AlphaFold
AlphaFold is a software package that provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and pusblished in Nature.
Cardinal
Texlive
TeX Live is a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro pacakges, and fonts that are free software, including support for many languages around the world.
Availability and Restrictions
Versions
The following versions are available on OSC clusters:
AFNI
AFNI (Analysis of Functional Neuro Images) is a leading software suite of C, Python, and R programs and shell scripst primarily developed for the analysis and display of multiple MRI modalities: anatomical, functional MRI (FMRI) and diffusion wieghted (DW) data. It is freely available (both as open source code and as precompiled binaries) for research purposes.
Availability and Restrictions
Versions
The following versions are available on OSC clusters:
Neuropointillist
Neuropointillist is an in-development R package which defines functions to help scientists to run voxel-wise models using R neuroimaging 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.
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 Owens and Pitzer clusters. These are the versions currently available:
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:
