Open science for Bio-Hacker

1.341 Aufrufe

Veröffentlicht am

Presentation Open Science for Bio-Hackers with an introduction into Open Science with applications for the DIY bio-hackers community.

Event: openscienceASAP meets Bricobio Biolab Montréal - Open Science for Bio-Hackers Google Hangout.

Video: https://www.youtube.com/watch?v=LxCb0GfEXIU
Blog: http://openscienceasap.org/stream/2015/03/23/video-open-science-for-bio-hackers/

Veröffentlicht in: Wissenschaft
0 Kommentare
0 Gefällt mir
Statistik
Notizen
  • Als Erste(r) kommentieren

  • Gehören Sie zu den Ersten, denen das gefällt!

Keine Downloads
Aufrufe
Aufrufe insgesamt
1.341
Auf SlideShare
0
Aus Einbettungen
0
Anzahl an Einbettungen
354
Aktionen
Geteilt
0
Downloads
4
Kommentare
0
Gefällt mir
0
Einbettungen 0
Keine Einbettungen

Keine Notizen für die Folie

Open science for Bio-Hacker

  1. 1. Stefan Kasberger OPEN SCIENCE Open and Reproducible Science See at https://creativecommons.org/licenses/by-sa/4.0/ for license details. ...for bio-hackers
  2. 2. Details Hangout 1st Google Hangout On Air + Recording Schedule ● Introduction Open Science (20min) ● Open Science for Bio-Hackers (5min) ● openscienceASAP (5min) ● Q&A (30min) #ASAPOnAir
  3. 3. Open Science Open Science is a movement, which makes scientific knowledge openly accessible and usable to all.
  4. 4. What is this all about ??
  5. 5. Open Definition Open Definition: “A piece of data or content is open if anyone is free to use, reuse, and redistribute it — subject only, at most, to the requirement to attribute and/or share-alike.”
  6. 6. What does this mean for Science?
  7. 7. Principles Research def. by Kraker et al. (2011): ● Open Data ● Open Source ● Open Access ● Open Methodology ● Open Peer Review Education ● Open Educational Resources
  8. 8. Open Access
  9. 9. Open Data ●
  10. 10. Open Source
  11. 11. Open Methodology InduktionDeduktion Theorie (allgemein) Empirie (speziell)
  12. 12. Open Peer Review
  13. 13. Open Educational Resources
  14. 14. All together = Open Science ● Open Access ● Open Data ● Open Source ● Open Educational Resources ● Open Methodology ● Open Peer Review
  15. 15. Why? accessible technology collaboration reproducability and so on...
  16. 16. Open Science for Bio-Hackers
  17. 17. Community ● Center for Open Science ● Sage Bionetworks ● Open Knowledge ● Mozilla Science Lab ● Biolabs
  18. 18. Open Source ● Etherpad: coll. Writing (brainstorming, many users, concepts) ● Git + GitHub: versioning of line-based files, (documentation, csv, software) ● R + Python: statistics, data preparation, etc. ● EMBOSS: package for molecular biology ● Bioblender: visualizing Protein Data Bank data ● LaTeX: document preparation software, writing paper etc.
  19. 19. Open Data Formats→ ● FASTA + FASTQ ● Rapid DNA Prototyping Standard
  20. 20. Open Data Repositories→ Repositories for your Data: ● Figshare ● national and disciplinary projects Public Data Repositories for you: ● ZooBank ● Protein Data Bank ● Global Biodiversity Information Facility ● Personal Genome Project ● International Plant Names Index
  21. 21. Open Access Journals→ → Directory of Open Access Journals (DOAJ) ● PLOS: PLOS One, PLOS Computational Biology, PLOS Genetics, PLOS Biology ● eLife ● BioMed Central ● PubMed Central ● bioRxiv
  22. 22. Open Access Coll. Writing→ ● Etherpad: collaborative writing, web ● Overleaf: coll. writing in LaTex, web
  23. 23. Open Methodology ● OpenWetWare ● Open Science Framework ● ScientificProtocols.org
  24. 24. Open Science as a Practice
  25. 25. Community
  26. 26. Blogging
  27. 27. Training
  28. 28. github.com/skasberger Knowledge is shareable! @stefankasberger
  29. 29. Slide 1 ● Image: Open Science logo by G.emmerich (CC BY-SA 3.0) ● Image: openscienceASAP logo by Stefan Kasberger (trademark) ● Image: Wired NDNAD Graphic - detail by Jer Thorpe (CC BY 2.0) ● Image: Creative Commons BY SA logo by Creative Commons (trademark) Slide 3 ● Image: Open Tin Can by Golden Swamp (CC BY-SA 2.0) Slide 4 ● Image: Open books by opensourceway (CC BY-SA 2.0) Slide 5 ● Quote: Open Definition by Open Knowledge ● Image: Open Knowledge Foundation logo by Open Knowledge (trademark) Slide 7 ● Image: Helix by Apers0n (public domain) ● Reference: The case for an open science in technology enhanced learning by Peter Kraker et al. Slide 8 ● Image: Open Access logo PLoS white by PLOS (CC0 1.0) ● Image: PLOS One logo by PLOS (CC BY-SA 3.0) ● Image: BioMed Central logo by BioMed Central (trademark) ● Image: bioRxiv logo by bioRxiv (trademark) ● Image: GIS Cellular Automata Using Artificial Neural Network for Land Use Change Simulation of Lagos, Nigeria screenshot by Stefan Kasberger (CC BY 4.0) Sources & References All trademarks and product names mentioned in this presentation are registered trademarks of the particular producer respectively corporation.
  30. 30. Slide 9 ● Image: Figshare logo by Anthony Salvagno (CC BY 3.0) ● Image: data.gov logo by data.gov (trademark) ● Image: NASA logo logo by National Aeronautics and Space Administration (public domain) ● Image: Worldbank logo by World Bank (trademark) ● Image: OpenStreetMap logo by OpenStreetMap (CC BY-SA 2.0) ● Image: Spreadsheet screenshot by Stefan Kasberger (CC BY 4.0) ● Image: JSON file screenshot by Stefan Kasberger (CC BY 4.0) Slide 10 ● Image: GitHub octocat by GitHub (trademark) ● Image: Open Source logo by Open Source Initiative (CC BY 2.5) ● Image: R project logo by R Foundation (GNU General Public License) ● Image: Python logo by Python Foundation (GNU General Public License) ● Image: tux by Larry Ewing: The copyright holder of this file allows anyone to use it for any purpose, provided that you acknowledge lewing@isc.tamu.edu and The GIMP if someone asks. ● Image: GPLv3 logo by Free Software Foundation (public domain) Slide 11 ● Image: Wordpress logo by WordPress (GNU General Public License) ● Image: Tubes by Greg Emmerich (CC BY-SA 2.0) ● Image: Induktion-Deduktion by WissensDürster (public domain) Slide 12 ● Image: Magnifying glass with infinite focus by Niabot (CC BY-SA 3.0) Slide 13 ● Image: Global OER logo by Jonathas Mello (CC BY 3.0 Unported) Slide 14 ● Image: Open Science logo by Greg Emmerich (CC BY-SA 2.0) Slide 15 ● Image: Kenneth Rogoff photo by International Monetary Fund (public domain) ● Image: Working Together Teamwork Puzzle Concept by lumaxart (CC BY SA 2.0 Generic) ● Image: Internet1 by Rock1997 (CC BY SA 3.0 Unported) ● Image: Magnifying glass with infinite focus by Niabot (CC BY-SA 3.0) Slide 17 ● Image: Mikrofoto.de-volvox-4 by Frank Fox (CC BY-SA 3.0 DE)
  31. 31. Slide 19 ● Image: Flu Genome Data Visualizer by Jer Thorp (CC BY 2.0) Slide 21 ● Image: PLOS One logo by PLOS (CC BY-SA 3.0) ● Image: PubMed Central logo by U.S. Government (public domain) Slide 22 ● Image: Overleaf screenshot by Stefan Kasberger (CC BY 4.0) Slide 23 ● Image: Goddard scientist Jennifer Eigenbrode by NASA Goddard Space Flight Center (CC BY 2.0) Slide 24 ● Image: openscienceASAP logo by Stefan Kasberger (trademark) Slide 25 ● Image: Content Mine hackathon Metalab photo by Stefan Kasberger (CC BY 4.0) Slide 26 ● Image: Wordpress Backend screenshot by Stefan Kasberger (CC BY 4.0) Slide 27 ● Image: Open Science training photo by Stefan Kasberger (CC BY 4.0) Slide 28 ● Image: Symmetry Of Life Forms On Earth by „This file is lacking author information.“ (CC BY 2.0) ● Image: GitHub octocat by GitHub (trademark) ● Image: openscienceASAP logo by Stefan Kasberger (trademark) ● Image: Creative Commons BY SA logo by Creative Commons (trademark)

×