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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

Tweet of the Week

 

Katharina Schiessl has been inundated with likes and congratulations for her research published in Current Biology this week. This is a game-changer for researchers aiming to engineer N-fixing into cereals – and her macro photos of nodules and a lateral root are stunning! Follow Kath @kathschiessl on Twitter.

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Harnessing tomato jumping genes could help speed-breed drought-resistant crops

Sep 16, 2019

Once dismissed as ‘junk DNA’ that served no purpose, a family of ‘jumping genes’ found in tomatoes has the potential to accelerate crop breeding for traits such as improved drought resistance.

Food of the Future: free online course launched to inspire the next generation of scientists

Aug 30, 2019

A new, free online course aimed at 16-19 year olds across Europe, funded by EIT Food and developed by the Gatsby Plant Science Education Programme (GPSEP) at the University of Cambridge alongside international partners, aims to inspire young people to study science so they can help to create food of the future.

How plants coordinate their biological clocks

Aug 15, 2019

New research from James Locke's group shows that clocks in plant seedlings can self-organise without a master.

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