Software Carpentry: an iDigBio staff perspective

Ever wondered where to start with analyzing a large biodiversity data set you've downloaded from iDigBio's portal or the iDigBio API? Wondering what software tools are available for cleaning your collections dataset or running some interesting queries? Finding a local Software Carpentry course is an excellent first step. On March 24-25, 2016, a 2-day workshop was held at the University of Florida in the newly reopened Reitz Union sponsored by ACIS and the UF Informatics Institute.  The course began with an introduction to the Unix Shell, followed by basic R and simple graphics, Git and GitHub for versioning and collaborative work, and culminated in learning some basic SQL commands and observing how all four components could be integrated into more complex scripting to answer more advanced research and collections data management questions. Two of the participants in this workshop were iDigBio staff members Shelley James and David Jennings who were keen to learn some new tricks and tools, indicating that even those in "the know" can still learn new techniques for data analysis!

While all of the lessons are available online via the Software Carpentry site ( for those self-motivated learners, it was extremely helpful to have the trainers and helpers available for all of those computer software and hardware quirks in addition to answering questions that arose in the process, which ultimately enhanced the learning experience. The trainers for this workshop were iDigBio staff member Matthew Collins, Henry Senyondo from UF's Wildlife Ecology, FLMNH graduate student Brian Stucky, Allison O'Dell from the Cataloguing and Discovery section of the UF library system, iDigBio associate François Michonneau, and learned helper Elise Morrison.

The take home message - don't be intimidated by taking a Software Carpentry course or new software developments for data analysis. Get over the ever-present learning curve, get out of the "what I know already works OK" scenario, and give it a go! Most importantly, all the participants at this workshop have now met knowledgeable and friendly trainers to ask for help when they hit a roadblock. iDigBio highly encourages students, researchers, and collections staff to take - or request - a Software Carpentry or Data Carpentry workshop at your institution to help with leaping off the data analysis dive board! If you need help, ask us at iDigBio, and we will do our best to assist.

-- Contributed by Shelley James and David Jennings