- published: 19 Jul 2012
- views: 56
Open notebook science is the practice of making the entire primary record of a research project publicly available online as it is recorded. This involves placing the personal, or laboratory, notebook of the researcher online along with all raw and processed data, and any associated material, as this material is generated. The approach may be summed up by the slogan 'no insider information'. It is the logical extreme of transparent approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'. The practice of open notebook science, although not the norm in the academic community, has gained significant recent attention in the research and general media as part of a general trend towards more open approaches in research practice and publishing. Open notebook science can therefore be described as part of a wider open science movement that includes the advocacy and adoption of open access publication, open data, crowdsourcing data, and citizen science. It is inspired in part by the success of open-source software and draws on many of its ideas.
Jean-Claude Bradley was a chemist who actively promoted Open Science in chemistry, including at the White House, for which he was awarded the Blue Obelisk award in 2007. He coined the term "Open Notebook science". He died in May 2014. A memorial symposium was held July 14, 2014 at Cambridge University, UK.
One outcome of his Open Notebook work is the collection of physicochemical properties of organic compounds he was studying. All of this data he made available as Open data under the CCZero license. For example, in 2009 Bradley et al. published their work on making solubility data of organic compounds available as Open data. Later, the melting point data set he collaborated on with Andrew Lang and Antony Williams was published with Figshare. Both data sets were also made available as books via the Lulu.com self-publishing platform.
He blogged extensively and contributed to at least 25 individual blogs. In an interview in 2008 with Bora Zivkovic titled "Doing Science Publicly", he spoke of his work and online presence. In 2010, he gave an extensive interview about the impact of Open Notebook science with Richard Poynder.
O or OPEN may refer to:
Jean-Claude Bradley introduces the concept of Open Notebook Science and the synthesis of anti-malarial compounds using the Ugi reaction. Topics briefly covered include Nature Precedings, JoVE, wikis, blogs, ChemSpider, automation, molecular docking, reaction optimization and the merits of carrying out research more openly. Presented on October 10, 2008 at Drexel University.
Part 1/3 of a presentation by Jean-Claude Bradley at the Biennial Conference for Chemical Education (BCCE) on July 29, 2008. The talk starts with an overview of Open Notebook Science using a wiki as a public lab notebook. An example of the usefulness of publishing failed experiments is detailed, showing how the version history of the wiki can be used to track the evolution of an organic chemistry experiment. Near the end of the talk an example of using automation to optimize a Ugi reaction is mentioned.
Jean-Claude Bradley presents at the American Chemical Society meeting on August 20, 2012. Examples are first presented to demonstrate how access to Open Notebooks can provide critical information not usually shared in the traditional publication process. The use of Google App Scripts to look up chemical properties allows for the use of Google Spreadsheets as a self-contained dashboard to plan and analyze chemical reactions. The concept of the Open Chemical Property Matrix (OCPM) is introduced and a smartphone app to suggest recrystallization solvents is then presented.
Cameron Neylon was interviewed on May 20th 2011 by Sarah Currier for the Centre for Research Communications. In this clip he defines open science and talks about his use of open notebook science. He gives his pitches for open science: (1) to other researchers, and (2) to funders, policy-makers and universities.
This is a short video showing the build and launch of Apache Zeppelin - a notebook web UI for interactive query and analysis. In this video we walk through using the tutorial notebook that comes with Zeppelin and discuss each step. This includes interactive querying and charting. Want to see something specific with Zeppelin that I avoided here? Leave a comment here or on my blog http://www.makedatauseful.com/zeppelin-notebook-tutorial-walkthrough/
Help us caption and translate this video on Amara.org: http://www.amara.org/en/v/Brhq/ http://grammarware.net/talks/#Open2012 http://www.softwarefreedomday.eu/2012/Open-Notebook-Computer-Science.html
This screencast concerns my research activities around Open Notebook Science as a way to archive subatomic SKOs. Since SKOs directly contribute to the body of knowledge (BOK), this presentation is submitted as a remote contribution to the SL(E)BOK @ SLE2012 workshop.
Jean-Claude Bradley presented at the University of British Columbia School of Libraries on April 2, 2008. The talk covered the implications of Open Notebook Science for storing and retrieving scientific information.
Jean-Claude Bradley presents on Open Notebook Science: Transparency in Research on October 23, 2012 at Georgia Tech for Open Access Week. Topics include solubility, melting points, a recrystallization app, the Chemical Information Retrieval class at Drexel University and the Open Chemical Property Matrix (OCPM).
Rufus Pollock was interviewed on April 29th 2011 by Sarah Currier for the Centre for Research Communications. In this clip he offers definitions of openness, open knowledge and open science, and talks about his work with The Open Knowledge Foundation. Includes discussion of his own research in open economics and 'open notebook social science'.
Jean-Claude Bradley introduces the concept of Open Notebook Science and the synthesis of anti-malarial compounds using the Ugi reaction. Topics briefly covered include Nature Precedings, JoVE, wikis, blogs, ChemSpider, automation, molecular docking, reaction optimization and the merits of carrying out research more openly. Presented on October 10, 2008 at Drexel University.
Part 1/3 of a presentation by Jean-Claude Bradley at the Biennial Conference for Chemical Education (BCCE) on July 29, 2008. The talk starts with an overview of Open Notebook Science using a wiki as a public lab notebook. An example of the usefulness of publishing failed experiments is detailed, showing how the version history of the wiki can be used to track the evolution of an organic chemistry experiment. Near the end of the talk an example of using automation to optimize a Ugi reaction is mentioned.
Jean-Claude Bradley presents at the American Chemical Society meeting on August 20, 2012. Examples are first presented to demonstrate how access to Open Notebooks can provide critical information not usually shared in the traditional publication process. The use of Google App Scripts to look up chemical properties allows for the use of Google Spreadsheets as a self-contained dashboard to plan and analyze chemical reactions. The concept of the Open Chemical Property Matrix (OCPM) is introduced and a smartphone app to suggest recrystallization solvents is then presented.
Cameron Neylon was interviewed on May 20th 2011 by Sarah Currier for the Centre for Research Communications. In this clip he defines open science and talks about his use of open notebook science. He gives his pitches for open science: (1) to other researchers, and (2) to funders, policy-makers and universities.
This is a short video showing the build and launch of Apache Zeppelin - a notebook web UI for interactive query and analysis. In this video we walk through using the tutorial notebook that comes with Zeppelin and discuss each step. This includes interactive querying and charting. Want to see something specific with Zeppelin that I avoided here? Leave a comment here or on my blog http://www.makedatauseful.com/zeppelin-notebook-tutorial-walkthrough/
Help us caption and translate this video on Amara.org: http://www.amara.org/en/v/Brhq/ http://grammarware.net/talks/#Open2012 http://www.softwarefreedomday.eu/2012/Open-Notebook-Computer-Science.html
This screencast concerns my research activities around Open Notebook Science as a way to archive subatomic SKOs. Since SKOs directly contribute to the body of knowledge (BOK), this presentation is submitted as a remote contribution to the SL(E)BOK @ SLE2012 workshop.
Jean-Claude Bradley presented at the University of British Columbia School of Libraries on April 2, 2008. The talk covered the implications of Open Notebook Science for storing and retrieving scientific information.
Jean-Claude Bradley presents on Open Notebook Science: Transparency in Research on October 23, 2012 at Georgia Tech for Open Access Week. Topics include solubility, melting points, a recrystallization app, the Chemical Information Retrieval class at Drexel University and the Open Chemical Property Matrix (OCPM).
Rufus Pollock was interviewed on April 29th 2011 by Sarah Currier for the Centre for Research Communications. In this clip he offers definitions of openness, open knowledge and open science, and talks about his work with The Open Knowledge Foundation. Includes discussion of his own research in open economics and 'open notebook social science'.
Jean-Claude Bradley presents on Open Notebook Science: Transparency in Research on October 23, 2012 at Georgia Tech for Open Access Week. Topics include solubility, melting points, a recrystallization app, the Chemical Information Retrieval class at Drexel University and the Open Chemical Property Matrix (OCPM).
Jean-Claude Bradley presents at the American Chemical Society meeting on August 20, 2012. Examples are first presented to demonstrate how access to Open Notebooks can provide critical information not usually shared in the traditional publication process. The use of Google App Scripts to look up chemical properties allows for the use of Google Spreadsheets as a self-contained dashboard to plan and analyze chemical reactions. The concept of the Open Chemical Property Matrix (OCPM) is introduced and a smartphone app to suggest recrystallization solvents is then presented.
Jean-Claude Bradley presents at the American Chemical Society meeting in New Orleans on April 6, 2008. The use cheminformatics tools such as SMILES, InChI, InChIKeys and JCAMP-DX to store and retrieve experimental information on a public laboratory notebook is detailed.
On June 3, 2014, Peter Murray-Rust and Michelle Brook delivered a lecture on "Open Notebook Science" at the Haus der Forschung in Vienna, Austria. They were talking about realising the value of published scientific research via open science. Their lecture was given as part of "New Trends in Scholarly Communication", a new lecture series initiated by IST Austria, Austrian Academy of Science, and the Austrian Science Fund.
Matthew McBride, a student in the Bradley lab at Drexel University, talks about "Leveraging Open Notebook Science for solubility and melting point predictions for optimizing reactions and recrystallizations" on August 20, 2012 at the American Chemical Society meeting in Philadelphia. Matt discusses his perspective of ONS as an undergraduate student and some of his findings over the summer as a Drexel STARS Scholar concerning optimizing reactions and recrystallizations.
This is a presentation by Jean-Claude Bradley at the Biennial Conference for Chemical Education (BCCE) on July 29, 2008. The talk starts with an overview of Open Notebook Science using a wiki as a public lab notebook. An example of the usefulness of publishing failed experiments is detailed, showing how the version history of the wiki can be used to track the evolution of an organic chemistry experiment. Near the end of the talk an example of using automation to optimize a Ugi reaction is mentioned.
Published on Dec 9, 2014 View slides for this presentation here: http://www.slideshare.net/PyData/matt-greenwood-scott-draves-the-polyglot-beaker-notebook PyData NYC 2014 The Beaker Notebook is a new open source tool for collaborative data science. Like IPython, Beaker uses a notebook-based metaphor for idea flow. However, Beaker was designed to be polyglot from the ground up. That is, a single notebook may contain cells from multiple different languages that communicate with one another through a unique feature called autotranslation. You can set a variable in a Python cell and then read that variable in a subsequent R cell, and everything just works – magically. Beaker comes with built-in support for Python, R, Groovy, Julia, and Javascript. In addition, Beaker also supports multiple ki...
Help us caption and translate this video on Amara.org: http://www.amara.org/en/v/Brhq/ http://grammarware.net/talks/#Open2012 http://www.softwarefreedomday.eu/2012/Open-Notebook-Computer-Science.html
Melissa Lewis http://www.pyvideo.org/video/3760/introduction-to-open-and-collaborative-data-analy https://pygotham.org/2015/talks/123/introduction-to-open-and-collaborative-data-analysis-with-pandas-and-ipythonjupyter-notebook Data munging is typically an involved and noisy process, but pandas -- especially using the notebook format -- make it easy to share and reproduce the process of analyzing data, from munging to analysis and even exploratory visualization! In this talk you'll get a glimpse of the pandas workflow and some tips for getting the most out of its use in the IPython/Jupyter notebook.
GraphTerm: A notebook-like graphical terminal interface for collaboration and inline data visualization Authors: Ramalingam Saravanan, Texas A&M; University Track: Reproducible Science The notebook interface, which blends text and graphics, has been in use for a number of years in commercial mathematical software and is now finding more widespread usage in scientific Python with the availability browser-based front-ends like the Sage and IPython notebooks. This talk will describe a new open-source Python project, GraphTerm, that takes a slightly different approach to blending text and graphics to create a notebook-like interface. Rather than operating at the application level, it works at the unix shell level by extending the command line interface to incorporate elements of the graphica...