Software Reproducibility using Containers (IN-PERSON)

IntermediatePrerequisitesNew

Congratulations! You have just created a new programme/script that is likely to be of use to other researchers. Naturally, you want to publish this software, others to use it and you to be cited. How hard can that step be? (SPOILER Alert – it’s harder than you think).

• This course explores the myriad challenges in producing code that works on other researchers’ computers and not just yours.
• We tour various possible software solutions and evaluate their suitability
• We examine the potential solution that is Software Containers (focusing on Docker).

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.
• Guidance on visiting Cambridge and finding accommodation is available here.

• Everyone is welcome to attend the courses, please review the relevant policies.

• Some Python Programming
• Familiarity with the Linux Command line & text editors

Number of sessions: 1

Challenges to software reproducibility, Virtual environments, Virtual Machines, Docker Containers

During this course you will learn about:

• The problem - things that could stop your software running on your peers’ computers
• The strengths and weaknesses of various solutions to the problem.
• How to create basic Docker containers to run software on target computers
• How to make your software according to the FAIR principles.

After this course you should be able to:

• Recognise the challenges of producing software that runs anywhere.
• Become familiar with terminology such as virtual environment, virtual machines & Software containers along with their strengths and weaknesses.
• Create simple Docker containers to run Python scripts and Notebooks.
• Use Container Registries to publish your containers to make them Findable, Accessible, Interoperable and Reusable.

Presentations, demonstrations and practicals

Machines will be set up and provided in the Training Room.

If you wish to use your own computer, then you need to install Docker, have a recent Python install and Virtualbox (newer Macs with M-series processors should install UTM instead of Virtualbox).

• Free for registered University of Cambridge students
• £ 60/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 120/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

1

• Introduction to the Unix command line (ONLINE LIVE TRAINING)
• Introduction to Python for Biologists (ONLINE LIVE TRAINING)