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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Computer Prototyping

Platform and Software Requirements

Our prototype 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.

Instructions

Accessing the Prototype

Our software is accessible at the following URL: http://rytaft.scripts.mit.edu/6.831/GR4/src/biomate_login.html.

Tasks to Evaluate

The following tasks can be helpful during the evaluation process:

1. Log in as a lab-bench biologist using the following login credentials (the canned data corresponds to what a lab-bench biologist might see):
   • username: alpha
   • password: beta
2. Use "Monte Carlo" script.
3. Use "Monte Carlo" script from history.
4. Browse your notes and look at your notes on "Monte Carlo".
5. Log in as a computational biologist using the following login credentials (the canned data corresponds to what a computational biologist might see):
   • username: gamma
   • password: delta
6. Create a new script.
7. Edit "Monte Carlo" script from history.

You might play with the interface. We have implemented enough of the functionality so that you should be able to see all of the screens we have designed. All buttons on the home screen should link to the correct screens (notes, history, add/edit a script, use a script), and buttons on these screens should show popups and tooltips with canned data. Selecting scripts other than "Monte Carlo" should not cause the interface to crash; you may not see any output or the output you see might not make sense.

Prototype information

Canned Elements

• You can login with only two username-password pairs as mentioned in the instructions.
• You can use only "Monte Carlo" script since we have created all of our screens with canned data corresponding to the "Monte Carlo" script which was used in our paper prototype scenario.
• The notes, instructions and parameters associated with "Monte Carlo" script are all canned.
• Clicking "Edit" for any script in the "History" popup shows an image of the "Create/Edit Script" screen with some items filled in, and is therefore not interactive.

Incompletely Implemented Elements

• Home/Login screen:
  • We did not implement the "create account" feature and the "login" functionality is incomplete in the sense that it uses canned data.
• Create/Edit a Script screen:
  • The "Delete" and "Edit" buttons do not allow you to delete or edit any parameter or static text.
  • The "View/Edit" buttons in the parameters table do not work.
  • Changing the "Alias" or "Prefix/Flag" in the parameters table does not update the draggable chunks.
  • Setting input type to "Flag" does not disable the "Required" checkbox.
  • We do not check for invalid or blank parameters.
• Use a Script screen:
  • From the "Generate Command" popup, Save to Notes and Copy to Clipboard do not work.
• General:
  • When you click buttons that would require mostly back-end work such as Save, Share, etc., nothing will be saved, even if feedback is displayed on the UI confirming the action.
  • When you click "Send" to send an email, nothing will be sent.