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 a Strategic Partnership with BioExcel CoE
The proposal will be reviewed by the executive board and we will follow-up with the next steps.
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.
The Scuola Normale Superiore (SNS) is an Italian public institute for higher education and research. SNS has very active groups in the field of Theoretical and Computational Chemistry linked with several international networks and societies (such as the Italian Biophysics Society, the European Society for Photobiology and the Italian Institute for Nuclear Physics and the Human Brain Project).
BioExcel is engaging in joint research work with SNS researchers on further development of multiscale modeling techniques. Our organizations are also organizing thematic meetings and dedicated schools in the area of biomolecular modeling using hybrid multiscale methods.
Multiscale Complex Genomics Virtual Research Environment (MuG VRE) supports the expanding 3D/4D genomics community by developing tools to integrate the navigation in genomics data from sequence to 3D/4D chromatin dynamics data. MuG VRE services include: personal user workspace, community-tailored tools and workflows and integrated user support. In addition, MuG offers training activities and community events, with the aim to enhance multidisciplinary communication and contribute to standardization in tools and methods.
BioExcel is engaging with MuG researchers on provisioning of tailored solutions such as VMs for the needs of the genomics community, defining a long-term collaborative framework for training, organizing thematic meetings, dedicated schools and educational webinars for increasing the adoption and expertise in biomolecular techniques within relevant genomics communities.
VI-SEEM provides networking and computational resources, application support and training, in both South East Europe and Eastern Mediterranean. It has supported the European vision of inclusive and smart growth, based on knowledge and innovation, enriching the European Research Area. The project unifies existing e-Infrastructures into an integrated platform to better utilize synergies, for an improved service provision within a unified Virtual Research Environment to be provided to scientific communities of high impact in the combined SEEM region.
BioExcel is partnering with VI-SEEM on dissemination of relevant information among the respective communities, promotion of BioExcel events to the VI-SEEM members in particular the Life Science groups, joint training activities including webinars and joint industry outreach activities.
Instruct-ERIC, through its centres, offers access to it’s infrastructure for researchers and industrial users, with support through training programmes and networking events. In addition, Instruct users are also offered services such as computational resources to conduct experimental analyses from structural data.
BioExcel is partnering with Instruct-ERIC to develop joint training programmes to cover technology advances and new data analysis and organise webinars to discuss computational services for user communities.
With a breadth of experience in software development, project management and community engagement, Software Sustainability Institute are working towards the advancement of cultivating better, more sustainable, research software.
Both organisations will work on activities such as development of quality marks for scientific software products and promotion of best practices for software sustainability within the Life Sciences community. BioExcel will also be engaging with Software Sustainability Institute by organising joint training programmes and webinars to facilitate exchange of expertise for user communities.
Iktos develops an innovative and user-friendly technology platform for deep-learning based de novo drug design.
BioExcel is partnering with Iktos on the application of advanced molecular modelling and simulation techniques for enhanced drug screening and design.