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Writing our first Bioconductor package as members of the CDSB community

Joselyn Chávez, Carmina Barberena Jonas, Emiliano Sotelo

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A recap of the Community of Bioinformatics Software Developers (CDSB in Spanish)

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Events held by the CDSB

Workshop 2018: Latin American R/BioConductor Developers Workshop

Workshop 2019: How to Build and Create Tidy Tools

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What is regutools?

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How it started?

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What we had at this point

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  • Functions
  • SQLite database

Building regutools as a package

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  • Functions improvement
  • Documentation
  • Vignette
  • Tests
  • Integrated workflow

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regutools team

Developers and Mentors

Developer Alumni

Regulondb Maintainer

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What can you do with regutools?

  • Connect to the RegulonDB database
  • Build a new object defined as a regulondb object

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What can you do with regutools?

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  • List datasets contained in the RegulonDB database
  • List columns called attributes from the datasets

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What can you do with regutools?

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  • Retrieve and filter data

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Importantly, the result of each function is by default a regulondb object which keeps the slots from the original object.

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What can you do with regutools?

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  • Extract and visualize regulatory networks

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What can you do with regutools?

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  • Search binding sites and retrieve them in multiple formats.

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Things we learned

Joselyn:

  • Modifying parameters into a function implies to run and sometimes update tests.
  • Implementing Travis CI App (Thanks to Leo) makes a big difference to test code.
  • It is better to write separate functions when we expect VERY different outputs.

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That was how these two functions born

Integration with Gviz

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Things we learned

Emiliano:

  • Working on a coding project collaboratively using github, slack.
  • Using R developer tools: devtools::test_coverage() makes writing unit tests a game.

Carmina:

  • Writing the code it's an important part of development but it's not all!

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The experience of submitting regutools to Bioconductor

We used guidelines to know important facts about the submitting process like:

  • There is a developers mail list.
  • How to create a SSH key to Github.

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But, the experience and guide from Leonardo and Alejandro was crucial to perform the submission process and understand build reports.

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Feedback during review process

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Some fixes:

  • Keep just one maintainer.
  • Remove the .Rproj file.
  • Add the NEWS file.
  • Adjust lines length and indentation.

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Good comments:

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Thanks a lot Nitesh!

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Current status of regutools

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Almost done but dealing with a Warning in the R CMD check

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Final thoughts

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The development process has been very rewarding as a collaborative and learning experience.

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We hope regutools will be a very useful tool for projects related with microbiological studies.