Computing Skills for Biologists: A Toolbox
This book grew out of the lecture notes for the graduate class Introduction to Scientiﬁc Computing for Biologists, taught by Stefano at the University of Chicago. We would like to thank all the students who took the class— especially those enrolled in Winter 2016 and 2017, who have test-driven the book. The class was also taught in abbreviated form at various locations: thanks to the TOPICOS students at the University of Puerto Rico Río Piedras, to those attending the 2014 Spring School of Physics at the Abdus Salam International Center for Theoretical Physics in Trieste, to the participants in the Mini-Course BIOS 248 at the Hopkins Marine Station of Stanford University, and to the students who joined the University of Chicago BSD QBio Boot Camps held at the Marine Biological Laboratory in Woods Hole, MA.
Several people read incomplete draﬅs of the book, or particular chapters. Thanks to Michael Afaro and anonymous referees for the critical and constructive feedback. Alison Kalett and her team at Princeton University Press provided invaluable support throughout all the stages of this long journey.
We are grateful to all the scientists who uploaded their data to the Dryad Digital Repository, allowing other researchers to use it without restrictions: it’s thanks to them that all the exercises in this book make use of real biological data, coming from real papers.
The development of this book was supported by the National Science Foundation CAREER award #1148867.
Stefano: I started programming late in my college years, thanks to a class taught by Gianfranco Rossi. This class was a real revelation: I found out that I loved programming, and that it came very naturally to me. Aﬅer learning a lot from my cousin and friend Davide Lugli, I even started working as a soﬅware developer for a small telephone company. In the ﬁnal year of college, programming turned out to be very useful for my honors thesis. I worked with Alessandro Zaccagnini, who introduced me to the beauty of LATEX. When I started graduate school, my advisor Antonio Bodini encouraged me to keep working on my computing skills. Stefano Leonardi convinced me to switch to Linux, pressed me to learn C, and introduced me to R. Many people are responsible for my computational toolbox, but I want to mention Daniel Stouﬀer, who gave me a crash course in svn,andEd Baskerville, who championed the use of Git. I thank my students and postdocs (in order of appearance Anna Eklöf, Si Tang, Phillip Staniczenko, Liz Sander, Matt Michalska-Smith, Samraat Pawar, Gyuri Barabás, Jacopo Grilli,
Madlen Wilmes, Carlos Marcelo-Sérvan, Dan Maynard, and Zach Miller) and the other members of the lab for coping with my computational quirks and demands, and for learning with me many of the tools covered in this book. Finally, I want to thank my parents, Gianni and Grazia for buying me a computer instead of a motorcycle, my brother Giulio, and my family, Elena, Luca & Marta, for love and support.
Madlen: I earned a ﬁve-year degree in biology without a single hour of computational training. That turned out to be a tremendous problem. Fellow PhD student Illka Kronholm took the time to teach R to the “German without humor.” Later, Ben Brachi generously shared his scripts and contributed to myﬂuencyinR.IamalsogratefultoMarcoMambelliwhointroducedmeto clustercomputingandhelpedmetogetagriponUnix.
My advisor and coauthor Stefano Allesina had, undoubtedly, the biggest impact on my programming skills. His course, Introduction to Scientiﬁc Computing, was my ﬁrst experience of a well-structured and constructive class centered on computing skills. And so the idea for this book was born, as I wished every student could have a resource to help overcome the initial steep learning curve of many computing skills, and use examples that were actually relevant to a biologist’s daily work. I am tremendously grateful to Stefano for agreeing to write this book together. In the process I not only became a more proﬁcient programmer and better organized scientist, but also felt inspired by his productivity and positive attitude.
My dad-in-law, George Wilmes, provided valuable feedback on every chapter and took care of my kids so I could work on this book. Last but not least I want to thank my parents and my husband John for helpful suggestions, love, and support.
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