BioExcel Deliverable D3.6 – Consultancy Support Proposals Update
Creators: name: Carter, Adam
name: Harrow, Ian
name: Badia, Rosa
name: Bonvin, Alexandre
name: Gapsys, Vytautas
name: de Groot, Bert
name: Hospital, Adam
name: Ippoliti, Emiliano
name: Matser, Vera
name: Melqiond, Adrien
name: Trellet, Mikael
name: White, Darren
Publisher: name: Zenodo
Year: 2019

description: BioExcel targets a broad and heterogeneous group of users from the biomolecular research community. Different kinds of consultancy and support will work best with different communities. In this project we have explored potential consultancy models through pilot use cases, contributed to a number of proposals for further related activities, and built solid foundations for future professional consultancy by building trust with potential customers. The project ran five Pilot Use Cases (UCs) which had an important role in bringing together work from across the project. The UC <em>Alchemical Free Energy Calculations in Biomolecules </em>covered the field of Free Energy Calculations, in which there is currently strong interest in the wider community, including drug discovery by pharmaceutical companies. It linked GROMACS with pmx, both codes being supported by BioExcel. <em>Molecular Recognition</em>, introduced a test bed where two BioExcel codes (HADDOCK and GROMACS) were used within the same automated workflow using the platform MDstudio, which will help to scale up and harvest of HPC/HTC resources in a simplified way. <em>Virtual Screening </em>was a collaboration with Nostrum Biodiscovery to study an important drug discovery process. <em>Multi-scale modeling </em>focused on validating a new highly parallel QM/MM interface of CPMD by applying the code to a state-of-the-art problem and comparing main results with the simulations performed with the original CPMD QM/MM interface. <em>Rapid turnaround cancer analysis pipeline for high throughput sequencing data </em>brought together existing processes into a new automated workflow and evaluated its suitability for an HPC implementation. The process of engaging with communities (and potential future customers) has been a gradual one. After an initial community landscaping exercise, several activities were begun to engage with communities of interest. Webinars proved a successful mechanism to begin engagement from the outset of the project; support forums provided a way for us to support existing users of the project’s codes from the start. As the project developed, there were opportunities to engage with communities face- to-face in smaller workshop meetings and the Community Forum, which was designed to bring members of different interest groups together. As well as supporting the wider community, considerable groundwork has been put in place to build a capability to offer professional consultancy, building trust with potential future customers. This groundwork included site visits and customised training for pharmaceutical companies such as Janssen and UCB. In addition, the project’s pilot use cases have provided insight into possible consultancy models and services such as webinars, forums and events which simultaneously allowed us to support best practice, share information about the centre, and learn more about the needs of the communities. The project has also provided opportunities for partners to engage in a number of new proposals, such as the consortium for Integrative Modelling of Antibodies (IMAbs) which includes UCB, AstraZeneca and MedImmune, some of which have led into further use-case work in BioExcel-2 which includes topics of specific interest to potential future industry clients.