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?•• Twitter: @egonwillighagen•• ORCID: 0000-0001-7542-0286••• of Bioinformatics - BiGCaT 24