The History and Purpose of Eco-Tools
By Gareth Russell, Columbia University (June 2004).
Motivation
Have you ever had to perform a complex ecological analysis, and found that your options were
- To download a piece of dedicated software which: a) is six years old since its last update, b) was written for an old operating system on a different platform, c) is outrageously expensive, d) requires an arcane input format e) has a poorly-designed interface and primitive graphics (if any), f) any combination of the above?
- To find various resources detailing the methods, and program it yourself?
I almost always take option (2), because I like to see what is really going on, and so that any mistakes are made by me, rather than the ‘black box’ that is pre-compiled code. But most people have neither the time nor the inclination to do this. So I decided to put together a set of numerical tools for ecological analysis that are available, free, to anyone with web access. What makes these tools different from other third-party offerings is that they are programmed in Mathematica (Wolfram Research), which is a high-level coding language, and the code is available for anyone to inspect. The idea is that the tools can be easily peer-reviewed, corrected, and improved over time.
I also hope that the site will make sophisticated tools for conservation available in developing countries where access to computing resources is limited. Eventually, I would like to see the site available in multiple languages. If you would like to volunteer to assist with this effort, contact me!
History
The idea for the Eco-Tools site was hatched in the summer of 2003, and the first, development version was begun on July 13th, 2003. This version was intended as a proof-of-concept, and used the free ‘amateur’ version of webMathematica as its engine.
Various ‘beta versions’ of tools were developed over the 2003–2004 academic year, mostly by me, with a couple coming from student projects.
The site made its public debut at the 2004 annual meeting of the Society for Conservation of Biology, which was held at Columbia University in the City of New York. Not coincidentally that is where I was based at the time!
Currently the site is based at the New Jersey Institute of Technology, where I am an assistant professor. It is housed on much better hardware than before. A revamped design, with updated modules, was made public in early 2006.
The Future
I believe that the Eco-Tools concept has enormous potential, and I am looking forward to getting input from others. My own thought is to follow the ‘working group’ approach of the National Center for Ecological Analysis and Synthesis (NCEAS). In this model there would be a series of working groups, each targeting a specific area (say, predicting time to extinction). A group would consist of modelers and managers, and would meet for a workshop to determine what the problems are that need solving and which mathematical approaches are available to do that. The approaches would be organized as far as possible into a hierarchy, from simple, generally-applicable techniques to more specialized tools. Example datasets would be chosen and technical references compiled. Following the workshop, a small programming team (e.g., myself, perhaps a post-doc or two) would translate the techniques into the Mathematica language, while a separate team works on writing up a short description of the techniques in ‘mid-level’ language, with references to technical articles. Once the working group is satisfied with these they would be put online and tested thoroughly.
That’s just one way in which Eco-Tools could develop. In terms of areas, I would very much like to implement tools for incorporating phylogenetic information into conservation-related analyses. My personal feeling is that many practitioners ignore the potential influence of phylogeny because it is “too hard” to implement. The existing tools, which are many, provide a classic example of problem (1) in the list above. As an extremely primitive beginning I have implemented a tool for calculating Moran’s I for a taxonomy or phylogeny as means of testing for phylogenetic autocorrelation in a trait. As the next step, I am working on a parser for Nexis format files.