98th ESA Annual Meeting (August 4 -- 9, 2013)

August 03 - 09, 2013

WK 12

Software Carpentry for Ecologists

Ecological research projects and analyses are increasingly dependent on programs of all sizes, many of them one-of-a-kind tools written by scientists themselves. Unfortunately, most ecologists are never taught the equivalent of good lab practices for software development, which means they are often less productive than they could be, and their software is often less reliable than it should be. Software Carpentry (http://software-carpentry.org) is a program designed to train scientists to build and use computational tools more efficiently so they can spend less time on the computer and more time doing science. Our day-long workshop will introduce four specific tools --- the Unix shell, version control, automated testing, and regular expressions --- that will help ecologists in the era of big data, simulation, and increasingly complex analyses. Each tool will facilitate ecological collaboration, research and data management. The Unix shell is the standard interface for all computing clusters and large database environments. Version control allows ecologists to keep track of their code more efficiently, and will make collaboration easier on large projects. A fundamental component to any kind of programming is making sure your code does what you intended. Learning automated testing will streamline this tedious process. Finally big data sets are not always what they seem, and often require further clean-up. Regular expressions are a powerful tool for the fuzzy searching of text to standardize variable names and inputs. Attendees will leave our workshop with a suite of powerful tools that streamline their research.