Category Archives: Events

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.

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.

 

Looking for a postdoc

With Gyuri leaving for Sweden, the laboratory is short of a postdoc. I am therefore looking for a new postdoc who could start in late 2016 or early 2017. Here below I past the ad I am circulating.

Postdoctoral position — Allesina Laboratory, University of Chicago

The Allesina laboratory at the University of Chicago is looking for a postdoc, starting in late 2016 or early 2017. The interests of the laboratory include ecological networks (food webs, mutualistic, competitive networks), community ecology, and theoretical ecology in general. The focus of the lab is on the development of new mathematical, statistical and computational methods for the analysis of ecological systems. More information on the research interests can be found here. A list of recent publications from the laboratory is here.

The candidate should have a strong mathematical background, be well-versed in statistics, and fluent in at least one of the programming languages used in the laboratory (C, python, R). Knowledge of Linux, Git, LaTeX, and SQL is a plus. Candidates with a background in mathematics or physics are also encouraged to apply.

To apply, please send an email including a CV, a brief description of research interests and experience, and the name of two letter writers to Stefano Allesina (sallesina@uchicago.edu).

Note: Gyuri Barabas and Matthew Smith will be at ESA Annual Meeting. If you are attending and are interested in this position, make sure to contact them to hear about life in the laboratory.

Joining NICO and PLoS Computational Biology

With the new year, I’ve been invited to join the Northwestern Institute on Complex Systems as an External Faculty, and the Editorial Board of PLoS Computational Biology.

nico-logoNICO is an institute dedicated to the study of complex systems, and is part of Northwestern University, in Evanston (a short train ride from Chicago). It is directed by Luis Amaral and Brian Uzzi, two of the best researchers working at the interface of networks and complex systems. I am very much looking forward to work with the faculty there, and I am very interested in the courses and conferences organized by the Center.

ploscb-logoPLoS Computational Biology is one of my favorite journals. I’ve published seven papers in the journal so far (three last year: 1, 2, 3), and I often reviewed and guest-edited for the journal. I am very happy to join the board as an Associate Editor, and I hope this will help increase the number of submissions from ecologists, as well as foster a dialogue between quantitative ecologists and other biologists interested in the computational, statistical, and mathematical aspects of the discipline.