Scipion¶

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy.

Policy¶

Scipion is available to users at HPC2N. Scipion is freely available and it’s source code is 100% open.

@article{DELAROSATREVIN201693, title = "Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy", journal = "Journal of Structural Biology", volume = "195", number = "1", pages = "93 - 99", year = "2016", issn = "1047-8477", doi = "https://doi.org/10.1016/j.jsb.2016.04.010", url = "http://www.sciencedirect.com/science/article/pii/S104784771630079X", author = "J.M. de la Rosa-Trevín and A. Quintana and L. del Cano and A. Zaldívar and I. Foche and J. Gutiérrez and J. Gómez-Blanco and J. Burguet-Castell and J. Cuenca-Alba and V. Abrishami and J. Vargas and J. Otón and G. Sharov and J.L. Vilas and J. Navas and P. Conesa and M. Kazemi and R. Marabini and C.O.S. Sorzano and J.M. Carazo", keywords = "Electron microscopy, Single particle analysis, Image processing, Software package, Workflows, Reproducibility", abstract = "In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es." } 

Overview¶

Scipion is an image processing framework for obtaining 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.

Scipion at HPC2N¶

On HPC2N we have Scipion available as a module on Kebnekaise. To see the available versions, login to Kebnekaise and do ml spider scipion.

Usage at HPC2N¶

Scipion is best used with its graphical frontend. To use the graphical frontend one should login to our Thinlinc based login node, see our support page for how to use ThinLinc.

Then, when you are logged in with ThinLinc, to use Scipion, load the Scipion module to add it to your environment.

You give this command to see which versions are available of Scipion:

ml spider Scipion

and you then do

ml spider Scipion/<version> 

to see how to load a specific version and its prereqisites.

ml GCC/8.2.0-2.31.1  OpenMPI/3.1.3 Scipion/2.0.0-Python-2.7.15    

ml GCC/8.2.0-2.31.1  CUDA/10.1.105  OpenMPI/3.1.3 Scipion/2.0.0-Python-2.7.15  

Setup¶

After loading the Scipion module, do

scipion config

This will create a scipion.conf file in $HOME/.config/scipion

Scipion also uses a separate directory for storing the projects in, the directory is defined in your scipion.conf file.

We recommend changing the SCIPION_USER_DATA definition in that file to use a directory in your project storage.

Differences in the GUI from standard installations¶

At HPC2N we have modified how to run the different protocols to be able to use the batch system more efficiently. When opening a Scipion protocol definition, the “Host” field have multiple entries.

The “localhost” entry can be used to run shorter, non-cpu intensive tasks, on the login node, or submit tasks to the batch system and run on CPUs only, good for any protocol that doesn’t utilize GPU resources. There is also a “GPU_batch_job” entry that can be used to submit GPU based tasks to the batch system.

When submitting tasks to the batch system one have to fill in the “project id” field. When using the “GPU_batch_job” selection one also have to choose GPU type to run on. Please read the support pages regarding how to use the GPU resources at HPC2N.

NOTE: Motioncor2 currently has a bug when running on the V100 GPUs and produces bad output. Use other GPUs.

Additional info¶

More information about Scipion and how to run it can be found on the Scipion home page.