[View this page as PDF](/blog/2007/09/21/09-33-08.277706/100.pdf)
Peter Murray-Rust [introduced me to the term Open Notebook
Science](http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=468) over lunch in
June this year.
In this post I will look a little at open science, as practiced by
chemists, and at a [recent DLib
colleagues of mine from Monash about the continuum of data form when it
is collected to when it is published, or curated, in the context of the
forthcoming Australian National Data Service (ANDS).
There are two points to this post:
1. A cheeky suggestion for a new term “Shared Notebook Science.” I assert that this is new because
> Your search - **"Shared Notebook Science class="spCh spChx201d">”** - did not match any documents.
Whereas “Open Notebook
Science” returns over 12,000
2. And a proposal for a new bit of infrastructure to help with both
Open and Shared varieties of data-driven research regardless of
whether it's broadly or narrowly accessible.
The term Open Notebook Science comes from Jean-Claude Bradley who has a
available](http://precedings.nature.com/documents/39/version/1) in PDF
and PowerPoint and [audio and
he talks about lots of tools that people can use for doing data-driven
Two slides stood out for me:
1. The blog as an integrative tool
2. The wiki as the laboratory notebook
There are lots of slides showing various data-driven research tools
– but you need some way to make that
research accessible to others and to provide the commentary that puts it
in context. The presentation is worth watching. My comment is that the
science would not have to be open for the tools to be useful.
The *Data Curation Continuum* doesn't discuss this aspect of the
practice of Science but it does look at data-flows. The authors note
that there's a requirement that access is **controlled, not open** for a
lot of researchers:
> The work of investigators in the DART project has indicated that many
> researchers are extremely conservative when it comes to granting
> access to research data. This appears to be associated with increasing
> competition in attracting research funds and having articles accepted
> by high-value publications. The recent move in Australia towards
> assessment of institutional research performance based on quality
> metrics (the Research Quality Framework class="spCh spChx2013">– DEST 2007) is only intensifying this.
> As a result, many researchers want tightly controlled access prior to
> publication. It is theoretically possible to provide the levels of
> access control demanded by researchers in a repository that also hosts
> open-access content, but separation of the two types of repositories
> may be a preferred solution. Post publication, there is some evidence
> that open access leads to increased accessibility and increased
> citation rates. This may encourage researchers to be less restrictive
> about access.
# 1 Shared Notebook science
I think that to cater to the access requirements noted by Andrew Treloar
et al you might need a “Shared
Notebook” approach as opposed to an
Open Notebook approach. That is, the benefits of a unifying tools like
Blogs and Wikis shared with colleagues but not open to all. ( I do
realize that there's a bit of baggage that comes along for the ride if
you substitute [Shared](http://en.wikipedia.org/wiki/Shared_source)for
Open, but I think the term fits.)
In fact I've worked on a “Shared
Notebook” project myself.
[RUBRIC](http://rubric.edu.au/). RUBRIC used a shared space in which to
work, which included a wiki, although our blogs were open-access. Read
Kate Watson and Chelsea Harper's
for more about how we got on.
So, some research needs to be kept under wraps, and some people are
happier collaborating withing a trusted community.
But whether we're talking Open or Shared, there's a need to promote
access and to communicate with peers. We need ways to do that on both
sides of what Andrew Treloar and co. call “the curation boundary”. Which brings us to my second point.
Making it easy to talk about data, right across the curation continuum.
# 2 New tools needed
Back to the Australian National Data Service, ANDS.
I think one contribution that USQ could make, in collaboration with
someone (and I'm thinking of chemists because I have made contact with
some) is to work out a generic service interface for making data easy to
embed into document, from the ephemeral through to published works.
Here's a workflow. I'll base it around [my earlier
example](http://ptsefton.com/blog/2007/06/22/cml_demo) of chemical
markup language but it could apply to any kind of data, big or small.
1. I make a new molecule.
Lets assume that it's a big one, so the Chemical Markup Language
that describes it is a **big** lump of XML.
(You have to suspend disbelief here. My first-year chemistry
lecturer, Julia James suggested that chemistry might not be my
vocation and pointed out that if I made up my mind quickly I could
withdraw without penalty. I did.)
2. I commit all the data about my molecule to the ANDS data service,
where I know it will be safe, and my colleagues can see it. This
includes the CML but also observations I have made (I'm getting
vague about the detail here, I know).
3. Now I want to tell people about my work. Some of them might find the
data because they are subscribed to a feed of some kind. Atom seems
like an appropriate protocol given the subject matter, but RSS if
you really must. But what about others who aren't using those tools
or who want to know a bit more about the context of my work?
4. In addition to automated dissemination I want to record stuff in my
notebook, which could be a wiki, or I may choose to blog it, maybe
I think what we need here is a way for me to chuck a link into my
document (for small amounts of data I would simply paste the data
in) and have helper software do the rest, making a print view of the
data and embedding live visualization tools into the web view of the
5. Later, wehn I start a paper, and I can copy/paste bits from the blog
and the Wiki into a document and have the ICE and the ANDS service
look after the details.
To support this I reckon we need a standard way to ask for **any data**
in the **range of views** we want, with software to make it easy to
write about it or call it up in a presentation. This is as necessary as
bibliography management via a tool like
[Zotero](http://www.zotero.org/), isn't it?
The software service would need to do something like this:
- Look at my data and work out that it's CML (or any one of hundreds
of other formats).
- Generate a 2D image for me to use in the print-view of my notes (may
not be important for wikis and blogs but ICE makes PDF for
everything and as you move towards publishing you want this view).
- Generate the HTML code needed to embed a useful visualization in my
- Insert all the right stuff in the right places without me having to
do anything, so I get a suitable live link from my notebook/blog to
the data with a useful visualization
ICE can already do some of this, and version 2, due in a couple of weeks
will be a good platform for this kind of service.