Hackathon on Resources for Modelling in Biology 2014 (HARMONY 2014)
Lead Research Organisation:
University of Manchester
Department Name: Computer Science
Abstract
United Kingdom
Organisations
- University of Manchester (Lead Research Organisation)
- University of Rostock (Collaboration)
- University of Connecticut Health Center (Project Partner)
- California Institute of Technology (Project Partner)
- Institute of Plant Genetics and Crop Plant Research (Project Partner)
- University of Toronto (Project Partner)
- Babraham Institute (Project Partner)
| Description | This grant supported a meeting to define standards in systems biology. Standards are procedures that help interchange scientific results, in this case in the form of computational models. The meeting allowed the definition of several new features in standards to encode models in mathematical and graphical formats. |
| Exploitation Route | This grant supported a meeting of worldwide researchers who work in software for systems biology. The outcome of the meeting was used by all the participants to further develop computational methods for systems biology. |
| Sectors | Chemicals,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Description | Combining standards for today's models |
| Organisation | University of Rostock |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | This is a collaboration, headed by researchers at Uni. Rostock, but including many others from universities in UK, EU, USA, Australia, and other countries. The project aims to encode the whole-cell model reported in Karr et al. 2012 (DOI:10.1016/j.cell.2012.05.044) using systems biology standards. The intention is not only to standardize the model but also to reveal where the standards are limiting and to expand them. This includes using several software applications including our own COPASI. My work on this project has been to lead a team of collaborators to encode a sub-section of the model, and to provide expertise on the use of COPASI. Finally I have been capturing suggestions for new functions in COPASI that would improve how simulation of whole-cell models. |
| Collaborator Contribution | The partners have been using systems biology standards (SBML and SED-ML mainly) to encode the Karr model. They use several software applications including our own COPASI. In addition they also use the ChEBI database as a reference for metabolites. |
| Impact | no outputs yet (paper in preparation) |
| Start Year | 2015 |
| Description | HARMONY 2014 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure for systems biology. Most of the time was devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. There were also several discussions of new additions to standards (SBML, SBGN, SED-ML). |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://co.mbine.org/events/HARMONY_2014 |