Mathematica
Mathematica is a mathematical computation program. It is capable in many areas of technical computing including but not limited to neural networks, machine learning, image processing, geometry, data science and visualizations.
Software
NVHPC
NVHPC, or NVIDIA HPC SDK, C, C++, and Fortran compilers support GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC® directives, and CUDA®. GPU-accelerated math libraries maximize performance on common HPC algorithms, and optimized communications libraries enable standards-based multi-GPU and scalable systems programming. Performance profiling and debugging tools simplify porting and optimization of HPC applications, and containerization tools enable easy deployment on-premises or in the cloud.
Clara Parabricks
Clara Parabricks is a powerful toolkit designed for genomic analysis. It is primarily designed for GPU computation.
CIAO
CIAO (also known as Chandra Interactive Analysis of Observations) is a X-Ray telescope analysis software package for astronomical observation. CIAO focuses on the Chandra X-ray observatory. It contains a toolset used to analyze fits files and is commonly used in conjuction with DS9 and Sherpa, and focuses on data flexibility.
DS9
SAOImageDS9 is a astronomical imaging and data visualization application. DS9 provides support for FITS images, binary tables, multiple frame buffers, region manipulation, and colormaps display options
Availability and Restrictions
The following versions of DS9 are available on OSC clusters:
WCStools
WCStools is a program package designed for working with Images and the World Coordinate System. The aim of WCStools is to provide methods for relating pixels taken common astronomical images to sky coordinates.
Availability and Restrictions
The following versions of WCStools are available on OSC clusters:
Cell Ranger
Cell Ranger is a cell analysis library for generate feature-barcode matrices, perform Analysis for RNA samples. Cell Ranger works in pipelines for it's RNA sequencing analysis which allows it to: process raw sequencing output, read alignment, generate gene-cell matrices, and can perform downstream analyses such as clustering and gene expression analysis.
Unblur
Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurrig due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format. Unblur generates frame sums that can be used in subsequent image processing steps and optionally applies an exposure-dependent filter to maximize the signal at all resolutions in the frame averages. Movie frame sums can also be calculated using Summovie, which uses the alignment resuls from a prior run of Unblur.
OpenCV
OpenCV is an open-source library that includes several hundreds of computer vision algorithms.
MotionCor2
MotionCor2 uses multi-GPU acceleration to correct anisotropic cryo-electron microscopy images at the single pixel level across the whole frame, making it suitable for single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.
Availability and Restrictions
Versions
The following versions are available on OSC clusters:
