Course Overview
From CodeRefinery welcome and information:
These days, computation is everywhere. Many people learn programming, but it’s much harder to learn how all of the things fit together in practice.
This course is aimed at supporting computational scientists’ skills so that they can:
- Do their science without barriers
- Produce higher quality, reproducible research
- Collaborate
The course programme includes:
- Reproducible research and FAIR data
- Social coding and open software
- Jupyter
- Documentation
- Software testing
- Modular code development
Similarly to what we propose for the first part of this workshop (about versioning and git), we plan to follow the streaming of this CodeRefinery lesson all together, with EMBL trainers at disposal in the (virtual or phisical) room as helpers or just local chair of the discussion.
Programme (tentative)
- Installation help and on-boarding – Wed (Sep 13), 14:30 – 16:00.
- Reproducible research, open source software – Tue (Sep 26), 09:00 – 13:30
- Documentation and Jupyter – Wed (Sep 27), 09:00 – 13:30
- Software testing and modular code development – Thu (Sep 28), 09:00 – 13:30
Technical Setup and important information (please read)
In order to be able to use the tools learned in their daily work after the course, participants are required to bring their own laptop. Please find all the information about the programme and requirements linked from the full workshop programme here . Also, followingly a summary of the requirement for all the three days modules together:
- install Git, Python, and Snakemake
- access Jupyter and JupyterLab, either through installing Miniconda or by accessing the EMBL JupyterHub
- install Sphinx and pytest as part of the Python environment
- optional, create a GitHub account to follow the demo exactly as in the tutorial. Alternatively, the EMBL GitLab can be used.
Registration
Please notice that Bio-IT helpers will not be available during this second part of the course. We will help with the initial troubleshooting of installations (Sep 13th) and during the first part (Sep 26-28th), for this last part instead you will be helped by the official CodeRefinery helpers, available through the online chat. For this reason, we only offer online registration for the second part and you will anyway need to register through the CodeRefinert website too.
Bookings
Bookings are closed for this event.