open science: examples in bioinformatics
DESCRIPTION
My #oaweeknl #oaweek2012 contribution.TRANSCRIPT
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Department of Bioinformatics - BiGCaT 1
Open Science
Examples of Bioinformatics
Egon Willighagen (@egonwillighagen)Dept. Bioinformatics – BiGCaT, Maastricht University
Open Access Week / Data Management 2012/10/23, Maastricht
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Department of Bioinformatics - BiGCaT 2
Warning and disclaimer!
• IANAL• I have too many slides
–But they will be available online later
• You are expected to tweet!–#oaweeknl–#oaweek2012–and #oaweekum ?
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Department of Bioinformatics - BiGCaT 3
Today's triangle
1. Science and Microscopes2. Open Science and Social Contracts3. Data Management
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Department of Bioinformatics - BiGCaT 4
Bioinformatics is ...
… development of new microscopes by which we study life.
(by finding new correlations and translate those into causal relations)
Wikipedia, Moisey, CC-BY-SA
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Department of Bioinformatics - BiGCaT 5
Not all microscopes works as expected
N. Jeliazkova, unknown license; claiming fair use
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Department of Bioinformatics - BiGCaT 6
Bioinformatics equipment
• Statistics (multivariate)• Computation• Data management
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Department of Bioinformatics - BiGCaT 7
Today's triangle (2nd round)
1. Science and Microscopes2. Open Science and Social Contracts3. Data Management
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Department of Bioinformatics - BiGCaT 8
Open Science
• Reproducibility!–How did that compound get synthesized?–Why can't I reproduce that cell line experiment??–Why are those data point errors suspiciously
distributed?–Can I apply that to my own data too?
There is no place in Science for trust.
“If there are two competing opinions but without arguments, we'll take mine.”
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Department of Bioinformatics - BiGCaT 9
Social Contract!
• Collaboration–Shared goal, shared ownership–More efficient and cheaper than other solutions
(e.g. consortium agreements, patents, IP)
• Impact for your research!–dissemination beyond 'friends'–#altmetrics
• Education– I will do as much as I can to make it easier for my
students to learn what I expect them to lean and more.
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Department of Bioinformatics - BiGCaT 10
Get more impact: Nature citations
• The Journal Impact Factor (JIF or IF) is a bad indicator of impact
• Less than half of the Nature papers has more than zero citations in past two years1. most Nature-worthy research has very
limited impact2. many papers get more cited than the
average Nature paper
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Department of Bioinformatics - BiGCaT 11
#altmetrics
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Department of Bioinformatics - BiGCaT 12
The 3 #openscience corner stones
• Knowledge (data, methods, conclusions) can be freely used
• It can be freely modified• It can be freely redistributed
(for #opendata, #opensource and #openstandards)
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Department of Bioinformatics - BiGCaT 13
Open Source Cheminformatics
• Metabolomics• Drug discovery• Toxicology
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Department of Bioinformatics - BiGCaT 14
O'Boyle et al., JChemInf, 2011
Blue Obelisk: Open Data, Open Source, Open Standards (or: interoperability)
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Department of Bioinformatics - BiGCaT 15
Today's triangle (2nd round)
1. Science and Microscopes2. Open Science and Social Contracts3. Data Management
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Department of Bioinformatics - BiGCaT 16
Labnote books
• Statistics–Sweave
• Computation–Log files
• Lab–Digitize images and
notes
Backup, easier to share, ...
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Department of Bioinformatics - BiGCaT 17
Version control: e.g. Git
commit 047ca7fc69d30a961209f6d480bc11e454f4bc56
Author: egonw <egonw@350a12d8-24d3-0310-83a6-a3e505aec109>
Date: Thu Feb 12 10:05:32 2004 +0000
Added artikelen subdirectory.
git-svn-id: svn+ssh://localhost/var/svn/runrepos@1 350a12d8-24d3-0310-83a6-a3e505aec109
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Department of Bioinformatics - BiGCaT 18
What about Dept. of Bioinformatics?
We take advantage of Open collaborations in our study of life.
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Department of Bioinformatics - BiGCaT 19
Be clear in what you want!
• Whatever license you pick, make sure that people know your wishes!
• Data without a license statement, is a potential gold mind, with a large legal department behind it waiting to feast.
(So, you move on to the next data set)
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Department of Bioinformatics - BiGCaT 20
Data sharing?
FigShare!
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Department of Bioinformatics - BiGCaT 21
DataDryad
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Department of Bioinformatics - BiGCaT 22
The Data Hub
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Department of Bioinformatics - BiGCaT 23
Conclusions
• Open Science–use it to your advantage; look at what
we achieved by everyone contributing their bit
– it improves science and education
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Department of Bioinformatics - BiGCaT 24
More info?
• Twitter: @egonwillighagen
• http://chem-bla-ics.blogspot.com/
• ORCID: 0000-0001-7542-0286
• http://www.blueobelisk.org/
• http://cdk.sf.net/
• http://openphacts.org/