What: Free participation, accommodation (for non-local delegates) and meals for members of C1net or another NIBB network
When: Monday 23 January 2017 – Friday 27 January 2017
Where: St James Hotel, 1 Rutland Street, Nottingham, Nottinghamshire, NG1 6FL
by C1net member and attendee Christian Gude
Scientists from all over the world, from Denmark to New Zealand, met in St James Hotel, Nottingham to gain insight in the building and use of structural metabolic models under the professional guidance of Prof. David Fell and Dr. Mark Poolman of Oxford Brookes University. The computational representation metabolic networks has been achieved through the program ScrumPy, a powerful tool in helping scientists represent and analyse complex metabolomes. With the aid of ScrumPy, scientists can import enzymatic databases of any organism and subsequently simulate changing growth conditions, gene knock-outs and projected yields of academically and industrially relevant metabolites.
The course taught the basics of the programming language Python, which is essential to manipulate data within ScrumPy. Interspersed by interesting talks on the mathematical background of network analysis, biotechnological applications of network analysis, flux balance analysis and how genome-scale models are built, we worked through practicals, which were designed to teach us not only how individual problems can be solved through Scrumpy, but also to show us its capabilities. Most participants are not likely to be using ScrumPy in their research, but they might have to communicate efficiently with the bioinformaticians who do. The communication between the dry and the wet sides of the lab is greatly facilitated by workshops such as these. The workshop gave me not only insight in how structural models are madebut also the ability to ask the right questions and an idea of what I can expect of our in-house bioinformatics experts. For example, I learned that I can anticipate very interesting findings towards interesting knock-out candidates in my system, but I can’t expect kinetic enzymatic data to be taken into consideration in a mere structural model, which was one of the things I was previously unaware of. The workshop concluded with three field reports on successful examples of how ScrumPy was used and a stimulating QA session.
“I am looking forward to attending further meetings!”
“An overall introduction to the topic was provided. Clearly it is quite a complicated topic and to fully benefit from metabolic modelling, much more training, or guidance, is required”.
“Hands-on experience of building and analysing structural metabolic models”
“Clearer understanding of colleagues work and also the advantages and limitations of structural modelling”
“I have understood the principles of how ScrumPy works, which helps me to communicate with bioinformaticians in my group”
86% thought the workshop was very/extremely well organised
75% thought the workshop length was just right
75% thought the pace was about right
92% thought the tutors were very/extremely skilled