skip to primary navigationskip to content
 

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

 

A bespoke hand-crafted necklace by Eva Hellmann illustrating the photosynthesis biochemical reaction.

Follow @Eva_in_the_net on Twitter

 

RSS Feed Latest news

People of Science

Dec 05, 2019

Professor Ottoline Leyser talks to Professor Brian Cox about her admiration for Nobel Prize winning geneticist, Barbara McClintock and explains the two great principles she uncovered.

Overlap in lateral root and nodule development brings self-fertilising cereals one step closer

Nov 16, 2019

A vision of creating crops that do not need chemical fertilisers is one step closer thanks to the recent discovery that a substantial overlap exists in the developmental programmes plants use for lateral roots and nitrogen-fixing nodules.

Hinchingbrooke School solves botanical crime scene

Nov 15, 2019

We were delighted to welcome Sixth Form students from Hinchingbrooke School to SLCU this week to meet our scientists and solve a botanic-inspired crime.

View all news