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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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.