Quick and clean: advanced Python for data science in biology


National course open for senior researchers or other professionals in biology, biochemistry and bioinformatics within all Swedish universities. PhD students are also welcome as long as they have some programming basics and have an urgent need for Python in their research.

The course is run by NBIS, the National Bioinformatics Infrastructure in Sweden, in collaboration with Chalmers University of Technology and Gothenburg University.

Application page

Important dates

Application open: March 1

Application deadline: April 30

Confirmation to accepted participants: May 2

Responsible teacher: Sergiu Netotea     sergiu.netotea@scilifelab.se

Course fee

A course fee of 1300 SEK will be invoiced to accepted participants.

 

Course content

Course material

The course is built around Python philosophy of being quick and clean (the so called Zen of Python) and thus assumes anything taking more than three days to learn is probably not worth the effort. In the first day it will start with a tutorial of Python as a language, and quickly inventory its uses as a general programming platform, ranked number five after Java and C*, along with basic devops. The second day is slightly more practical: a language is the sum of its third-party libraries, plus how it handles on different platforms. You will make introductory steps into the famous libs that made Python, along with R, the lingua-franca of data science, and test it on different computing environments. The third day it will be your effort that counts: you will pick one real omics subject from a given task list or you will use Python in your project under our assistance.

Note: Lectures and exercises will take place May 16, 17 and 19. May 18 is set aside for independent work (no lecture hall booked or TA:s present).

 

Learning outcomes

Anyone thinking they will master anything in only three days is of course naive. The three days of advanced Python will give you confidence in your abilities and hitch you higher on the learning curve, least it will help you understand more accurately if you can become a master bioinformatician yourself or you need to hire one. If your need of Python is very specific (as I expect it should) it will also set you on the right path to getting things done. An additional benefit is learning proper devops: how to handle your project, how to use Git, Jupyter and Docker, cloud and GPU computing, etc.

Entry requirements

The course is primarily aimed at senior researchers or other professionals in biology, biochemistry and bioinformatics. PhD students are also welcome as long as they have some programming basics and have an urgent need for Python in their research. Besides your initial ability with programming and Python we think that the nature of your interest for using it is what really counts. Do you need Python to solve real problems in your field? Do you want to improve the reproducibility of your research? Are you passionate about computing and data science? Did you worked with NBIS before, or planning to?

Selection criteria

Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

 

Venue

Room KS41, Kemigården 4,
SE-412 96 Göteborg
Chalmers University of Technology