SynthSys

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Enhancing agricultural productivity

Our world is built on plants. Plants provide all of our food and a significant proportion of our fuel and industrial raw materials. They do this through the process of photosynthesis - the conversion of sunlight into "new plant". Understanding photosynthesis is one of the keys to improving agricultural productivity to meet the rising demands of an increasing population and the linked problems of decreasing fossil fuel availability and rapid, detrimental climate change.

With these aims in mind, SynthSys at the University of Edinburgh perform research into genetic and chemical regulation in biological systems. SynthSys uses cutting-edge approaches, from experimental synthetic biology to theoretical computer science, and applies them to experimental systems to gain insight into intracelluar processes like photosynthesis.

Software plays a fundamental role in SynthSys's work, and in particular the Systems Biology Software Infrastructure (SBSI) is a core research platform for them. SBSI provides an open-source suite of tools for model construction and analysis, including parameter optimisation and data visualisation, with associated databases of models and experimental data.  The Software Sustainability Institute is helping SynthSys develop SBSI to meet new challenges in data analaysis.

SynthSys and the Software Sustainability Institute

As with many important pieces of research software, SBSI exhibits some of the classic symptoms of organic growth and "legacy-itis". With the rapid increase in the size and complexity of biological data sets more and more is being asked of legacy biological analysis software, and in certain places cracks are beginning to show.

The Software Sustainability Institute will work closely with biologists, mathematicians and software developers at SynthSys to refactor and re-engineer some of the key numerical components of the SBSI system. The aim is to add both capability and capacity to a core research platform for the group, enabling it to work with larger and more complex data than is currently possible.

The Institute's work on SBSI is funded by SynthSys as part of the EU Framework 7 TiMet project.

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