The Open Science Workshop at PSB 2009
A recap by Shirley Wu
BMIR RIP 1/15/09

2 hours of talks + 1 hour discussion
Phil Bourne
Drew Endy
Larry Hunter
Russ Altman
Steven Brenner
Style, text, photos borrowed from Cameron Neylon

If you couldn’t make it...

If you couldn’t make it...
Microblogging
Slides
Webcasts
http://tinyurl.com/psb09-openscience

“Open Science?”
What is it?
Why should I care?
http://flickr.com/photos/good-karma/710068054/

“Open Science?”
The movement that advocates making
changes to the research process that
make more of the outputs of research
accessible in an effective and timely way
more stuff,
more available,
more quickly
http://flickr.com/photos/good-karma/710068054/

If a million
post-docs
repeat a
million
experiments...
http://flickr.com/photos/heymans/480396810/

... and 25% of
those don’t
work...
http://flickr.com/photos/cliche/120070310/

... how much
taxpayers’
money is that?
http://flickr.com/photos/luismimunoznajar/2093185804/

Make research
more...
efficient
effective
accessible
http://flickr.com/photos/luismimunoznajar/2093185804/

“We argue in good faith
from shared evidence to
shared conclusions.”
- Lee Smolin

“I never had an idea that
couldn’t be improved by
sharing it with as many
people as possible…”
- Bill Hooker

Idea
Develop
Read
Publish Fund
Process Plan
Record

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Publish Fund
Process Plan
Record

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Web 2.0

Protocols
Experimental record
Data
Literature
http://flickr.com/photos/virtualsugar/316200555/

http://flickr.com/photos/65068167@N00/158070855

http://flickr.com/photos/zanotti/314391903/
http://flickr.com/photos/65068167@N00/158070855

Workshop agenda
• Identify challenges and next steps for
Open Science
• Discuss:
• Current approaches and practice
• Development of tools
• Socio-cultural issues

Keynote: Phil Bourne
Open Science:
One Person’s View and What
We Are Doing About It
The research contract is changing
The relationship between scientist and publisher will be
different

Keynote: Phil Bourne
Open Science:
One Person’s View and What
We Are Doing About It
What’s missing?
• Seamless integration between data and publications
• Seamless integration of the authoring and publishing
process
• Association of publications with multimedia
• Professional networking akin to social networking

Keynote: Phil Bourne
Open Science:
One Person’s View and What
We Are Doing About It

Keynote: Phil Bourne
Open Science:
One Person’s View and What
We Are Doing About It

Tool development
David de Roure
The myExperiment approach
towards open science

Tool development
Nigam Shah
How bio-ontologies enable
open science
Open science requires structured content
Generation of structured content requires automated and
collaborative curation
NCBO provides services that address these needs:
Ontology services
Annotator services
Data services

Social issues
CF Quo
Community annotation in
translational bioinformatics:
lessons from Wikipedia
Picture by Hay Kranen

Social issues
CF Quo
Community annotation in
translational bioinformatics:
lessons from Wikipedia
Few users, many edits
Many users, few edits
Picture by Hay Kranen

Social issues
CF Quo
Community annotation in
translational bioinformatics:
lessons from Wikipedia
If 0.01% of users
contribute...
Picture by Hay Kranen

Social issues
CF Quo
Community annotation in
translational bioinformatics:
lessons from Wikipedia
Picture by Hay Kranen

Social issues
CF Quo
Community annotation in
translational bioinformatics:
lessons from Wikipedia
... you need
millions of users
Picture by Hay Kranen

Social issues
Heather Piwowar
Measuring the adoption of
open science sharing data
How much is shared, not shared?
Who is sharing and who isn’t?
Why do people share or not share?

Social issues
Heather Piwowar
Measuring the adoption of
open science sharing data
40% said data sharing was discouraged during
their training
80% said sharing was too much effort
Obstacles are publishing, control, and cost

Social issues
Heather Piwowar
Measuring the adoption of
open science sharing data
Benefits are personal as well as societal
People will share if they think it really helps others
It would be easier if there was more help, better
tools and guidelines

Main themes
“If you build it, they won’t come.”
- Sean Mooney
The design of tools cannot be divorced from the cultural
and social issues that surround them
Community building is just as important as tool building
Need active conversation between users and builders

Main themes
“You cannot manage what you cannot measure.”
- Lord Kelvin
Does any of this actually provide benefits, and if so, to whom?
What is the return on investment?
Without this it is difficult to convince anyone of anything

Tools?
Specific tools are required
(persistent identity, good
repository systems)
Build the service and the
community
http://www.flickr.com/photos/gaetanlee/2792436526/

Policy?
Standards and methods of
citation are at the core of
good science
Focus on specific actions
with measurable
outcomes
Identify successes (and
celebrate), identify failures
(and learn)
http://flickr.com/photos/amrufm/2351316712/

Funding?
Infrastructure
Research on research
http://flickr.com/photos/luismimunoznajar/2093185804/

Improving the research process
is an area for (experimental) research
that requires the same
rigour, standards, and funding
as anything else that we do

http://tinyurl.com/psb09-openscience