CodeRefinery: Scientific Software Development

Lisanna Paladin   2022-09-20   Comments Off on CodeRefinery: Scientific Software Development

Date(s) - 2022-09-20 - 2022-09-29
09:00 CEST - 12:30 CEST


About CodeRefinery

CodeRefinery acts as a hub for FAIR (Findable, Accessible, Interoperable, and Reusable) software practices. It currently focuses on the Nordic/Baltic countries, but aims to expand beyond this region. CodeRefinery aims to operate as a community project with support from academic organizations.

If you are familiar with The Carpentries workshops, you can consider CodeRefinery ones as "the next step" into software development, as targeted to a more advanced audience. Find more information here.

CodeRefinery, although mostly targeting Nordic countries, offers possibilities of attendance for non-Nordic researchers. You could either follow the stream (more information followingly) or, if we will collect enough registrations, we will set up a training room at EMBL with helpers at your disposal during the course. If you are interested in this possibility, please register here by the 11th of September.

About the course

Course goals

In this course, you will become familiar with tools and best practices for scientific software development. This course will not teach a programming language, but we teach the tools you need to do programming well and avoid common inefficiency traps. The tools we teach are practically a requirement for any scientist that has to do their own programming. The main focus is on using Git for efficiently writing and maintaining research software.


All times are in Europe/Stockholm time (CEST). The schedule includes frequent breaks.

Day 1 (Tue, Sep 20)
8:50 – 9:00 connecting time, icebreaker
9:00 – 9:20 Welcome and practical information
9:20 – 12:30 Introduction to version control – part 1/2

Day 2 (Wed, Sep 21)
8:50 – 9:00 connecting time, icebreaker
9:00 – 12:30 Introduction to version control – part 2/2

Day 3 (Thu, Sep 22)
8:50 – 9:00 connecting time, icebreaker
9:00 – 12:30 Collaborative distributed version control

Day 4 (Tue, Sep 27)
8:50 – 9:00 connecting time, icebreaker
9:00 – 9:15 Mini-intro
9:00 – 11:15 Reproducible research and FAIR data
11:15 – 12:30 Social coding and open software

Day 5 (Wed, Sep 28)
8:50 – 9:00 connecting time, icebreaker
9:00 – 10:45 Jupyter
10:45 – 12:30 Documentation

Day 6 (Thu, Sep 29)
8:50 – 9:00 connecting time, icebreaker
9:00 – 10:45 Software testing
11:00 – 12:15 Modular code development
12:15 – 12:30 Concluding remarks and where to go from here

How to join

This is an informal and interactive event with type-along lessons, live coding, and exercises. Learners are divided into exercise teams for interactivity – register with a friend! The workshop will be held online, see options at how to join:

  • Everyone watches the main teaching via a livestream at If you register, you can get emails and link to ask questions.
  • You can also register here to request us to set up a room, in order to follow the course together with other EMBL participants and with helpers at your disposal.


Bookings are closed for this event.