Thursday, July 19, 2007

Biodiversity on the Desktop

In earlier posts, I described my vision of an Encyclopedia of Life (EoL) where the web and your desktop environment are blurred or mashed together. In such a manner, I envisioned a tool where users and contributors to EoL could maintain either a public or private working space to mix and mash data from multiple sources with those in their own hard drives.

One of the grandiose dreams I had was the ability to create a private, content management-like community within EoL in which co-authors of a proposed manuscript like a taxonomic revision could merge their datasets, grab data from third party sources if useful (e.g. GenBank, GBIF, etc.), and collectively work on the manuscript. Upon completion of the manuscript, there may be some elements of use to EoL that the authors could later push out, which in no way diminishes the value of their publication or would cause editors to frown and reject the paper, but offers immediate value to the public at large. Granted I'm not totally clear on how this will work, but I really don't think it would be completely unrealistic. But, what I can't stress enough, is that EoL cannot be like WikiSpecies where contributors have to sit and author content solely for use in WikiSpecies. Rather, it absolutely must have a system that can somehow slip into the workflow of biologists. I'm now convinced that such a vision is not science fiction.

I watched a few Adobe AIR (Adobe Integrated Runtime - code named Apollo) videos this morning and got thoroughly fired-up about the possibilities. Google has been working on an offline API, which looks pretty good, but AIR blows all this out of the water because it allows a developer to maintain an application's presence on the desktop. Further, it can be integrated into the operating system. So, imagine working on a manuscript with a handful of colleagues and be notified with a desktop toast pop-up when he/she has completed his/her revisions or sections of the manuscript, or if a dataset in EoL suddenly became available while the manuscript was being prepared.

The really cool thing from a web developer's perspective is that AIR uses existing web programming tools, i.e. the learning curve to create these cross-platform applications is quite shallow because code can be repurposed for either the web or the least that's the impression I get from watching a few of these videos. Here's one such video where Christian Cantrell demonstrates a few simple applications built on AIR...just mentally substitute Amazon for EoL and you get my drift.

Now, all this stuff is really cool and there is indeed the potential for EoL or the totally unknown "MyEoL" to truly transform the science of biology because it can & should slip into biologists' workflows. Of course, there's no reason why multiple flavours of these AIR desktop applications couldn't be built for children, amateur naturalists, scientists, or however EoL sees its user base. In fact, what I'd really like to see is a BioBlitz class of user where observational data can be merged across interest groups at any geographic scale in their respective desktop applications. An Encyclopedia is great, but we ultimately want people to use the encyclopedia and go outside with fellow human beings to look at, count, touch, or otherwise experience life on our planet. Each flavour of the desktop application can be customized to do different chores or expose different aspects of the EoL system to various classes of end users. The first step then is to nail the needs and design these applications around them. So, here are a few questions to kick-start this process, at least for biologists/systematists who are excited about EoL but just don't believe there will ever be time for them to contribute content:

1. When conducting a taxonomic revision, what are the significant organizational and communications impediments that have slowed down the process?
2. What data sets are vital to conducting an effective revision?
3. What desktop software applications are critical when conducting a revision? [remember, because AIR is on the desktop, there may be an opportunity here to automate file type transformations produced by one provider/database/spreadsheet to the applications required to actually analyze the data]

#2 above will be a challenge and will require that data providers produce similarly structured APIs (e.g. DiGIR, TAPIR, OpenSearch, and the like). This I believe, is where EoL has to take firm leadership. What it needs now is a demo application like that produced by Adobe and Christian Cantrell so we can all visualize this dream. Currently, the EoL dream is very fuzzy and has lead to a lot of miscommunication and confusion. e.g. isn't this just WikiSpecies? THEN, EoL absolutely must write some recipes for content providers to start sharing their data in a manner like what Google does with their Google Maps API. The selling point will be iconographic and link-back attribution for content providers, which can be constructed already if all content providers used a system like OpenSearch, MediaRSS, GeoRSS, and various other RSS flavours to open their doors.

1 comment:

David Shorthouse said...

Follow up...

If you want to see what I think is the best application to date that uses AIR, check out Finetune Desktop.