about
iugo-cafe.org is a project to develop web-based tools for scientific collaboration. In the early 2000s, a radical change began in how scientists work together. Web-based collaboration among scientists via wikis, easy access to e-publications, and data-sharing took off, first slowly and then explosively. However, in one area, sharing of code needed for scientific analysis, scientists have lagged behind far behind computer programmers. Since the 1990s, computer programmers have experienced rapid increases in productivity by sharing code and using open-source code. Code-sharing allows fields to progress more rapidly because multiple people don't have to go through the drudgery of coding the same tasks or algorithms. Science, in contrast, does not have effective ways for scientists to code-share; the tools used by computer programmers are impenetrable for most scientists and simply not used by scientists (except to a very, very limited degree). At the same time, science has become more and more computationally intensive and scientific inference (statistics) requires programming algorithms that are more and more beyond the reach of most scientists.
Iugo-cafe came about as an experiment to understand the blocks to web-collaboration among scientists and later to experiment with tools that would facilitate code-sharing. The idea was to learn by doing and at the same time to create something that would be of use to our own groups of scientists. The project was lead by scientists in the Mathematical Biology group at the Northwest Fisheries Science Center and supported by NOAA/NMFS.
The project led to the development of four tools:
Chinook
Chinook is a simple content management php toolkit for making interactive websites. It was designed by and for scientists to facilitate on-line workshops. However it is a quite generic tool and could be used many ways. You are welcome to try it out at the demo site: Chinook Demo Site. If you would like to see a Chinook site being used to provide online statistical workshops, go here Random Pursuits.
Greenboxes
The goal of Greenboxes is to create a network of ecological-oriented code sharing sites. The first site is FishBox and is populated with code by ecological statisticians at NWFSC. You are welcome and encouraged to peruse this site and use the code therein FishBox. If you want to upload your own code to a Greenbox site, you can do that at EcologyBox. Greenboxes has been extremely useful at making our research more efficient.
Sculpin
Sculpin is a lightweight code sharing interface for organizing and freely distributing software code. It is intended to facilitate code sharing by people who are not computer geeks. It has a simple interface to enable people to create personal pages for sharing code with just a few mouse clicks. Sculpin is the engine behind Greenboxes.
Minnow
Minnow is a pdf annotation tool. You can upload a pdf and then have interactive discussions about them. You are welcome to try out minnow on its demo site: Minnow Demo Site. Minnow was our first experiment and did not prove to be very useful for our group.
Developers
The project leader for Iugo-cafe is Eli Holmes. Other developers are Brice Semmens, Ben Weintraub (programmer), and Howard Coleman (programmer). Go to Developers for info on the developers.
Support
Website maintenance is supported by NOAA/NMFS funding. Development of Chinook and Sculpin were supported by an NWFSC Internal Grant (a competitive program to support innovative pilot projects at NWFSC).