Transcript NeylonDrexelNov07

A Beginner’s Guide to Open
Science
(Not for beginners but by beginners)
Cameron Neylon
School of Chemistry, University of Southampton
&
Science and Technology Facilities Council,
Rutherford Appleton Laboratory, Oxfordshire
The problem
• Too much data being
collected
• Too spread out over too
many computers and
people
• Often not accessible or
not properly indexed
• Data gets lost as
computers are retired
and people leave
Objectives for an e-notebook
1. Storing, recording, and preserving data
2. Tracking samples and sample movements
3. Monitoring researcher progress and problems
4. Machine readable data structure to track
relationships between samples/data
Implementation of e-lab book
• Blog based format
• Purpose built engine
• Fully flexible system
with arbitrary metadata
• Full record of changes
(not currently easily
accessible)
http://chemtools.chem.soton.ac.uk/projects/blog/ “Bio Blogs”
http://blogs.openwetware.org/scienceintheopen
Discussion
Implementation of e-lab book
• Blog based format
• One poster per item
• Templates enable
automated posting and
metadata capture
• Aim to develop a web
service interface
http://chemtools.chem.soton.ac.uk/projects/blog/ “Bio Blogs”
http://blogs.openwetware.org/scienceintheopen
Discussion
Objectives for an e-notebook
1. Storing, recording, and preserving data

2. Tracking samples and sample movements

3. Monitoring researcher progress and problems

4. Machine readable data structure to track
relationships between samples/data

What is this to do with ‘Open’?
What do we mean by ‘Open’?
'No insider information‘ – Jean-Claude Bradley
Possible issues with ONS
• ‘Being scooped’
– The biggest fear and
probably not actually a
serious problem
• Being embarrassed
– This is what actually
scares people
• Requires effort,
discipline, and a bit of
persistence
• Legal issues…safety
and ethics…politics?
Other approaches to ONS
Impressions of ONS approaches
• The initial motivation for doing ONS/using an enotebook has a strong effect on form
• For most laboratory research strict data
structures will always break
• Different viewers have different needs
• The simple notebook/journal has advantages of
paper notebooks but also disadvantages
• Flexible metadata is crucial
• Templates provide a very effective way of
capturing metadata and increasing useability
Linking web services together
Workflow by
Duncan Hull
Linking web services together
Linking web services together
Linking web services together
Where next?
• Small group of people doing ONS and a variety of
other similar projects ongoing
• Small benefits being seen but community size and
connectivity needs to grow
• Many of the tools we use do not yet provide the clear
advantages to persuade people to move from paper
• Communication beyond traditional publishing needs
aggregators and indexes
• ‘Open Science’ requires a series of cultural shifts in
how scientists work, communicate, and are evaluated.
Acknowledgements
• Lab Blog development and implementation
Andrew Milsted, Professor Jeremy Frey
• Lab work and blog use
Jennifer Hale, Wendy Smith, Joseph She
• Funding
BBSRC grant BBD00652X1, UK E-science
programme through platform grant to JGF
Links
• Our lab blogs (pick one of the “Bio Blogs”)
http://chemtools.chem.soton.ac.uk/projects/blog/
• Timeline view of one of the Lab Blogs
http://chemtools.chem.soton.ac.uk/projects/timeline/
blogs.php?id=13
• Discussion of related issues with the Lab Blog
including technical and ‘social’ issues
http://blog.openwetware.org/scienceintheopen