Software

Connectome

Connectome is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

DSI Studio

DSI Studio is a tractography software tool that maps brain connections and correlates findings with neuropsychological disorders. It is a collective implementation of several diffusion MRI methods, including diffusion tensor imaging (DTI), generalized q-sampling imaging (GQI), q-space diffeomorphic reconstruction (QSDR), diffusion MRI connectometry, and generalized deterministic fiber tracking.

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:

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:

PETSc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism. The supported libraries include f2cblaslapack, superlu, ptso, metis, parmetis, mumps, hypre and scalapack.

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.

NetCDF-Serial

NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netcdf library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

For mpi-dependent codes, use the non-serial NetCDF module.

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 discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

Availability and Restrictions

Versions

Connectome Workbench is available on Owens and Pitzer clusters. These are the versions currently available:

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