Collaborative platforms for streamlining workflows in Open Science

Transcript

1. Collaborative platforms for streamlining workflows in Open Science Konrad U. F¨ orstner, Gregor Hagedorn, Claudia Koltzenburg, M. Fabiana Kubke, Daniel Mietchen July 30th, 2011 – OKCon 2011, Berlin
2. About this work Wiki base version of the manuscript: http://is.gd/openworkflows
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. Knowledge generation Again: Collaborative - increase the number of brains involved Again: Formalization - e.g. argument maps which link to results and literature http://www.flickr.com/photos/diana_blackwell/2597258115/ – CC-BY by flick user diana blackwell
10. Final publication Little effort: linking to the major outcomes and putting them into the scientific context http://www.flickr.com/photos/yorkjason/3265889476/ – CC-BY by flickr user yorkjason
11. 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 the communities http://www.flickr.com/photos/tallkev/256810217/ – CC-BY by flickr user tallkev
12. Implementation - Reputation Microcontribution ⇒ Microattribution (e.g. ORCID based) http://www.flickr.com/photos/tallkev/256810217/ – CC-BY by flickr user tallkev
13. Implementation - Licenses Ideally: Public domain / CC0 (see Panton Principle) http://www.flickr.com/photos/subcircle/500995147 – CC-BY by flickr user subcircel
14. Implementation - Funding Long term aim: Funding agencies require the usage of such Open Science workflows (worked for OA) – CC-BY by flickr user therichbrooks
15. Dealing with the cultural clash via a gradual approach Proposed infrastructure but with fine granular access control and a smaller number of participants. http://www.everystockphoto.com/photo.php?imageId=1761122 – source: The Library of Congress
16. 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
17. http://www.flickr.com/photos/nateone/3768979925/ – CC-BY by flick user nateone