amplicon sequencing |
| Mafft (ver. 7.471) | Yes | Multiple sequence alignment tool for nucleotide/protein sequences — high speed/accuracy |
| Medaka (ver. 1.7.3) | Yes | Consensus & variant calling tool for Oxford Nanopore Technologies long-reads |
| Metaphlan2 (ver. 2.6.0, 2.7.7) | Yes | Tool for profiling microbial community composition (species/strain) from metagenomic data |
| Metaphlan3 (ver. 3.0.2) | Yes | Updated version of MetaPhlAn pipeline for metagenomic profiling |
| Metaphlan4 (ver. 4.0.6) | Yes | Next-generation of MetaPhlAn suite with updated databases/algorithms |
| Nanofilt (ver. 2.8.0) | Yes | Filtering tool for long-read sequencing data (Nanopore/PacBio) based on quality/length |
| Plink (ver. 1.90b6.21) | Yes | Whole-genome association analysis toolset (GWAS, population genetics) |
| Raven (ver. 1.8.1) | Yes | Genome assembler for long-reads (Nanopore/PacBio), efficient in time/memory |
| Saige (ver. 0.44.6.5) | Yes | Scalable mixed-model association tests for large biobank data (GWAS) |
| Samtools (ver. 1.9, 1.10) | Yes | Toolkit for processing SAM/BAM/CRAM alignment files: sorting, indexing, viewing, variant calling |
| SRA Toolkit (ver. 3.0.1) | Yes | Toolkit for accessing and retrieving sequencing data from NCBI’s Sequence Read Archive |
| STAR (vera2.7.5c) | Yes | Spliced-transcript aligner, ultra-fast alignment of RNA-seq reads (splice-aware) |
| Strelka2 (ver. 2.9.10) | Yes | Small-variant caller (SNPs/indels) optimized for tumour/normal and germline workflows |
| Trapd | Yes | A burden-testing tool for rare variants, designed to compare case variant burdens against publicly-available summary-level control data |
| Trimmomatic (ver. 0.39) | Yes | Flexible readtrimming tool for Illumina sequencing: adapters, quality, length filters |
| VEP (ver. 101) | Yes | Variant Effect Predictor: annotates effects of genomic variants (genes, transcripts, regulatory) |
| Varscan (ver. 2.4.4) | Yes | Variant caller for low-frequency variants, indels and copy-number in sequencing data |
| Vcftools (ver. 0.1.17) | Yes | Tools for manipulating and analysing VCF files (filtering, summarising, annotation) |
| Vep (ver. 101, 104.3, 108.2) | Yes | Variant Effect Predictor: annotates effects of genomic variants (genes, transcripts, regulatory) |
| Vsearch (ver. 2.15.0) | Yes | Open-source alternative to USEARCH: clustering, dereplication, chimera detection of sequences |
Other
| Software | Open Source? (or Licensed) | Description |
| Agisoft PhotoScan | No | Photogrammetry software for 3D reconstruction from imagery. |
| Apptainer (ver. 1.1.6) | Yes | A container/virtualisation runtime focused on reproducibility & HPC usage. |
| Blender (ver. 2.7) | Yes | Open-source 3D modelling, animation, rendering tool. |
| Git (ver. 1.8.3.1. 2.41.0) | Yes | Distributed version control system widely used for software development. |
| Hashcat | Yes | High-performance password recovery / hash-cracking tool. |
| R (ver. 3.4.0, 3.5.3, 3.6.3,4.1.0) | Yes | Free software environment for statistical computing and graphics. |
| Singularity (ver. 3.2.1, 3.4.1, 3.11.4) | Yes | Containerisation platform designed for HPC / reproducible compute environments. |
Programming Tools and Compilers
| Software | Open Source? (or Licensed) | Description |
| Conda/Anaconda (ver. 4.7.5, 4.7.10, 4.13.0, 23.1.0) | Free and Paid version | Cross-platform package and environment manager (especially for Python/R), and distribution of scientific packages. |
| CUDA Toolkit (ver. 8.0, 9.2, 10.1, 11.4), cuDNN | Proprietary | GPU-accelerated development toolkit: libraries, compilers, runtimes for heterogeneous/parallel computing on NVIDIA GPUs. |
| GNU Compiler Collection (ver. 4.8.5, 5.4.0,7.3.0, 8.3.0, 11.2) | Yes | The standard free compiler suite for C, C++, Fortran, and other languages — widely used in open-source and research. |
| Intel Parallel Studio (ver. 2015)/ IntelMPI (ver. 4.0.3) | Proprietary | Commercial high-performance development suite with Intel’s compilers, libraries, MPI, threading tools for parallel computing. |
| Jaer 1.8.1 | Yes | Software likely related to event-based vision (Dynamic Vision Sensors) – used in certain research contexts. |
| OpenACC (3.1) | Yes | Compiler directive standard for parallel computing targeting GPUs or accelerators (e.g., “#pragma acc”). |
| OpenCL (3.0) | Yes | Framework for writing programs that execute across heterogeneous platforms (CPUs, GPUs, FPGAs etc). |
| OpenCV (4.5) | Yes | Open-source computer vision and machine learning library — real-time image/video processing across multiple languages/platforms. |
| OpenMPI (ver. 1.10.7, 3.1.1, 4.0.5, 4.1.1) | Yes | High-performance Message Passing Interface library for parallel/distributed computing (clusters, supercomputers). |
| Mamba (1.4.4) | Yes | Fast drop-in alternative to Conda for package/environment management, optimized performance for dependency resolution. |
| Perl (ver. 5) | Yes | High-level scripting language, often used for system-administration, text processing, rapid prototyping. |
| Python (ver. 2.7, 3.6) | Yes | Widely-used high-level programming language in research, science, engineering, scripting, data-analysis. |