open science for bio-hacker
TRANSCRIPT
Stefan Kasberger
OPEN SCIENCEOpen 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
Researchdef. by Kraker et al. (2011):
● Open Data
● Open Source
● Open Access
● Open Methodology
● Open Peer Review
Education
● Open Educational Resources
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
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 [email protected] 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)