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.