US Partnering Award: Systems Biology of Plants and Algae, from Molecular Networks to Informatics Infrastructure.

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
 
Description The travel award supported visits; we also met our partners at two conferences; we organised three further workshops in 2016-2018.
Exploitation Route Other labs will use the output of our workshops. Multiple clock research groups studying plant and algal clocks are now linked in the UK circadian clock club.
Sectors Agriculture

Food and Drink

Manufacturing

including Industrial Biotechology
 
Description Multiple workshops and visits have been funded, including international researchers and students as proposed, contributing to the development of skilled research staff, now with greater experience of international networking, presentation and critical thinking.
 
Description Cyverse UK 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Organisation of 2018 UK plant and algal clocks meeting
Collaborator Contribution Speaker at 2018 UK plant and algal clocks meeting
Impact None so far; yes multi-disc between computer science and plant science
Start Year 2018
 
Title Arabidopsis Framework Model, version FM-lite nested in version FM-life 
Description Two new computational models, implemented in the rule-based language Chromar: - FM-lite for the vegetative growth of Arabidopsis thaliana, including modifications to use real weather data. - FM-life for the entire lifecycle of Arabidopsis, from seed to seed. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact So far only academic publications 
URL https://github.com/azardilis/ChromarFM
 
Title Chromar and its implementation in Haskell 
Description Chromar is a rule-based modelling language, implemented in the general-purpose programming language Haskell. Chromar supports multi-scale models that create and destroy agents; it extends the formalisms simialr to coloured Petri nets using externally-defined functions (fluents, useful to represent meteorological or experimental inputs) and observables (model outputs that are calculated from the primary agents and their attributes). This makes it helpful in multi-scale applications such as whole-organism models, in our case the Arabidopsis Framework Model. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Academic publications, so far. New application, where model is used in optimal control of plant growth conditions. Zardilis participated in the iHaskell hackathon to gain support of Chromar in this interactive interface. 
URL https://github.com/azardilis/Chromar