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