Introduction

Today’s translational research era calls for innovative solutions to enable researchers and clinicians to build bridges between the microscopic (molecular) and macroscopic (human) scales. This requires building both transversal and vertical connections between techniques, researchers and clinicians to provide them with an optimal e-Science toolbox to tackle societal health challenges.

At the microscopic level, proteins and their intricate network of interactions are the mainstay of any cellular process. Disruption and perturbations in those networks are at the onset of many diseases. Dissecting these networks at atomic detail is therefore invaluable, as this will pave the route to a mechanistic understanding of biological function and provide the first essential step toward the development of new drugs. To achieve this, structural biologists have to resort to an arsenal of various biochemical, biophysical and computational techniques, share data of various natures and collaborate, which is at the core of integrative structural biology. The ESFRI project INSTRUCT aims at unifying the structural biology landscape into a pan-European infrastructure. On the e-Infrastructure side, the WeNMR virtual research community (VRC) has set the first steps toward providing e-Science solutions for integrative structural biology by bringing together the NMR and SAXS research communities (and currently expanding to include the fast growing cryo- Electron Microscopy community), establishing standard computational workflows and services through easy-to-use web interfaces and making efficient use of the European Grid Infrastructure (EGI). It serves a worldwide community of 4500+ registered users, with a sustained growth over the years, connections to Asia-Pacific and America (e.g. with the Open Science Grid). To date the WeNMR VRC has access to >100’000 CPU cores via the EGI infrastructure, running several millions of jobs and with a significant impact as measured by large number of peer-reviewed scientific publications.

At the macroscopic level, the explosion of medical data in the clinical setting of the past 20 years has led researchers to develop procedures aimed to exploit them in an efficient way to perform scientific analyses and improve patient care and diagnostic. This clinical data explosion, while opening unprecedented avenues for scientific exploration, has as consequence that exploitation of these large datasets can only be efficiently done in few laboratories worldwide, thus jeopardizing the potential impact of this kind of research. In order to address those issues in the area of brain and neurodegenerative disease research, the NeuGrid4You (N4U) project has built a virtual research environment (>6000 cores and >20 TB physical space) where neuroscientists and clinicians in Europe and worldwide can securely upload, use and share brain feature extraction algorithms paired with access to computational power, large image datasets and specialized support & training. This has provided the fuel to a better understanding of the pathophysiological mechanisms of diseases, the development of markers of disease activity and progression and, in the long term, will boost the drug discovery process for neurodegenerative and other brain diseases.

Now the time has come to build bridges between the microscopic and macroscopic worlds in order to facilitate both the transversal and vertical integration and sharing of techniques and knowledge needed to tackled health challenges, which is what this competence center is about.

Objectives

The main objective of MoBrain is to lower barriers for scientists to access modern e-Science solutions from micro to macro scales (O0). By building on grid- and cloud-based infrastructures and on the existing expertise available within WeNMR and N4U and by integrating molecular structural biology and medical imaging services and data, MoBrain will kick-start the development of a larger, integrated, global science virtual research environment for life and brain scientists worldwide. The mini-projects defined in MoBrain are geared toward facilitating this overall objective, each with specific objectives to reinforce existing services, develop new solutions and pave the path to global competence center and virtual research environment for translational research from molecular to brain. 

Tasks

  • T1: Cryo-EM in the cloud: bringing clouds to the data
  • T2: GPU portals for biomolecular simulations
  • T3: Integrating the micro- (WeNMR/INSTRUCT) and macroscopic (NeuGRID4you) virtual research communities
  • T4: User support and training

Deliverables

  • D6.4 Fully integrated MoBrain web portal (OTHER), M12 (02.2016) - by T3
  • D6.7 Implementation and evaluation of AMBER and/or GROMACS (R), M13 (03.2016) - by T2
  • D6.12 GPGPU-enabled web portal(s) for MoBrain (OTHER), M16 (06.2016) - by T2&3
  • D6.14 Scipion cloud deployment for MoBrain (OTHER), M21 (11.2016) - by T1