BioMate

Lab-bench biologists find it difficult to use many existing tools for their data analysis. These tools are generally command-line computer programs written by computational biologists. Computational biologists do not have time to create user-friendly interfaces for their programs, and often find themselves spending a lot of time helping lab-bench biologists run their programs. This creates a burden for all involved: lab-bench biologists cannot move forward with their data analysis, and computational biologists cannot move forward with their research.

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Implementation

Accessing the Prototype

Our software is accessible at the following URL: http://rytaft.scripts.mit.edu/6.831/GR5/src/biomate_login.html.

Platform and Software Requirements

Our software can run on any modern browser and any operating system. We have tested our code on several browsers and it seems to work best on Chrome.

Summary of Contribution

Avanti Shrikumar
  • Implemented most of the programmer-facing interface
  • Wrote code to dynamically generate the lab-bench biologist view on-the-fly
Rebecca Taft
  • Implemented most of the lab-bench biologist-facing interface
  • Wrote classes to interact with the Parse backend
Sumaiya Nazeen
  • Designed and implemented most of the home screen and login/sign up screens
  • Implemented script-sharing functionality using Mailgun-Parse Cloud code
All 
  • Fixed bugs and implemented small features on all screens
  • No labels

2 Comments

  1. Unknown User (jks@mit.edu)

    • Presentation:
      • Good motivation for your user interface, but it could have been better scripted.
      • For example, explaining why the user might want to use the history feature, as opposed to just showing the history overlay.
    • Usability:
      • Great unified interface between computational and lab-bench biologists.
      • Should be able to navigate home by clicking BioMate logo
      • Consider in-app sharing/notifications between BioMate users
      • When creating a param, errors should have louder feedback (red tooltip)
      • Safety/Learnability: Difficult to grasp the differences between instructions/caveats, warnings/tooltips. Consider simplifying.
      • History and saved parameters:
        • Right now, can only save one set of parameters per script. Might be useful to save multiple parameter sets (e.g. short run vs. long run for different number of iterations).
        • If you can save different parameter settings, might make sense to associate each run in the history with a set of parameters as well. In that sense, each item in the history is a complete trial that you can run.
      • Larger icons at top needed for navigation to homepage, and between creating and using scripts.
      • Seems like the script automatically saves when I make changes to parameters - is the save button necessary? Maybe 'Save As' could be 'Make Copy', and 'Save and Share' could just be 'Share'. The word save is repeated three times...feels redundant.
    • Completeness:
      • Excellent job implementing the back-end.
      • Very minor bug: alert pops up when you navigate away from an edited script, without saving (e.g. clicking home button).

    1. Unknown User (rytaft@mit.edu)

      Hi Jeremy,

      Sorry if I didn't make this clear when presenting, but you can save as many sets of parameter values per script as you like. They are not associated with a particular run in History, but when you click "Load Parameters", you can see a list of all the different parameter values you have saved along with the date they were saved.

      Thanks,

      Becca