Science Ajar? From Open Access to Intelligently Accessible ...€¦ · Science Ajar? From Open...
Transcript of Science Ajar? From Open Access to Intelligently Accessible ...€¦ · Science Ajar? From Open...
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Science Ajar? From Open Access to Intelligently
Accessible Data in Open Notebooks
Jeremy G. Frey
University of Southampton
05/12/2014 Beyound Open Access
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A Chemist’s Digital Aura
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A Chemist’s Digital Aura
http://mosaically.com/PhotoMosaic/3289771f-0bf3-49bf-bc8a-1810167096ff
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05/12/2014 The future of laboratory data 4
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http://commons.wikimedia.org/wiki/File:ISS-30_Ice_floes_along_the_Kamchatka_coastline.jpg
Reducing and Managing Uncertainty
05/12/2014 Beyound Open Access
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Coherent diffraction Imaging for lens-less soft x-ray microscopy
Key is computational phase reconstruction, which using GPU, can be done in time comparable to the experimental acquisition time. GPU cluster will enable ensemble solution and thus estimate the uncertainty in the reconstructing, but would need on demand.
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Air/Water slab MD simulation
Computational power now available means that sufficient accuracy and low uncertainty can be obtained for a whole series of small and large water slabs allowing the surface contribution to the total energy to be reliably “observed” and entropy contributions to surface tension derived.
Surface area per molecule
Tota
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Reducing Uncertainty
• What is already known?
• Who is doing what?
• How was a result obtained?
• Access to Data
• Integration of Data.
• Provenance & Planning
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Intelligent (Open) Access to Data
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https://royalsociety.org/policy/projects/science-public-enterprise/Report/
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05/12/2014 Beyound Open Access
http://www.nature.com/news/confusion-over-publisher-s-pioneering-open-data-rules-1.16409
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05/12/2014 Beyound Open Access
http://blogs.nature.com/news/2014/11/gates-foundation-announces-worlds-strongest-policy-on-open-access-research.html
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05/12/2014 Beyound Open Access
“In theory, there is no difference
between theory and practice.
But, in practice, there is.”
Unknown (possibly Yogi Berra or Manfred Eigen)
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05/12/2014 Beyound Open Access
http://news.bbc.co.uk/1/hi/technology/8388485.stm
Methods are as important as the data
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05/12/2014 Beyound Open Access
http://editorsupdate.elsevier.com/short-communications/journal-cortex-launches-registered-reports/
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05/12/2014 Beyound Open Access
http://www.nature.com/news/ocean-observatory-project-hits-rough-water-1.16406
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05/12/2014 Beyound Open Access
http://997waystobeagreatspeaker.com/2010/12/how-to-tell-a-story/
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THE NARRATIVE What is the story? What is the how and the why?
05/12/2014 Beyound Open Access
Skills we need are story telling skills not data mining skills Clive Humby DE/2014 Keynote
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Faraday’s laboratory notebooks are also remarkable in the amount of detail that they give about the design and setting up of experiments, interspersed with comments about their outcome and thoughts of a more philosophical kind. All are couched in plain language, with many vivid phrases of delightful spontaneity…. Peter Day, ‘The Philosopher’s Tree: A Selection of Michael Faraday’s Writings’
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THE INTERNET AND THE WEB WWW
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Scientific Data Value Chain
• Does the Web currently/have the potential to disrupt or support the data value chain?
http://www.dreamingnewmexico.org/food/ff-local-foodshed
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USER GENERATED CONTENT
Web 2.0 & Semantic Web
Nature Chemistry
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QUALITY?
05/12/2014 Beyound Open Access
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http://www.opsrules.com/supply-chain-optimization-blog/bid/282916/Why-You-Shouldn-t-Waste-Effort-Improving-Forecast-Accuracy
Accuracy
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DIGITAL RESEARCH NOTEBOOKS
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MoreTea: Tablet Interface and RDF World 05/12/2014
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LabTrove: Easy Communication
Images and sketch commenting
Highly inter-linked report
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Digital and Physical Worlds
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Open Notebook Science
• Certainly not always the way to work! – IPR, Commercial, long term projects, recognition
issues, etc
• But – Makes connection much easier if the data and
processes are “Open”
– Easy to export & access of “Linked-Data”
It is not necessary to change. Survival is not mandatory.
W. Edwards Deming
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LabTrove Open Notebooks
Mat Todd’s Malaria Project
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LabTrove -> RSS -> Email / Twitter
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http://upload.wikimedia.org/wikipedia/commons/4/41/Looking_through_the_Trees_in_Spearywell_Wood_-_geograph.org.uk_-_424274.jpg
Finding the “Wood” From the “Trees”
05/12/2014 Beyound Open Access
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http://en.wikipedia.org/wiki/Plantation#mediaviewer/File:Pinus_taeda_plantation.jpg
Organized Data - Metadata - Linking - Networks/Graphs
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A big proportion of our users are
not really adding
metadata!
05/12/2014 Beyound Open Access
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Chemistry blogs results
50 chemistry-related blogs – 10,436 ‘tags’
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05/12/2014 Beyound Open Access
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NASA results
53 NASA blogs – 1226 ‘tags’
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Metadata
• User Created
• Metadata Sentence
–Attempt to get verbs (processes) as well as nouns (things)
Toki Pona
http://en.wikipedia.org/wiki/Toki_Pona
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learning Research Thesis
Reading collection
Thes
is
Rev
isio
n
Effo
rt
do
cum
ent
org
aniz
e
Pla
n
Sub
mit
Research student thesis writing often involves dealing with the consequences of having delayed the (huge) organization effort to the point of writing up
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Time
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Smart Tea Project
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P2 - Plans & Provenance
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Graph/Network provides intuitive navigation
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VALIDATION
Publication@Source
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“The Laboratory”
• A laboratory is an Integration of people and equipment
• A complex socio-technical system
• Disrupted or integrated by digital infrastructure?
• How to support (a) people to do what they are best at doing and (b) computers to undertake what they can do best and (c) ensure that they can work together.
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DISSEMINATION IS PART OF THE RESEARCH
Bringing dissemination in to the lab… use and re-use of data… the digital research notebook
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“Engrooved*”
* concept highlighted in teaching by Paul Trowler
– http://www.brad.ac.uk/sustainable-universities/media/sustainableuniversities/Keynote-Prof-Paul-Trowler.pdf
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http://www.todayandtomorrow.net/2010/02/22/quarter-mile-groove/
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The System adapted from Atul Gawande 2014 Reith Lectures
• “Primitive idea” – You ought to do x.
• Medieval approach – You must do x! You must follow the standards
– Will will take away your grant….!
• Modern world(?) – Becomes the norm, make it easy to do
– Checklists
– Feedback loops
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All I am saying is that now is the time to develop the technology to deflect an asteroid
We must speed up the knowledge discovery process
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Re-imagining Scientific Research
A “Social Machine” of experienced researchers, technology &
information
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LABORATORIES OF THE FUTURE
http://lab-on-chip.gene-quantification.info/
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Everything is Awesome, Everything is cool when you're part of a team
The Lego Movie
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IDCC 2014 Meeting San Francisco http://www.dcc.ac.uk/events/idcc14/programme-presentations
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The samples you need may already be available
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05/12/2014 Beyound Open Access
http://www.nature.com/polopoly_fs/1.16429!/menu/main/topColumns/topLeftColumn/pdf/516131a.pdf
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The Art of Asking the Right Question
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He who asks a question is a fool for five minutes; he who does not ask a question remains a fool forever.
—Chinese Proverb
Why is asking a good question on Quora (20 credits per follower) more rewarding than writing a good answer (10 credits per upvote)?
http://www.quora.com/Why-is-asking-a-good-question-on-Quora-20-credits-per-follower-more-rewarding-than-writing-a-good-answer-10-credits-per-upvote
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Acknowledgements
• My research group – Chemists & Computer Scientists – UG project students, PG, and Post-Docs – Visitors
• My colleagues – Chemistry, Physics & ORC, Computing, Engineering, – Statistics/ Mathematics
• Funding – University of Southampton, Chemistry – EPSRC, RCUK, JISC/Jisc, IBM, Microsoft, TSB, Lonza
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Trust me Mort - no electronic communications
superhighway, no matter how vast and sophisticated,
will ever replace the art of the schmooze
Thank you for listening