Your mission: Create an open workspace
that showcases a fully reproducible analysis!
Do you have a pet workflow or favorite notebook? Have you thought about sharing them with the world, but keep pushing it off? Here's your opportunity to get it done, feel good about it AND win a trip to Switzerland in July!
We've all been in the situation of needing to share our tools and methods with a collaborator, or wanting to build on someone else's work for our own research. We've made a lot of progress toward making it easier to share, collaborate, and build on previous computational biology work by adopting best practices like version control, containers and so on. But there can still be a big gap between handing over the code and enabling others in the field to actually run it and reproduce the work. Let's show how much easier it can be with a showcase of working examples in an environment like Terra that integrates code, data and execution.
Through this friendly contest, we want to challenge the Terra community to raise the bar in how we share computational methods with each other. The best workspace wins (we're crowdsourcing evaluations based on overall ease of reproducibility, including clarity and completeness of workspace documentation... and science chops!). By showcasing a variety of reproducible workspaces, we hope to demonstrate the high value benefits to the entire community of Open Science approaches that boost computational reproducibility.
For some background reading on computational reproducibility, see this blog post.
If you don't already have a Terra account, follow these instructions to create one and provision it with free credits to cover compute and storage costs for your project.
Clone this template workspace, making sure to give your workspace a name that follows this convention: TOSC19-NAME where NAME can be anything you choose (doesn't have to be capitalized). This is your master workspace.
Populate your master workspace with any data, tools and/or notebooks necessary to perform the analysis you want to showcase. Make sure everything in there is okay to share publicly! You are solely responsible for complying with data privacy and data use restrictions. Your workspace description should include sufficient documentation to reproduce your analysis without any additional help from you.
Do all your testing in fresh clones so your master workspace stays clean of past runs and output files.
Once you're satisfied with your work, share your master workspace with email@example.com to enter it into the contest.
Our team will review your workspace and email you to ask for your explicit permission to make it fully public and list it on the contest page.
The Grand Prize is a roundtrip to Basel, Switzerland to attend the joint ISMB/ECCB* and BOSC** conference, July 21-25. Flights, hotel accommodation, and conference registration are all included in this prize. The winner will be expected to attend the conference and may be asked to give a short oral presentation about the workspace.
*ISMB: International Society for Computational Biology
**BOSC: Bioinformatics Open Source Conference
The first runner-up will win $5,000 in Google credits.
Second runner-up will win $2,500 in Google credits.
Entry submissions will open May 17 and close June 17. Judging will open May 20 and close June 20.
Entries will be judged based on the following criteria:
Ability for anyone to run the full analysis easily
Opportunity to customize relevant parameters of the analysis
Clarity and completeness of the documentation
Coolness of the science (as a tiebreaker)
Judging will be crowdsourced to the Terra community. We will invite all Terra users to try out the workspaces entered into the contest, and each workspace will include a link to a short google form with the scoring rubrics. Contestants are welcome to advertise their workspace(s) as widely as they like. Judges are not obligated to review all workspaces, but we do encourage everyone to review more than one workspace as this will provide some useful perspective for scoring entries.