Problem

Much of the knowledge produced by biological research is passed down by oral tradition.

This makes it difficult for newcomers to enter the field.

Solution: OpenWetWare

OpenWetWare's contributions

Easy and collaborative content generation Digitization of biological knowledge, as it is generated

Labs on OpenWetWare

Integrating OpenWetWare into research

Examining Communication

Ethnomethodology: A sociological discipline which focuses on the ways in which people make sense of their world, display this understanding to others, and produce the mutually shared social order in which they live. (Wikipedia)

Discourse Analysis

Dysfunctionality of Model Publishing

Systematization and Data Standards

• A
• B

YeastPheromoneModel.org

YeastPheromoneModel.org

Data standards

Rigid, one-way communication

Model Construction and Documentation

• YeastPheromoneModel.org -- Ty Thomson, MIT
• Agile Informatics project -- Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP

Models Are Poorly Communicated

Knowledge generated during model building is lost!

It is difficult to:

1. construct a new model
2. build on published models
3. evaluate published models
4. involve experimentalists

What About MIRIAM, SBML, etc?

1. MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
2. SBML - Systems Biology Markup Language

OK for publishing, but too complicated for discovery!

Can we design something more "agile" while utilizing and respecting the established standards?

1. systematize data
2. follow so-called "80/20" rule
3. "living" models
4. wikis foster communication

OpenWetWare's success

• 2,800 contributors
• 100 labs
• 1.5 million pageviews per month
• 275,000 sessions per month

http://openwetware.org