CORDIS

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CORDIS

Centre of Excellence for Biomolecular Research

Fact Sheet

Reporting

Results

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Project information

BioExcel

Grant agreement ID: 675728

Project website

Start date

1 November 2015
End date

31 December 2018

Funded under:

H2020-EU.1.4.1.3.

Overall budget:

€ 4 782 286,25
EU contribution

€ 4 782 286

Coordinated by:

KUNGLIGA TEKNISKA HOEGSKOLAN

Sweden

Objective

Life Science research has become increasingly digital, and this development is accelerating rapidly. Biomolecular modelling techniques such as homology modelling, docking, and molecular simulation have advanced tremendously due to world-leading European research, resulting in extreme demands for better computational performance and throughput as these tools are used in applied research and industrial development. This research has direct influence on our daily life in areas such as health and medical applications, the development of new drugs, efficient drug delivery, biotechnology, environment, agriculture and food industry. Life Science is one of the largest and fastest growing communities in need of high-end computing, and it is a critically important industrial sector for Europe. However, compared to some other disciplines, the use of e-Infrastructure is still relatively new - many advanced techniques are not applied commercially due to limited experience. It requires significant support to:
• Make e-Infrastructure useable by researchers who are not computing experts,
• Improve the performance and applicability of key life science applications,
• Handle large amounts of data in computational workflows.

BioExcel proposes to tackle these challenges by establishing a dedicated CoE for Biomolecular Research, covering structural and functional studies of the building blocks of living organisms - proteins, DNA, saccharides, membranes, solvents and small molecules like drug compounds - all areas where with large academic and industrial users bases in Europe. Specifically, BioExcel will
• Improve the efficiency and scalability of important software packages for biomolecular research;
• Improve the usability of ICT technologies for biomolecular researchers in academia and industry;
• Promote best practices and train end users in making good use of both software and e-Infrastructure.
• Develop appropriate governance structures and business plans for a sustainable CoE.

Programme(s)

H2020-EU.1.4.1.3. - Development, deployment and operation of ICT-based e-infrastructures

Topic(s)

EINFRA-5-2015 - Centres of Excellence for computing applications

Call for proposal

H2020-EINFRA-2015-1

See other projects for this call

Funding Scheme

RIA - Research and Innovation action

Coordinator

KUNGLIGA TEKNISKA HOEGSKOLAN

Address

Brinellvagen 8
100 44 Stockholm

Sweden

Activity type

Higher or Secondary Education Establishments

EU Contribution

€ 1 084 750

Website

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Participants (10)

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UNIVERSITEIT UTRECHT

Netherlands

EU Contribution

€ 279 000,25

FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA)

Spain

EU Contribution

€ 225 000

FORSCHUNGSZENTRUM JULICH GMBH

Germany

EU Contribution

€ 259 773,75

THE UNIVERSITY OF EDINBURGH

United Kingdom

EU Contribution

€ 1 001 226

THE UNIVERSITY OF MANCHESTER

United Kingdom

EU Contribution

€ 345 875

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Germany

EU Contribution

€ 598 411

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV

Germany

EU Contribution

€ 315 000

FORWARD TECHNOLOGIES AB

Sweden

EU Contribution

€ 264 500

BARCELONA SUPERCOMPUTING CENTER - CENTRO NACIONAL DE SUPERCOMPUTACION

Spain

EU Contribution

€ 225 000

IAN HARROW CONSULTING LTD

United Kingdom

EU Contribution

€ 183 750

Project information

BioExcel

Grant agreement ID: 675728

Project website

Start date

1 November 2015
End date

31 December 2018

Funded under:

H2020-EU.1.4.1.3.

Overall budget:

€ 4 782 286,25
EU contribution

€ 4 782 286

Coordinated by:

KUNGLIGA TEKNISKA HOEGSKOLAN

Sweden

Project information

BioExcel

Grant agreement ID: 675728

Project website

Start date

1 November 2015
End date

31 December 2018

Funded under:

H2020-EU.1.4.1.3.

Overall budget:

€ 4 782 286,25
EU contribution

€ 4 782 286

Coordinated by:

KUNGLIGA TEKNISKA HOEGSKOLAN

Sweden

Periodic Reporting for period 2 - BioExcel (Centre of Excellence for Biomolecular Research)

Reporting period: 2017-05-01 to 2018-12-31

Summary of the context and overall objectives of the project

The goal of the BioExcel project was to establish a Centre of Excellence for Biomolecular Research (BioExcel) that becomes a central hub for biomolecular modeling and simulations. The centre 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). It is contributing to important societal challenges in Health and Food and has wide impact in Academia as well as Industry, particularly the Pharma, Biotech, Chemical, and Food industries.

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:
The final releases of the pilot applications provide much improved performance and scalability. GROMACS, in particular, comes with support for all current CPU and accelerator platforms, including expected future exascale systems, with more than double performance since the start of BioExcel; and our novel QM/MM interface of CPMD has shown to scale efficiently on all the Tier-0 resources, enabling QM/MM simulations with CPMD for PRACE projects. Significant efforts have also been spent on reducing the time-to-solution for common free energy and sampling simulations of small systems – identified as a priority from industrial and academic users – by enabling ensemble simulations that automatically optimize sampling. HADDOCK, which is an example of an HTC application has been expanded with options that will make it run much more efficiently in a massive, distributed exascale scenario.

Objective 2. Excellence in Usability:
We have developed a rich library of biomolecular building blocks covering the most common needs of researchers. Workflows, based on those blocks, have been successfully tested and launched for wider adoption. Web-based portals such as HADDOCK and PMX have been updated to provide excellent user experience. The role of BioExcel within ELIXIR has grown to become the main contributor of best practices in the domain of structural and computational biomolecular science. A key element of interoperability is the emerging Common Workflow Language, which BioExcel and ELIXIR have adapted early on and helped evolve as a community standard, while we are also supporting more interactive workflow environments like KNIME, Galaxy and Jupyter Notebook.

Objective 3. Competence-building among academia and industry:
The results have been disseminated widely to the community and industry. We were involved in the organisation of over 30 events. Highlights include impact through activities with large bio-infrastructures such as ELIXIR; countries from the EU 13 area (via VI-SEEM VRE); international foothold (via MolSSI, US, FDA/BioCompute); good relationships established with industry contacts from several pharma companies, including site-visits to Janssen and UCB. The webinar series have been very popular, some of them with over 1000 views. Our training program has been refined, and support material in the knowledgebase expanded. Our support forum, AskBioExcel, is being well-used: as a whole, the forum has had about 21,000 page views from logged-in users, about 210,000 page views, and the top posts on this forum have been viewed over 2000 times.

Objective 4. Work towards a sustainable structure:
The business plan was refined and finalized. We have identified several products and services (particularly workflows and training) suitable for commercialization. They have been analyzed in terms of the current market and competitor landscape, and further tested during a focus group meeting with pharma industry representatives. Various funding schemes and modalities were extensively studied. Viable governance and legal structures were identified. Registration of a legal entity is planned for 2019.

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 providers, software developers, 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 be drastically 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.
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.
Results: We have developed a rich library of biomolecular building blocks covering the most common needs of researchers. Workflows, based on those blocks, have been successfully tested and launched for wider adoption.

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. It contributes to improved research output and fosters the international competitiveness of European academia & industry.
Results: We ran numerous topical workshops, hands-on and training events to address the gaps which were identified in the beginning of the project. Highlights include the impact through activities with large bio-infrastructures such as ELIXIR; countries from the EU 13 area (via VI-SEEM VRE); international foothold (via MolSSI, US); industrial support (site-visits to Janssen and UCB). The webinar series have been very popular, some with over 1000 views. Our training program has been refined, and support material in the knowledgebase expanded.

Logo of BioExcel Center of Excellence

Services and solutions provided by BioExcel CoE

Project information

BioExcel

Grant agreement ID: 675728

Project website

Start date

1 November 2015
End date

31 December 2018

Funded under:

H2020-EU.1.4.1.3.

Overall budget:

€ 4 782 286,25
EU contribution

€ 4 782 286

Coordinated by:

KUNGLIGA TEKNISKA HOEGSKOLAN

Project information

BioExcel

Grant agreement ID: 675728

Project website

Start date

1 November 2015
End date

31 December 2018

Funded under:

H2020-EU.1.4.1.3.

Overall budget:

€ 4 782 286,25
EU contribution

€ 4 782 286

Coordinated by:

KUNGLIGA TEKNISKA HOEGSKOLAN

Sweden

Events

BioExcel Summer School on Biomolecular Simulations 2020

22 June 2020 -

26 June 2020

Pula, Italy

7 May 2020

Project information

BioExcel

Grant agreement ID: 675728

Project website

Start date

1 November 2015
End date

31 December 2018

Funded under:

H2020-EU.1.4.1.3.

Overall budget:

€ 4 782 286,25
EU contribution

€ 4 782 286

Coordinated by:

KUNGLIGA TEKNISKA HOEGSKOLAN

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Last update: 9 September 2019

Record number: 198303

Permalink: https://cordis.europa.eu/project/id/675728

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Periodic Reporting for period 2 - BioExcel (Centre of Excellence for Biomolecular Research)

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