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Resources software - Life Science
| Name | Version | Description | Topic | Availability | Target user |
|---|---|---|---|---|---|
| Amber | 16 (MARCONI), 22 (M100), 2020 (G100) |
Molecular Dynamics on Biomolecules |
Chemistry, Life Science, Physics | GALILEO100, MARCONI, MARCONI100 | academic |
| Apbs | 3.0.0(G100) |
APBS solves the equations of continuum electrostatics for large biomolecular assemblages. |
Life Science | GALILEO100 | all |
| Autodock-gpu | 4.2.6 |
The AutoDock Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function. |
Life Science | MARCONI100 | all |
| CPMD | 4.3 (G100, M100, MARCONI) |
Plane wave and pseudopotential implementation of Density Functional Theory |
Chemistry, Life Science, Physics | GALILEO100, MARCONI, MARCONI100 | all |
| Ctiffind | 4.1.14 |
CTFFIND is a program for finding CTFs of electron micrographs. |
Life Science | MARCONI100 | all |
| DeePMD | 2.0 (M100) 2018 (MARCONI) |
DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. |
Chemistry, Deep Learning, Life Science, Physics | MARCONI100 | all |
| DL_POLY | 4.08 |
General purpose classical molecular dynamics (MD) simulation software |
Chemistry, Life Science, Physics | MARCONI | academic |
| Dssp | 3.1.4 |
Calculates DSSP (dictionary of protein secondary structure) entries from PDB entries |
Chemistry, Life Science | MARCONI100 | all |
| Fsl | 6.0.5.1 |
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
Bioinformatics, Life Science | GALILEO100 | academic |
| GATK | 4.0(MARCONI) 4.2.0 (G100) |
GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. |
Bioinformatics, Life Science | GALILEO100, MARCONI | academic |
| GROMACS | 2020.6 (MARCONI), 2022 (M100), 2021.3 (G100) |
GROningen Machine for Chemical Simulations - Molecular Dynamics on Parallel Computers |
Chemistry, Life Science, Physics | GALILEO100, MARCONI, MARCONI100 | all |
| Illumina_genome_Mus_musculus | mm10 |
Ready-To-Use Reference Sequences and Annotations |
Life Science | GALILEO100 | academic |
| LAMMPS | 23jun2022 (G100) 29sep2021 (M100) 12dec2018 (MARCONI) |
Molecular Dynamics Simulator (classical dynamics) |
Chemistry, Life Science, Physics | GALILEO100, MARCONI, MARCONI100 | academic |
| NAMD | 2.14 (G100, M100) 2.12 (MARCONI) |
Scalable molecular dynamics for biomolecular modeling |
Chemistry, Life Science | GALILEO100, MARCONI, MARCONI100 | academic |
| Neuron | 7.6.7 |
NEURON simulation environment |
Life Science | MARCONI | all |
| R | 4.2.0 (G100) 3.6.1 (Marconi) 4.0.1 (M100) |
Statistical computing and graphics |
Bioinformatics, Engineering, Life Science, Maths Libraries | GALILEO100, MARCONI, MARCONI100 | all |
| Relion | 3.1.2 |
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM) |
Life Science | MARCONI100 | all |
| Seqtk | 1.3 (G100) |
Seqtk is a fast and lightweight tool |
Life Science | GALILEO100 | academic |
| Sra | 3.0.0(Galileo100) 2.8.1 (Marconi) |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archive and download them locally |
Bioinformatics, Life Science | GALILEO100, MARCONI | all |
| Stacks | 2.59 |
Software pipeline for building loci from short-read sequences |
Life Science | GALILEO100 | all |
| Trimmomatic | 0.39 |
A flexible read trimming tool for Illumina NGS data |
Bioinformatics, Life Science | GALILEO100, MARCONI, MARCONI100 | all |
| Varscan | 2.4.2 (G100, Marconi) |
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. |
Bioinformatics, Life Science | GALILEO100, MARCONI | all |