Science Tools 2.0

This week’s topic is “other web 2.0 applications”. In my opinion, this is one of the more exciting developments at the interface between science and technology over the last 5 years or so, it's also rapidly changing. The major themes in this area (as I see them) are:

- increasing integration between data sources and/or analysis strategies
- accessibility and low learning curves
- resource availability

In some cases, this simply amounts to using standard web 2.0 tools (e.g., wikis and blogs) in order to organize and present scientific information in useful ways, in other cases these tools are novel applications developed with a specific purpose in mind. I’ve linked to some resources that I’ve found useful or think are cool. This list is heavily biased toward the type of resources that I use most (phylogenetics and biodiversity informatics), feel free to add others in the comments.

Increasing integration
GBIF - Global Biodiversity Information Facility
Genbank
Scratchpads - Customizable collaboration for taxonomic research
Phylota - Mike Sanderson's database that packages genbank into phylogenetically useful clusters
dryad - Nescent funded data repository

Accessibility
Tree tapper - Former CPBer Brian O'Meara's Nescent postodoctoral project.
Phylowiki - phylogenetics tutorials as a wiki, developed as part of the Bodega Applied Phylogenetics Course
OpenWetWare - lab notebooks, blogs, protocols, etc.
BEAST user guide - example of using a wiki to develop a user guide to complicated software
Cipres - popular phylogenetic inference methods made easy
iTOL - tree visualization
automated tree inference - mor (rDNA fungal phylogeny), MatriPhy (my package, still in development, link goes to turtle example)

Resource availability
Genome browsers
RDP -ribosomal database
Treebase - database of phylogenies
uBIO - database of taxonomic information
Museum collections: specimens - MaNIS, ORNIS, HerpNET; fieldnotes
EoL - Encyclopedia of Life
Biodiversity heritage library - an effort to digitize all the biodiversity literature in 10 natural history museum libraries
Cipres - Free access to some computing resources at the San Diego Supercomputer Center


One could also argue that new online “rapid publication” journals are part of this trend (E.g. Zootaxa, Zookeys, PLoS one). I’ve only had one experience with this type of journal to date and found it to be really great for certain types of papers, I’d be interested to hear about other’s experiences.

In many ways, science is only beginning to take advantage of web 2.0 technologies and I think most would agree that there is a lot of potential for more development in this area. Aside from discussing the utility and the impact that these tools have had on science already, I would also be interested in discussing what resources people think are currently missing and what future developers should be aiming for.