Collaborations


Collaborations are an integral part of our goals to provide support and impact within the wider community. In addition to the ongoing efforts of each of the partners, the CoE has formalized several strategic and collaborative partnerships through Memorandums of Understanding (MoUs).

How to become a partner

As a first step, we recommend that you get in contact with BioExcel personnel whose work is most closely related to your area of research. After discussion of your interest, please fill out together with your contact person the short proposal for partnership.

Download the template: Proposal for an Strategic Partnership with BioExcel CoE

The proposal will be reviewed by the executive board and we will follow-up with the next steps.

Established partnerships

   The Open PHACTS Foundation is a registered charity dedicated to sustaining and developing the Open PHACTS Discovery Platform, with an interest in data standards, interoperability and public understanding of drug discovery science. It is part of a large community of researchers and developers from industry, academia and small businesses.

The platform provides access and query of publicly-available pharmacological linked data in a single integrated, open infrastructure. One of the BioExcel pilot use cases is harnessing the Open PHACTS platform as a source of pharmacological data.

ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access services that are vital for their research.

The collaboration framework between Elixir and BioExcel includes work on the http://bio.tools database, adoption of API libraries and workflow specifications, joint efforts towards adoption and performance evaluation of the common workflow language (CWL) in selected workflows, as well as joint webinar series.

The Molecular Sciences Software Institute (MolSSI) serves as a nexus for science, education, and cooperation serving the worldwide community of computational molecular scientists. The Institute supports advances in software infrastructure, education, standards, and best-practices that are needed to enable the molecular science community to open new windows on the next generation of scientific Grand Challenges.

BioExcel’s cooperation with MolSSI allows to strengthen the links with the US research communities. Joint activity plans include joint projects involving scientists on both sides, sharing of expertise and/or biomolecular software, exchange of students or teaching material, and organizing joint training events and promotion of other ongoing activities.

Within the Division of Molecular and Computational Toxicology at Vrije Universiteit Amsterdam (VUA), the Biomolecular Simulation and Modeling team develops, implements and applies advanced in silico models to study and predict protein-ligand binding from (HPC) simulation. In the context of the IMI-JU eTOX project and the current NL-eScience project Enhanced protein-drug binding prediction, the team integrates molecular dynamics and other advanced modeling approaches into efficient heterogeneous workflows for the purpose of binding affinity prediction, protein engineering or other applications.

The workflow frameworks developed by the group of Daan P. Geerke are a valuable addition to the work at BioExcel. As part of our collaboration, the frameworks will be extended with support for our core applications HADDOCK and GROMACS, as well as organization of joint webinars and training events.

  HPCE3 project started on May 1st 2017 aims to maintaining the persistence of a high-quality service of transnational access to the most advanced HPC infrastructures available in Europe for European research. The project is based on a programme of visits, in the form of traditional transnational access, with researchers visiting HPC centres and/or scientific hosts who mentor them scientifically and technically. The visitors are funded for travel, accommodation and subsistence. They are provided with an amount of computing time suitable for the approved project. The calls for applications are issued four times a year and published online at www.hpc-europa.eu

Our two organizations will collaborate on dissemination of relevant information among the respective communities, and exchange of expertise in sustainability development.