The Scientist Article on Electronic Lab Notebooks

Amber Dance has written an article in The Scientist (2010-05-01) Digital Upgrade: How to choose your lab’s next electronic lab notebook. This is basically a quick overview of different Electronic Lab Notebooks (ELNs) that should be helpful for people researching what is currently available in that space.

There was some coverage of Open Notebook Science and Steve Koch and I were quoted. Ironically my contribution appeared in the "Cons" section :)

Pros

• The format is unconstrained—you can set up any categories, and as many users and pages, as you want—and fast to set up.
• Open notebooking attracts collaborators. Koch counts three collaborations that wouldn’t have happened if he weren’t on OpenWetWare. And his students build professional networks well before they author a paper.

Cons

• Wikis were not designed with scientific data in mind. For example, it’s hard to make a table, Koch says.
• Open notebook science “does limit where you can send your work,” says Jean-Claude Bradley, a chemist at Drexel University in Philadelphia, who also uses an open wiki notebook. His lab sticks to journals that accept preprints.
• Posting online voids international patent rights, although US patents are still possible.

In my opinion, one of the biggest "Pros" wasn't listed in that section: the free cost. (That was mentioned elsewhere though) When you see the costs of some of these other commercial systems, that has to be a factor for many people trying to make a decision.

If privacy is an issue wikis can certainly be made private, although I'm not sure if that is possible on OpenWetWare. It can be done for $5/month on Wikispaces, the wiki we use for lab notebooks - although then it wouldn't be Open Notebook Science.

Concerning Steve's Con of wikis being difficult to use to store data, that is true. However combining the use of a wiki with Google Spreadsheets has completely resolved that issue for us. With our ability to automatically export an archive of the notebook (as HTML) and spreadsheets (as XLS) into an integrated archive, the two platforms operate essentially as if they were a single system.

ONS Solubility Book: Edition 3 with Notebook Archive

Edition 3 (2010-02-11) of the ONS Solubility Challenge book is now available.

We've been trying for some time to find a way to conveniently take a snapshot of our Open Notebooks and all associated raw data files. This could serve as a way to back up all of our work as well as provide a means of finding out the state of knowledge for a project at a given moment in time. There is also a tremendous benefit to confidently using the best of free hosted Web2.0 services out there (e.g. GoogleDocs and Wikispaces) without being concerned with changes in policies or access down the road.

Our recent use of the ONS Challenge Solubility book to periodically create releases of summarized data has opened up a convenient opportunity. And yesterday the last piece of the puzzle fell into place. Through a combination of fairly quick manual and automated tasks, Andrew Lang and I are able to push out a full snapshot of all relevant files and lab notebook pages and associate it with an edition of the book.

As described below, the archive is accessible interactively on a server, as a zip download or as a CD from LuLu. Perhaps we can also find a home on library servers in the future.

More details are provided in the preface for Edition 3 (2010-02-11):

This is the first edition to include a full archive of the ONS Challenge notebook. A space export from Wikispaces provides an initial version of all the HTML pages in the notebook with local hyperlinks to copies of all images and files uploaded onto the wiki. All of the Google Spreadsheets are automatically downloaded as Excel spreadsheets and placed in the same "files" folder as the images. NMR spectra, stored as JCAMP-DX files, are placed in the "spectra" folder. All of the HTML pages are reformatted to provide local references to both Excel spreadsheets and the JCAMP-DX files.

The notebook archive is meant to represent a snapshot of the state of all source documents at the time of the publication of an edition of this book. When used from a server with web services running, clicking on links to the spectra will allow interaction via a browser interface, including zooming in or out and integration of the NMR spectrum. When accessed in stand-alone mode after downloading or directly from a CD, everything will work the same, except that JCAMP-DX files must be open from JSpecView running on the desktop. Excel files will retain any calculations in the cells of the original Google Spreadsheets but dynamic values generated from calling web services - such the script that automatically integrates NMR spectra - will be frozen as simple values. However the link to the web service used will be stored in the cell as a comment. Links to external websites are not crawled and embedded Google Spreadsheets or videos are not copied. These will work but will reflect live data on the web.

The February 11, 2010 version of the notebook archive is available on a hosted site, on a CD or by download.

Andy and Shirley's new ONS Logos

Some new ONS logos are available to specify a researcher's intent in making their lab notebook available online. Options include full Open Notebook Science (All Content - Immediate) or more restrictive forms (Selected Content or Delayed).

Andrew Lang updated his logos, including options for multiple sizes:




Shirley Wu also contributed these:





The logos can be downloaded from the ONS claims website. Clicking on them should link either directly to the lab notebook or to the ONS claims page, where a brief description of the intended meaning can be found.