Software

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.

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:

VisIt

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool for visualizing data defined on two- and three-dimensional structured and unstructured meshes.

 

HMMER

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMS). HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models.

Availability and Restrictions

Versions

HMMER is available on the OSC clusters. These are the versions currently available:

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.

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