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Open Notebook Science by Mind Map: Open  Notebook Science
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Open Notebook Science

What is Open Notebook Science (ONS)?

Practice of making the entire primary record of a research project available online in real-time, or as near real-time as possible.

Practice is similar to keeping a paper notebook in lab, Key difference: OPEN ACCESS

Things that go in the notebook:

Minimum, methods/protocols, raw data, processed data

Going the extra mile, project outline, equipment lists and details, negative results/failed experiments, experimental elaborations, explanations on how results were obtained, nuances with experiment setup, excessive details

Types of Open Notebooks

Blog Format

Wordpress.com, Andy Maloney - UT Austin, https://andymaloney.wordpress.com/, Alex Haddad - UNM, http://alexhaddadnm.wordpress.com/, Steve McIntyre -, http://climateaudit.org/

Tumblr, Damian J. - UT Austin, http://damianjimenez.tumblr.com/

Self hosted Wordpress, Carl Boettiger, http://www.carlboettiger.info/research/lab-notebook, Me, http://research.iheartanthony.com, Maria Benitez - UNM (308L Open Notebook Experiment), http://mbenitez.iheartanthony.com/sample-page/, John Espinoza - UNM (308L Open Notebook Experiment), http://j2phenom.iheartanthony.com/

Google Docs

My Google Doc Notebook, https://docs.google.com/folder/d/0Bwbdciapt4QZNWY5YWZmOGItNzE2Ni00NzdjLWIxY2QtMjUxNGI5ZDFhMzAz/edit

Brian Josey - UNM (308L Open notebook experiment), https://docs.google.com/folder/d/0BzJAt7upwcA4ZGI3NTQ2ZmQtMDk1Yy00MzQ5LWFjNDItZWFmNzAxNmQ4OWIw/edit#

Stephen Pietromonaco - UNM (308L Open Notebook Experiment), https://docs.google.com/folder/d/0BzTcQmjt2CwMNGI0YzczN2YtNDhlMS00MTNmLWIwMjktYzYzMGFjNDlhYWM0/edit#

Wiki

Jean-Claude Bradley - Drexel University, http://usefulchem.wikispaces.com/All+Reactions

Openwetware.org, Raf Aerts, http://openwetware.org/wiki/User:Raf_Aerts/Notebook/Open_Coffee, my OWW notebook (pre-IheartAnthony), http://openwetware.org/wiki/User:Anthony_Salvagno/Notebook/Research, Tons more!, http://openwetware.org/wiki/Lab_Notebook

GitHub wiki (see below)

CMS

Drupal

Joomla

Other

LabTrove, Cameron Neylon - Science and Technology Facilities Council, http://biolab.isis.rl.ac.uk/camerons_labblog

GitHub, Rob Olendorf - UNM, https://github.com/olendorf, Brandon Middleton - UNM (308L Open Notebook Experiment), https://github.com/bmiddl01

Archived (.pdf), http://www.jeremiahfaith.com/open_notebook_science/jeremiah_faith_lab_notebook.pdf

Friendfeed

Evernote

My notebook

Project Planning

http://research.iheartanthony.com/2012/03/29/handrite-notes/

http://research.iheartanthony.com/2011/12/02/preplanning-for-ddw-with-e-coli-thread/#comments

Protocols

http://research.iheartanthony.com/2012/05/30/yeast-in-di-ddw-30-60-and-99-d2o-trial-3-setup/

All protocols, http://research.iheartanthony.com/tag/setup/

Equipment

http://research.iheartanthony.com/experiments-product-details/

Live Results

http://research.iheartanthony.com/2011/09/08/the-crumley-spreadsheet/

Raw and Interpreted Data

http://research.iheartanthony.com/2012/05/30/hourly-yeast-growth-trial-3-results/

http://figshare.com/articles/Hourly_Yeast_Growth_in_DDW,_DI_Water,_30_,_60__and_99__D2O/92159

Failed Experiments

All entries for an entire failed experiment, http://research.iheartanthony.com/category/water-type-effects-on-organism-growth/rc2/?orderby=date&order=ASC

Conclusions

http://research.iheartanthony.com/2012/04/26/ddw-and-30-d2o-starter-culture-analysis/

Project Fundraising

http://research.iheartanthony.com/scifund-links/my-project/

http://research.iheartanthony.com/tag/scifund/

Community

Comments provide real-time peer review/critique, http://research.iheartanthony.com/2012/02/10/help-me-pay-for-going-to-scio12/, https://docs.google.com/document/d/1R4AWpVd2-da4pLB2KgkrAI7KPIXyLQ6PkKkzHJCeHXo/edit

Get to ask questions about experiments, products, etc, http://research.iheartanthony.com/2011/08/23/openpcr-understanding-the-final-hold-issues/#comments

Debate Science Issues, http://research.iheartanthony.com/2012/02/23/why-bother-publishing-in-a-journal-2/#comments

Ask questions to the world, http://research.iheartanthony.com/2012/01/23/crowdfunding-for-science/

Project Planning, http://research.iheartanthony.com/2011/12/02/preplanning-for-ddw-with-e-coli-thread/#comments

My experiences

Phys 308L Electronics Lab - The ONS Experiment

http://2012juniorlab.iheartanthony.com/

Motivations, to create a test community of open scientists, understand interactions between scientists online, discover pros/cons of various notebooking platforms, observe notebooking behaviors

Mentoring

ONS success stories

sharing experiences with different notebook platforms, What's the best platform?, How do I get started?

How to maintain an open notebook

open notebooks for everyone

conversations with many in the open science community

NSF IGERT for open research and ONS

https://docs.google.com/document/d/1lmk7VhAMyj_EuJuuv7Es4za8w2BmUwST_aYOUI3tf00/edit

This presentation can be accessed via my open notebook

http://research.iheartanthony.com/2012/06/24/presentation-for-science-at-risk-meeting/