Open Science Examples of Bioinformatics  Egon Willighagen (@egonwillighagen)  Dept. Bioinformatics – BiGCaT, Maastricht Un...
Warning and disclaimer!• IANAL• I have too many slides     – But they will be available online later• You are expected to ...
Todays triangle1. Science and Microscopes2. Open Science and Social Contracts3. Data ManagementDepartment of Bioinformatic...
Bioinformatics is ...… development ofnew microscopesby which we studylife.(by finding new correlationsand translate those ...
Not all microscopes works as expected        N. Jeliazkova, unknown license; claiming fair useDepartment of Bioinformatics...
Bioinformatics equipment• Statistics (multivariate)• Computation• Data managementDepartment of Bioinformatics - BiGCaT   6
Todays triangle (2nd round)1. Science and Microscopes2. Open Science and Social Contracts3. Data ManagementDepartment of B...
Open Science• Reproducibility!    – How did that compound get synthesized?    – Why cant I reproduce that cell line experi...
Social Contract!• Collaboration    – Shared goal, shared ownership    – More efficient and cheaper than other solutions   ...
Get more impact: Nature citations• The Journal Impact Factor (JIF or IF)  is a bad indicator of impact• Less than half of ...
#altmetricsDepartment of Bioinformatics - BiGCaT   11
The 3 #openscience corner stones• Knowledge (data, methods,  conclusions) can be freely used• It can be freely modified• I...
Open Source Cheminformatics• Metabolomics• Drug discovery• ToxicologyDepartment of Bioinformatics - BiGCaT   13
Blue Obelisk: Open Data, Open Source,Open Standards (or: interoperability)OBoyle et al., JChemInf, 2011Department of Bioin...
Todays triangle (2nd round)1. Science and Microscopes2. Open Science and Social Contracts3. Data ManagementDepartment of B...
Labnote books• Statistics   – Sweave• Computation   – Log files• Lab   – Digitize images and     notesBackup, easier tosha...
Version control: e.g. Gitcommit047ca7fc69d30a961209f6d480bc11e454f4bc56Author: egonw <egonw@350a12d8-24d3-0310-83a6-a3e505...
What about Dept. of Bioinformatics?We take advantageof Opencollaborations inour study of life.Department of Bioinformatics...
Be clear in what you want!• Whatever license you pick, make sure  that people know your wishes!• Data without a license st...
Data sharing?FigShare!Department of Bioinformatics - BiGCaT   20
DataDryadDepartment of Bioinformatics - BiGCaT   21
The Data HubDepartment of Bioinformatics - BiGCaT   22
Conclusions• Open Science     – use it to your advantage; look at what       we achieved by everyone contributing       th...
More info?• egon.willighagen@gmail.com• Twitter: @egonwillighagen• http://chem-bla-ics.blogspot.com/• ORCID: 0000-0001-754...
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Open Science: examples in bioinformatics

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Open Science: examples in bioinformatics

  1. 1. Open Science Examples of Bioinformatics Egon Willighagen (@egonwillighagen) Dept. Bioinformatics – BiGCaT, Maastricht University Open Access Week / Data Management 2012/10/23, MaastrichtDepartment of Bioinformatics - BiGCaT 1
  2. 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 ?Department of Bioinformatics - BiGCaT 2
  3. 3. Todays triangle1. Science and Microscopes2. Open Science and Social Contracts3. Data ManagementDepartment of Bioinformatics - BiGCaT 3
  4. 4. Bioinformatics is ...… development ofnew microscopesby which we studylife.(by finding new correlationsand translate those intocausal relations) Wikipedia, Moisey, CC-BY-SADepartment of Bioinformatics - BiGCaT 4
  5. 5. Not all microscopes works as expected N. Jeliazkova, unknown license; claiming fair useDepartment of Bioinformatics - BiGCaT 5
  6. 6. Bioinformatics equipment• Statistics (multivariate)• Computation• Data managementDepartment of Bioinformatics - BiGCaT 6
  7. 7. Todays triangle (2nd round)1. Science and Microscopes2. Open Science and Social Contracts3. Data ManagementDepartment of Bioinformatics - BiGCaT 7
  8. 8. Open Science• Reproducibility! – How did that compound get synthesized? – Why cant 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 butwithout arguments, well take mine.”Department of Bioinformatics - BiGCaT 8
  9. 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.Department of Bioinformatics - BiGCaT 9
  10. 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 years 1. most Nature-worthy research has very limited impact 2. many papers get more cited than the average Nature paperDepartment of Bioinformatics - BiGCaT 10
  11. 11. #altmetricsDepartment of Bioinformatics - BiGCaT 11
  12. 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)Department of Bioinformatics - BiGCaT 12
  13. 13. Open Source Cheminformatics• Metabolomics• Drug discovery• ToxicologyDepartment of Bioinformatics - BiGCaT 13
  14. 14. Blue Obelisk: Open Data, Open Source,Open Standards (or: interoperability)OBoyle et al., JChemInf, 2011Department of Bioinformatics - BiGCaT 14
  15. 15. Todays triangle (2nd round)1. Science and Microscopes2. Open Science and Social Contracts3. Data ManagementDepartment of Bioinformatics - BiGCaT 15
  16. 16. Labnote books• Statistics – Sweave• Computation – Log files• Lab – Digitize images and notesBackup, easier toshare, ...Department of Bioinformatics - BiGCaT 16
  17. 17. Version control: e.g. Gitcommit047ca7fc69d30a961209f6d480bc11e454f4bc56Author: 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@1350a12d8-24d3-0310-83a6-a3e505aec109Department of Bioinformatics - BiGCaT 17
  18. 18. What about Dept. of Bioinformatics?We take advantageof Opencollaborations inour study of life.Department of Bioinformatics - BiGCaT 18
  19. 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)Department of Bioinformatics - BiGCaT 19
  20. 20. Data sharing?FigShare!Department of Bioinformatics - BiGCaT 20
  21. 21. DataDryadDepartment of Bioinformatics - BiGCaT 21
  22. 22. The Data HubDepartment of Bioinformatics - BiGCaT 22
  23. 23. Conclusions• Open Science – use it to your advantage; look at what we achieved by everyone contributing their bit – it improves science and educationDepartment of Bioinformatics - BiGCaT 23
  24. 24. 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/Department of Bioinformatics - BiGCaT 24
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