Apps Database
This is a database of the software supported at the ACI-REF institutions. By clicking on the column headings, you will sort on that column. You can search on any term in the database and it will return all of the matches to that term in the database. Here are brief descriptions of the Columns:
- Package: name of package
- Category: broad categorization of the package with four possible entries - Applications, Programming Tools, Libraries and Utilities
- Tag: additional categorization which can be used to narrow searches, based on the functionality of the package
- Version: the version installed; can be multiple
- Site: Clemson, Harvard, Hawaii, USC, Utah, Wisconsin
- Contact: ACIREF who works with package
- Expertise Level: installation only, novice user, intermediate user, experienced user
| Package | Category | Tag | Versions | Site | Contact | Expertise Level |
|---|---|---|---|---|---|---|
| Package | Category | Tag | Versions | Site | Contact | Expertise Level |
| 7zip | Utilities | File compression | 9.13 | Utah | Martin Cuma | Installation Only |
| abaqus | Applications | engineering | 6.12 | Wisconsin | Christina Koch, Lauren Michael | Installation Only, Installation Only |
| abaqus | Applications | Computer aided engineering, finite element | 6.14-1, 6.14-2 | Utah | Anita Orendt, Martin Cuma | Installation Only, Installation Only |
| abinit | Applications | Condensed Matter Physics, Physics | 8.8.1 (D) | Utah | Wim Cardoen | Installation Only |
| abinit | Applications | chemistry, electronic structure, quantum chemistry | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| abyss | Applications | Bioinformatics, Genomic sequencing | 2.1.2 (D) | Utah | Brett Milash | Installation Only |
| acml | Libraries | Math | 2.7.0, 3.0.0, 4.0.0, 4.1.0, 4.4.0 | Utah | Wim Cardoen | Intermediate User |
| aladin | Applications | Astronomy | 7.015b | Utah | ||
| allpaths-lg | Applications | genomics | 52488 | Utah | Anita Orendt | Installation Only |
| AllpathsLG | Applications | 50081 | Harvard FAS | Bob Freeman | Intermediate User | |
| amber | Applications | chemistry, Computational chemistry, CUDA, molecular dynamics | amber14-GPU | Utah | Wim Cardoen | Installation Only |
| amber | Applications | chemistry, molecular dynamics | amber14 | Utah | Anita Orendt, Wim Cardoen | Novice User, Installation Only |
| amber | Applications | chemistry, molecular dynamics | amber15 (amber14 with ambertools15) | Utah | Anita Orendt | Novice User |
| amber | Applications | chemistry, molecular dynamics, molecular mechanics | amber12 | USC | ||
| amber | Applications | chemistry, molecular dynamics, molecular mechanics | amber14 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| amber | Applications | biochemistry, molecular dynamics | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| anaconda (python) | Programming Tools | Python | 5.1.0 (Python 2.7.14, 3.6.4) | Utah | Wim Cardoen | Installation Only |
| angsd | Applications | Genomic analysis, genomics | 0.917, 0.916, 0.911 | Utah | Anita Orendt | Installation Only |
| ansys | Applications | C, computational fluid dynamics, Computer aided engineering, engineering, Finite difference, fluid dynamics | 12.1, 14.0, 14.5, 15.0, 16.1 17.1(D) | Utah | Anita Orendt, Martin Cuma | Installation Only, Installation Only |
| Ansys Electronics Desktop | 16.1, 17 | Utah | Martin Cuma | Installation Only | ||
| apache | Utilities | File transfer | 2 | Harvard FAS | Aaron Kitzmiller | Experienced User |
| apache-ant | Programming Tools | 1.9.7 | Utah | Anita Orendt | Installation Only | |
| asciidoc | Utilities | Text editor | 8.6.9 | Utah | Wim Cardoen | Installation Only |
| augustus | Applications | genomics | 3.3 | Utah | Anita Orendt | Installation Only |
| autoconf | Programming Tools | Build tools | 2.68 | Harvard FAS | Aaron Kitzmiller | Intermediate User |
| autoconf | Applications | Build tools | 2.69 | Utah | Martin Cuma, Wim Cardoen | Intermediate User, Intermediate User |
| autodock | Programming Tools | chemistry, Molecular Docking | 4.2.5.1 | Utah | Anita Orendt | Novice User |
| automake | Programming Tools | Build tools | 1.11.1 | Harvard FAS | Aaron Kitzmiller | Intermediate User |
| AutoSeg | Applications | brain imaging, image processing, visualization | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| avbin | Utilities | Video Decoding | 7, 8.1 | Utah | Martin Cuma | Installation Only |
| AVL | Applications | computational fluid dynamics, engineering, fluid dynamics | 2013.1 | Utah | Anita Orendt | Installation Only |
| bamtools | Applications | 2.3.0 | Harvard FAS | Bob Freeman | Intermediate User | |
| bamtools | Applications | genomics | 2.5.1 | Utah | Anita Orendt | Installation Only |
| Bazel | Applications | Build tools, C, Compilers, Compilers and Tools, Tools | 10/27/2016, 0.5.1 (D) |
Utah | Wim Cardoen | Installation Only |
| bbcp | Utilities | File transfer | 10.08.29.00.0, 12.08.17.00.0 | Utah | Martin Cuma | Installation Only |
| bcbio-nextgen | Applications | 20140611 | Harvard FAS | Bob Freeman | Intermediate User | |
| bcftools | Applications | genomics | 1.6 | Utah | Anita Orendt | Installation Only |
| bcl2fastq2 | Applications | genomics | 2.17 | Utah | Anita Orendt | Installation Only |
| BEAST | Applications | Bioinformatics, Phylogenetic analysis | 1.8.1, 2.1.0 | Sean Cleveland | Intermediate User | |
| bedtools | Applications | Genetics, Genomic analysis | 2.24.0 | Utah | Anita Orendt | Installation Only |
| berkeley-nlp | Applications | Bioinformatics, Natural Language Processing | 1.1 | Utah | ||
| bernese | Applications | Astronomy, Global Navigation | BERN50 | Utah | Martin Cuma | Installation Only |
| binutils | Programming Tools | Build tools | 2.25 | Utah | Martin Cuma | Novice User |
| Bioinformatics Brew | Utilities | Build tools | 2014-05-09 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| bioperl | Programming Tools | genomics | 1.5.1, 1.6.1 | Utah | Martin Cuma | Installation Only |
| bioperl | Libraries | Genetics, perl | 1.6.1 | Harvard FAS | Bob Freeman | Experienced User |
| biopython | Libraries | Python | 1.60 | Harvard FAS | Bob Freeman | Intermediate User |
| bismark | Applications | genomics | v0.17.0, v0.12.2 | Utah | Anita Orendt | Installation Only |
| blacs | Libraries | Math | 1.1 | Utah | Martin Cuma | Intermediate User |
| blast | Applications | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | ||
| blast | Applications | Genomic alignments, Genomic sequencing | 2.3.0+ | Utah | Anita Orendt | Installation Only |
| blast2go | Applications | 2.5.0 | Harvard FAS | Bob Freeman | Intermediate User | |
| blat | Applications | Genomic alignments, Genomic sequencing | 34 | Utah | Anita Orendt | Installation Only |
| boost | Libraries | Utility | 1.40.0, 1.41.0, 1.50.0, 1.54.0, 1.55.0 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| boost | Libraries | C++ | 1.54.0 | Utah | Wim Cardoen | Intermediate User |
| boost | Libraries | C | 1.54.0, 1.58.0(i) (D), 1.59.0 (g), 1.66.0 (g) (D) | Utah | Wim Cardoen | Intermediate User |
| boost | Libraries | C++ | Wisconsin | Christina Koch, Lauren Michael | Installation Only, Installation Only | |
| boost | Libraries | C++ | 1.47.0, 1.51.0, 1.55.0 | USC | ||
| bowtie | Applications | Genomic alignments | v1-0.12.5, v2-2.0.0-beta7 | Utah | Anita Orendt | Installation Only |
| bowtie | Applications | genomics | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| bowtie | Applications | genomics | 1,2 | Harvard FAS | Bob Freeman | Installation Only |
| bsoft | Applications | Structural biology | 1_8_6 | Utah | Anita Orendt | Installation Only |
| bwa | Applications | genomics | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| bwa | Applications | genomics | 0.7.10 | Utah | Anita Orendt | Installation Only |
| bzip2 | Libraries | File compression | 1.0.6 | Utah | Wim Cardoen | Installation Only |
| c++ | Programming Tools | Scripting language | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| Cadence | Applications | engineering | ~ 2015 | Utah | Martin Cuma | Installation Only |
| cantera | Applications | chemistry, engineering, Python | 2.2.0(D), 2.1 | Utah | Wim Cardoen | Installation Only |
| carpy | Applications | Astronomy, Python | 2013-06-17 | Utah | Wim Cardoen | Installation Only |
| CASAVA | Applications | 1.8 | Harvard FAS | Bob Freeman | Intermediate User | |
| cbc | Library | Applied Math | 2.9.7 | Utah | Wim Cardoen | Installation Only |
| CCP4 | Applications | Crystallography tools | 6.4.0 | Utah | Anita Orendt | Installation Only |
| cctools | Applications | Batch Systems | 6.1.1 | Utah | Wim Cardoen | Installation Only |
| cdo | Applications | Atmospheric Sciences | 1.8.2 | Utah | Martin Cuma | Installation Only |
| cellranger | Applications | Genomic analysis | 3.0.0 | Utah | Brett Milash | Installation Only |
| cfitsio | Libraries | C, File Reading/Writing, Fortran, R | 3.24, 3.310, 3.35, 3.370(g)(D) | Utah | Wim Cardoen | Installation Only |
| cgl | Applications | Genome Annotation, genomics | 0.08 | Utah | Anita Orendt | Installation Only |
| charmm | Applications | chemistry, molecular mechanics | Utah | Anita Orendt | Intermediate User | |
| charmm | Applications | chemistry, molecular mechanics | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| chimera | Applications | chemistry, Molecular viewers | 1.9, 1.10 | Utah | Anita Orendt | Novice User |
| circos | 0.69-5 | |||||
| circos | Applications | genomics, visualization | 0.69-5 | Utah | Anita Orendt | Installation Only |
| cleartk | Applications | Bioinformatics, Machine learning, Natural Language Processing | 1.4.1 | Utah | ||
| clhep | Libraries | Math | 2.2.0.3 | Utah | Wim Cardoen | Installation Only |
| Clustalw | Applications | 2.0.12 | Harvard FAS | Bob Freeman | Experienced User | |
| cluto | Applications | Bioinformatics, C, Clustering, Machine learning | 2.1.1 | Utah | ||
| cmake | Programming Tools | Build tools | 3.7.2 (D) |
Utah | Wim Cardoen | Intermediate User |
| cmake | Programming Tools | Build tools | 2.8.12 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| cmake | Programming Tools | Build tools | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| cmaq | Applications | Air quality modeling, Atmospheric Sciences | 5 | Utah | Wim Cardoen | Installation Only |
| CMG | Applications | C, Computer aided engineering, engineering | 2012.105.G | Utah | Anita Orendt | Installation Only |
| CodeBlocks | Programming Tools | C, C++, Fortran, IDE | 16.01 | Utah | Wim Cardoen | Installation Only |
| comsol | Applications | Computer aided engineering | 3.2, 4.1, 4.3, 4.4 (D) | Utah | Martin Cuma | Installation Only |
| comsol | Applications | earth system modeling, fluid dynamics, geophysical modeling, multiphysics | 43, 44b, 50 | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User |
| coot | Applications | chemistry, Crystallography tools, Molecular viewers, visualization | version-0.8-4968 | Utah | Anita Orendt | Installation Only |
| copro-seq | Applications | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | ||
| CPAN | Libraries | perl | Harvard FAS | Bob Freeman | Experienced User | |
| CSD | Applications | chemistry, Crystallography tools | 2016 | Utah | Anita Orendt | Experienced User |
| ctakes | Applications | Bioinformatics, Natural Language Processing, UML | 3.1.1 | Utah | ||
| ctf | Applications | Electron microscopy analysis, Structural biology | 4.1.13, 4.1.8, 4.0.7 | Utah | Anita Orendt | Installation Only |
| cuda | Programming Tools | GPU | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| cuda | Libraries | CUDA | 6.0, 6.5 | USC | ||
| Cudnn | Libraries | Machine learning | 8.0(D) | Utah | Wim Cardoen | Installation Only |
| cufflinks | Applications | genomics | 2.2.1 | Harvard FAS | Bob Freeman | Intermediate User |
| cufflinks | Applications | Genomic sequencing, genomics | 2.0.2, 2.1.2(D) | Utah | Anita Orendt, Wim Cardoen | Installation Only, Installation Only |
| curl | Applications/Utilities | File transfer | 7.35.1, 7.49.1, 7.54.1(D) | Utah | Wim Cardoen | Installation Only |
| cwf | Libraries | Atmospheric Sciences | 3.2.2, 3.3.0_54 (D) | Utah | Wim Cardoen | Installation Only |
| cyana | Applications | chemistry, NMR Structure, R | 2.1 | Utah | Anita Orendt | Installation Only |
| cytoscape | Applications | Network Analysis, visualization | 3.2.1 | Utah | Wim Cardoen | Installation Only |
| DAGMan | Utilities | Batch Systems | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| dakota | Applications | Math | 5.3 | Utah | Martin Cuma | Installation Only |
| dakota | Programming Tools | Toolkits | 5.4 | Wisconsin | Christina Koch, Lauren Michael | Installation Only, Installation Only |
| DARS | Applications | computational fluid dynamics, Computer aided engineering | 2.12.005 | Utah | Martin Cuma | Installation Only |
| dcm4che | Applications | Healthcare | 2.0.25 | Utah | ||
| ddt | Programming Tools | Debugging, Profiling | 4.2.2 | Utah | Martin Cuma | Intermediate User |
| degrib | Applications | Atmospheric Sciences | 1.90, 1.94 | Utah | Martin Cuma | Installation Only |
| delft3d | Applications | engineering | Utah | Wim Cardoen | Installation Only | |
| DLPOLY | Applications | molecular dynamics | 4.07 | Utah | Martin Cuma | Installation Only |
| DNAnexus SDK | Programming Tools | Bioinformatics | 0.231.0 | Utah | ||
| DNAnexus Upload Agent | Applications/Utilities | Bioinformatics | 1.5.27 | Utah | ||
| dock | Applications | chemistry, Molecular Docking | 3, 6.1, 6.4, 6.5 | Utah | Anita Orendt | Novice User |
| docker | Utilities | Build tools | 0.8.1 | Harvard FAS | Aaron Kitzmiller | Novice User |
| ds9 | Applications | Astronomy, visualization | 7.3.2 | Utah | Anita Orendt | Installation Only |
| dssp | Applications | C, chemistry, Computational chemistry, Structural biology | 2.0.4, 2006 | Utah | Anita Orendt | Installation Only |
| eautils | Applications | Genomic sequencing, genomics | 1.1.2-806 | Utah | Anita Orendt | Installation Only |
| Eigen | Libraries | Math | 2.0.17 | Utah | Wim Cardoen | Installation Only |
| eigensoft | Applications | Genetic trait analysis, Genetics | 6.0.1 | Utah | Anita Orendt | Installation Only |
| eland | Applications | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | ||
| EMAN2 | Applications | Electron microscopy analysis, Structural biology | 2.3, 2.22, 2.2, 2.12 | Utah | Anita Orendt, Wim Cardoen | Installation Only, Installation Only |
| EMBOSS | Applications | 6.4.0 | Harvard FAS | Bob Freeman | Novice User | |
| esmf | Applications | earth system modeling | 6.3.0rp1 | Utah | Wim Cardoen | Installation Only |
| exonerate | Applications | Genomic alignments, genomics | 2.2.0 | Utah | Anita Orendt | Installation Only |
| expat | Libraries | XML parser | 2.1.0 | Utah | Martin Cuma | Installation Only |
| Fasta | Applications | Genomic sequencing | fasta-36.3.6d | Utah | Anita Orendt | Installation Only |
| fastqc | Applications | Genomic sequencing, genomics | 0.11.4 | Utah | Anita Orendt | Installation Only |
| fastqc | Applications | 0.10.1 | Harvard FAS | Bob Freeman | Experienced User | |
| FastTree | Applications | Genomic alignments | 1.2.9 | Utah | Anita Orendt | Installation Only |
| fastx_toolkit | Applications | 0.0.13 | Harvard FAS | Bob Freeman | Intermediate User | |
| fastx_toolkit | Applications | Genomic sequencing, genomics | 0.0.13 | Utah | Anita Orendt | Installation Only |
| fbat | Applications | Genetic trait analysis, Genetics | 2.0.3 | Utah | Anita Orendt | Installation Only |
| fdt | Utilities | File transfer | 0.9.20 | Utah | Wim Cardoen | Installation Only |
| fdtd | Applications | Finite difference, Maxwell equation solver | 8.9.201 | USC | ||
| ffmpeg | Utilities | Video Decoding | 6/7/2013 | Utah | Wim Cardoen | Installation Only |
| ffmpeg | Utilities | Video Decoding | 2.4.2 | Harvard FAS | Bob Freeman | Installation Only |
| ffmpeg | Utilities | Video Decoding | 2.2.4 | Wisconsin | Christina Koch, Lauren Michael | Installation Only, Installation Only |
| fftw | Libraries | Math | 3.3.4(D), 2.1.5 | Utah | Martin Cuma, Wim Cardoen | Experienced User, Installation Only |
| fftw | Libraries | Math | 3.3.3, 2.1.5 | Utah | Martin Cuma, Wim Cardoen | Experienced User, Experienced User |
| fftw | Libraries | Math | 2.1.5,3.3.3 | USC | ||
| fftw | Libraries | C++ | Wisconsin | Christina Koch, Lauren Michael | Installation Only, Installation Only | |
| fftw | Libraries | Math | 3.3.4, 2.1.5 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| findbugs | Programming Tools | Debugging | 1.3.9 | Utah | ||
| FindEM | Applications | Electron microscopy analysis | 2 | Utah | Anita Orendt | Installation Only |
| fitsverify | Applications | Data tools | 4.17(D) | Utah | Wim Cardoen | Installation Only |
| focus | Applications | Electron microscopy analysis, Structural biology | 1.1.0 | Utah | Anita Orendt | Installation Only |
| fortran | Programming Tools | Scripting language | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| frealign | Applications | Electron microscopy analysis | 9.11 | Utah | Anita Orendt | Installation Only |
| frealix | Applications | Electron microscopy analysis | 1.1 | Utah | Anita Orendt | Installation Only |
| freebayes | Applications | genomics | 1.0.2-16 | Utah | Anita Orendt | Installation Only |
| freesurfer | Applications | brain imaging, image processing, visualization | 4.1.8 | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User |
| freesurfer | Applications | brain imaging, Healthcare, Image Tool, visualization | 5.0.0 | Utah | ||
| freetype | Libraries | C | 2.3.12, 2.4.11, 2.5.3(D) | Utah | Wim Cardoen | Installation Only |
| freud | Applications/Utilities | C, chemistry, Computational chemistry, molecular dynamics | 0.6.1 | Utah | Wim Cardoen | Installation Only |
| g2 | Libraries | Graphics | 0.72 | Utah | Anita Orendt | Installation Only |
| gate | Applications | Natural Language Processing | 6.0, 7.0 | Utah | ||
| gatk | Applications | Genomic analysis | 3.7 | Utah | Anita Orendt | Installation Only |
| gaussian | Applications | Computational chemistry | g03 | USC | ||
| gaussian09 | Applications | chemistry, Computational chemistry, Molecular viewers, quantum chemistry | Utah | Anita Orendt | Experienced User | |
| Gaussian16 | Applications | C, chemistry, Computational chemistry | C.01, B.01, A.03 | Utah | Anita Orendt | Experienced User |
| gawk | Applications | File conversion, File Reading/Writing, R | 4.1.3(D) | Utah | Wim Cardoen | Intermediate User |
| gcc | Programming Tools | Compilers | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| gcc | Programming Tools | Compilers | 4.7.2 | Harvard FAS | Aaron Kitzmiller | Novice User |
| gcc | Programming Tools | C, Compilers, Fortran | 4.4.7(D), 4.7.2, 4.8.4, 4.9.2, 5.4.0 | Utah | Wim Cardoen | Experienced User |
| gcc | Programming Tools | Compilers | 4.6.2, 4.8.1 | USC | ||
| gcta | Applications | Genetic trait analysis | 0.92.9 | Utah | Anita Orendt | Installation Only |
| gdal | Library | Atmospheric Sciences | 1.9.2, 1.10.0, 2.0.1, 2.3.1(D) | Utah | Wim Cardoen | Installation Only |
| gdlib | Libraries | image processing | 2.1.1(D) | Utah | Wim Cardoen | Installation Only |
| geant4 | Applications | particle physics simulation | 4.10.01.p01(D) | Utah | Wim Cardoen | Installation Only |
| gempak | Applications | Atmospheric Sciences | 5.11.1, 7.1.0, 7.3.0 (D) | Utah | Martin Cuma | Installation Only |
| genesis-sim | Applications | Neuroscience | 2.3 | Utah | Wim Cardoen | Installation Only |
| genetorrent | Utilities | File transfer, genomics | 3.8.5a | Utah | Anita Orendt | Installation Only |
| GenomeAnalysisTK | Applications | 3.2.2 | Harvard FAS | Bob Freeman | Intermediate User | |
| geomview | Applications | visualization | 1.9.4 | Utah | Anita Orendt | Installation Only |
| geos | Libraries | Math | 3.2.2, 3.3.8, 3.4.2, 3.5.0(D) | Utah | Wim Cardoen | Installation Only |
| ghc | Programming Tools | Haskell | 7.6.3(D) | Utah | Wim Cardoen | Installation Only |
| git | Programming Tools | versioning | 1.9.3 | USC | ||
| git | Programming Tools | versioning | 1.7.1 | Harvard FAS | Aaron Kitzmiller | Experienced User |
| git | Programming Tools | versioning | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| git | Programming Tools | versioning | 1.8.1.1, 1.8.3.4, 1.8.4.1(D), 2.10.0, 2.10.0-c7 | Utah | Wim Cardoen | Intermediate User |
| globus | Utilities | File transfer | 4.0.7 | Utah | ||
| globus | Utilities | File transfer | 5.2.3 | USC | ||
| glpk | Libraries | Math | 4.35 | Utah | Wim Cardoen | Installation Only |
| gluster | Utilities | Filesystem | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| Gmap | Applications | Genomic alignments, genomics | 2014-06-10, 2011-09-07 | Utah | Anita Orendt | Installation Only |
| gmp | Libraries | Toolkits | 5.1.0, 6.0.0, 6.1.0 | Utah | Wim Cardoen | Installation Only |
| gmt | Applications | Graphing | 5.1.2_r14049, 4.5.11 | Utah | Anita Orendt | Installation Only |
| gnuplot | Applications | Graphing | 4.4.3, 4.6.0, 5.0.3 (D) | Utah | Martin Cuma, Wim Cardoen | Intermediate User, Installation Only |
| Google Test & Mock | Applications | C++ | 05/25/2016 | Utah | Wim Cardoen | Experienced User |
| grace | Applications | Graphing | 5.1.24 | Utah | ||
| grads | Applications | earth system modeling, visualization | 2.0.2.oga.2 | Utah | Martin Cuma | Installation Only |
| graphicsmagick | Applications | Graphics | 1.4 | Utah | Wim Cardoen | Installation Only |
| grib | Libraries | I/O | 1.12.3 | Utah | Martin Cuma | Installation Only |
| gromacs | Applications | chemistry, molecular dynamics, molecular mechanics | 5.0 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| gromacs | Applications | molecular dynamics, molecular mechanics | 4.6.6, 5.0.2 | USC | ||
| gromacs | Applications | biochemistry, molecular dynamics | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| gromacs | Applications | chemistry, molecular dynamics | 5.0.4s, 5.0.4d, 2016.4s, 2016.4d(D) | Utah | Wim Cardoen | Installation Only |
| gsl | Libraries | Math | 1.16 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| gsl | Libraries | C, Math | 1.15, 1.16, 2.1, 2.2.1 (D) | Utah | Wim Cardoen | Intermediate User |
| guidance | Applications | Genomic alignments, genomics | 2.02,2.01 | Utah | Anita Orendt | Installation Only |
| gurobi | Libraries | Math | 5.6.0 | USC | ||
| hadoop | Libraries | Hadoop | 1.1.2 | USC | ||
| Harminv | Applications | Applied Math, chemistry | 1.4 | Utah | Wim Cardoen | Installation Only |
| Harp | Applications | Astronomy | 1.0.beta (D) | Utah | Wim Cardoen | Installation Only |
| haskell-platform | Programming Tools | Haskell | 2.0.0(D) | Utah | Wim Cardoen | Installation Only |
| hdf4 | Libraries | I/O | 4.2.9 | Utah | Martin Cuma | Intermediate User |
| hdf5 | Libraries | I/O | 1.8.14 (D), 1.8.12 | Utah | Martin Cuma | Intermediate User |
| hdf5 | Libraries | I/O | 1.8.12 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| hdf5 | Libraries | I/O | 1.8.12 | USC | ||
| hdf5 | Libraries | I/O | 1.8.14, 1.8.12 | Utah | Martin Cuma | Intermediate User |
| hdf5 | Library | I/O | 1.8.14, 1.8.16, 1.8.17-c7 | Utah | Martin Cuma, Wim Cardoen | Intermediate User, Intermediate User |
| hdf5 | Libraries | I/O | 1.8.14, 1.8.12 | Utah | Martin Cuma, Wim Cardoen | Intermediate User, Intermediate User |
| hdfeos | Libraries | I/O | 5.1.13, HDF-EOS2, HDF-EOS5 | Utah | Martin Cuma | Installation Only |
| hdfview | Utilities | GUI | 2.5p3_64, 2.11.0 (D) | Utah | Martin Cuma | Installation Only |
| healpix | Applications | visualization | 3.11(D) | Utah | Wim Cardoen | Installation Only |
| helyx-os | Applications | computational fluid dynamics, fluid dynamics, GUI | 2.3.0 | Utah | Anita Orendt | Installation Only |
| hisat | Applications | Genomic alignments, genomics | 0.1.6-beta | Utah | Anita Orendt | Installation Only |
| hisat2 | Applications | Genomic alignments, genomics | 2.0.4 | Utah | Anita Orendt | Installation Only |
| HMMer | Applications | 3.1 | Harvard FAS | Bob Freeman | Experienced User | |
| hmmer3 | Applications | genomics | 3.1b2 | Utah | Anita Orendt | Installation Only |
| homer | Applications | Genomic analysis | 5.4(D) | Utah | Wim Cardoen | Installation Only |
| HOOMD | Applications | C, chemistry, Computational chemistry, GPU, molecular dynamics | 2.3.1 (dp)(D), 2.3.1 (sp) | Utah | Wim Cardoen | Installation Only |
| hpctoolkit | Programming Tools | Profiling, Toolkits | 5.3.2 | Utah | Martin Cuma | Intermediate User |
| hpctoolkit | Programming Tools | Profiling | 5.3.2 | USC | ||
| hpctoolkit-externals | Programming Tools | Profiling, Toolkits | 5.3.2 | Utah | Martin Cuma | Intermediate User |
| hpctraceviewer | Programming Tools | Profiling, Toolkits | 5.3.2 | Utah | Martin Cuma | Intermediate User |
| hpcviewer | Programming Tools | Profiling, Toolkits | 5.3.2 | Utah | Martin Cuma | Intermediate User |
| hsi | Utilities | File transfer | 4.0.1.3 | Utah | Martin Cuma | Installation Only |
| htar | Utilities | File compression | 4.0.1.3 | Utah | Martin Cuma | Installation Only |
| HTC Software Portability | Other | HTC | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| HTC Workflow | Other | HTC | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| htcondor | Utilities | Batch Systems | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| httplog | Utilities | File backup, File compression | 2.1 | Utah | ||
| Humann2 | Applications | genomics, metagenomics, microbial genomics | Utah | Anita Orendt | Installation Only | |
| hypre | Libraries | Math | 2.9.0b, 2.10.1 (D) | Utah | Martin Cuma | Installation Only |
| idba | Applications | Bioinformatics | 1.1.1 | Utah | ||
| idl | Programming Tools | IDE | 8.1, 8.2, 8.2.3, 8.3, 8.4, 8.5.1 (D) | Utah | Martin Cuma | Installation Only |
| idv | Applications | Atmospheric Sciences, R, Radar processing, visualization | 5.2 | Utah | Anita Orendt, Martin Cuma | Installation Only, Installation Only |
| IGV | Applications | visualization | 2.* | Harvard FAS | Bob Freeman | Intermediate User |
| imagemagick | Applications | image processing | 6.5.6-10, 6.9.0-4(D) | Utah | Wim Cardoen | Installation Only |
| infernal | Applications | Genomic sequencing | 1.1.1 | Utah | ||
| inrich | Applications | Genomic analysis | 1.1 | Utah | Anita Orendt | Installation Only |
| intel | Programming Tools | Compilers | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| intel | Programming Tools | Compilers and Tools | Cluster Studio 2015 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| intel | Programming Tools | Compilers | 12.1.1, 14.0 | USC | ||
| intel | Programming Tools | C, Compilers, Fortran | 2013, 2015, 2016(D), 2017 (D c7) | Utah | Martin Cuma, Wim Cardoen | Experienced User, |
| intelpy | Programming Tools | Python | 2.7.12, 3.5.2 | Utah | Wim Cardoen | Experienced User |
| Interproscan | Applications | 5.3 | Harvard FAS | Bob Freeman | Intermediate User | |
| ioapi | Libraries | Atmospheric Sciences | 3.1, 3.1 | Utah | Martin Cuma | Installation Only |
| isl | Libraries | Applied Math, Math | 0.17, 0.12 | Utah | Wim Cardoen | Installation Only |
| jasper | Library | Graphics, Toolkits | 1.900.1(D) | Utah | Wim Cardoen | Installation Only |
| java | Programming Tools | Scripting language | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| jdk | Programming Tools | Build tools, C, Compilers, Java | 1.8.0_25, 1.7.0_67(D) | Utah | Wim Cardoen | Experienced User |
| Jellyfish | Applications | 1.1.11 | Harvard FAS | Bob Freeman | Intermediate User | |
| julia | Programming Tools | Scripting language | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| Julia | Programming Tools | C, Compilers, Compilers and Tools, Tools | 0.3.7, 0.4.0, 0.4.5, 0.5.0, 0.6.0 (D) | Utah | Wim Cardoen | Intermediate User |
| kallisto | Applications | Genomic sequencing | 0.42.2(D) | Utah | Wim Cardoen | Installation Only |
| king | Applications | Genomic analysis, genomics | 1.4 | Utah | Anita Orendt | Installation Only |
| kiva | Applications | computational fluid dynamics | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| lammps | Applications | molecular dynamics, molecular mechanics | 8-Jul-13 | USC | ||
| lammps | Applications | chemistry, molecular dynamics | 11Aug17(D) | Utah | Wim Cardoen | Intermediate User |
| lammps | Applications | molecular dynamics, particle physics simulation | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| LibElemental | Libraries | Applied Math, Math | 08262015(D) | Utah | Wim Cardoen | Installation Only |
| LibFlame | Library | Applied Math, Math | 08182015(D) | Utah | Wim Cardoen | Installation Only |
| libxml2 | Utilities | XML parser | 2.9.1 | Utah | Martin Cuma | Installation Only |
| libyaml | Library | C | 0.1.5(D), 0.1.6 | Utah | Wim Cardoen | Installation Only |
| LLVM | Programming Tools | C, Compilers, Debugging | 3.7.0(D) | Utah | Wim Cardoen | Intermediate User |
| lmod | Utilities | Tools | 6.0.1(D) | Utah | Wim Cardoen | Experienced User |
| lobSTR | Applications | Genomic sequencing, genomics | 4.0.6 | Utah | Anita Orendt | Installation Only |
| log4j | Programming Tools | Debugging | 1.2.14 | Utah | Wim Cardoen | Installation Only |
| lrzip | Utilities | File compression | 0.552 | Utah | Wim Cardoen | Installation Only |
| lsdyna | Applications | engineering, finite element | 8.1.0-smp, 8.0-smp | Utah | Anita Orendt | Installation Only |
| lua | Programming Tools | Lua | 5.1.4-2, 5.1.4.8, 5.1.5(D) | Utah | Wim Cardoen | Installation Only |
| luarocks | Programming Tools | Compilers and Tools, Lua, Scripting language | 2.1.2(D) | Utah | Wim Cardoen | Installation Only |
| lucene | Applications | Indexing/Searching | 1.4.1, 3.5.0 | Utah | ||
| lumerical | Applications | Finite difference, Maxwell equation solver | 8.15.736, 8.16.1022 | Utah | Anita Orendt | Installation Only |
| lvg | Applications | Natural Language Processing | 2010, 2014 | Utah | ||
| maestro | Applications | chemistry, Molecular viewers | 2015-4 | Utah | Anita Orendt | Novice User |
| Magma | Library | Applied Math, CUDA, GPU, Math | 2.0.1 | Utah | Wim Cardoen | Installation Only |
| mahout | Libraries | Machine learning | 0.5 | Utah | ||
| Maker2 | Applications | Genome Annotation, genomics | 2.28 | Utah | Anita Orendt | Installation Only |
| marvin | Applications | Molecular viewers | 6.1.2 | Utah | Anita Orendt | Installation Only |
| mathematica | Applications | Integrated Development Environment | 10.0.0 | USC | ||
| mathematica | Applications | Applied Math, Math | 10.4.1, 11.0.0, 11.0.1, 11.1.1 (D) | Utah | Wim Cardoen | Intermediate User |
| Matlab | Programming Tools | Scripting language | 2011, 2013, 2014 | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User |
| matlab | Applications | Integrated Development Environment | 2014a | USC | ||
| matlab | Applications | engineering, Graphing, Math | R2011a, R2011b, R2012a, R2012b, R2013a, R2013b, R2014a, R2014b, R2015a, R2015b, R2016a, R2016b (D) | Utah | Martin Cuma | Experienced User |
| Matlab Compiler | Programming Tools | Compilers | 2011, 2013, 2014 | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User |
| matplotlib | Libraries | Python | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| maven | Programming Tools | Toolkits | 3.0.4, 3.2.1, 3.2.5, 3.3.3 (D) | Utah | Wim Cardoen | Intermediate User |
| maxquant | Applications | chemistry | 1.6.3.3 | Utah | , Anita Orendt | , Installation Only |
| MEEP | Applications | engineering, Finite difference, Maxwell equation solver | 1.3 | Utah | Wim Cardoen | Installation Only |
| meme | Applications | Bioinformatics, genetic maps, Genetics, Genomic sequencing, genomics | 4.11.2 | Utah | Wim Cardoen | Installation Only |
| mercurial | Programming Tools | versioning | 3.6(D) | Utah | Wim Cardoen | Installation Only |
| merlin | Applications | Genetics | 1.1.2 | Utah | Anita Orendt | Installation Only |
| MET | Applications | Atmospheric Sciences | 4.1 | Utah | Anita Orendt | Installation Only |
| metamap | Applications | Bioinformatics, Natural Language Processing | linux_2014,linux_2013, linux_2012, linux_2011v2, linux_2011 | Utah | ||
| metaphlan2 | Applications | genomics, metagenomics, microbial genomics | 2.2.0 | Utah | Anita Orendt | Installation Only |
| Metis | Library | Applied Math, finite element | 5.1.0 | Utah | Wim Cardoen | Installation Only |
| Microsoft R Open | Applications | R | 3.4.3 | Utah | Wim Cardoen | Intermediate User |
| midas | Applications/Utilities | Data Storage | 3.2.8 | Utah | Wim Cardoen | Installation Only |
| minx | Applications | visualization | 3.0<>(D) | Utah | Wim Cardoen | Installation Only |
| miranda | Applications | genomics | 3.3a | Utah | Anita Orendt | Installation Only |
| mirdeep2 | Applications | genomics | 2.0.0.8 | Utah | Anita Orendt | Installation Only |
| mirth | Applications | Healthcare | 1.8.2.4472.1351 | Utah | ||
| modeller | Applications | homology modelling, Protein modeling and analysis | 9.9 | Utah | Anita Orendt | Installation Only |
| modules | Utilities | Environment modules | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| molden | Applications | Molecular viewers | 4.4, 4.6, 4.7 | Utah | Anita Orendt | Novice User |
| mopac | Applications | chemistry, Computational chemistry, semiempirical quantum chemistry | 2012 | Utah | Anita Orendt | Novice User |
| mothur | Applications | Bioinformatics, metagenomics | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| mothur | Applications | genomics | 1.35.1 | Utah | Anita Orendt | Installation Only |
| motion-correct | Applications | 1.0(D) | Utah | Martin Cuma | Installation Only | |
| MPB | Applications | Materials modeling | 1.5 | Utah | Wim Cardoen | Installation Only |
| mpc | Libraries | C, Math | 1.0.1, 1.0.3 | Utah | Wim Cardoen | Installation Only |
| mpfr | Libraries | C, Math | 3.1.1, 3.1.2, 3.1.4 | Utah | Wim Cardoen | Installation Only |
| mpi | Programming Tools | MPI | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| mpich | Programming Tools | MPI | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| mpich2 | Programming Tools | MPI | 1.3.1..10,1.5 | USC | ||
| mpich2 | Libraries | Parallelization | 3.1.1, 3.1.2, 3.1.4, 3.2(D) | Utah | Martin Cuma, Wim Cardoen | Experienced User, Experienced User |
| mplus | Applications | Analytics | 7.4 | Utah | Anita Orendt | Installation Only |
| MrBayes | Applications | Phylogenetic analysis | 3.2.3 | Harvard FAS | Bob Freeman | Intermediate User |
| MrBayes | Applications | phyologenetic analysis | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| MRTSwath | Utilities | Atmospheric Sciences | 10152014(D) | Utah | Wim Cardoen | Installation Only |
| MultiNest | Applications | Math | 3.4(D) | Utah | Wim Cardoen | Installation Only |
| MUMmer | Applications | 3.23 | Harvard FAS | Aaron Kitzmiller | Installation Only | |
| mvapich | Programming Tools | MPI | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| mvapich2 | Libraries | MPI | 2.0 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| mvapich2 | Libraries | Parallelization | 1.9, 2.0, 2.1, 2.2 (D) | Utah | Martin Cuma | Experienced User |
| MySQL | Applications | Data tools | 5* | Harvard FAS | Aaron Kitzmiller | Experienced User |
| NAMD | Applications | chemistry, molecular dynamics, molecular mechanics | 2.9 | USC | ||
| namd | Applications | biochemistry, molecular dynamics | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| namd | Applications | molecular dynamics, Molecular viewers | 2.10 | Utah | Martin Cuma | Installation Only |
| nboview | Applications | electronic structure, Molecular viewers | 1.1 | Utah | Anita Orendt | Installation Only |
| ncarg | Utilities | Atmospheric Sciences | 5.1.1, 6.0.0, 6.1.0, 6.1.2 | Utah | ||
| ncbi-blast | Applications | 2.2.* | Harvard FAS | Bob Freeman | Experienced User | |
| ncbrowse | Utilities | Graphing, visualization | 1.67 | Utah | ||
| ncdu | Utilities | Machine Metrics | 1.10(D) | Utah | Wim Cardoen | Installation Only |
| ncl | Programming Tools | Scripting language | 6.0.0, 6.1.0, 6.1.2 | Utah | ||
| nco | Applications | Atmospheric Sciences | 4.2.0, 4.4.4 | Utah | Martin Cuma, Wim Cardoen | Installation Only, Installation Only |
| ncview | Applications | Atmospheric Sciences | 1.93g, 2.1.2, 2.1.2 | Utah | Martin Cuma | Installation Only |
| ndt | Utilities | Network performance | 3.5.6(D) | Utah | Wim Cardoen | Installation Only |
| neon | Applications | HTTP and proxy server | 0.25.5, 0.26.3, 0.28.4, 0.29.0, 0.30.0(D) | Utah | Wim Cardoen | Installation Only |
| netcdf-c | Libraries | I/O | 4.3.2, 4.3.3.1, 4.4.1-c7 | Utah | Martin Cuma, Wim Cardoen | Installation Only, Installation Only |
| netcdf-cxx | Libraries | I/O | 4.2.1, 4.3.0-c7 | Utah | Martin Cuma, Wim Cardoen | Installation Only, Installation Only |
| netcdf-f | Libraries | I/O | 4.4.0, 4.4.4-c7 | Utah | Martin Cuma, Wim Cardoen | Installation Only, Installation Only |
| netcdf-perl | Libraries | I/O | 1.2.4 | Utah | Martin Cuma | Installation Only |
| neuroconstruct | Applications | Neuroscience | 1.3.6 | Utah | Wim Cardoen | Installation Only |
| neuron | Applications | Neuroscience | 7.2(D) | Utah | Wim Cardoen | Installation Only |
| nfs | Utilities | Filesystem | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| nginx | Applications/Utilities | HTTP and proxy server | 1.7.8(D) | Utah | Wim Cardoen | Installation Only |
| ngsTools | Applications | Genetics, genomics | 1.0.0 | Utah | Anita Orendt | Installation Only |
| novocraft | Applications | Genomic alignments, genomics | 2.07.11 | Utah | Anita Orendt | Installation Only |
| numpy | Libraries | Python | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| nwchem | Applications | chemistry, Computational chemistry | 6.1, 6.3 | Utah | Anita Orendt | Experienced User |
| octave | Programming Tools | Scripting language | 3.6.3, 3.6.4, 3.8.0(D) | Utah | Wim Cardoen | Installation Only |
| OMA | Applications | Phylogenetic analysis | 0.99 | Harvard FAS | Bob Freeman | Intermediate User |
| omega | Applications | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | ||
| Open Science Grid | Other | HTC, OSG | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| openbabel | Applications | chemistry, File conversion | 2.3.2 | Utah | Anita Orendt | Intermediate User |
| openblas | Libraries | Math | 0.2.8, 0.2.7, 0.2.7_mt | Utah | Wim Cardoen | Experienced User |
| openblas | Libraries | Math | 0.2.8 | Utah | Wim Cardoen | Experienced User |
| openblas | Libraries | Math | 0.2.12, 0.2.13, 0.2.14 | Utah | Wim Cardoen | Experienced User |
| opencv | Applications | C, Computer vision, Machine learning | 2.4.9(D) | Utah | Wim Cardoen | Installation Only |
| opencv | Libraries | Computer vision | 2.4.8 | USC | ||
| OpenFoam | Applications | computational fluid dynamics, engineering, fluid dynamics | 2.4.0,v1606+, 4.1 | Utah | Anita Orendt | |
| openFOAM | Applications | computational fluid dynamics | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| openjpeg | Library | Graphics | 1.5.2(D) | Utah | Wim Cardoen | Installation Only |
| openkim | Applications | chemistry | 1.2.1, 1.1.11, 1.0.1,1.7,1,1.7.2(D) | Utah | Wim Cardoen | Installation Only |
| openmpi | Programming Tools | MPI, Parallelization | 1.6.5, 1.8.2, 1.10.0, 1.10.2 (D), 2.0.1 | Utah | Martin Cuma, Wim Cardoen | Experienced User, Experienced User |
| openmpi | Libraries | MPI | 1.8.1 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| openmpi | Programming Tools | MPI | 1.6.4,1.8.1 | USC | ||
| openmpi | Programming Tools | MPI | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| OpenMRS | Applications | Healthcare | Demo-1.6.0 | Utah | ||
| opennlp | Libraries | Natural Language Processing | 1.5.3, 1.5.0, 1.4.3 | Utah | ||
| osg | Utilities | Batch Systems | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| ovito | Applications | Molecular viewers | 2.9.0 | Utah | Anita Orendt | Installation Only |
| packmol | Applications | molecular dynamics | 14.225 | Utah | Anita Orendt | Installation Only |
| pandaseq | Applications | Genomic sequencing, genomics | 2.9 | Utah | Anita Orendt | Installation Only |
| pandoc | Utilities | File conversion | 1.11.1(D) | Utah | Wim Cardoen | Installation Only |
| panoply | Applications | Graphing | 4.0.3 | Utah | Martin Cuma | Installation Only |
| papi | Programming Tools | Profiling | 5.2.0 | Utah | Wim Cardoen | Installation Only |
| papi | Programming Tools | Profiling | 5.3.0 | USC | ||
| parallel | Utilities | Virtual Machine | 20130722, 20150322(D) | Utah | Wim Cardoen | Installation Only |
| paraview | Applications | visualization | 5.3.0 | Utah | Anita Orendt, Martin Cuma | Installation Only, |
| parmetis | Library | Applied Math, finite element | 4.0.3 | Utah | Martin Cuma | Novice User |
| pcre | Applications/Utilities | perl | 8.37 | Utah | Wim Cardoen | Installation Only |
| pdb2pqr | Utilities | File conversion | 1.9.0 | Utah | Anita Orendt | Installation Only |
| pear | Applications | genomics | 0.9.6 | Utah | Anita Orendt | Installation Only |
| peridigm | Applications | Physics | Peridigm | Utah | Martin Cuma | Installation Only |
| perl | Programming Tools | Scripting language | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| perl | Scripting language | 5.18.1, 5.10.0, 5.10.1 | Utah | Martin Cuma | Installation Only | |
| Perl | Programming Tools | Scripting language | 5 | Harvard FAS | Aaron Kitzmiller, Bob Freeman | Experienced User, Experienced User |
| petsc | Libraries | Math | 3.6.1 | Utah | Martin Cuma | Installation Only |
| petsc | Libraries | Math | 3.4.1 | USC | ||
| pgi | Programming Tools | Compilers | 13.10,13.3 | USC | ||
| pgi | C, Compilers | 15.1, 15.7 (D) | Utah | Martin Cuma | Experienced User | |
| phase | Applications | genetic maps | 2.1.1 | Utah | Anita Orendt | Installation Only |
| phast | Applications | Genomic analysis, Genomic modeling, genomics | 1.3(D) | Utah | Wim Cardoen | Installation Only |
| phenix | Applications | Crystallography tools | 1.9-1692 | Utah | Anita Orendt | Installation Only |
| picard | Applications | Genomic sequencing, genomics | 1.55, 1.122. 2.1.1(D) | Utah | Anita Orendt, Wim Cardoen | Installation Only, Installation Only |
| pigz | Utilities | File compression | 2.1.6 | Utah | Martin Cuma | Installation Only |
| plink | Applications | Genomic analysis, genomics | 1.09, 1.07 | Utah | Anita Orendt | Installation Only |
| prank | Applications | Genomic alignments, genomics | 170427 | Utah | Anita Orendt | Installation Only |
| prest | Applications | Genomic analysis, genomics | 4.09 | Utah | Anita Orendt | Installation Only |
| proj | Libraries | Applied Math | 4.6.1, 4.7.0, 4.9.0(D) | Utah | Wim Cardoen | Installation Only |
| pssac2 | Applications | geophysical modeling | 11042014(D) | Utah | Wim Cardoen | Installation Only |
| puppet | Utilities | Configuration Management | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| PyMOL | Applications | Molecular viewers, visualization | 1.8.6,1.7.0, 1.6.0 | Utah | Anita Orendt | Installation Only |
| python | Programming Tools | Scripting language | 2, 3 | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User |
| Python | Programming Tools | Scripting language | 2,3 | Harvard FAS | Aaron Kitzmiller, Bob Freeman | Experienced User, Experienced User |
| python | Programming Tools | Scripting language | 2.7.11, 3.5.2 (D), 3.6.3 | Utah | Wim Cardoen | Experienced User |
| python | Libraries | Python | 3.3.3 | USC | ||
| q3c | Utilities | Database | 1.4.15, 1.4.19, 1.4.23(D) | Utah | Wim Cardoen | Installation Only |
| qiime | Applications | genomics, metagenomics, microbial genomics | 1.9.1 | Utah | Anita Orendt | Installation Only |
| qiime | Applications | Bioinformatics, metagenomics, phylogenetics | 1.7.0 | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User |
| qiv | Utilities | Image viewer | 2.3.1 | Utah | Martin Cuma | Installation Only |
| QRNA | Applications | Genomic sequencing, genomics | 2.0.3c | Utah | Anita Orendt | Installation Only |
| Qt | Programming Tools | GUI | 4.6.0, 4.8.2, 4.8.4, 4.8.6, 5.4.1(D) | Utah | Wim Cardoen | Installation Only |
| Quantum Espresso (QE) | Applications | C, chemistry, Computational chemistry, materials | 5.3.0, 5.0.3, 5.0.2, 4.3.1 | Utah | Anita Orendt | Intermediate User |
| R | Applications | Integrated Development Environment | 2.15.3, 3.1.1 | USC | ||
| R | Programming Tools | IDE | 3.3.1, 3.3.2(D), 3.4.1 | Utah | Martin Cuma, Wim Cardoen | Novice User, Intermediate User |
| R | Programming Tools | Scripting language | 2, 3 | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User |
| radx | Libraries | C | 20140113(D) | Utah | Wim Cardoen | Installation Only |
| RAxML | Applications | Phylogenetic analysis | 7.7.6 | Harvard FAS | Aaron Kitzmiller | Installation Only |
| rclone | Utilities | File transfer | 1.17,1.21. 1.22, 1.24 | Utah | ||
| RDPTools | Applications | Genomic analysis | 2016-06-09 | Utah | Anita Orendt | Installation Only |
| rdp_classifier | Applications | genomics, metagenomics | 2.2 | Utah | Anita Orendt | Installation Only |
| rdseed | Applications/Utilities | File conversion | 4.7, 5.3.1 | Utah | Anita Orendt | Installation Only |
| relion | Applications | Electron microscopy analysis | 2.0.4 ,2-beta, 1.4, 1.3, 1.2, 1.1 | Utah | Anita Orendt | Installation Only |
| RepeatMasker | Applications | Genomic sequencing | 4.0.3 | Utah | Anita Orendt | Installation Only |
| RepeatMasker | Applications | 4.0.5 | Harvard FAS | Bob Freeman | Experienced User | |
| rnahybrid | Applications | genomics | 2.1.2 | Utah | Anita Orendt | Installation Only |
| root | Applications | Data tools | 6.03.03, 6.03.04 (D) | Utah | Wim Cardoen | Installation Only |
| Rosetta | Applications | Protein modeling and analysis | 3.5, 2016.13 | Utah | Anita Orendt | Installation Only |
| RSEM | Applications | Expression analysis | 1.2.16 | Harvard FAS | Bob Freeman | Experienced User |
| rsem | Applications | genomics | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | |
| rsem (RNA-Seq by Expectation-Maximixation) | Applications | genomics | 1.3.0 | Utah | Anita Orendt | Installation Only |
| RSL | Library | Atmospheric Sciences, Radar processing | 1.49 | Utah | Wim Cardoen | Installation Only |
| RStudio | Programming Tools | R | 0.99.903 , 1.0.153(D) | Utah | Wim Cardoen | Intermediate User |
| ruby | Programming Tools | Scripting language | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| Ruby | Programming Tools | Scripting language | 1.9.3 | Harvard FAS | Aaron Kitzmiller | Novice User |
| rzip64 | Utilities | File compression | 3 | Utah | Martin Cuma | Installation Only |
| SAC | Applications | 101.5c, 101.6a (D) | Utah | Martin Cuma | Installation Only | |
| samstat | Applications | Genomic sequencing, genomics | 1.08 | Utah | Anita Orendt | Installation Only |
| samtools | Applications | 0.1.17,0.1.19,1.0 | Harvard FAS | Bob Freeman | Experienced User | |
| samtools | Applications | Genomic alignments, genomics | 1.5,1.2 (D), 1.1, 0.1.11, 0.1.18 | Utah | Anita Orendt | Installation Only |
| sas | Applications | Analytics | 9.4, 9.2_phase2 | Utah | Anita Orendt | Installation Only |
| scala | Programming Tools | Scala | 2.10.5, 2.11.5(D) | Utah | Wim Cardoen | Installation Only |
| scalapack | Libraries | Applied Math, Math | 2.0.2 | Utah | Wim Cardoen | Novice User |
| scipy | Libraries | Python | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| seqprep | Applications | genomics | 1.1 | Utah | Anita Orendt | Installation Only |
| shapefile | Library | C | 1.3.0 | Utah | Martin Cuma | Installation Only |
| sickle | Applications | Genomic sequencing, genomics | 1.33 | Utah | Anita Orendt | Installation Only |
| SignalP | Applications | 4.1 | Harvard FAS | Bob Freeman | Intermediate User | |
| slony | Utilities | Database | 2.2.1 | Utah | Martin Cuma | Installation Only |
| slurm | Utilities | Batch Systems | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| slurm | Utilities | Resource Management | 14.11.4, 14.03.8, 14.03.7 | Utah | Martin Cuma | Intermediate User |
| SLURM | Utilities | Runtime | 14 | Harvard FAS | Bob Freeman | Intermediate User |
| smoke | Applications | Air quality modeling, Atmospheric Sciences | 3.1 | Utah | Wim Cardoen | Installation Only |
| SNAP | Applications | genomics | 2013-02-16 | Utah | Anita Orendt | Installation Only |
| SNAP (Sentinel Application Platform) | Applications | earth system modeling, image processing | 6.0 | Utah | Anita Orendt | Installation Only |
| snappy | Utilities | File compression | 1.1.2 | Utah | Wim Cardoen | Installation Only |
| SOAPdenovo2 | Applications | Genomic alignments, genomics | 2.04-r240 | Utah | Anita Orendt | Installation Only |
| sod | Applications/Utilities | geophysical modeling | 3.2.6 | Utah | Martin Cuma | Installation Only |
| software testing | Other | software testing | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| solo | Applications | Atmospheric Sciences | 3-20140711 | Utah | Wim Cardoen | Installation Only |
| sortmerna | Applications | genomics | 2.0 | Utah | Anita Orendt | Installation Only |
| SPAdes | Applications | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | ||
| Spades | Applications | genomics, metagenomics | 3.7.0 | Utah | Anita Orendt | Installation Only |
| specex | Applications | Astronomy, Physics | 10132015(D) | Utah | Wim Cardoen | Installation Only |
| sphinx | Utilities | 2.0.4 | Utah | Wim Cardoen | Installation Only | |
| spider | Applications | image processing | 21.02 | Utah | Anita Orendt | Installation Only |
| SQL | Programming Tools | Data tools | 9* | Harvard FAS | Aaron Kitzmiller, Bob Freeman | Experienced User, Experienced User |
| sqlite3 | Utilities | Database | 3.8.0.2, 3.7.13, 3.6.22 | Utah | Martin Cuma | Installation Only |
| squid | Utilities | Proxy | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| sra-toolkit | Applications | Data tools, genomics | 2.5.2 | Utah | Anita Orendt | Installation Only |
| Stacks | Applications | genetic maps, phylogenetics, population genomics | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | |
| stanford-nlp | Applications | Bioinformatics, Natural Language Processing | 3.3.1, 1.3.4 | Utah | ||
| STAR | Applications | Genomic alignments, genomics | 2.5 | Utah | Anita Orendt | Installation Only |
| star-ccm+ | Applications | C, Computer aided engineering, engineering | 5.04.006, 7.04.006, 8.06.007, 9.04.009, 9.06.011, 10.02.010, 11.02.009, 11.04.10 (D) | Utah | Martin Cuma | Installation Only |
| starcd | Applications | C, Computer aided engineering, engineering | 3.26, 4.16, 4.06, 4.02 | Utah | Martin Cuma | Installation Only |
| SU2 | Applications | computational fluid dynamics | 4.0 | Utah | Martin Cuma | Installation Only |
| suitesparse | Libraries | Math | 4.4.3, 4.4.5(D) | Utah | Wim Cardoen | Installation Only |
| sundials | Library | Applied Math, Math | 2.6.2 (D), 2.6.1 | Utah | Wim Cardoen | Installation Only |
| svn | Programming Tools | versioning | 1.8.3 | Utah | Wim Cardoen | Installation Only |
| swish | Utilities | XML parser | 2.4.7 | Utah | Wim Cardoen | Installation Only |
| szip | Utilities | File compression | 2.1(D) | Utah | Martin Cuma | Installation Only |
| tassel | Applications | Genetic trait analysis, Genomic analysis, genomics | 5.0 | Utah | Anita Orendt | Installation Only |
| tcltk | Programming Tools | Scripting language | 8.4.20(D), 8.5.12, 8.5.9 | Utah | Wim Cardoen | Installation Only |
| tecplot | Applications | visualization | 2018rC1 | Utah | Anita Orendt | Installation Only |
| texinfo | Applications | Utility | 6.0 | Utah | Wim Cardoen | Installation Only |
| texlive | Applications | 2014 | Utah | Wim Cardoen | Intermediate User | |
| tinker | Applications | Computational chemistry, molecular dynamics, molecular mechanics | 8.2.1 | Utah | Anita Orendt | Installation Only |
| TMHMM | Applications | 2.0c | Harvard FAS | Bob Freeman | Intermediate User | |
| tophat | Applications | 2.0.13 | Harvard FAS | Bob Freeman | Experienced User | |
| tophat | Applications | Bioinformatics, Genomic analysis | 2.0.4(D) | Utah | Wim Cardoen | Installation Only |
| tophat | Applications | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | ||
| totalview | Programming Tools | Debugging | 8.14.0, 8.15.0, 2016.01, 2016.05 (D) | Utah | Martin Cuma | Experienced User |
| TransDecoder | Applications | 2013, 2014 | Harvard FAS | Bob Freeman | Intermediate User | |
| trilinos | Applications | Math | 11.12.1 | Utah | Anita Orendt | Installation Only |
| trimmomatic | Applications | genomics | 0.33 | Utah | Anita Orendt | Installation Only |
| Trimmomatic | Applications | 0.30,0.32 | Harvard FAS | Bob Freeman | Experienced User | |
| trim_galore | Applications | Genomic analysis, genomics | 0.3.3 | Utah | Anita Orendt | Installation Only |
| trinity | Applications | genomics | 2.2.0 | Utah | Anita Orendt | Installation Only |
| Trinity | Applications | 2013, 2014 | Harvard FAS | Bob Freeman | Experienced User | |
| trinity | Applications | Wisconsin | Christina Koch, Lauren Michael | Novice User, Novice User | ||
| Trinotate | Applications | 2013, 2014 | Harvard FAS | Bob Freeman | Experienced User | |
| udunits | Applications | Atmospheric Sciences | 2.2.19, 2.2.25 (D) | Utah | Martin Cuma | Installation Only |
| uima | Applications | apache-uima-as-2.6.0 | Utah | |||
| umls | Applications | Healthcare | Utah | |||
| unphased | Applications | Genetic trait analysis, Genetics | 3.1.5 | Utah | Anita Orendt | Installation Only |
| Unrar | Applications/Utilities | File compression | 5.3.11 | Utah | Wim Cardoen | Installation Only |
| usearch | Applications | Genomic analysis, genomics | 6.1.544 | Utah | Anita Orendt | Installation Only |
| useq | Applications | Genomic sequencing, genomics | 7.9.3 | Utah | ||
| usf (Uppsala Software Factory) | Applications | Crystallography tools, Structural biology | Utah | Anita Orendt | Installation Only | |
| vaast | Applications | Genomic analysis, genomics | 2.1.6, 2.1.3 | Utah | Anita Orendt | Installation Only |
| vapor | Applications | Atmospheric Sciences, visualization | 1.5.2, 2.0.2, 2.2.4, 2.5.0 | Utah | Martin Cuma | Installation Only |
| vasp | Applications | materials, molecular dynamics | Wisconsin | Christina Koch, Lauren Michael | Experienced User, Experienced User | |
| vat | Applications | Genomic analysis, genomics | 2.0.1 | Utah | Anita Orendt | Installation Only |
| vcftools | Applications | Genomic analysis, genomics | 0.1.11, 0.1.7, 0.1.14-20 (D) | Utah | Anita Orendt | Installation Only |
| Velvet | Applications | 1.2.10 | Harvard FAS | Bob Freeman | Intermediate User | |
| velvet | Applications | Wisconsin | Christina Koch, Lauren Michael | Intermediate User, Intermediate User | ||
| VisIt | Applications | visualization | 2.10.0, 2.10.1, 2.10.2, 2.10.3 (D) | Utah | Martin Cuma | Novice User |
| VisualSFM | Applications | visualization | 0.5.26 | Utah | Anita Orendt | Installation Only |
| vmd | Applications | chemistry, visualization | 1.9.2, 1.9.3(D) | Utah | Anita Orendt | Intermediate User |
| voronoi | Library | Applied Math, C, Delaunay triangulation, Math | 0.4.5, 0.4.6(D) | Utah | Wim Cardoen | Installation Only |
| weblogo | Applications | genomics | 2.8.2 | Utah | Anita Orendt | Installation Only |
| weka | Applications | Machine learning | 3.6.12 | Utah | Martin Cuma | Novice User |
| wgrib | Applications | Atmospheric Sciences | 1.8.0 | Utah | Martin Cuma | Installation Only |
| wgrib2 | Applications | Atmospheric Sciences | 2.0.2 | Utah | Martin Cuma | Installation Only |
| wien2k | Applications | C, chemistry, Computational chemistry | 14.2 | Utah | Anita Orendt | Installation Only |
| wxWidgets | Libraries | C | 2.9.4 | Utah | Wim Cardoen | Installation Only |
| xerces | Utilities | XML parser | c-3.1.1(D) | Utah | Wim Cardoen | Installation Only |
| xz (lzma) | Applications | File compression | 5.2.2 | Utah | Wim Cardoen | Installation Only |
| zeromq | Library | 4.0.5, 4.1.3(D) | Utah | Wim Cardoen | Installation Only | |
| zlib | Library | C, Compilers, Compilers and Tools, Tools | 1.2.7 | Utah | Wim Cardoen | Installation Only |