I’m currently writing two manuscripts that each have a substantial data modelling component. Some of our previous papers have included computer code, but it was straightforward enough to have the code as a supplementary file or in a GitHub repo and leave it at that. Now with more substantial computation in the manuscript, I was wondering how best to describe it. How much detail is required?
How much explanation should be in the main text, how much is in supplementary information and how much is simply via commenting in the code itself?
I asked for recommendations for excellent cell biology papers that had a modelling component, where the computation was well described.
I got many replies and I’ve collated this list of papers below so that I can refer to them and in case it is useful for anyone who is also looking for inspiration. I’ve added the journal names only so that you can see what journals are interested in publishing cell biology with a computational component. Here they are, in no particular order:
- This paper on modelling kinetochore-microtubule attachment in pombe. Published in JCB there is also a GitHub repo for the software, kt_simul written in Python. The authors used commenting and also put a PDF of the heavy detail on GitHub.
- Modelling of signalling networks here in PLoS Comput Biol.
- This paper using Voronoi tesselations to examine tissue packing of cells in EMBO J.
- Two papers, this one in JCB featuring modelling of DNA repair and this one in Curr Biol on photoreceptors in flies.
- Cell movements via depletion of chemoattractants in PLos Biol.
- Protein liquid droplets as organising centres for biochemical reactions is a hot topic. This paper in Cell was recommended.
- Final tip was to look at PLoS Comput Biol for inspiration, searching for cell biology topics. Papers like this one on Smoldyn 2.1.
Thanks to Hadrien Mary, Robert Insall, Joachim Goedhart, Stephen Floor, Jon Humphries, Luis Escudero, and Neil Saunders for the suggestions.
The post title is taken from “The Arcane Model” by The Delgados from their album Peloton.