An initiative funded by the BBSRC to development an agri-ecology specific Nextflow pipeline community and development program.
Our goal is to help researchers develop Nextflow code, teach basic/advanced topics around the UK and build functional pipelines to super charge UK research.
Agri-ecology research is critical for our understanding of the natural environment and the security of our food supply.
However, tooling lags behind other research fields such as medicine; this bottleneck is holding back research and the speed at which this critical research gets published. In addition, research is often not reproducible, accessible or scalable.
We are currently accepting expressions of interest in the program.
If you want us to build a pipeline or help you build a pipeline, let us know!
Follow this URL, to fill in a form about the kind of project you want us to build/help with.
We will get back to as soon as possible, and let you know how we can help.
1. BUILDING
We will develop (within end-user communities) reproducible, easy-to-use, modular bioinformatics pipelines suitable for the most useful analyses required by ecologists in the application of omics data to address critical ecological questions. Specifically, we will use Nextflow, a world leading pipeline development structure to create these pipelines.
2. TESTING
Once we have developed our pipelines, we will ensure each module has unit testing (using nf-test), as well as end to end pipeline tests with example data. Alongside our ambassadors and partner labs we can ensure pipelines are continuously tested and improved, so they remain active and relevant.
3. TRAINING
We address this mismatch by building resource bridges between ecologists – especially those working at the interface of insect ecology and agriculture - and bioinformatics; we will empower them with the autonomy to access and use the most appropriate cutting-edge analyses. Let’s remove the black box of bioinformatics!
4. COMMUNITY
Finally, while fulfilling the previous steps, we will build a community of pipeline developers in the UK. Pipeline development should be collaborative, interactive and accessible, so we will be hosting additional networking and hackathon events to build a community of developers that will compliment code devlopment.
- Who are we ?
- What services can we provide ?
- Examples of current pipelines
- Who are our current research partners ?
- Citations