Centre of Excellence for Biomolecular Research
- Website: https://bioexcel.eu
- Started: November 1, 2015
- Duration: 3+3.5 years
- Project reference: https://cordis.europa.eu/project/id/823830 https://cordis.europa.eu/project/id/675728
The centre facilitate the use of high-performance computing (HPC) and high-throughput computing (HTC) in biomolecular research, both in academia and industry.
The BioExcel project aims to improve the performance, efficiency, scalability and accessibility of software for biomolecular modelling (in particular GROMACS, HADDOCK, CP2K, PMX), allowing such tools to be scaled up to run on larger supercomputer systems, while also making them easier for biomolecular researchers to use on computational infrastructures by providing training and guidance on best practices and integration with commonly used workflow systems such as CWL, KNIME, Galaxy, Apache Taverna or COMPSs.
As a Centre of Excellence, BioExcel gathers biomolecular consultants with experience in both HPC/HTC and the life sciences, who can assist both academic and industrial researchers with using and improving tools for computational biomolecular research.
eScience Lab contributions
In the BioExcel-2 project we are involved in:
- WP2: Convergence of HPC/HPDA and Improved Usability (deputy lead)
- T2.1: Application building blocks for computational biomolecular simulations
- T2.2: Definition, development and specification of workflow prototypes and demonstrators
- T2.4: Convergence of High Performance Computing (HPC) and High-Performance Data Analytics (HPDA)
- T2.5: Provisioning and maintaining a Workflow Environment
- T2.6: Retaining usability, interoperability and reproducibility in Exascale workflows (task lead)
- WP3: Community, Support and Use Cases
- T3.1: Use Case Support
- T3.2: Community Participation
- T3.3: In-Depth Support
- T3.4: Standards and Best Practice (task lead)
- T3.5: User & Community Needs Analysis
- T3.6: Challenge Participation and Support
- WP4: Dissemination and Training
- T4.1: Evaluate and test virtual learning environment
- T4.2: Promotion and outreach
- T4.3: User training
- T4.4: Capacity building and knowledge transfer
- T4.5: Collaboration
We will be building on our extensive experience and engagement with Common Workflow Language (CWL) and Research Objects as well as fostering links between BioExcel communities and related projects like ELIXIR, EOSC and BioConda.
We developed and maintain the CWL Viewer with support from BioExcel. We are contributing to the BioExcel Building Blocks (BioBB) library, translating workflows into CWL and assisting with the development of their tutorial material. We are also assisting with registering BioBB workflows on WorkflowHub.