Open Notebook Science
Thanks to Beth Ritter-Guth's efforts to clarify the definition of
terms relating to Open Source Science, a good discussion has evolved
on the Blue Obelisk mailing list. Peter Murray-Rust has made the point
that this term may be confused with Open Source Software. However, as
Peter notes in a follow-up post, Jamais Cascio from WorldChanging has
used this definition of Open Source Science, which is fairly
consistent with our use of it in UsefulChem:
...research already in progress is opened up to allow labs anywhere
in the world to contribute experiments. The deeply networked nature
of modern laboratories, and the brief down-time that all labs have
between projects, make this concept quite feasible. Moreover, such
distributed-collaborative research spreads new ideas and
discoveries even faster, ultimately accelerating the scientific
process.
In Open Source Software, the code is made available to anyone to
modify and repurpose. What we have been trying to do with UsefulChem
is to provide the analogous entity for chemical research, which is raw
experimental data along with the researcher's interpretation in a
format that anyone can easily re-analyze, re-interpret and re-purpose.
A good example of re-purposing is using some results and observations
from a failed experiment in a way that was never intended by the
original researcher. This just doesn't happen regularly in science
because failed experiments are almost never included in publications.
Unfortunately, in addition to the confusion with Open Source Software,
others are using the term Open Source Science to mean discussions
about pre-prints of regular journal articles.
To clear up confusion, I will use the term Open Notebook Science,
which has not yet suffered meme mutation. By this I mean that there is
a URL to a laboratory notebook (like this) that is freely available
and indexed on common search engines. It does not necessarily have to
look like a paper notebook but it is essential that all of the
information available to the researchers to make their conclusions is
equally available to the rest of the world. Basically, no insider
information.
posted by Jean-Claude Bradley at 4:04 AM
4 Comments:
* Jean Claude
This is really useful - I think "Open Notebook Science" captures
both the description and the spirit.
I am also exceited by the recipes you list in the example. I have
spent the w/e trying to work out how to parse such text into
CMLReact and feeling quite confident. It is possible that we can
converge on a CMLReact representation that suits both your
requirements and yours. Then we have a completely machine-readable
book. So that if you feel what is on your site is the complete
record I think we have real possibility. Put it in Bioclipse as a
plugin and ...
More on this in a few days.
By Blogger Peter Murray-Rust, at 2:29 PM
* This is a great new term, Jean-Claude. I believe, as Peter does,
that this new term "captures both the description and the spirit"
of your work.
This is precisely what I hoped would happen when I took on this
project; I hoped to facilitate a useful discussion among "open
chemists" about the terms used to discuss the work they share.
By Blogger Beth Ritter-Guth, at 4:21 PM
* Hey this is great! So good to see scientists taking initiative to
make their knowledge accessible (isn't that what science is all
about?).
The next step is to make these open notebooks as user friendly as
possible. I mean this from the perspective of both the person
entering the information, and the one using it.
Hopefully the Wiki format is comfortable markup to use, was it
difficult for everyone in the lab to learn? The output of the
notebooks must be similarly usable, what possibilities might exist
for creating live summaries and tabular data?
Hope to see more great innovation in this area!
By Blogger Michael, at 4:39 AM
* Michael
Where applicable we are creating tables where similar experiments
can be compared - see here for example
There is also a table of contents of the experiments that gives
the notebook a familiar interface to a regular paper notebook.
By Blogger Jean-Claude Bradley, at 4:52 PM
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