The current system of publishing scientific papers hampers scientific advancement in particular ways. I’d like to diagnose the problems so that new publishing efforts (like PLoS ONE) can be shaped to remedy them. I believe that a major flaw in the modern journal system is that it discourages complete treatments of the literature.

Isfahan, Iran has one of the most beautiful plazas in the world. A gorgeous book about that city has been redone and includes a full-page version of this photograph I took of its Friday Mosque. I hope the book, Isfahan: Pearl of Persia gets the readers it deserves. I also highly recommend visiting Iran yourself.

https://www1.gotomeeting.com/register/422340144 Fri, May 22, 2009 3:00 PM – 3:30 PM CDT description: http://blog.enthought.com/?p=116 They will try to record it for later playback.

Earlier I wrote about the open-source free tools I use to plot and analyze my data—Python and R. One of the most time-consuming and fiddly parts of making graphs for our papers is the need to: plot multiple subsets of the data (different experimental conditions), sometimes with double axes make a whole array of plots, one for each of the experimental participants’ data I’ve been doing this in python with scipy by coding an outer loop

In my graduate school days, we had something called ‘The Scathing Wall’, a small bulletin board which provided some outlet for one of our greatest frustrations—dealing with the reviews that came back from a journal after we had submitted a manuscript.

My scientific workflow includes email between myself and lab members and collaborators, annotations on previously published papers, adding information and ideas to the lab wiki, Python programs to create visual displays and run experiments with them, and Python and R code to plot the results and do the statistical analysis.

I’ve transitioned to all open-source software for my science. The Python language and its libraries VisionEgg and Psychopy are more than sufficient to code my perception experiments. For data analysis, I’ve gotten pretty far with the SciPy library for Python, which has probability distributions, function minimization, Fourier transforms, etc. The Matplotlib library makes it easy to make plots in a way familiar for old MATLAB users like me.

For data analysis, I switched from using MATLAB, partially motivated by a desire to support open source, to using R. But my experiments nowadays are written in Python, so I decided to try analyzing the data with Python as well. SciPy is an open-source library that helps with this, and duplicates a lot of MATLAB functionality to make it easier to switch from MATLAB.

The conventional encyclopedia: old and unimproved! Here is a preprint of my entry for the The Sage Encyclopedia of Perception with headword “The Binding Problem”. The hardcopy version of the encyclopedia will be a massive 1100-page tome with hundreds of contributors.

I’m releasing an interactive tutorial suitable for either individual learning or in the context of a class wherein each student, or pair of students, has a computer. I used it for my third-year psychology university students. Before beginning the 100-minute class, most had little idea how connectionist networks could store memories or compute visually guided action.

Nature has published a news item by Declan Butler on the finances of one of its competitors: the open-access PLoS journals, using language that puts the organisation and its journals, especially PLoS ONE, in a negative light.