Both Crop Scientists and Systems Biologists model biology, but their expertise cannot easily be linked to address Food Security, in part because their models are so different. In building our web portal (www.plasmo.ed.ac.uk) for diverse models from ecology to systems biology, we showed that Simulistics' Simile software can handle both types of model. However, none of the standard biological modelling languages is broad enough to represent the resulting models. SynthSys integrates leading UK researchers in languages for modelling biological systems. We aim to develop a candidate standard, based on our past and current work, that would be suitable as a modelling framework to represent Digital Organisms in future.
You will be trained on cutting‐edge models from both fields, using Simile’s graphical interface. Physiological experiments will be conducted on Arabidopsis plants, to extend and validate Crop‐Science‐style models to a range of growth conditions. A broadly‐applicable modelling standard will be developed for multi‐scale models in plant science, from biochemical pathways to a field of varying plants. UML class diagrams, the most widely‐used graphical formalism in computer science, will represent the disaggregation of each biological level into its components (tissue to cells, metabolism to pathways, etc.). Mapping the standard into Simile will provide the user interface and modelling tools, linking the example models as a test case for the community.
The project will provide dual expertise training in plant science and modelling, with experience in commercial software development, in the outstanding, interdisciplinary environment of SynthSys. First-class academic credentials in a numerate discipline are required to take advantage of this unusual opportunity.
Further details are provided at www.amillar.org/PhDs_2013.htm
Funding Notes:
The supervisory team: Prof. Andrew Millar FRS, School of Biological Sciences (main supervisor); Prof. Vincent Danos, School of Informatics, Director of SynthSys; Dr. Robert Muetzelfeldt, Simulistics Ltd.
Only online applications from home or UK resident EU nationals will be accepted for this BBSRC Industrial CASE studentship, by 31st May 2013: http://www.ed.ac.uk/studying/postgraduate/degrees?id=12&cw_xml=details.php
Contact andrew.millar@ed.ac.uk for informal enquiries.
References:
www.synthsys.ed.ac.uk; www.simulistics.com; www.plasmo.ed.ac.uk; www.amillar.org.
Salazar J.D., Saithong T., Brown P.E., Foreman J., Locke J.C.W., Halliday K.J., Carré I.A., Rand D.A., Millar A.J. (2009) Prediction of Photoperiodic Regulators from Quantitative Gene Circuit Models. Cell, 139: 1170‐1179.