Open Notebook Science

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Open Notebook Science by Mind Map: Open  Notebook Science

1. What is Open Notebook Science (ONS)?

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

1.1.1. Practice is similar to keeping a paper notebook in lab

1.1.1.1. Key difference: OPEN ACCESS

1.2. Things that go in the notebook:

1.2.1. Minimum

1.2.1.1. methods/protocols

1.2.1.2. raw data

1.2.1.3. processed data

1.2.2. Going the extra mile

1.2.2.1. project outline

1.2.2.2. equipment lists and details

1.2.2.3. negative results/failed experiments

1.2.2.4. experimental elaborations

1.2.2.4.1. explanations on how results were obtained

1.2.2.4.2. nuances with experiment setup

1.2.2.4.3. excessive details

2. Types of Open Notebooks

2.1. Blog Format

2.1.1. Wordpress.com

2.1.1.1. Andy Maloney - UT Austin

2.1.1.1.1. https://andymaloney.wordpress.com/

2.1.1.2. Alex Haddad - UNM

2.1.1.2.1. http://alexhaddadnm.wordpress.com/

2.1.1.3. Steve McIntyre -

2.1.1.3.1. http://climateaudit.org/

2.1.2. Tumblr

2.1.2.1. Damian J. - UT Austin

2.1.2.1.1. http://damianjimenez.tumblr.com/

2.1.3. Self hosted Wordpress

2.1.3.1. Carl Boettiger

2.1.3.1.1. http://www.carlboettiger.info/research/lab-notebook

2.1.3.2. Me

2.1.3.2.1. http://research.iheartanthony.com

2.1.3.3. Maria Benitez - UNM (308L Open Notebook Experiment)

2.1.3.3.1. http://mbenitez.iheartanthony.com/sample-page/

2.1.3.4. John Espinoza - UNM (308L Open Notebook Experiment)

2.1.3.4.1. http://j2phenom.iheartanthony.com/

2.2. Google Docs

2.2.1. My Google Doc Notebook

2.2.1.1. https://docs.google.com/folder/d/0Bwbdciapt4QZNWY5YWZmOGItNzE2Ni00NzdjLWIxY2QtMjUxNGI5ZDFhMzAz/edit

2.2.2. Brian Josey - UNM (308L Open notebook experiment)

2.2.2.1. https://docs.google.com/folder/d/0BzJAt7upwcA4ZGI3NTQ2ZmQtMDk1Yy00MzQ5LWFjNDItZWFmNzAxNmQ4OWIw/edit#

2.2.3. Stephen Pietromonaco - UNM (308L Open Notebook Experiment)

2.2.3.1. https://docs.google.com/folder/d/0BzTcQmjt2CwMNGI0YzczN2YtNDhlMS00MTNmLWIwMjktYzYzMGFjNDlhYWM0/edit#

2.3. Wiki

2.3.1. Jean-Claude Bradley - Drexel University

2.3.1.1. http://usefulchem.wikispaces.com/All+Reactions

2.3.2. Openwetware.org

2.3.2.1. Raf Aerts

2.3.2.1.1. http://openwetware.org/wiki/User:Raf_Aerts/Notebook/Open_Coffee

2.3.2.2. my OWW notebook (pre-IheartAnthony)

2.3.2.2.1. http://openwetware.org/wiki/User:Anthony_Salvagno/Notebook/Research

2.3.2.3. Tons more!

2.3.2.3.1. http://openwetware.org/wiki/Lab_Notebook

2.3.3. GitHub wiki (see below)

2.4. CMS

2.4.1. Drupal

2.4.2. Joomla

2.5. Other

2.5.1. LabTrove

2.5.1.1. Cameron Neylon - Science and Technology Facilities Council

2.5.1.1.1. http://biolab.isis.rl.ac.uk/camerons_labblog

2.5.2. GitHub

2.5.2.1. Rob Olendorf - UNM

2.5.2.1.1. https://github.com/olendorf

2.5.2.2. Brandon Middleton - UNM (308L Open Notebook Experiment)

2.5.2.2.1. https://github.com/bmiddl01

2.5.3. Archived (.pdf)

2.5.3.1. http://www.jeremiahfaith.com/open_notebook_science/jeremiah_faith_lab_notebook.pdf

2.5.4. Friendfeed

2.5.5. Evernote

3. My notebook

3.1. Project Planning

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

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

3.2. Protocols

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

3.2.2. All protocols

3.2.2.1. http://research.iheartanthony.com/tag/setup/

3.3. Equipment

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

3.4. Live Results

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

3.5. Raw and Interpreted Data

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

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

3.6. Failed Experiments

3.6.1. All entries for an entire failed experiment

3.6.1.1. http://research.iheartanthony.com/category/water-type-effects-on-organism-growth/rc2/?orderby=date&order=ASC

3.7. Conclusions

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

3.8. Project Fundraising

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

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

3.9. Community

3.9.1. Comments provide real-time peer review/critique

3.9.1.1. http://research.iheartanthony.com/2012/02/10/help-me-pay-for-going-to-scio12/

3.9.1.2. https://docs.google.com/document/d/1R4AWpVd2-da4pLB2KgkrAI7KPIXyLQ6PkKkzHJCeHXo/edit

3.9.2. Get to ask questions about experiments, products, etc

3.9.2.1. http://research.iheartanthony.com/2011/08/23/openpcr-understanding-the-final-hold-issues/#comments

3.9.3. Debate Science Issues

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

3.9.4. Ask questions to the world

3.9.4.1. http://research.iheartanthony.com/2012/01/23/crowdfunding-for-science/

3.9.5. Project Planning

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

4. My experiences

4.1. Phys 308L Electronics Lab - The ONS Experiment

4.1.1. http://2012juniorlab.iheartanthony.com/

4.1.2. Motivations

4.1.2.1. to create a test community of open scientists

4.1.2.2. understand interactions between scientists online

4.1.2.3. discover pros/cons of various notebooking platforms

4.1.2.4. observe notebooking behaviors

4.2. Mentoring

4.2.1. ONS success stories

4.2.2. sharing experiences with different notebook platforms

4.2.2.1. What's the best platform?

4.2.2.2. How do I get started?

4.2.3. How to maintain an open notebook

4.3. open notebooks for everyone

4.3.1. conversations with many in the open science community

4.4. NSF IGERT for open research and ONS

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

5. This presentation can be accessed via my open notebook

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