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* |
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
