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BioExcel Report Summary

Project ID: 675728
Funded under: H2020-EU.

Periodic Reporting for period 1 - BioExcel (Centre of Excellence for Biomolecular Research)

Reporting period: 2015-11-01 to 2017-04-30

Summary of the context and overall objectives of the project

The goal of the Centre of Excellence for Biomolecular Research (BioExcel) is to become a central hub for biomolecular modeling and simulations. It will enable better science by improving the most popular biomolecular software and spreading best practices and expertise among the communities through consultancy and training. Research and expertise in the centre covers structural and functional studies of the main building blocks of living organisms - proteins, DNA, saccharides, membranes, solvents and small molecules such as drug compounds.

The centre includes competence on dynamics, docking, screening and simulations of these building blocks, as well as analysis, refinement and classification of experimental structural data. Our expertise also covers techniques to model interactions between molecules, hybrid-QM/MM methods (targeting enzyme reactions) and coarse-level models (bridging applicability to higher levels of structural organization).

The specific goals of the centre are:
• Improve the performance, efficiency, and scalability of selected software packages of high importance for biomolecular Life Science research on next-generation HPC systems.
• Improve the usability of ICT technologies for biomolecular researchers, both in academia and industry. According to user needs, efficient workflow environments with associated data handling and integration of simulation and analysis codes will be devised.
• Promote best practices and train end users to make best use of both software and computational infrastructure.
• Develop appropriate governance structures and a sustainable business plan

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Objective 1. Excellence in Biomolecular Software:
Updates to the three core applications GROMACS, HADDOCK and CPMD, as well as PMX have been released. The releases come with improved performance and scalability as well as reliability via implemented unit tests and continuous integration infrastructure utilization. Clear roadmaps for future work have been set with particular focus towards future exascale capabilities. We have engaged in collaborations with vendors such as NVidia, Intel etc. to adapt the codes for taking advantage of upcoming technologies. In addition, preparatory work on ensemble/throughput computing has been undertaken to facilitate further exascale usage patterns.

Objective 2. Excellence in Usability:
We have analysed the state of the art and identified technological gaps, which need to be filled in order to improve the usability of the applications as means towards increased productivity and reliability of computational research. We have built the testbed infrastructure in parallel with major work on the BioExcel cloud portal. Several workflows have been designed based on the pilot use cases and one of them has been already run across 6 different environments using 3 different workflow managers each. We supported the development of the Common Workflow Language (CWL), which has seen great interest by organizations such as ELIXIR and the US Food and Drug Administration (FDA). We have very close interactions (and a signed MoU) with ELIXIR and our contributions have been praised in its reports.

Objective 3. Competence-building among academia and industry:
We have developed a comprehensive training program based on a competency profile comprised of 31 competencies for 3 different user groups. We have identified the existing gaps and planned our training activities towards filling those that are most urgent and provide biggest value by the available expertise and resources. We have collected an extensive number of existing training material which has been provided via the knowledge resource center. We have carried 28 training events across Europe and Asia of 3 were organized specifically as part of the training program. In order to engage with the wider communities, we have established interest groups on 7 different topics. Our forum ( is very much used as a support center for some
of the codes. We are running very popular webinar series, which have attracted a few thousand views at the time of this report.

Objective 4. Work towards a sustainable structure:
We have developed a business plan for sustainable center operations. The plan is based on information gathered through surveys with BioExcel partner institutions, EU HPC centers and related projects and initiatives. The plan outlines different scenarios based on the available funding income. We have studied the potential modalities and funding options as means for long-term support of the center. Under our initiative, we organized meetings on sustainability with other CoEs and VREs. Viable governance structures have been identified and will be the basis for consideration in following phases of the project. We have signed three MoUs with important strategic partners in Europe and USA.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

BioExcel acts as a bridge between e-Infrastructure resource providers, software developers for biomolecular applications, academic and industrial researchers within molecular life science, and other key stakeholders in computing. In so doing, BioExcel stimulates collaborative software development and use of e-Infrastructure for the benefit of European innovation and competitiveness, primarily via three core innovations:

Innovation 1: More efficient, scalable, and functional software
Impact: Through increasing the efficiency, scalability, and functionality of key biomolecular software, the computational costs will drastically be reduced providing a shorter time to solution, better exploitation of the available hardware, and thus reducing the development cycle and increasing the effectiveness of key products such as new drugs.
Current results: We have delivered code releases with improved performance and scalability, new features introduced and support for cutting-edge hardware platforms.

Innovation 2: Improved access to data- and e-Infrastructures
Impact: Lowering the barrier to access data and e-Infrastructures will facilitate the uptake of computational technologies in the target sectors, improve their efficiencies and thus again directly contribute to increased efficiency and competitiveness.
Current results: We have developed most of the necessary application building blocks and workflow units. The HPC, cloud and accelerator environments for workflow execution are operational and have been integrated with the necessary data resources and first tests have been carried out.

Innovation 3: Improved competence among academia and industry
Impact: By increasing the competence on using computational methods, providing support, and related training programs, BioExcel provides an innovative portfolio of services by building on scientific and technological excellence. It will contribute to improved research output and foster the international competitiveness of European academia & industry.
Current results: We have defined competency profiles of specific user groups and developed a specific training program to address the urgent gaps. The program includes workshops with hands-on sessions, webinar series and an online knowledge resource center. Extensive support has been provided via the forums at and the respective codes’ mailing lists. We established 7 interest groups for additional targeted support and engagement. We have been working closely with several related initiatives for greater impact, e.g. ELIXIR, Open PHACTS, WestLife and MuG VREs.

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