Scipion is an application framework developed as a collaboration between many institutions including the Instruct Image Processing Center (I2PC) in Madrid to help the Structural Biology community to process Cryo Electron Microscopy (CryoEM) data. Scipion is developed as a plugin-based workflow management system that integrates many important software packages available in the field.

Scipion is a desktop application and the user interacts with it through a GUI developed in python and Java. ScipionCloud, previously offered as an EGI AppDB image, has been converted to a web service that can be used by Instruct users to deploy a cluster in EOSC cloud resources to keep processing data acquired at a CryoEM facility. This cluster has Scipion installed as well as most of the plugins and external packages used by the community, all ready to be used. In this first prototype only a single Scipion node is deployed but the next version will deploy a slurm elastic cluster using one of the core EGI services, EC3. Worker nodes will only be created when the workload requires it, ensuring an optimum usage of cloud resources. 


Added-value EOSC integration


SCIPION service has moved from a static image that needed to be deployed directly on a specific site to a fully web service that is easy to use thanks to the integration of some of the EOSC core services. Now INSTRUCT users can access the service at the IM dashboard using her ARIA (the identity provider developed by Instruct) credentials and deploy a cluster on EOSC cloud resources by clicking on a button and providing some input through a guided wizard. All this is accomplished by using the following services:

  • Authentication: The portal to deploy Scipion service (currently the IM dashboard) integrates the EGI Check-in service that allows INSTRUCT users to keep using her ARIA (the identity provider developed by Instruct) credentials.
  • Elastic cluster deployment: Currently IM service is used to deploy a single Scipion node but the next version will use EC3 and SLURM to deployan elastic cluster on EOSC cloud resources or public clouds such as AWS EC2. Scipion can send jobs through SLURM which is totally integrated with EC3.
  • EOSC cloud resources: The cluster might be deployed on EOSC federated cloud if user credentials permit it.

Related documents

Users can find documentation on how to use the application as well as tutorials and information useful to integrate new protocols as plugins.

  • Dedicated documentation about the ScipionCloud service can also be found there at the following URL:

and in the github repo

Relevant links

Related publications

The following publications are related to the Scipion framework:

  • Other related publications can be found here.

The service was presented at the EGI conference in 2021 with the title ‘Towards FAIR CryoEM workflows in EOSC’.

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