A quick trip through openness, freedom and transparency

Intro Open Source Creative Commons Open Access Open Science / Knowledge THM

Konrad Forstner, Bork Group, EMBL

http://konrad.foerstner.org

September 8th, 2007, Barcelona

Disclaimer

Fasten your seat belts! This willbe a rushed journey through alot of topics that have someimportant concepts in common.

It is an introductionary talk:

⇒ just an appetiser⇒ some simplifications

Sometimes techy

Starting consensus

We need to agree that

Openness

Freedom

Transparency

are essential for a functional anddemocratic scientific community andfor society in general.

Open Source Software

What is it?

Open source software is computersoftware that is published under alicense that gives the freedom to use,modify and redistribute it.

Closed Source Software:Only the executable program(binary) is available.

Open Source Software:Source code and executableprogram are available.

FLOSS/FOSS/OSS licenses

(Free)/(Libre)/Open-Source Software

Make software “free as in freedom, not as infree beer”.

Most important examples:

GNU General Public License (“copyleft”)BSD License

Important freedoms that Open Source licenses give

The freedom to use

The freedom to copy

The freedom to make derivatives

The freedom to redistribute(also the modified versions)

Advantages

Transparency

Potentially higher quality/security due to peer-review by thecommunity

Independence of vendors

Modification/adaptation to personal needs possible

Reusablity of code ⇒ faster development

Free/low costs ⇒ affordable for everybody

Some examples you might be familiar with

Mozilla Firefox (Web browser)

OpenOffice (Office Suite)

GNU/Linux (Operating system)

Gimp (Graphics editor)

Some less obvious examples that you use for sure

Apache (Web server)

BIND (DNS server)

Google (adapted version of GNU/Linux on their servers)

Some examples you might be familiar with

Mozilla Firefox (Web browser)

OpenOffice (Office Suite)

GNU/Linux (Operating system)

Gimp (Graphics editor)

Some less obvious examples that you use for sure

Apache (Web server)

BIND (DNS server)

Google (adapted version of GNU/Linux on their servers)

Creative Commons licenses

What is it?

The default copyright ( c© all rights reserved) restricts creativityand cultural development in the digital age. Creative Commonslicenses make it easy for creators to define the freedom of theircreations.

Use for ...

Images

Select a license by choosing conditions

Attribution

No derivative works

Non-commercial

Share alike

Open Access

What is it?

Open Access is a publishing conceptwith immediate, free and unrestrictedonline access to scholarly publications.

Open Access

Current closed-access scenario

1. Scientist is paid by the public todo research

2. Scientist writes publication andgives all the rights to publisher

3. Other scientists (if they can)buy the publication with publicmoney

⇒ public pays twice and loses rights to the publisher

⇒ access to knowledge is limited to people who can pay for it

Open Access

Publishing with Open Access

Publishing using an Open Access publisher

Author keeps rights (often a Creative Commons license is used)Different business models: fee or non-fee-based used

Open access self-archiving

In addition to the traditional publication the article is archivedin central repository (e.g. arXiv, Nature Precedings)

⇒ Immediate access to the generated knowledge for everybody

Open Access

Advantages

No financial hurdles for readers

Higher scientific impact

Author keeps the rights

Computational text analysispossible (necessary due togrowing amount of literature)

Open Science / Knowledge

Sometime I have the feeling people forget ...

that scientists are payed by thepublic to generate knowledge forthe public.

that delayed/restricted access toresults/data/knowledgehampers scientific progress andmaybe even costs lives.

that “negative” results are alsoresults.

the question if the “paper” isreally the optimal form ofcommunicating science in theinternet age.

Example 1: PloS One

An online-only Open Access journal

Pre-publication peer review but notfiltered by scientific relevance (= don’tcare about impact factor)

Users can rate and discuss articlesafter publication

Example 2: Science Commons

Aim is “removing unnecessary legaland technical barriers to scientificcollaboration and innovation.”

E.g. The Biological Materials TransferAgreement Project (MTA): lower thecosts of transferring physical biologicalmaterials (DNA, cell lines, modelanimals etc.)

Example 3: Wikipedia

... and family: Wikibooks,Wikiversity etc.

An easy way of teaching a broadaudience and communicatescience to the public

Example 4: OpenWetWare

“Sharing of information, know-how, andwisdom among researchers and groups whoare working in biology & biologicalengineering.”

Wiki-based platform

Example 5: Open Notebook Science

Online version of the classicallab notebook

Making the way of discoveriestransparent

Instant publication of results

Instant feedback from colleagues

Example 6: Wikiscience

Article hosted on a wiki

All versions are stored

Constantly improving

Many contributors

Micropublications

Yes, there are currently problems like

Fear of being scooped as blog/wikicontributions are not officialpublications

or not accepted by journals as alreadypublished in blogs/wikis

No credit system for this kind ofscientific contribution

⇒ Problems are cultural not technical!

⇒ Luckily there are grass root projectswhere people start to play around withthe new concepts.

Take home messages

The concepts of openness, freedom and transparency canimprove a lot of fields.

Science is one of them and you can help.

LearnTestDiscussSpread the wordQuestion the current status

Acknowledgements

Thanks to ...

An uncountable amount of people whodiscuss their opinions and ideas online

Bernd Ahlers who ignited my OpenSource fire

Let’s open it

Selected references and Image sources/attribution

Reference

http://www.opensource.org

http://creativecommons.org/

http://www.plosone.org/

http://sciencecommons.org/

http://wikipedia.org/

http://openwetware.org

http://www.edge.org/3rd culture/kelly06/kelly06 index.html

Image sources

Seatbelt sign http://flickr.com/photos/davescunningplan/236094576/hanging fishes http://flickr.com/photos/rastafabi/369869352/Shell http://flickr.com/photos/96dpi/501424695/ Freedom http://flickr.com/photos/dazzied/427180864/Shipping containers http://flickr.com/photos/16543356@N00/150898441/Container train http://flickr.com/photos/telstar/163503065/Container trucks on an American highway http://flickr.com/photos/87913776@N00/422603859/i have no idea why that caged bird does a damn thing http://flickr.com/photos/emdot/135529627/Creative Commons Logo http://flickr.com/photos/purzlbaum/239202519/Filters Showcase http://flickr.com/photos/denverjeffrey/300338550/Open Access Logo http://open-access.net/de/austausch/downloads/Hardship in the streets of Varanasi (India) http://flickr.com/photos/ahron/266050467/Tree of Knowledge http://flickr.com/photos/knilram/64366434/Note Book http://flickr.com/photos/prashant zi/289482096/Collaboration http://flickr.com/photos/fncll/145149313/tough grass http://flickr.com/photos/zachk/109921799/Corkscrew http://flickr.com/photos/awrose/121085717/(The other images were created by myself)

About this document

Created in LATEX using the beamer class, pdfLATEX and emacs.Gimp and Firefox were used to take screen shots of websites.

All these programs run on OpenBSD.

http://www.latex-project.org

http://latex-beamer.sourceforge.net

http://www.tug.org/applications/pdftex

http://www.gnu.org/software/emacs

http://www.mozilla.com/en-US/firefox/

http://www.gimp.org/

http://www.openbsd.org

Published under the Creative Commons Attribution 3.0 License

http://creativecommons.org/licenses/by/3.0/

Document version 1.0 2007/08/08

A quick trip through openness, freedom and transparency

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