collaborative platforms for streamlining workflows in open science
DESCRIPTION
TRANSCRIPT
Collaborative platforms for streamliningworkflows in Open Science
Konrad U. Forstner, Gregor Hagedorn, Claudia Koltzenburg,M. Fabiana Kubke, Daniel Mietchen
July 30th, 2011 – OKCon 2011, Berlin
About this work
Wiki base version of the manuscript:
http://is.gd/openworkflows
Problem: There are many gaps in the scientific process
Time consuming and often annoying
Loss of information
http://www.flickr.com/photos/eirikref/403363597 – CC-BY by flick user eirikref
A proposal for improved scientific workflow
Seamless transition from bench to publication
Based on Virtual Research Environments (VRE)
Transparency, reproducibility & reusability
Formalization
Reputation system included
http://commons.wikimedia.org/wiki/File:Future73nb.jpg – PD
Conception and project planning
Utilizing collective intelligence
Management tools can help to handle complex projects
http://www.flickr.com/photos/marksurman/3604105727/ – CC-BY by flick user marksurman
Experiments and data generation
More automation needed (ideally via Open Hardware)
Formal language to design/program experiments
http://www.flickr.com/photos/kaibara/2072160194/ – CC-BY by flick user kaibara
Data storage = data release
Publish data immediately in a machine-readable form
Every entity gets an unique identifiers (⇒ referable)
http://www.flickr.com/photos/wilhei/109404222/ – CC-BY by flick user wilhei
Data analysis
Scripting / programming or recording of GUI-tool actions
Good examples: Taverna or Galaxy
Grid computing if needed / possible
http://commons.wikimedia.org/wiki/File:Plastic_tape_measure.jpg – CC-BY by Wimedia Commons user Pastorius
Knowledge generation
Again: Collaborative - increase the number of brains involved
Again: Formalization - e.g. argument maps which link toresults and literature
http://www.flickr.com/photos/diana_blackwell/2597258115/ – CC-BY by flick user diana blackwell
Final publication
Little effort: linking to the major outcomes and putting theminto the scientific context
http://www.flickr.com/photos/yorkjason/3265889476/ – CC-BY by flickr user yorkjason
Implementation - Technology
Most needed building blocks are available (as FLOSS) –“just” need to be connected
Open standards needed
Domain specific solutions should be created by thecommunities
http://www.flickr.com/photos/tallkev/256810217/ – CC-BY by flickr user tallkev
Implementation - Reputation
Microcontribution ⇒ Microattribution (e.g. ORCID based)
http://www.flickr.com/photos/tallkev/256810217/ – CC-BY by flickr user tallkev
Implementation - Licenses
Ideally: Public domain / CC0 (see Panton Principle)
http://www.flickr.com/photos/subcircle/500995147 – CC-BY by flickr user subcircel
Implementation - Funding
Long term aim: Funding agencies require the usage of suchOpen Science workflows (worked for OA)
– CC-BY by flickr user therichbrooks
Dealing with the cultural clash via a gradual approach
Proposed infrastructure but with fine granular access control and asmaller number of participants.
http://www.everystockphoto.com/photo.php?imageId=1761122 – source: The Library of Congress
Take home messages in a nut shell
All steps of the research process can be represented in /connected to VREs
Gaps between the steps are minimized
Gain of transparency, reproducibility & reusability
Main problems are not technical but cultural/political
http://www.flickr.com/photos/marcoarment/3129076932 – CC-BY by flickr user marcoarment
http://www.flickr.com/photos/nateone/3768979925/ – CC-BY by flick user nateone