BioDynaMo: a bit of history, to understand the future

It all began in 2014, when Prof. Marcus Kaiser (then based at Newcastle University, now based at Nottingham University) was awarded institutional seed funding to investigate collaborative opportunities with other institutions. This was in the context of his Human Green Brain Project, and led to a conversation with CERN, and I (a Postdoc in his lab) was sent to Geneva in July 2014. There, I met Dr Marco Manca at CERN Directorate General who was working as a senior research fellow on bio-medically relevant topics. We came up with the ideas underpinning BioDynaMo, and wrote a project proposal. We presented the project to the CERN Medical Applications Council, then having its first steps, chaired by Dr Steve Myers, and obtained its green light to further develop the proposal and demonstrate a buy-in from within CERN research community.

 

As part of our lobbying we reached out to Dr Alberto di Meglio, Head of CERN openlab. CERN openlab is a platform for facilitating collaboration between CERN, industrial stakeholders, and, upon initiative of Alberto di Meglio for that cycle of activity, academic institutions. Also Dr Fons Rademakers, Chief Research Officer at CERN openlab, was involved in this discussion. The project was deemed interesting but had to be broken down and made compatible with the openly framework, so we came back to office to develop a detailed Project Statement of Work, including the overall aims, required resources and a time plan including milestones.

On November 11th, 2014 I gave a talk on the project at the CERN openlab Healthcare Workshop, which was the first time the ideas were presented to a general audience.

 

In June 2015, a framework agreement between CERN and Newcastle University, defining the terms to collaborate, was signed by the legal teams of both institutions. This agreement was  further concretised in the CERN openlab V Project Agreement, which was signed in December 2015. In addition to Newcastle University and CERN, it also included additional partners Intel, Innopolis University and Kazan University (for the records, GSI Helmholtz Center was also a signatory of the agreement, but was not involved in the BioDynaMo initiative at the time, as the “optimisation of code” umbrella also covered activities on other software from the high energy physics community).

 

In Sep 2015, the Intel Modern Code Developer Challenge was launched, originating from a collaboration involving Newcastle University, CERN and Intel. As the base code developer, I wrote agent-based simulation code that had to be optimised in the context of this competition. It attracted thousands of students from all over the world, and helped us with regard to the implementation of a high-performance computing core for agent-based modelling. In particular, we managed to obtain a speedup of 595x as described in the study (Gonzalez-de-Aledo et al., Adv Eng Softw, 2018).

 

In Sep 2016, I started an Fellowship funded by the Medical Research Council of the UK, a so-called MRC Skills Development Fellowship (MR/N015037/1). This fellowship titled “Computational modeling of retinal development” provided significant support (costed at £274,477) for research on retinal development, and my lab contributed to the BioDynaMo core as well as the neuroscience module.

 

In June 2018, I started a different Fellowship funded by the Engineering and Physical Sciences Research Council of the UK, a so-called EPSRC UKRI Innovation Fellowship (EP/S001433/1) that is costed at £502,399. This Fellowship is titled “Computational modelling of cryopreservation of biological tissue”. Here, we extend BioDynaMo for the modelling of the cryopreservation of cells and tissues, and we are currently preparing a manuscript on this extension named “CryoDynaMo”.

 

To date, the BioDynaMo project has become a formal international collaboration. This step towards a consortium-led initiative was realised in July 2019, when the BioDynaMo Collaboration Agreement was drafted and signed by Newcastle University and CERN. Since then, we have significantly grown and now include also the University of Cyprus (admitted on Aug 2019), GSI Helmholtz Center (Aug 2019), Immunobrain Checkpoint (Aug 2019), University of Geneva (Jun 2020), the University of Surrey (Oct 2020) and SCImPULSE Foundation (Oct 2020). I have been elected Spokesperson of the collaboration, thus liaising with external stakeholders and potential partners, and chair the Collaboration Board. The project coordination also set up a Technical Committee, coordinating the development and supervising the quality of contributed code, whose chair is currently CERN’s Fons Rademakers.

biodynamo_team_2015.jpg

Photo of BioDynaMo team members in 2015.