Microbial ecologists today face critical computational barriers. The rapid increase in the quantity of data acquired by modern sequencing instruments makes analysis by hand infeasible, and even software developed just a few years ago cannot scale to modern data sets. As a result, making advanced, scalable algorithms and large-scale computational resources available to end-users is necessary to advancing our understanding of microbial ecology. One challenge many face when developing software for the first time is the gap between writing a script that can run on a single processor and writing a script that will scale to a larger cluster. A second is that knowledge required for a project is often distributed among many individuals, including software developers, subject matter experts and experts in the use of specific computer systems. Although computation can be a language that bridges many disciplines, additional ‘glue’is often needed to make the requirements mutually comprehensible to diverse members of a project team.

One approach to this ‘glue’is represented by IPython (Pérez and Granger, 2007), which provides tools for interactive and parallel computing that support online collaboration. The IPython notebook allows users to combine code, text (including mathematical expressions), figures, and so on, into a single document. These documents are accessed through a web browser and can be simultaneously edited by multiple collaborators. The resulting environment is analogous to Google Docs, but aimed at scientific computation. Beyond document writing, these notebooks can execute arbitrary code in the Python programming language, providing a framework where documentation, software and results are combined in one place, and code can be edited, annotated and re-run dynamically to immediately show how the results change. IPython also provides tools to run computations in parallel, with a high-level interface that eases the transition from a classic serial script to a parallel environment. The power of the IPython approach is especially apparent when it is coupled to cloud computing,