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Software Development

Here, some of the public software projects developed at the Sainsbury Laboratory, University of Cambridge will be described. We have divided the projects into Bioinformatics / Image Processing / Modelling.

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

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.

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Behind the scenes with our researchers

Jul 19, 2018

Go behind the scenes with SLCU researcher Dr Annalisa Rizza to find out about her work.

SLCU Director presented OlChemIn Award 2018

Jul 09, 2018

SLCU Director, Professor Ottoline Leyser, was presented with the OlChemIn Award 2018 in recognition of her outstanding research on plant hormones.

Edwige Moyroud awarded Linnean Society Bicentenary Medal

May 24, 2018

Dr Edwige Moyroud has been honoured by the Linnean Society of London with the 2018 Bicentenary Medal for her discoveries on the evolution and development of nanoscale architecture in flower petals.

Elliot Meyerowitz awarded prestigious Gruber Prize

May 14, 2018

Professor Elliot Meyerowitz has been awarded the 2018 Gruber Genetics Prize by the Gruber Foundation for his "groundbreaking work in identifying the basic regulatory and biochemical mechanisms underlying the development of plants."

HFSP funding to investigate cellular growth and stresses in plants

Apr 11, 2018

SLCU's Professor Henrik Jönsson is part of an international collaboration that has received funding from the Human Frontier Science Program (HFSP) to develop the first integrated model in plants investigating the effects from cellular growth and stresses on nuclear shape and genetic activity.

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