BioBash Workshops: How It All Began

BioBash Workshops: How It All Began

Let’s be honest here: in the begining, Genialis employed mostly computer scientists and while we have trouble grasping the basic concepts of molecular biology, we can intuitively think in Python clauses and command-line arguments. So it took a wet-lab biologist to remind us the life scientist out there need also something else beside the complex analysis platforms that we had been developing: they want the basics explained in plain language. Recently, a lot of resources at Genialis are spent on developing and delivering the BioBash Workshops. This is our way of making our knowledge of programing and NGS data analysis available to interested researchers in life sciences.

The effort is now lead by Luka Ausec, yet we met him almost by chance — my colleague Klemen interviewed him about general problems in bioinformatics sometime in November last year. Luka is a microbiologist and a self-taught bioinformatician who has mastered Python and loads of data analysis skills while working on his PhD. He is one of those biologists with enough persistence to learn the skill on his own. And, as he can testify, it wasn’t easy.

But why is that? Why do many biologists end up using only BLAST, Excel, and a few online databases? I believe there are two main reasons for that.

Whole New World
Firstly, to start analyzing raw data by yourself, you need to understand the underlying technologies used to produce the data in the first place. But this is the easy part for the biologist. Then you need to know what are the possible workflows to analyze the data, but more importantly, you need to understand which (usually command line) tools to use at which step in the process, what are the data formats and so on. Finally, you need to actually use the tools, and this is where most people get stuck. Compiling tools, running scripts or making their own is far from intuitive for newcomers. This is not surprising and is a direct consequence of not getting any training.

Lack Of Good Data Analysis Courses
Second, there are few really good courses and workshops which would lead a data analysis beginner through all the hurdles during the first steps in data analysis. Too many workshops just focus on copy-pasting commands without thoroughly explaining the logic behind them. Even just getting Linux up and running can be challenging for researchers only working in Windows. Bioinformatics courses taught at life science universities are only slowly becoming useful and going beyond using browser-based applications. What is more, the pace of the development of new tools is hard too keep up with in the school programmes, and there is often a need for a trusted source to bring the life-science researchers up to date with their computers.

Learning By Doing
This is why Luka came up with an idea of BioBash Workshops: Let’s create something newcomer biologists really need when starting with data analysis. A series of workshops that begin from scratch and explain the obvious bits, too. We only expect our Essentials workshop participants to know how to turn on the computer. However, we don’t stop at the mere foundations, there are also workshops for those who already master the basics. In either case, the guiding principle is “Learning By Doing”, and the workshop is 90% a hands-on experience, participants learn as they actually do the analyses and write code.

Our mission at Genialis is to empower the biologists to perform data analysis themselves and become autonomous in their research. We hope to achieve this goal by organizing more BioBash workshops around Europe in the future and by providing intuitive data analysis software tools for biologists.

Hope to see you around!