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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

 

SLCU Reopening Site

(for staff & students)

 

University of Cambridge Guidance 

 

We would like to thank NHS staff, key workers and volunteers who are working tirelessly throughout the ongoing coronavirus pandemic in the UK. Our thoughts are with those whose health is impacted here in the UK and around the world.

 

 

Supported by the Gatsby Charitable Foundation

RSS Feed Latest news

New insights could help plants fortify walls against root pathogens

Sep 03, 2020

Sainsbury Laboratory Cambridge University (SLCU) researchers, as part of a multidisciplinary international team, have uncovered a mechanism controlling subtle changes to the architecture of cell walls in plant roots that bolsters their defence against Phytophthora palmivora without negatively affecting plant growth.

Giles Oldroyd elected as member of EMBO

Jul 10, 2020

Professor Giles Oldroyd is among 63 other scientists from around the world elected this year as Members and Associate Members of the European Molecular Biology Organisation (EMBO).

Cells in tight spaces – how the cytoskeleton responds to different cell geometries

Jul 09, 2020

Inside every living cell, there is a network of protein filaments providing an interior scaffold controlling the cell’s shape called the cytoskeleton. Research from the Sainsbury Laboratory Cambridge University (SLCU) suggests that this relationship might actually be two-way, with cell geometry itself having the capacity to influence the organisation of the cytoskeleton in living plant cells.

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