MRIQC
MRIQC is a program that provides automatic prediction of quality and visual reporting of MRI scans.
Availability and Restrictions
Versions
The following versions are available on OSC clusters:
Software
fMRIPrep
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
Trinity
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Availability and Restrictions
The following versions of Trinity are available on OSC clusters:
Software Refresh - May 2020
OSC will be refreshing the software stack for Owens and Pitzer on May 19, 2020. This will be done in a system-wide downtime. During the software refresh, some default versions will be changed to be more up-to-date. Information about the new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
HDF5-Serial
HDF5 is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids.
For mpi-dependent codes, use the non-serial HDF5 module.
Connectome Workbench
Connectome Workbench is an open source, freely available visualization and analysis tool for neuroimaging data, especially data generated by the Human Connectome Project.
Availability and Restrictions
Versions
Connectome Workbench is available on Pitzer and Cardinal clusters. These are the versions currently available:
LS-PrePost
LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.
Availability and Restrictions
Versions
The following versions of ls-prepost are available on OSC clusters:
QGIS
QGIS is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, Windows and Android and supports numerous vector, raster, and database formats and functionalities.
Availability and Restrictions
Versions
The following versions of QGIS are available on OSC clusters:
Gaussian
Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems.
Gurobi
Gurobi is a mathematical optimization solver that supports a variety of programming and modeling languages.
Availability and Restrictions
Versions
The following versions of bedtools are available on OSC clusters:
