Scipion on-demand service in the cloud

Scipion is an image processing framework used to obtain 3D maps of macromolecular complexes using cryo Electron Microscopy, developed by the researchers of CNB-CSIC. This is a clear example of a community self-developed solution that can be integrated for support in generic Clouds (public and private).

It has emerged as the solution offered by the Instruct Image Processing Center (I2PC) to European scientists accessing the European Research Infrastructure for Structural Biology (Instruct). Scipion is a desktop application that can be installed on personal desktops as well as big servers or clusters. Even though installation and configuration is intended to be as easy as possible there are some specific parts that could be more complex, such as MPI setup or GPU configuration.

Besides, for a standard cryo-EM processing common desktop machines are clearly insufficient in terms of computing capability and storage, which could a problem for many scientists that might not have access to powerful servers or GPUs. However, computing may also take place in distributed and decentralized environments and in this way, cloud is a new form of accessing computing and storage resources on demand. To effectively use cloud infrastructures ScipionCloud was developed, resulting in a full installation of Scipion both in public and private clouds, accessible as public ‘‘images”, that include all needed cryoEM software and just requires a Web browser to work as if it was a local desktop.

These images could be used to easily deploy instances in the EGI Federated Cloud using the EGI AppDB VM operations dashboard. Besides, in the context of the Westlife project an alternative option to the use of fixed images has been developed. This uses the cloud orchestration tool Cloudify with the configuration management tool Puppet to automatically deploy and configure ScipionCloud software on a single machine or cluster in the EGI Federated Cloud. These two existing options allow to easily deploy on-demand servers or clusters in the cloud with ready-to-use Scipion software that could be used by cryoEM scientists to start processing their data.