Homo biologicus informaticus

Summary

I got invited by the Graduate School Experimental Plant Sciences (EPS) to give a lecture on data management scientific programming and good practices. While mostly aimed at bioinformatics, it is far from being restricted to genomics. The presentation I’ve shaped was intended to give a good overview of what needs to be learned by the newest generation of life scientists.
You don’t have to be an expert in code to actually benefit from better code and data know-how and good practices!

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The Study Group stories! The PLoS Biology paper is out!

Summary

After nearly a year of intense brainstorming, our story on building Study Groups is out in the open. Sarah and I act as community leads in Madison-Wisconsin (USA) and Amsterdam (Netherlands) at our respective Universities. Our communities of practice in scientific programming are affiliated to Mozilla Science Lab Study Groups foster and support Life Scientists lost under a data avalanche. Communities of practice in scientific programming help to break the impostor syndrome, network with other researchers engaged in programming and data analysis, break organisation silos that keep different fields and expertise separated, etc.

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How to organise code-review sessions for researchers

I’d like to organise code-review sessions in the near future with the aim of helping scientists to produce better more efficient code. Nonetheless, also having some documentation and testing would be nice!
I’ve compiled a few great resources and tips from the web in this blog post.
Hope it helps you if you’d like to organise similar things.
Cheers!

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Building the executive team of the Study Group

Yesterday, I organised a kick-start meeting to create a team of researchers that will lead the Study Group activities for the upcoming year.
With some experience and some further reading (see the other blog posts), I made a small agenda to convey the main information about the Study Group, its missions, values and what it takes to become a member.
I hope it helps others in organizing their own Study Group at their institution. Cheers!

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Sociocraty: a process to reach decision making

From the Wikipedia article on sociocraty that helps to make a policy on decision making. The question is: what type of decision making policy do we want for a local community of practice in scientific programming. If we stick to the community values (see related post), then it should be a democratic and respectful decision making process. For now, there is no explicit structure which means that we need to implement one.

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Starting your own company in the Netherlands

For some time now and after some discussion, I decided to start my own data analysis company and named it “biodata services”. The domain name www.biodataservices.nl is registered but I need to build the corresponding website and come up with a portfolio of the related activities!

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Building your own community of practice

Together with a list of scientists, I have recently written an article entitled “Building a local community of practice in scientific programming for Life Scientists”. This manuscript is under review for PLoS Biology at the time and already available on bioXriv here.

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