Open science resources
Open source platforms
New technologies and techniques drive discovery.
We share our innovations, ideas, tools and techniques openly to support scientists worldwide.
Alongside publishing in scholarly journals, presenting at conferences, and engaging with the wider scientific community, we share data, software, information, image processing, modelling applications, and biological resources, including:
- Bioinformatics
- Image processing
- Modelling
- Laboratory tools
- Software
- Model organisms
- Data
Bioinformatics
SecretSanta
Open-source software tool that automates the rapid and accurate prediction of secretomes
The SecretSanta package provides an R interface for the integrative prediction of extracellular proteins that are secreted via classical pathways. Automated pipelines created within the SecretSanta framework can be applied to large protein sets to facilitate comparison of secretomes across multiple species or under various conditions. Source code, installation instructions, documentation and use case scenarios are available on GitHub.
Image Processing
Costanza image segmentation software
Costanza is an open source segmentation tool developed by the Jönsson Group to identify nuclei in 3D confocal data or cells with membrane marked (mainly used in 2D). It was originally developed in Java and is accessible via different interfaces.
Image analysis/quantification
AMFinder
Automatic Mycorrhiza Finder (AMFinder) is an open-source software tool developed by the Schornack Group. It uses deep learning to automatically identify and quantify arbuscular mycorrhizal (AM) fungal colonisation in plant roots.
The tool uses convolutional neural networks (CNNs) to analyse ink-stained root images. It provides a reproducible and faster alternative to manual, human-scored microscopy.
Modelling
Cytosim cytoskeleton simulation
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.
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.
Data
Schornack Lab data and resources
A Zenodo repository of publicly available data and resources including scientific posters, microscopy, protein structure models and plant acession data.