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 led by Eli Holmes 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. To see a Chinook site being used to provide online statistical workshops, go here Random Pursuits.

Sculpin

Sculpin is a lightweight interface for organizing and 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.

FishBox

Sculpin is the engine (code) behind FishBox. FishBox is a site for sharing code by ecological statisticians at NWFSC.

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.

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).