Computing skills for biologists

The cover, featuring art by Desmond Paul Henry

After years in the making, “Computing Skills for Biologists — a Toolbox” is finally out!

The book covers many topics, including the Unix shell, programming in Python and R, LaTeX, and relational databases. It shows how these tools can be integrated to build powerful pipelines for the automated, rigorous and reproducible analysis of biological data.

You can find the book on the website of Princeton University Press, or on Amazon and other sellers.

You can find more information on the dedicated website computingskillsforbiologists.com

A big thanks to my co-author Madlen Wilmes, to Alison Kalett and her team at PUP, and to the students who helped us making the material more interesting and fun.

Random zoo

When will I be in Lotka?

In a new paper, Carlos, José, Jacopo, Kent and I tackle this simple problem: if we take a Lotka-Volterra system with random parameters, and let the dynamics elapse, how big will the final, persistent community be?

You can read the paper here:

Carlos A. Serván, José A. Capitán, Jacopo Grilli, Kent E. Morrison & Stefano Allesina
Coexistence of many species in random ecosystems
Nature Ecology & Evolution, 2018

I’ve written a short blog post for Nature Ecology & Evolution Community, telling the story behind the paper, which you can read here.

A News & Views piece by Shaopen Wang accompany the paper. This work was highlighted in Nature Physics by Federico Levi. This paper was also mentioned in an article in Quanta Magazine.

Network Spandrels

Biological networks show strong departures from simple models of random graphs. For example, they display broader degree distributions, high modularity, and strong preponderance of certain motifs.

One might be tempted to interpret these features as a signal of a selective force pruning the space of possible networks, resulting in empirical networks possessing certain features.

In one of my all-time favorite papers, Ricard Solé & Sergi Valverde proposed an alternative explanation: these features might be by-products of how the network was assembled. They dubbed this the “network-spandrel” hypothesis, referencing the famous paper by Gould & Lewontin.

In a new paper just published in Ecology Letters, Dan Maynard, Carlos Serván and I show a simple model of ecological assembly where by slightly tweaking the rules of assembly we can obtain dramatically different network structures—a paradigmatic case of network spandrels:

Daniel S. Maynard, Carlos A. Serván & Stefano Allesina
Network spandrels reflect ecological assembly
Ecology Letters, 2018

Notably, the idea of network spandrels will be the focus of a Satellite Session at NetSci 2018 in Paris. The satellite is being organized by many of the current and past collaborators of the lab.

 

3 ≫ 2

In a new paper published today in Nature, we show that Higher-Order Interactions (HOIs) can have dramatic effects on the dynamics of ecological systems.

Jacopo Grilli, György Barabás, Matthew J. Michalska-Smith & Stefano Allesina
Higher-order interactions stabilize dynamics in competitive network models
Nature, 2017

I have written a short “Behind the paper” post for the Nature Ecology & Evolution Community, which you can find here.

James O’Dwyer has written a News & Views commentary.

Rob Mitchum has covered this work for the Computation Institute‘s website.

I have presented this work at several conferences. Here’s a video of my talk at the BES annual meeting in Liverpool (Dec 2016, ~30 mins):