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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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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Today's triangle

1. Science and Microscopes2. Open Science and Social Contracts3. Data Management

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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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Not all microscopes works as expected

N. Jeliazkova, unknown license; claiming fair use

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Bioinformatics equipment

• Statistics (multivariate)• Computation• Data management

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Today's triangle (2nd round)

1. Science and Microscopes2. Open Science and Social Contracts3. Data Management

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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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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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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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#altmetrics

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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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Open Source Cheminformatics

• Metabolomics• Drug discovery• Toxicology

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O'Boyle et al., JChemInf, 2011

Blue Obelisk: Open Data, Open Source, Open Standards (or: interoperability)

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Today's triangle (2nd round)

1. Science and Microscopes2. Open Science and Social Contracts3. Data Management

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Labnote books

• Statistics–Sweave

• Computation–Log files

• Lab–Digitize images and

notes

Backup, easier to share, ...

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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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What about Dept. of Bioinformatics?

We take advantage of Open collaborations in our study of life.

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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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Data sharing?

FigShare!

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DataDryad

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The Data Hub

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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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More info?

• egon.willighagen@gmail.com

• Twitter: @egonwillighagen

• http://chem-bla-ics.blogspot.com/

• ORCID: 0000-0001-7542-0286

• http://www.blueobelisk.org/

• http://cdk.sf.net/

• http://openphacts.org/