Software

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.

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:

Scipion

SCIPION is an image processing framework fo robtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

SPM

SPM is made freely available to the [neuro]imaging community, to promote collaboration and a common analysis scheme across laboratories. The software represents the implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package.

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:

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