Loading…
BCC2020 has ended
➞ Set your timezone before doing anything else on this site (home page, on the right)
Limit what is shown by Type, Category, or Hemisphere
Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

Back To Schedule
Saturday, July 18 • 03:31 - 06:00
Bionitio: building better bioinformatics tools with batteries included II

Sign up or log in to save this to your schedule, view media, leave feedback and see who's attending!

This is the second part of a two-session workshop. If you register for one, you are required to also register for the other.

Software development is a central part of bioinformatics, but for many reasons software quality is not always prioritised, leading to problems in maintenance, usability and reproducibility. Adopting software engineering best practices at the beginning of a project can address these problems, but this is often not done due to lack of time and/or experience. This workshop covers the essentials of good programming practices and provides you with tools and knowledge to build high quality bioinformatics software from the outset. We will introduce Bionitio (https://github.com/bionitio-team/bionitio), a tool for quickly creating new software projects with important features and infrastructure already included.

Learning Outcomes
  • By the end of the workshop you will have:
  • Created a new software repository
  • Committed it to GitHub
  • Set up continuous integration testing
  • Used test-driven-development to add a new feature to the program
  • Learnt about good practices in software development and why they are useful
  • Learnt how to use a tool (bionitio) to automate this for future projects.

Target audience

Bioinformaticians with beginner to intermediate level of programming experience who want to apply good software engineering practices in their daily work. Experience with the Unix command-line is assumed. Basic familiarity with Python (or similar languages) is an advantage.

Requirements

  • You'll need to bring a laptop with Unix (e.g. an Apple Mac or Linux).
  • Windows users: please install Putty.
  • Before attending the workshop, please set up a GitHub account (free, https://github.com/join).



Speakers
avatar for Anna Syme

Anna Syme

Bioinformatician, Royal Botanical Gardens, Melbourne, Australia
avatar for Bernie Pope

Bernie Pope

Victorian Health and Medical Research Fellow, Melbourne Bioinformatics, University of Melbourne
I am an Associate Professor at The University of Melbourne. My research focuses on applying computational techniques to biological questions, especially related to Human Genomics and Cancer.


Saturday July 18, 2020 03:31 - 06:00 EDT
Training B