Open Workshop

One of us (RS) initiated the Open Workshop as an experiment to bring together the populations of curious laymen, experienced wet biologists, and software engineering talent in the East Bay area, and all three of these groups were represented in the attendees of the workshop. In addition, several working bioinformaticians contributed.

The project was structured to give an introduction and purpose to looking at a variety of publicly available biological data. The first five meetings each were spent on a category of biological data: chromosomal sequences; individual open reading frames; microarray data; quantitative proteomics data in 2D Polyacrylamide Gel Electrophoresis; and quantitative proteome data from Gas Chromatography/ Mass Spectroscopy. In each of these sessions, data was gathered from public sources and participants worked. Attendance ranged from 25 to 30 participants. As a public-scientific interface event, hands on work with data and computers was quite engaging and several useful scripts were written to process the data in python and R.

The following two months of biweekly data analysis sessions were less fully attended, with an average of 2-4 participants. Possible reasons for this decline include lack of understanding of the subject matter or technical skills needed to fully participate, inability to commit to an extended project, and unclear direction or incentives to continue. The more open ended nature of data interpretation and analysis is also a difficult process to relate to an introductory courss; it was difficult for newcomers to biology to attach to these tasks.

Future workshops may be structured into beginner, intermediate and advanced levels that would be more accessible to participants from diverse educational backgrounds and will likely be shorter in length to reduce attrition. Another idea is to take on a project with the sole goal of doing that project, rather than anticipating publishable results. As an experiment, the workshop did succeed in bringing together a range of talent and covered a broad set of biological data.

Slides for these sessions are available at http://boundaryconditions.org/biology.html. When we have completed screening out parts, scripts, data collected and analysis for this project will be made available here: https://bitbucket.org/ronbo/glowingplantparts