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Software Development

Here, some of the public software projects developed at the Sainsbury Laboratory, University of Cambridge will be described. We have divided the projects into Bioinformatics / Image Processing / Modelling.

Bioinformatics

Ara-BOX-cis

araboxcic.org This tool provides ways of visualising the network of bHLHs/bZIPs and their predicted regulatory targets among genes that are expressed in seedlings and that contain perfect G-boxes (CACGTG) within 500bp upstream of their TSS.  A more detailed description of how this network was generated can be found at https://doi.org/10.1101/128371.


Image Processing

Costanza

Image segmentation software implemented as an ImageJ plugin (Java) and batch mode version developed by the Jönsson group. It can be used for 2D membrane segmentation (e.g. Jönsson et al (2006), PNAS) and 3D nuclei segmentation (e.g. Meyer et al (2017), eLife.  More information and src code at Costanza


Modelling

Organism

The Organism-Tissue Simulator is a C++ software for simulating biological systems developed by the Jönsson group. It has been used to simulate plant tissues, bacteria colonies and budding yeast colonies. More information can be found on the gitLab page.

 

 

Supported by the Gatsby Foundation

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Noisy gene atlas to help reveal how plants ‘hedge their bets’ in race for survival

Jan 24, 2019

As parents of identical twins will tell you, they are never actually identical, even though they have the same genes. This is also true in the plant world. Now, new research by Sainsbury Laboratory Cambridge University (SLCU) is helping to explain why ‘twin’ plants, with identical genes, grown in identical environments continue to display unique characteristics all of their own.

How trees and turnips grow fatter – researchers unlock the secrets of radial growth

Jan 09, 2019

Plant science researchers from SLCU and the University of Helsinki have identified key regulatory networks controlling how plants grow ‘outwards’, which could help us to grow trees to be more efficient carbon sinks and increase vegetable crop yields.

SLCU helps reveal another layer in the strigolactone signalling pathway

Nov 23, 2018

An interdisciplinary collaboration between structural biologists and plant scientists has revealed another layer in the signalling pathway of strigolactone – a plant hormone that plays a key role in shoot branching and other plant development processes.

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