D3.1 – Specification of data/ API requirements - M9
D3.1 report contains the results of analysis of API needs for the modules to be properly integrated. Most interfaces concern data format and parameters. It describe LiGen modules, with overviews of each module’s goal, input/output and command line arguments. The interfaces of the LiGen modules have been updated to build flexible workflow, also including external tools. Most of the already existing modules of LiGen have been refactored to consider the new defined interfaces. For GROMACS work has focused on requirements for automatic topology and parameter generation, and automatically decide simulation length to reach a target precision. The document also shows examples of module composition for more complex workflows, including Virtual Screening, pre-processing, docking, scoring and free energy calculations. and considers a preliminary analysis for the HyperQueue tool to manage submission of the workflows. In summary, API needs have been analyzed and reviewed and interfaces for modules development have been defined, as well as settling on common input/output standard formats. Consistency between application concepts (e.g., data types) has been verified, and a plan for API evolution has been defined that will pave the way for subsequent D3.2 and D3.3 deliverables.
D3.2 Data translators
and code
Extensions to existing data translators when possible, and implementation of new ones either as scripts, standalone programs or in the original applications to allow exchange of data and interact within the solution.
This work has been highly successful. While there will be additional efforts in the second half of the project to fully integrate with newly developed interfaces, in particular to better identify and handle broken, incorrect or simply unsupported molecules (for a particular parameter set the user has selected), the achievements here have allowed us to execute our first trial benchmark tests of large-scale free energy and docking workflows.