Page History

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.

{html}<STYLE>.pagetree2 a{font-size:16px; }
--></STYLE>{html}
{pagetree2:BioMate}

_Click on a page above for a specific section._


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

[Design One 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 therefore be comfortable providingpresenting a command to the system in a way towhich specifyspecifies 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 As mentioned above, this design allows computational biologists to directly enter the command as it would be run in the command line and have the system perform parsing for them. This is extremely efficient for the programmercomputational biologist since they have already created the script to be run in the command line and are very familiar with the syntax for doing so.

* &nbsp;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, butdespite it is very learnableits learnability. 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 therefore important that the computational biologist verify the parameters for his or her script before submitting them;. howeverHowever, 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 lab-bench biologist, hopefully reducing errors.

* The desktop metaphor provides a solid degree of safety for the lab-bench biologist because it is a familiar interface and reduces the probability of getting lost in the system, or accidentally clicking on the wrong link (by virtue of using icons). Furthermore, the lab-bench biologist's interface with a script provides on-the-fly command feedback when they change the options or parameters for a particular script. Of course, lab-bench biologists would generally not be able to distinguish righta orcorrent wrongcommand from an aincorrect command (the primary issue this system seeks to resolve\!), but this feature could improvesimprove safety forin cases where lab-bench biologists become sufficiently familiar with a script to recognize errors in the command, or when computational biologists seekgo to test their interface for a script by previewing the view for lab-bench biologists.

h3. Design Two

h4. Storyboard

[Design Two Storyboard|BioMate Design 2 Storyboard]

h4. Analysis

h3. Design Three

h4. Storyboard

[Design Three Storyboard|BioMate Design 3 Storyboard]


h4. Analysis