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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.

Coronavirus

 

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RSS Feed Latest news

2020 Waddington Medal

Mar 29, 2020

SLCU Director Professor Ottoline Leyser has been awarded the 2020 Waddington Medal by the British Society for Developmental Biology (BSDB).

Discovery of expanding pectin nanofilaments that manipulate plant cell shapes

Feb 27, 2020

Scientists have discovered new filamentous structures within plant cell walls that influence cell growth and help build complex three-dimensional cell shapes.

Random gene pulsing generates patterns during development of living systems

Feb 19, 2020

A team of Cambridge scientists working at the intersection between biology and computation has found that random gene activity helps patterns form during development of a model multicellular system.

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