allaway/ideas

ideas for scientific projects

ideas

I have a some alright ideas for projects, but maybe some of them are occasionally good ideas or actionable in the right hands. Here's a running list.

If you happen to stumble upon this repo and are interested in collaborating on one or more of these projects, let me know!

If you are not interested in collaborating (totally fine) but are planning on working on one of these projects, please file an issue so I can mark it off as in progress.

idea	description	in progress?	who's working on it
schwannomatosis STR mining	synodos schwannomatosis WGS dataset - check for pathogenic(?) STR expansions
nf1 canine comparative study	use dataset from https://www.nature.com/articles/s41597-019-0149-8 to interrogate NF1 biology in mammary tumors
automate manual compound curation	get a bunch of medicinal chemists in a room to rate structures and then develop predictive models using the ratings as training data. It seems like the manual process of triaging molecules is unavoidable even when using ADME tools. Could we develop computational methods to resolve that manual curation step??
automate manual dose-response curation	get a bunch of preclinical researchers to categorize dose response curves for activity (i.e. efficacious compounds, non efficacious compounds to train a model to predict the efficacy of any given curve. There is often a lot of manual curation and triaging that goes on - 4/5 parameter logistic regression is not the be-all and end all of determining whether a compound is efficacious
NF1 tumors - viral integration?	run a method like p-dip on WGS data, or another appropriate method on RNA-seq data	yes	@parnaljoshi
NF symptom tracking app	measure pain, tumor burden, medication, diet, sleep; could generate important research data while providing value to patients
design scientific software	what design patterns work best? how much information is too much?