Closed tlnagy closed 8 years ago
Sounds great! You could also add:
Those shouldn't be a problem! I updated the original post.
@martinkampmann Here's an example configuration file:
# This is an example configuration file. Whitespace is important.
# Settings pertaining to the library design
library:
genome:
num_genes: 500
num_guides_per_gene: 5
frac-increasing-genes: 0.02
frac-decreasing-genes: 0.1
guides:
crispr-type: CRISPRn # either CRISPRi or CRISPRn
frac-high-quality: 0.9 # fraction of high quality guides
mean-high-quality-kd: 0.85 # mean knockdown by a high quality guide (CRISPRi only)
screen:
type: facs # either facs or growth
representation: # integer value, how much larger are samples than the library
- transfection: 10
- selection: 10
- sequencing: 10
bin-size: 0.25 # size of tail to sample from, must be between 0 and 0.5 (FACS only)
std-noise: 1
num-bottlenecks: 10 # (Growth only)
Some of the descriptions can be improved still
That looks great! I like the descriptions in comments, and we can always have a little more explanation in a separate document, or a supplemental table in the paper.
I agree. I definitely want at least an overview to make it into the README that is shown on the github page of the project.
Currently, the only way to run a custom experiment is to write a full julia file and put it into the
src/exps/
directory. Something like a yaml text file could be much more user friendly. See https://github.com/dcjones/YAML.jlYAML is nice because unlike other structured text files (e.g. JSON) it is also easy to read and supports comments.
I'm collecting a list of interesting "knobs" that users might want to turn:
Library "knobs"
Screen "knobs"
@martinkampmann Thoughts?