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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 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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_Click on a page above for a specific section._

h2. Paper Prototyping

h3. Prototype Photos

| !IMG_1329.png|border=1,width=350,align=center! \\
This is the home screen that both computational biologists and lab-bench biologists see. Our first high-level task was for computational biologists to add a new script, so they clicked "Add/Edit Script". | !IMG_1327.png|border=1,width=350,align=center! \\
This is the screen that computational biologists see after clicking "Add/Edit Script". By clicking "Add text" and "Add parameters", they can construct the command structure that lab-bench biologists will use to run their script. They can also enter caveats and user instructions for the lab-bench biologist, then save or share the script. | !IMG_1318.png|border=1,width=350,align=center! \\
This is the popup that a computational biologist sees when clicking "Add text" from the "Add/Edit script" screen. This is where they enter static text in the command such as "perl montecarlo.pl" or "\| less". |
| !IMG_1317.png|border=1,width=350,align=center! \\
This is the popup that a computational biologist sees when clicking "Add parameter" from the "Add/Edit script" screen. This is where they enter information about each of the parameters that the lab-bench biologist will have the option of setting when running the script. \\ | !IMG_1319.png|border=1,width=350,align=center! \\
This is the popup that a computational biologist sees when clicking "Share" from the "Add/Edit script" screen. Here they have the option of sharing the script with their existing contacts in BioMate or entering an email address. | !IMG_1329.png|border=1,width=350,align=center! \\
This is the home screen that both computational biologists and lab-bench biologists see. Our second high-level task was for lab-bench biologists to run a script, so they clicked "Run Script". \\ |
| !IMG_1335.png|border=1,width=350,align=center! \\
This is the screen that lab-bench biologists see after clicking "Run Script". By clicking "My Notes on Monte Carlo", they can view any notes they have previously created on the Monte Carlo script. By clicking "Instructions", they can view any caveats or instructions written by the programmer. Then the lab-bench biologist can enter the parameters and generate the command. \\ | !IMG_1314.png|border=1,width=350,align=center! \\
This is the popup that a lab-bench biologist sees when clicking on "Instructions" from the "Run script" screen. It shows both caveats and instructions shared by the computational biologist. | !IMG_1316.png|border=1,width=350,align=center! \\
This is the popup that a lab-bench biologist sees when clicking "Generate Command" after entering the required and optional parameters. Here they can copy the command and paste it into a terminal to run. They also have the option of saving the command to their notes. |
| !IMG_1330.png|border=1,width=350,align=center! \\
This is the popup that a lab-bench biologist sees when adding a note on a particular script. They can see all previous notes on this script as well as previous versions of the command they have saved to their notes. | !IMG_1332.png|border=1,width=350,align=center! \\
This is the popup a lab-bench biologist sees when clicking on "Save Parameters" from the "Run Script" screen. This allows them to save all the parameters for a particular run with a unique name. | !IMG_1333.png|border=1,width=350,align=center! \\
This is the popup that a lab-bench biologist sees when clicking on "Load Parameters" from the "Run Script" screen. This allows them to load parameter that they have previously saved for the given script. \\ |

h2. Briefing

h3. Lab-Bench Biologist

You are a lab-bench biologist. You frequently collaborate with a computational biologist in another lab who writes scripts to analyze the data that you have generated in your lab. Sometimes you want to be able to run these scripts yourself because you want to analyze many different datasets and don’t want to bother your collaborator each time you have some new data. The problem is that you are not comfortable using a command-line interface, but your collaborator does not have time to create a fancy GUI for you to run each of their scripts.
We have provided a tool here that allows your collaborator to easily create a GUI for their script and share it with you. You will use the GUI to input the parameters that you want to run the script with. After specifying the parameters, you will be able to press a button to generate the correct command-line syntax for running the script, which you will then cut and paste into the terminal to run.
You are a lab-bench biologist. You frequently collaborate with a computational biologist in another lab who writes scripts to analyze the data that you have generated in your lab. Sometimes you want to be able to run these scripts yourself because you want to analyze many different datasets and don’t want to bother your collaborator each time you have some new data. The problem is that you are not comfortable using a command-line interface, but your collaborator does not have time to create a fancy GUI for you to run each of their scripts.
We have provided a tool here that allows your collaborator to easily create a GUI for their script and share it with you. You will use the GUI to input the parameters that you want to run the script with. After specifying the parameters, you will be able to press a button to generate the correct command-line syntax for running the script, which you will then cut and paste into the terminal to run.

h3. Compuational Biologist

You are a computational biologist. You frequently collaborate with lab-bench biologists in another lab and write scripts to analyze the data that they have generated in their lab. Sometimes your collaborators want to be able to run these scripts themselves because they may want to analyze many different datasets and don’t want to bother you each time they have some new data. The problem is that your collaborators are not comfortable using a command-line interface, but you do not have time to create a fancy GUI for them to run each of your scripts.

We have provided a tool here that allows you to specify the command-line structure of your script and generate a user-friendly GUI for your biologists. The biologists will use the GUI to input the parameters they want to run the script with. After specifying the parameters, the biologists will be able to press a button to generate the correct command-line syntax for using your script, which they will then cut and paste into the terminal to run.

h2. Scenario Tasks

h3. Lab-Bench Biologist

# You would like to run a simulation using a Monte Carlo script which has been written for you. First, find the interface for that script.
# Now, make a note for yourself saying that you are going to try running the script on the file ‘abc.txt’ in your home directory.
# Next, generate the command for the script which prints verbose output to the terminal, runs for 2000 iterations, and is run on the file ‘abc.txt.’
# You realize that the command as generated above causes the script to run for too long. Make a note for yourself saying that 2000 iterations takes too long. Also include the command you just used.
# You are leaving for the day, but would like to return to work on this tomorrow. Save your current configuration so you don’t have to input all the settings you currently have all over again when you come back.
# It’s a new day\! Now, go back to the Monte Carlo script interface, but this time generate the command which does the same thing as you did yesterday except runs the script for only 100 iterations.

h3. Computational Biologist

# Create a new interface for a Monte Carlo script you have written.
# Build the interface for the command ‘perl /home/X/montecarlo.pl \[-v\] <INPUT_FILE> \| less’, where “-v” is a flag for verbosity and “<INPUT_FILE>” is a required parameter and specifies the file path. Make sure that the lab-bench biologist knows that this path is absolute.
# Edit the Monte Carlo script interface you just created to add an optional parameter which will allow the lab-bench biologist to specify the number of iterations the script runs for. The flag for this is “-n” and the default value should be 100.
# Make sure the lab-bench biologist is aware that this command will print its output to the terminal. Also, it should be suggested to not run the simulation for more than 10,000 iterations. Finally, add a description explaining what a Monte Carlo simulation does, and leave your contact information for the lab-bench biologist in case they require clarifications.
# Share the Monte Carlo script interface you have created with your collaborator “V”.
# &nbsp;

h2. Observations: Monday's User Testing Session (Round 1)

h3. User Testing Descriptions

h3. Changes for Round 2

h2. Observations: User Testing on People From B Lab (Round 2)

h3. User Testing Descriptions

h3. Issues to Consider/Resolve