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Stefan Kasberger
OPEN SCIENCE
Open and Reproducible Science
See at https://creativecommons.org/licenses/by-sa/4.0/ for
license details.
...for bio-hackers
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
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 — subject
only, at most, to the requirement to attribute
and/or share-alike.”
What does this mean for
Science?
Principles
Research
def. by Kraker et al. (2011):
●
Open Data
●
Open Source
●
Open Access
●
Open Methodology
●
Open Peer Review
Education
●
Open Educational Resources
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 Peer Review
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,
(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.
Open Data Formats→
●
FASTA + FASTQ
●
Rapid DNA Prototyping Standard
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
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
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 (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.
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)
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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Open science for Bio-Hacker

  • 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. 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. Open Science Open Science is a movement, which makes scientific knowledge openly accessible and usable to all.
  • 4. What is this all about ??
  • 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. What does this mean for Science?
  • 7. Principles Research def. by Kraker et al. (2011): ● Open Data ● Open Source ● Open Access ● Open Methodology ● Open Peer Review Education ● Open Educational Resources
  • 14. All together = Open Science ● Open Access ● Open Data ● Open Source ● Open Educational Resources ● Open Methodology ● Open Peer Review
  • 17. Community ● Center for Open Science ● Sage Bionetworks ● Open Knowledge ● Mozilla Science Lab ● Biolabs
  • 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. Open Data Formats→ ● FASTA + FASTQ ● Rapid DNA Prototyping Standard
  • 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. 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. Open Access Coll. Writing→ ● Etherpad: collaborative writing, web ● Overleaf: coll. writing in LaTex, web
  • 23. Open Methodology ● OpenWetWare ● Open Science Framework ● ScientificProtocols.org
  • 24. Open Science as a Practice
  • 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. 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. 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)