Cameron Neylon

Following on from my post there has been lots of discussion both in the
comments to the post and also support and ideas on other blogs. I also
had a good talk (I know, face to face, how archaic :) with Jeremy Frey
about the idea. Here I want to collate a few of the comments and ideas.

[Jean-Claude](http://usefulchem.blogspot.com) makes a very good point in
a comment on the original post.

> I think that the role of funding is to ramp up an existing
> infrastructure of people already committed to participating. If I got
> more money I could support more students, get more chemicals,
> equipment like automated reactors, etc. Testers could get more
> resources to do more samples, modelers like Rajarshi could also get
> more assistance, etc. But, like open source software, the open source
> science core motor relies on the participation (even if limited) of
> people who have already bought into the concept.

I believe it will be possible, with resources,Â  to expand this more
rapidly than we otherwise could. This is based on my assumption that if
we can offer a well put together laboratory practical session or project
that works 'out of the box' then most undergraduate teaching departments
will jump at the opportunity. But it is important as Jean-Claude makes
clear that people really do buy in to the central concept; that it is
the open aspect of this that could make it successful.

Anna Croft makes a comment that echoes what virtually every other person
I've talked to raises as a concern (so I'm not picking on Anna, its just
that I happen to have her comment in text).

> \[...\]One thing thatâ€™s been slightly bothering me is data
> reliability. By using undergraduates we are relying on potentially
> problematic data. ie, without excellent prac skills, or with hidden
> problems (such as gone off reagents, which might go unrecognised) many
> reactions may be reported as not working that may work in the hands of
> another worker.\[...\]

I will reply to that with Jean-Claude's response which very much echoes
my own thinking.

> We have to move away from the concept of â€œtrusted sourcesâ€? that
> can be relied upon to be completely accurate without providing
> adequate proof. Providing links to all the raw data is absolutely key
> and lets us use information from undergraduates, postdocs and machines
> with minimal assumptions.

He then goes on to discuss this with respect to the work he is doing
with Brent Friesen and the fact that the students will be taking
pictures of their reactions. Now they may not be uploading these to
flickr but this does raise an issue which will be a big one to resolve
which is how to manage the data. This ties in with the discussion I have
been having with Frank Gibson about data models. We will clearly need to
think very carefully about how the data is captured and how it is
reported. What happens if we find out after the event that a reagent was
dodgy, that a set of assays are wrong? What data structure will allow
this to be properly managed?

Pawel Szczesny (spelt correctly this time I hope!) goes even further
suggesting;

> \[...\] this made me think about going even bigger. What about setting
> aim to develop a data model/framework for majority of scientific
> experiments, not only in chemistry? Significant portion of
> bioinformatics and molecular biology could be easily (at least I hope
> it would be easy) captured in such framework. \[...\]

While I agree tackling the problem is very worthwhile, I think it's too
big an issue to handle as the core of the project. That said development
in this area should obviously tie in and the data store could make a
good resource for developing such models. Keep thinking about the re-use
of this data, because that's where the long term gains are and that's
where we will be most effective making the case for Open Data (which we
clearly [still need to
do](http://feeds.feedburner.com/~r/PetermrsBlog/~3/265058858/)) .

[Peter Murray-Rust
agrees](http://feeds.feedburner.com/~r/PetermrsBlog/~3/264997239/) that
using the tools his group has developed could help out here.

> \[...\] suggested we can do theoretical calculations on these. With a
> modern machine this takes a few hours to get very good accuracy, and
> that could be run on the studentsâ€™ own machines. We have developed
> CML-based technology as in CrystalEye which can represent this in
> semantic fashion. The whole material should take about a terabyte --
> not challenging by todayâ€™s standards.Â  And it could all be stored
> in Pubchem, or Chemspider or Amazon or even an institutional
> repository. \[...\]

And goes on to express some concerns about the challenges of getting
people to buy in;

> Of course not all reactions will work, and some of the undergraduates
> will make mistakes (thatâ€™s how education works!).Â  But itâ€™s a
> great vision. The main problem is that most chemists are very
> conservative and undergraduates do the same experiment year after
> year. This would take some effortâ€¦

I think this is less of an issue than people might think, as long as, as
I said above, you can deliver the guts of the practical to the lab
organizer on a plate. This means in practice that rolling this kind of
thing out means sending people into each new department and really
holding people's hands throught the first run through. People who run
undergraduate labs would love to do something new (and the combi-chem
angle can help to deliver that) but they don't have the time resources
to get things working. To my mind that means that providing those
resources to get it to work is crucial to taking this forward as a
project. This suggests, to me, running the programme out of a foundation
that employs staff both to get things working in the first place and
then to deliver those to new labs.

Funding is obviously an issue here. Some things we can do with no
further resources, at least none beyond the considerable work that Brent
and Jean-Claude are already putting in. How does this work at Dominican?
Can we do it on a small scale at Bangor or at Southampton as final year
projects? Jeremy Frey also had some good ideas on possible funding
sources. The [Wellcome Trust](http://www.wellcome.ac.uk/) runs a [public
engagement](http://www.wellcome.ac.uk/Funding/Public-engagement/index.htm)
programme (see particularly [Society
Awards](http://www.wellcome.ac.uk/Funding/Public-engagement/Grants/Society-Awards/index.htm))
and is also one of the few agencies that actually have a [funding
programme for drug lead
discovery](http://www.wellcome.ac.uk/Funding/Technology-transfer/Awards/Seeding-Drug-Discovery/index.htm).
Another obvious resource to tap into would be the [Science Leaning
Centre](http://www.sciencelearningcentres.org.uk/WebPortal.aspx?page=8)
at Southampton University. There are other funding agencies that would
be interested if this could be taken into schools so a key question he
asked was;

> Is it possible to define experiments that could be done at high school
> level?

If this were possible it opens up a lot more opportunities, as well as
widening the public involvement, and engaging school kids in real
science.

Jeremy's second main point was that if you are selling this as an
educational programme then you have to be able to expand it into other
areas (materials, inorganic chemistry, physics, maths, cell biology,
medicine?). I think we could see the drug discovery concept as a
template that could be replicated for other fields or other experiments
(combinatorial solid state materials is one potential area).

Anyway, many ideas, lots of possibilities. Let's keep the conversation
going.


Following on from my post there has been lots of discussion both in the comments to the post and also support and ideas on other blogs. I also had a good talk (I know, face to face, how archaic :) with Jeremy Frey about the idea. Here I want to collate a few of the comments and ideas. Jean-Claude makes a very good point in a comment on the original post. I believe it will be possible, with resources,Â

Publicaciones de Rogue Scholar

Open drug discovery in the undergraduate lab