Bioinformatics training at the Norwegian Veterinary Institute

Earlier this month, I got something that most academics regard as something akin to a miracle – I got steady employment. I now have a work contract without an end date!Earlier this month, I got something that most academics regard as something akin to a miracle – I got steady employment. I now have a work contract without an end date!

I’ve now been working at the Norwegian Veterinary Institute for two years. These have been two very good years, I’ve had opportunity to work on many interesting projects.  The Institute has quite a broad portfolio of responsibilities – it is tasked with diagnostics, surveillance, monitoring, risk assessments and giving scientific advise to the government on a whole slew of issues. Considering the inroads into various fields that bioinformatics and sequencing have been making the last 10 years, it is not surprising that this now has come to the Institute as well. However, it has also gradually been noticeable that I am the only one at the Institute that can do the things that I do. I have at times become a roadblock.

So, in good Software Carpentry tradition, I’ve been working on training people. This fall we are now able to put this training on a more formal footing – we are starting up a year-long course aimed at training around 20 people to become for the most part self driving bioinformaticians. And, again in good Software Carpentry tradition, I am writing about it in case somebody has feedback and/or would like to do something similar themselves.

The course is slated to run for about a year, and we’ve estimated that people will use approximately one day a week on participation. The course will proceed in two distinct stages, with an introductory lecture series followed by a hands-on practical course

Open introductory lectures
The first part of this course consists of a lecture series that is open to all at the Institute. This series is meant to give people unfamiliar with bioinformatics and sequencing an introduction to what bioinformatics is, what kinds of problems you can solve with it, how to design studies, the methods that are involved in analysis, and so forth. This part has already started, this week we are continuing with the 3rd lecture in the series.

After the open introductory part, around 20 people will be selected for further participation in the practical part.  This part of the course will proceed in four stages:

Bioinformatics infrastructure workshops
The Institute is a pure windows shop. Thus, most of the people here have little to no experience working within the kind of infrastructure that is commonly used for bioinformatics. Due to the pure windows shop factor, we have chosen to use the HPC resources at the University of Oslo for analyses. To interact with the UiO systems, we have opted for going with windows laptops with virtualbox on them, with a biolinux image. That will put the learners on a unix platform with tools that can be used when/if needed while also enabling easy interaction with the HPC cluster. However, to effectively use this kind of a setup, our learners need to know quite a few things. Thus we will be introducing them to VMs, how to use the shell, and how to interact with the UiO computers (including the queueing system). We will also teach them a bit of basic R and python programming. Fortunately, we don’t have to invent the wheel ourselves here – Software and Data Carpentry has a lot of already existing material that we will use for this part. This part is planned as whole day hands on workshops.

We will subsequently divide the participants into three working groups. Not all people are interested in the same kinds of things, and it takes time to learn something properly. Through discussions with people at the Institute, we have figured out that people are primarily interested in comparative genomics, transcriptomics and metagenomics. Each separate group will have their own mentor. From this point onwards the workshops will be one half-day every week, with homework.

Case study workthrough
Once the common infrastructure part is done, we will have the students working in their separate groups. They will first be working through a case study that is known to their mentor. They will work through that case, and through that become familiar with common analyses within their fields.

Working with their own data
They will then proceed to working with their own data, solving their own specific problems. This work will be done under the guidance of their mentor.

Writing up a paper
We have also decided to include writing up a paper based on their own data into this course. Getting the figures and the tables created is one thing, and writing it up and formulating the results is something else. It can be hard to figure out exactly what your results are saying, and thus we decided to include that in the course too.

As is evident from the description above, this is quite an extensive program. I am very happy that I will not be doing this on my own. The Institute has hired two people in 20% positions to work on this with me. The others are Arvind Sundaram, who works at the Norwegian Sequencing Centre, and Thomas Haverkamp, who is at the Biology department at the University of Oslo. During this year, I will be mentoring the comparative genomics group, Arvind will be mentoring the transcriptomics group, while Thomas will be mentoring the metagenomics group.

All in all, I am very exited that we are able to start this course now, and I look forward to help upskill people at my Institute. However, I also have to admit that it is bit terrifying being responsible for the further education of this many people. But, we have to start somewhere, and I am fortunately not going it alone (another thing that Software Carpentry has taught me). I’d also very much like to hear from people who have done similar things, even if on a smaller scale. I also aim to write about this regularly here, to get more feedback and possibly help and inspire others who would like to do similar things.