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Sainsbury Laboratory

 

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.

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Latest news

Blushing plants reveal when fungi are growing in their roots

23 July 2021

Scientists have created plants whose cells and tissues ‘blush’ with beetroot pigments when they are colonised by fungi that help them take up nutrients from the soil.

Alpine plant spins its own flavonoid wool

17 June 2021

Like the movie version of Spider-Man who shoots spider webs from holes in his wrists, a little alpine plant has been found to eject cobweb-like threads from tiny holes in specialised cells on its leaves.

Plants get a faster start to their day than we think

7 June 2021

To describe something as slow and boring we say it’s “like watching grass grow”, but scientists studying the early morning activity of plants have found they make a rapid start to their day – within minutes of dawn.