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Software Development

Open source software developed by Sainsbury Laboratory researchers that is free to use and explore.

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

Cytosim

Cytosim is a cytoskeleton simulation designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It is a versatile base that has been used to study actin and microtubule systems in 1D, 2D and 3D. It is built around a core cross-platform C++ engine. It runs on UNIX, Mac OSX, GNU/Linux and within Cygwin on Windows. The code is modular and extensible, making Cytosim a convenient base that can be customized to meet particular tasks.

More information can be found on the Cytosim Gitlab page.

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 Charitable Foundation

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Integrating maths and plant science to explain how plant roots generate a hormone gradient

Feb 18, 2021

The research team that developed a biosensor that first recorded that a distinct gradient of the plant growth hormone gibberellin correlated with plant cell size has now revealed how this distribution pattern is created in roots.

New research team joins SLCU

Nov 13, 2020

Chris Whitewoods will join the SLCU research leadership team to head a new research group focused on understanding how plants pattern themselves in three dimensions.

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