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h1. *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 leb-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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h2. Scenario

Our scenario involves a lab-bench biologist V. who seeks to run an experiment using a script written by X., a computational biologist.

# V. tells X. via e-mail that she needs to use a Monte Carlo simulation script which he wrote
# X. uses BioMate to create an interface for his Monte Carlo script.
# X. shares his script with V. on BioMate
# V. contacts X. again saying that she wants to be able to specify the number of iterations for his script
# X. edits his Monte Carlo script interface to provide the ability to modify the number of iterations
# V. access the update script through BioMate and obtains the command she needs
# V. notices that 1000 iterations works well for her, so she makes a (personal) note on BioMate to remind her of this later. She saves the current configuration of this script in her history.
# Some time later, V. goes back to BioMate because she wants to run the Monte Carlo script on a different input file. She pulls up her history and views the Monte Carlo script which she previously saved. She edits the parameter she wants changed and uses the modified output provided.

h2. Individual Design Sketches

h3. Sumaiya

!Sumaiya's design 1.png|thumbnail,border=1!

!Sumaiya's design 2.png|thumbnail,border=1!

!Sumaiya's design 3.png|thumbnail,border=1!

h3. Rebecca

!beccas_drawings 1.png|thumbnail,border=1!

!beccas_drawings 2.png|thumbnail,border=1!

!beccas_drawings 3.png|thumbnail,border=1!

h3. Avanti

h3. Michael

!maddox_sketch_1.jpg|thumbnail,border=1!

!maddox_sketch_2.jpg|thumbnail,border=1!

!maddox_sketch_3.jpg|thumbnail,border=1!

h2. Storyboard

h3. Design One

h4. Storyboard

[Link to Storyboard|BioMate Design 1 Storyboard]

h4. Analysis

Overall, Design One focuses on providing distinct user experiences for lab-bench biologists and computational biologists. This approach can be useful if their roles tend to overlap little or not at all. 

h5. Learnability

* Following the paradigm described above paradigm, this design leverages a traditional desktop metaphor to simplify the interface for lab-bench biologists as much as possible. Since lab-bench biologists would often come onto BioMate searching for a particular script, this metaphor parallels what one might expect when looking for a file on a desktop computer. In this case, maintaining metaphorical consistency should increase learnability for the lab-bench biologist.

* Furthermore, we propose an automatic command parser for the computational biologist to facilitate the creation of an interface for a partiuclar script. Computational biologists are very familiar with the command line, and would be comfortable providing a command in a way to specify all the options and allowed values in a single line, as is often done in *nix man pages. This external consistency should increase learnability for the computational biologist.

h5. Efficiency

* This interface allows computational biologists to directly enter the command as it would be run in the command line. This is extremely efficient for the programmer since they have already created the script to be run in the command line and are very familiar with the syntax for doing so.

* The down-side of this feature, however, is that it may be very difficult for us to implement a parser to determine which fields to present to the lab-bench biologist. It also encourages computational biologists to not bother with writing notes for each of their parameters since they can generate a working interface so quickly.

* This interface is not as efficient for a lab-bench biologist, but it is very learnable. We would probably need to incorporate some keyboard shortcuts for this interface to be efficiently used by a lab-bench biologist "power user" with a lot of experience with the system.

h5. Safety

* The computational biologist could easily enter a typo in their command. Since the system itself has no a priori knowledge of what certain commands should be, this introduces the possibility of creating a valid interface for a script which is in fact incorrect. It is important that the computational biologist verify the parameters for his or her script before submitting them; however, enforcing this may be difficult with this streamlined approach. For example, we could present the computational biologist with the option of previewing the corresponding view for the biologist, hopefully reducing errors.

h3. Design Two

h4. Storyboard

[Link to Storyboard|BioMate Design 2 Storyboard]

h4. Analysis

h3. Design Three

h4. Storyboard

[Link to Storyboard|BioMate Design 3 Storyboard]


h4. Analysis