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:

Version Pitzer
3.0.8 X*
* Current default version

You can use module spider scipion to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Scipion is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

All scipion code and plugins, are licensed under the GPL3 (http://www.gnu.org/licenses/gpl-3.0.html)

Now, Scipion interacts, and in some cases installs 3rd party software with its own LICENCE that must be observed.

So, it is under the user responsibility to check the license of each of the software scipion is installing.

In most cases, if not all, software is free available for academic use and industry but there are few exceptions where industry users are not granted for a free usage. You must check each case.

Usage

Usage on Pitzer

Set-up

To configure your environment for use of scipion, run the following command: module load scipion. The default version will be loaded. To select a particular scipion version, use module load scipion/version. For example, use module load scipion/3.0.8 to load SCIPION 3.0.8

Scipion/3.0.8 was built with gnu/9.1.0, openmpi/4.0.3-hpcx, cuda/10.1.168, and hdf5/1.12.0.

Plugins

The following plugins are installed

scipion-em-xmipp
scipion-em-resmap
scipion-em-sphire
scipion-em-localrec
scipion-em-bsoft
scipion-em-ccp4
scipion-em-cryoef
scipion-em-spider
scipion-em-imagic

 

Further Reading

Supercomputer: 
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