Update README.md

README.md

@@ -1,10 +1,10 @@
 [![Tests](https://github.com/fowler-lab/sbmlsim/actions/workflows/tests.yaml/badge.svg)](https://github.com/fowler-lab/sbmlsim/actions/workflows/tests.yaml)
 
 # sbmlsim
-Create upsampled/artificial datasets of bacterial alleles for training machine learning models
+Python package to create upsampled/artificial datasets of alleles of bacterial genes to test training advanced machine learning models such as graph-based convolutional neural nets. If successful, then real data can be collected to train the model.
 
-## design thoughts
-* class-based design with `Sample` or `Batch` -- the latter with have the iterator within the object. Plan is to try `Batch`
+## high-level design
+* class-based design with `Sample` or `Batch` objects e.g.
 
 ```
 batch = sbmlsim.Batch(n_samples=10,...)
@@ -16,20 +16,5 @@ for i in range(n_samples):
     samples = sbmlsim.Sample(n_res=3, n_sus=2, resistant_mutatations = options.resistant_mutations, random_seed=42...)
 ```
 
-* methods for producing output
-
-## coding thoughts
-
-* python package or CLI with an entrypoint `import sbmlsim` or `sbmlsim --n_res 3 ..` or both -> package first
-* protect `main`? -> not sure we can as is a private repo so don't push to `main`!
-* use pull requests where we ask one other people for a review
-* unit tests run by GitHub Actions on push -> simple system just for testing, used SARS-CoV-2, or HPV, or made up virus
-* use `black` as makes easier to read, run as we go, maybe install an extension in VSCode to run `black` automatically upon save
-* use linting?? No.
-* Google convention for docstrings
-
-## how to write?
-
-* post in `#general` and then push when done
-* 
-
+## research outputs
+To be added once pre-printed.