There are three kind of softwares, the supercomputing software is used through a terminal, with a queue system, you can read the manual at the Picasso documentation section.

The virtual software can be accessed through a virtual desktop, after doing login in this web page you will see a new menu item to access your virtual desktop.

To use the web software you don´t need to have an account, you can access it clicking here.

Annotation

annotsvv3.1Terminal

brakerv2.1.5Terminal

dfast_corev1.2.18Terminal

eggnog-mapperv2.1.6Terminal

genotev0.5b1Terminal

interproscanv5.44.79v5.54.87TerminalAnotación de proteinas

lionv171220Terminal

prokkav1.12v1.14.5Terminal

scbi_variantsvcurrentTerminalhtml generation

sma3v2v2.1v2.1_perlv2.2Terminal

snpeffv4.2v4.3v4.4v5eTerminal

unifamv1.0.0Terminal

vepv95.2Terminal

Chemistry

ABCClusterv2.1Terminal

fhi-aimsv150518v150518_impiv151012v151012_vibv211217ManualTerminalFritz Haber Institute ab initio molecular simulations is an accurate all-electron, full-potential electronic structure code package for computational materials science

gatev8.2v9.1_gcc7.5.0Terminal

molcasv7.8v7.8_ompv8.0v8.0gpuv8.01(default)v8.2v8.2_gfortv8.2_modifv8.2_mpi_modifv8.4v8.4_2022v8.4_amd_intelv8.4_completov8.4_nv8.4betav8.4beta_intelvopen_22.6_gcc12.2.0vopen_22.6_mklManualTerminalMolcas allow an accurate ab initio treatment of very general electronic structure problems for molecular systems

moldenv5.1v7.1Terminal

quantumespressov5.1v6.5_intelv6.8_gccv7.1_aocc_OMPv7.1_gpuManualTerminalQuantum Espresso is a suite for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

siestav4.1.5v4.1.5_omp_mpiv4.1.5_omp_mpi_gcc11v4.1.5_omp_mpi_gcc11_testTerminalperforms electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids

topmodv09Terminal

Functional analysis

Ingenuity-PathwayvlastManualWebModel, analyze, and understand the complex biological and chemical systems at the core of life science research with IPA

home_biov0922Terminal

humann2v0.11.2Terminal

Gene expression

R-Bioconductorv3.5.1v3.6.0v4.0.2v4.1.0(default)v4.1.0_sinv4.1.2_visv4.1.2_vis_sinv4.2.1_visTerminalR statistical language

controlfreecv11.6Terminal

mirdeep2v2Terminal

Genetic variations

TEtoolkitv160206Terminal

bayescanv2.1Terminal

cambav012312Terminal

cnvkitv0.9.9Terminal

deepvariantv1.2.0Terminal

dellyv0.7.2v080115Terminal

encorev20121120Terminal

freebayesv1.3.6Terminal

gappav0.8.1Terminal

gatkv3.1v3.5v3.6.0v4.1.2.0v4.2.2.0(default)Terminal

lamplinkv1.11Terminal

mrbayesv3.2.3Terminal

mutectv20141110Terminal

phenolyzerv0.1.8Terminal

pilonv1.23Terminal

pradav1.2Terminal

repenrichv2_20170822v20150918Use onlineTerminalRepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

vcflibv20150325Terminal

Genome assembly

abyssv1.3.5v2.3.5Terminal

allpaths-lgv52488Terminal

amosv3.1.0Terminal

bwav0.5.9v0.7.5av0.7.12(default)Terminal

copev1.1.3v1.2.5_gccTerminal

cortexv1.0.5.21Terminal

discovarv52488Terminal

eulerv120408Terminal

falconv20160425Terminal

finisherscv2.0.29Terminal

gam-ngsv20131210Terminal

garmv0.7.3Terminal

kalignv2Terminal

kmergeniev1.7051Terminal

masurcav1.9.5v3.2.4v4.0.9Terminal

miniav1.4683Terminal

minimap2v2.9Terminal

mspacv261120Terminal

mummerv3.22v4rc1Terminal

newblerv2.8Terminal

oasesv0.2.08(default)v0.2.08_vel1.2.08TerminalDe novo transcriptome assembler for very short reads

operamsv0.8.3Terminal

pb_assemblyv20210110TerminalPAcbio assembly

platanusv1.2.1v1.2.4Terminal

raconv1.5.0Terminal

ragtagv2.1.0Terminal

rayv1.7.0v2.3.1Terminal

roche454v2.8v2.9(default)Terminal

samstatv1.5.1(default)v1.09Terminal

scarpav0.22Terminal

scipiov1.4Terminal

sgav0.9.43v0.10.14(default)v0.10.14_10kTerminal

smrtanalysisv3.0.2Terminal

soap3dpv2.3.169Terminal

soapdenovo_transv1.03TerminalA de novo transcriptome assembler designed specifically for RNA-Seq

spadesv3.5.0v3.7.1v3.10.1v3.14v3.15.4Terminal

sspacev3.0Terminal

stringtiev1.3.1cv1.3.3bv2.2.1Terminal

suttav1.0Terminal

tophatv1.4.1v2.0.4v2.0.8bv2.0.10v2.0.13v2.1.0Terminal

wenganv0.2Terminal

Genomics tools

agentv2018Terminal

augustusv3.1v3.2.3v3.3Terminal

bactopiav20220127Terminal

bamutilv20190625Terminal

baypassv2.1Terminal

bcl2fastqv2.17.1.14v2.20(default)v2.20_gcc7Terminal

bedopsv2.4.39v2.4.40Terminal

biocodev1.0Terminal

centrifugev1.0.3v1.0.4Terminal

circexplorer2v2.3.8Terminal

colonyv2.0.6.5Terminal

exome_depthv1.1.10Terminal

expansionhunterv5.0.0TerminalThere are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat

fgbiov1.4.0Terminal

genometoolsv1.3.5v1.5.9Terminal

genotoolboxv20131009TerminalGenoToolBox is a collection of scripts used to manipulate genomic data

glimmer-mgv0.3.1Terminal

gtdb-tkv1.7.0Terminal

krakenv2.1.2Terminal

kronav2.4Terminal

map-rseqv1.2.1Terminal

meganv5Terminal

memev5.1.1Terminal

metaeukv2020Terminal

metamosv1.2Terminal

mmseqsv20220324Terminal

mrepsv2.5Terminal

multiqcv1.6v1.11v1.11_testv1.13aTerminal

musclev2010Terminal

prankv270417Terminal

predicthaplov0.4Terminal

pyaniv0.2.10Terminal

pyphillinv20220118Terminal

qapv1.2.1Terminal

qurev0.99971Terminal

repeatmaskerv4.1.0Terminal

repeatoirev20131009Terminal

rmblastv2.9.0Terminal

sambambav0.6.6v0.8.1Terminal

seqbusterv3.1Terminal

seqclusterv20150226Terminal

shorahv0.82Terminal

snippyv040419Terminal

sparccv050319Terminal

tombov1.5Terminal

viquasv1.3Terminal

yampv0.9.5.3Terminal

Image processing

blenderv2.74Terminal

fijiv1.48iTerminal

fslv5.0.10Terminal

icyv1.4.3.5Terminal

imafish_mlv20160311Terminal

imagejv1.47Terminal

imagemagickv6.9.0-4Terminal

instant-ngpv170522Terminal

jasperv2.0.14Terminal

meshroomv2021.1Terminal

povv3.7Terminal

webpv0.4.0Terminal

Libs

anacondav11-2020v39.4.9.2v2021.05versionTerminal

armadillov6.700.6Terminal

beaglev2.1Terminal

berkely-dbv4.3.29v6.2.23Terminal

bisonv3.0.2Terminal

boostv1.36v1.44v1.55v1.64Terminal

byaccv1.9Terminal

bzip2v1.0.6Terminal

cudav4v5v6Terminal

fftwv2.1.5_intel_mpiv3.3.3v3.3.3_intelv3.3.4v3.3.7_intel_mpiv3.3.10_ompi4_gcc7.5v3.3.10_ompi4_gcc11Terminalfast FFT compiled with intel compilers

filezillav3.29.0Terminal

flexv2.5.3Terminal

foam-extendv1.6v3.1v3.1_con1.6.5TerminalThe goal of this project is to open the OpenFOAM CFD toolbox to community contributed extensions.

freetypev2.5.3Terminal

gapv4r5Terminal

geant4v10.5v10.7.2_gcc7.5.0ManualTerminaltoolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science

gem5v220422Terminal

glewv1.12.0Terminal

glibv2.0Terminal

globalarraysv5.8.1Terminal

glpk_oldv4.65Terminal

gmpv6.1.2v6.1.2_gcc_4.9.1Terminal

gslv1.16v2.1v2.1_intelTerminal

h5pypv1.10.6.1a0Terminal

hdf5v1.8.12(default)v1.8.12_gccv1.8.12_gcc4v1.8.12_gcc4_mpiv1.8.12_intel_f_mpiv1.10.1_intelv1.10.5_gcc7.5.0_mpi1v1.10.5_mpichv1.10.5_mpich_gcc4v1.10.5_mpich_gcc7v1.12.0v1.12.0_gcc11v1.12.0_intelmpiv1.12.1_api16_gcc7.5.0_ompi3v1.12.1_api16_gcc7.5.0_ompi4v1.12.1_exav1.12.1_exa_cmakev1.12.1_gcc7.5.0_mpi1v1.12.1_gcc7.5.0_mpi3v1.12.1_gcc7.5.0_mpi3_nv1.12.1_gcc7.5.0_mpi4v1.12.1_gcc11v1.12.1_intel21TerminalHDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections

htslibv1.14v1.16Terminal

lapackv3.4.2(default)v3.5.0v3.6.0v3.8.0v3.9.1v3.10.0_gcc7.5.0vmal_3.8.0TerminalLinear Algebra PACKage

libatlasv3.10.1Terminal

libcurlv7.50.3Terminal

libdbv4.6Terminal

libgdalv2.1.3Terminal

libgit2v161220Terminal

libpcrev8.38v8.41Terminal

libpngv15Terminal

libyamlv0.1.4Terminal

libzmqv4.3.4Terminal

mavenv3.2.1v3.8.1Terminal

metisv5.1.0_gcc7.5.0v5.1.0_gcc11v5.1.0_intel2013v5.1.0_intel2021ManualTerminalSerial Graph Partitioning and Fill-reducing Matrix Ordering

mpfrv3.1.5Terminal

netCDFv1.12.1_pnet_intelv4.3.0v4.4.0_gccv4.4.2_gcc_fortranv4.4.2_gcc_fortran_mpiv4.7.0_intelv4.7.2_gcc4v4.7.2_gcc7v4.7.2_gcc9v4.8.0_gcc7v4.8.0_gcc7.5.0_mpiv4.8.0_gcc7.5.0_mpi3v4.8.0_gcc11v4.8.0_intelmpiv4.8.1_exav4.8.1_gcc7.5.0_mpi3v4.8.1_gcc7.5.0_ompi3_hdf51.12.1Api16v4.8.1_gcc7.5.0_ompi4_hdf51.12.1Api16v4.8.1_gcc11v4.8.1_intel214v4.8.1_intel214_cv4.8.1_intel214_c_fortranv4.9.0_c_fortran_gcc12.2.0_mpi4.1.4Use onlineTerminalNetwork Common Data Form (NetCDF) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data

openblasv0.3.21Terminal

opencvv2Terminal

openfoamv2.2.0v2.2.0_unpatchedv2.3.0v2.3.1v4_v1706Use onlineTerminalfluid dynamcis (CFD) software package

platypusv1.0.4Terminal

proj4v4.9.3Terminal

pytorchv0.4.1v1.11.0Terminal

rootv6.16v6.24.06_gcc7.5.0ManualTerminalA modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage

scalapackv2.0.2(default)v2.0.2_gccv2.0.2_intelv2.1.0_gcc7.5.0v2.1.0_gcc11v2.1.0_gcc11_nTerminalScalable Linear Algebra PACKage

sparsehashv2.0.2v2.0.3Terminal

swigv3.0.8Terminal

tauv2.30.1Terminal

tensorflowv0.9v1.12v1.15.5v2.0.0v2.3.0v2.3.0_pytorch_171v2.3.0_wandb_lastv2.4.0v2.5.0v2.5.0_libsv2.8.0v2.9.1v2.10.0Terminalopencv with tensorflow 2.2

wxv3.0.3Terminal

zlibv1.2.8v1.2.11Terminal

Molecular simulation

amberv12v12mpiv16vcudaTerminal

cpmdv3.13.2v3.15.3Terminal

gromacsv2022.2v2022.3_impiTerminal

lammpsv1feb14(default)Terminal

mdynamixv5.2.6Terminal

namdv2.8plumedv2.9v2.13b1vnb_2017_07_24Terminal

vaspv4.6v5.2v5.3.3(default)v5.3.3_vtstv5.3.5_vtstv5.4.1v5.4.1.05Feb16v5.4.1.05Feb16_testv5.4.1gnuTerminalVASP (Vienna Ab initio Simulation Package) is a program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics

Mpi

impiv4.1.0.024Terminal

openmpi_aoccv4.1.1Terminal

openmpi_gccv1.10.6_gcc7.5.0v3.1.6_gcc7.5.0v3.1.6_gcc12.2.0_ucxv4.1.1_exav4.1.1_gcc7.5.0(default)v4.1.1_gcc11.1.0v4.1.2_gcc7.5.0v4.1.4_gcc9.5.0_cudav4.1.4_gcc12.2.0_ucxTerminalMPI library

openmpi_intelv1.6.1v4.1.1Terminal

ucxv1.13.1Terminal

Music tools

ffmpegv2013.05.15Terminal

flacv1.2.1Terminal

id3v0.15Terminal

lilypondv2.16.2Terminal

soxv14.4.1Terminal

timidityv2.14.0Terminal

uuid-runtimev2.17.2-9Terminaluuid generating tool

Oceanography

FVCOMv3.1.6v3.2.0Terminal

delft3dv7545Terminal

hermesv1.0.2v2.1.2Terminal

ncov5.0.3Terminal

Optimizers

amplv20200501v20200501_user_licv20210425v20220424TerminalAMPL is an algebraic modeling system used for optimization.

coin-orv1.7.4Terminal

ipoptv3.12.8Terminal

Physics

CST_Studiov2022Terminal

basiliskv130319Terminal

pandapowerv2.6.0v2.6.0_nTerminal

parallel_bilbyv1.1.3TerminalBayesian inference library, primarily for inference of compact binary coalescence events in interferometric data

Programming languages

Rv3.5.1v3.6.0v4.0.2v4.1.0(default)v4.1.0_sinv4.1.2_visv4.1.2_vis_sinv4.2.1_visTerminal

aoccv3.2.0Terminal

bioperlv1.4v1.6.1(default)v1.7.7Terminal

chapelv1.6.0v1.6.181212v1.10.0Terminal

cmakev2.8.8v3.5.1v3.13.1v3.21.4Terminal

cplexv12.6.3cmv20.1.0v20.1.0_21v20.1.0_21nTerminal

degeneshunterv0.98v0.99.13Terminalcomprehensive protocol for the analysis of transcriptional data

gccv4.4.7v4.5.4v4.6.2v4.9.1v4.9.4v5.5.0v7.2.0v9.2.0v9.5.0v11.1.0v12.2.0Terminal

glpkv4.65Terminal

gov1.11.1v1.14(default)Terminal

intelv2013.1.117v2021.2v2021.4(default)v2021.4_sinmpiv2022.3Terminal

javav1.6.0_18vjdk-7u40vjdk-8u121vjdk-17.0.1vjre-7u21vjre-7u40vjre-8u60vjre-8u211vjre-8u301(default)Terminal

llvmv3.9.1Terminal

mathematicav11.2v12.3Terminal

matlabvR2007bvR2011bvR2012bvR2013bvR2014avR2014bvR2015b(default)vR2015b_jvmvR2015b_runtimevR2017bvR2019bvR2019b_runtimeTerminalMatlab numeric calculus programming and simulations

nasmv2.15.05Terminal

nodejsv6.11.3Terminal

nvhpcv20.9v20.9_nompiTerminal

octavev4.0.1v5.1.0Terminal

perlv5.8.9v5.14.2v5.28.2Terminal

pgiv13.6Terminal

pythonv2.7.18v3.8.8v3.8.10Terminal

rubyv1.9.3p327(default)v1.9.3p327_with_Rv2.2.2p95v2.3.4v2.3.8v2.4.1v2.7.2TerminalRuby programming language

singularv4.2.1Terminal

uprofv3.4.502Terminal

Quantum

qiskitv0.8.2v0.37.1v0.37.2_gpuv0.38.0v0.39.0_mpiTerminal

Read mapping

bowtiev1.0v2.1.0v2.2.4v2.2.9v2.4.4v1.1.2v1_0.12.8v2_2.0.0-beta7TerminalRead mapping utility

gem3v3.6Terminal

gmapv7Terminal

gsnapv7Terminal

Sequences matching

blastv2.2.20Terminal

blast_plusv2.2.26+v2.2.27+v2.2.27+_stdv2.2.28+v2.2.29+v2.2.29_pipesv2.2.30+(default)v2.10.1+v2.12.0+Terminalfind matches between input and databases

blatv34Terminal

clustalv1.2.0_omegav2.1Terminal

diamondv0.9.22v2.0.13Terminal

exoneratev2.2.0Terminal

gpu_blastv2.2.28+Terminal

hmmerv3.1b1v3.1b2v3.3.2Terminal

lastzv1.04.22Terminal

platypusvcv0.8.1Terminal

scbi_distributed_blastv0.0.5TerminalDistributed blast+ using scbi_mapreduce

Sequences preprocessing

bbmapv36.11v37.68v38.50bTerminal

cdhitv4.5.4v4.8.1Terminal

cellrangerv7.0.0Terminal

cellranger-arcv2.0.1TerminalCell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage

cutadaptv3.4Terminal

deeptoolsv3.5.1Terminal

fastq-mcfv1.1.2Terminal

hydrav0.5.3Terminal

ngs_qcv2.3Terminal

phredv0.020425.cTerminal

seqtrimbbv2.1.3v2.1.8Terminal

Tests

Rv4.1.0_oldv4.1.0_visTerminal

REDItoolsv2.0Terminal

artaiosv2.1Terminal

bbmapv38.92Terminal

biobambamv2.0.180Terminal

bwav0.7.8Terminal

bwa_memv2.2.1Terminal

checkmv1.1.3Terminal

enveomicsv1.3.4Terminal

fftwv3.3.9v3.3.9_openmpi3Terminalfast FFT compiled with intel compilers

gmapv2021_augTerminal

gnuplotv5.4.2Terminal

gsnapv2021_augTerminal

hyprev2.11.2_mpi1_gcc7.5.0v2.11.2_mpi4_gcc7.5.0v2.22.0v2.22.0_mpi1_gcc7.5.0v2.22.0_ompi3_gcc7.5.0TerminalHYPRE is a library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers.

idbav1.1.3Terminal

iqtreev1.6.12Terminal

juliav1.7.2Terminal

lapackv3.2.1v3.10.0_gcc11TerminalLinear Algebra PACKage

matlabvR2020bTerminalMatlab numeric calculus programming and simulations

maxbinv2.2.7Terminal

megahitv1.2.9Terminal

mesmerv5.2Terminal

nanofiltv2.8Terminal

nanoplotv1.2Terminal

nanostatv1.5Terminal

prodigalv2.6.3_gcc11TerminalProdigal provides fast, accurate protein-coding gene predictions in GFF3, Genbank, or Sequin table format. It does not need to be provided with any training data, and instead automatically learns the properties of the genome from the sequence itself, including RBS motif usage, start codon usage, and coding statistics. Handles gaps and partial genes.

quastv5.0.2_gcc11Terminal

satsuma2v2020Terminal

squeezemetav1.3Terminal

tabixv0.2.6Terminal

Transcriptome assembly

cufflinksv2.0.2v2.1.1v2.2.1Terminal

pricev0.17.2Terminal

rsemv1.1.21v1.2.7v1.2.12Terminal

trinityv2.10.0v2.10.0.bkpv2.14.0vr2012.10.05vr2013.08.14vr2013.11.10vr2014.04.13p1vr2016.03.17_v2.2.0vr2017.02.05_v2.4.0TerminalTranscriptome assembly software

Transcriptomics tools

alphafoldv20210907Terminal

annocriptv0.2Terminal

capmirseqv20140618Terminal

circomparav20190910Terminal

imrepv20190910Terminal

kallistov0.43.0Terminal

methyldackelv0.6.1Terminal

miarmav1.5Terminal

mireaderv2Terminal

msisensorprov1.2.0Terminal

nanocountv0.2.5Terminal

pitav07Terminal

squidv1.3Terminal

starchipv20190910Terminal

tidditv3.3.2Terminal

transdecoderv20140704TerminalTransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks

viennaRnav2.2.10Terminal

Utils

apsv0.1v0.2v0.9(default)v1.0Terminal

artv04022013Terminal

asperav3.9.6Terminal

autoflowv0.8.7vdevvlast(default)voldTerminal

chromonomerv1.10Terminal

circosv0.67-7Terminal

dimemasv5.4.2Terminal

dna2pepv1.1Terminal

dotv2.49.2Terminal

embossv6.6.0v6.6.0_nTerminal

evefv1.0v1.1v2.0Terminal

extraev3.8.0Terminal

fqbinv0.9Terminal

ghostscriptv8.64Terminal

gnuplotv4.4.2v4.6.5Terminal

graphvizv2.49.2Terminal

inelasticav1.3.7Terminal

latexv3.14v3.14_singTerminal

lep_anchorv20200310Terminal

lep_map3v20200115Terminal

libgdv2.1.1Terminal

minicondav3Terminal

mysqlv5.6.23Terminal

ncbi_cpp_toolkitv12.0.0v21.0.0TerminalNCBI toolkit for C++

nextflowv20.10Terminal

pandocv2.2.1v2.11v2.17.0.1Terminal

parallelv20150322Terminal

paraverv4.8.2Terminal

parse_nanov01Terminal

picrustv1.1.3v1.1.4v2.0.3v2.5Terminal

portraitv1.1Terminal

prosplignv1.0.0Terminal

pydrive2v0.14.0Terminal

qualimapv2.2v2.2.1Terminal

rdkitv20140902v20150301Terminal

resv1.0Terminal

resmapv1.1.4Terminal

rtg-corev3.6Terminal

sam2countsv20131126v20131126_oldTerminalConvert SAM mapping results to reference sequence counts

singularityv3.5.3v3.7.2Terminal

solexaqav3.1.4Terminal

sparkv3.0.0_h3.2Terminal

splignv1.39.8Terminal

statav17Terminal

vcev6.0.2Terminal

vcftoolsv0.1.11v20160205Terminal

vtcv0.9.2Terminal

wombatv20140828v20171103v20200225(default)Terminal

Visualization

amirav550Terminal

paraviewv5.6.0Terminal

pymolv1.7.4Terminal

relionv1.3v1.4v2_beta_161031v2_beta_161031_guiManualTerminalRelion employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

vis5dv1.3.0bTerminal

xcrysdenv1.5.32Terminal