Stefan Kasberger
OPEN SCIENCE
Open and Reproducible Science
See at https://creativecommons.org/licenses/by-sa/4.0/ for
lic...
Details Hangout
1st Google Hangout On Air + Recording
Schedule
●
Introduction Open Science (20min)
●
Open Science for Bio-...
Open Science
Open Science is a movement, which
makes scientific knowledge openly
accessible and usable to all.
What is this
all about ??
Open Definition
Open Definition:
“A piece of data or content is open if anyone is
free to use, reuse, and redistribute it ...
What does this mean for
Science?
Principles
Research
def. by Kraker et al. (2011):
●
Open Data
●
Open Source
●
Open Access
●
Open Methodology
●
Open Peer R...
Open Access
Open Data
●
Open Source
Open Methodology
InduktionDeduktion
Theorie
(allgemein)
Empirie
(speziell)
Open Peer Review
Open Educational Resources
All together = Open Science
●
Open Access
●
Open Data
●
Open Source
●
Open Educational Resources
●
Open Methodology
●
Open...
Why?
accessible
technology
collaboration
reproducability
and so on...
Open Science for
Bio-Hackers
Community
●
Center for Open Science
●
Sage Bionetworks
●
Open Knowledge
●
Mozilla Science Lab
●
Biolabs
Open Source
●
Etherpad: coll. Writing (brainstorming, many
users, concepts)
●
Git + GitHub: versioning of line-based files...
Open Data Formats→
●
FASTA + FASTQ
●
Rapid DNA Prototyping Standard
Open Data Repositories→
Repositories for your Data:
●
Figshare
●
national and disciplinary projects
Public Data Repositori...
Open Access Journals→
→ Directory of Open Access Journals (DOAJ)
●
PLOS: PLOS One, PLOS Computational Biology,
PLOS Geneti...
Open Access Coll. Writing→
●
Etherpad: collaborative writing, web
●
Overleaf: coll. writing in LaTex, web
Open Methodology
●
OpenWetWare
●
Open Science Framework
●
ScientificProtocols.org
Open Science as a Practice
Community
Blogging
Training
github.com/skasberger
Knowledge is shareable!
@stefankasberger
Slide 1
●
Image: Open Science logo by G.emmerich (CC BY-SA 3.0)
●
Image: openscienceASAP logo by Stefan Kasberger (tradema...
Slide 9
●
Image: Figshare logo by Anthony Salvagno (CC BY 3.0)
●
Image: data.gov logo by data.gov (trademark)
●
Image: NAS...
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....
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Open science for Bio-Hacker

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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
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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)

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