Bioexcel Deliverable 2.1 – State Of The Art And Gap Analysis

Adam Hospital, Anna Montras, Stian Soiland-Reyes, Alexandre Bonvin, Adrien Melquiond, Josep Lluís Gelpí, Daniele Lezzi, Steven Newhouse, Jose A. Dianes, Mark Abraham, Rossen Apostolov, Emiliano Ippoliti (+2 others)
2016 Zenodo  
This deliverable describes the state of the art and gives a technological gap analysis in the portable environments for computing and data resources of BioExcel. We review the commonly used technologies for computational infrastructures, a selection of workflow managers for computational biology and three important repositories for biomolecular data. We then provide a catalogue of tools that are supported by BioExcel partners, which will become the building blocks used in the pipelines and
more » ... versal workflow units of our pilot use cases. We then describe the seven BioExcel pilot use cases. To help identify potential issues in developing the corresponding pipelines, the use cases have been individually described and analyzed, focusing on the set of functionalities (from the tool catalogue and elsewhere) that form a complete workflow. Interoperability between building blocks and data models are explored using workflow diagrams. Finally, we summarize the technological gaps for each use case. We analyzed the user feedback from WP3 to highlight key focus areas for BioExcel's future work. From the initial WP3 survey together with previous HADDOCK and GROMACS surveys we identified three main areas of potential user interest: Interoperability, usability and remotely accessible tools. For the interoperability issue, we found that the need for manual interaction needs to be reduced, for instance by incorporating workflow managers to integrate processes and input/output data. For the usability part, we found that improvements could be made to the main codes (GROMACS, HADDOCK and CPMD) to ease their usage, such as web portals providing assistance on how to run, install or use advanced configuration options. Finally, we realized that a high number of users would be interested in using remote tools, although several concerns have been raised about this, namely data privacy, reliability, and lack of control. Based o [...]
doi:10.5281/zenodo.263963 fatcat:o2v7ogjmnbauhn7txp2buz3pem