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December 6, 2022

5 Reasons to Bring Web Apps Into Your Bioinformatics Work

Many research teams share static results between working group members, like image files or documents, but this can slow progress down. Feedback can be difficult to give and difficult to incorporate. Next time a bioinformatics project is wrapping up, think about dynamic result sharing with a web app! Here’s why:

  1. No more emailing documents back and forth! Bioinformaticians have to go back to code repeatedly over a project’s lifecycle. They need feedback from team members who have varying technical skills, so usually after they code everything needed for a figure or report, discussion moves off their working platform and into email attachments. This can slow everyone down — colleagues have to manually review graphs, and bioinformaticians have to comb back through their code to incorporate changes. Web apps allow colleagues, at all technical levels, to interact with the data via drop down menus, text boxes, buttons, and sliders.
  2. Web apps encourage proactive experimental planning. Deeply considering the analytical framework for one task will make it easier to prepare for the next. Even using user-friendly tool sets, apps can be an investment — they should be made carefully and align with future work or incoming data. This is a two-way street and gives structured foresight for future data ingestion and even experimental planning: having discussions in the planning phase between all parties that are going to touch the data ultimately makes your science better.
  3. You can standardize plot elements. Even among highly experienced bioinformaticians, people really vary in how they set up axes, select color schemes, mark error bars, etc. This variation can cause confusion, especially for colleagues who need to make quick, clear inferences from these plots. It’s hard to establish standards on these details without extremely lengthy documentation. Building a web app, with core plots and interactive elements, provides a good framework to make standards actionable.
  4. Design is fun and encourages empathy. Design meetings are where you get to bust out the white board! It gets everyone involved on one common task, using visual, symbolic language. Designing an app together involves discussing and understanding how users will look at, and move through, the visual cues in front of them and how they’ll want to interact with the framework. Too often, people can get siloed and frustrated at each other instead of at the structural framework that they’re working with.
  5. There’s a lot of neat tools to choose from! If you’re a data-centric R team: Shiny. Python? Check out Dash by Plotly, Viola, or Streamlit. There are many others for a huge variety of languages and requirements. What they all have in common is active communities — if you have questions or develop work you’re excited to share, there are many dedicated forums where you can get support and cheers. Whatever your team’s existing tools and preferences are, we’re confident you’ll find a web app option that fits.

If you enjoyed reading about web apps and would like to learn more, check out the on-demand webinar, How to Build, Run, and Deploy Bioinformatics Apps to the Cloud in Minutes. Code Ocean bioinformatician Emily So illustrates an end-to-end web app process using Shiny on the Code Ocean platform!

Tag(s): Bioinformatics

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