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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 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