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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.

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Plants feel the heat

Feb 13, 2018

Sainsbury Laboratory scientists have solved a 79-year-old mystery by discovering how plants vary their response to heat stress depending on the time of day.

Fast-talking plants increase flower production within 24-hours of soil nutrient application

Jan 24, 2018

The molecular mechanisms enabling plants to quickly adapt their rate of flower production in response to changing nutrient levels in soil have been revealed by researchers at the Sainsbury Laboratory at the University of Cambridge.

Re-wiring cells by crossing kingdoms

Jan 22, 2018

Game-changing synthetic biology developments that could help address global health and agriculture challenges will be examined at a three-day international synthetic biology symposium at the Sainsbury Laboratory, University of Cambridge, this spring (16-18 April 2018).

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