As part of the IBH BBSRC Barley EU Network project led by Isabelle Colas and involving researchers from Hutton, University of Dundee and IPK, Sebastian Raubach from the Information & Computational Sciences Department was invited to present his work on bioinformatics research software development at the Leibniz Institute of Plant Genetics and Crop Plant Research (more commonly known as IPK).
Sebastian Raubach (IBH and ICS)
His talk on “Everything Everywhere All at Once” as part of the genetics seminar series was very well attended and received. The presentation was followed by chats with genebank curators, other research software engineers in the bioinformatics group and researchers in the automated phenotyping group.
The visit included a tour of the PhenoSphere – a set of large chambers in which environmental conditions can be strictly controlled (light, wind, temperature, humidity, CO2 concentration). The first chamber contains a rhizotron system in which root and shoot development can be monitored while the second chamber houses a container system in which large soil containers are used to simulate field-like conditions.
During the second week of the trip, the Breeding API (https://brapi.org) consortium met in the city of Protestant Reformation – Wittenberg Germany. The Breeding API is an international effort to enable interoperability among plant breeding databases and tools. So basically, it’s about trying to teach all these software tools to play nice and talk the same language to further the areas of plant research and breeding.
The hackathon event was co-hosted by IPK and attendees arrived from all over the world including the USA, Mexico, Philippines, Kenya, Germany and the UK among others. The Hutton has been involved in BrAPI since its conceptualisation as a Bill and Melinda Gates supported project and ICS staff have been attending hackathons on a regular basis, either virtually or in person. Our main interest has been to establish closer links with the other BrAPI participants to learn more about their systems, workflows, and challenges. Additionally, ensuring our software tools for phenotypic data collection, plant genetic resources data storage as well as genotypic, phenotypic and pedigree data visualization are widely known and compatible with other group’s tools is essential.
During the hackathon we focused on adding support for loading trials data into our pedigree visualization tool Helium (https://helium.hutton.ac.uk) so it can be visualized on top of the pedigree structure. This will further increase the usability of Helium within the BrAPI community and generally.
Overall, it was a very enjoyable trip that allowed us to make new connections and strengthen old ones.
Sebastian Raubach
The only hiccup I had was a slight fiasco with the electric hire car I got due to a mix-up and its unexpectedly miniscule range. I’m all for doing my bit for the environment, so initially the prospect of zipping about in a wee electric car seemed exciting. This was soon shattered after finding out that the 2-hour drive (140 miles) required stopping twice to recharge and quickly became a 6-hour trip. Finding charging points you can pay at with a credit card turned out to be the second big surprise of the day and panic soon set in when the range dropped to 15 miles with only an educated guess of where to find a charging point that would accept credit cards as well as have a compatible charging port.