Cameron Neylon

Following on fromÂ [Science Online
09](http://www.scienceonline09.com/index.php/wiki/)Â and particularly
discussions on [Impact Factors and researcher
incentives](http://www.scienceonline09.com/index.php/wiki/Reputation_authority_and_incentives/)Â (also
onÂ [Friendfeed](http://friendfeed.com/e/ff6e8043-e771-45ec-9ff6-9bddff241017/Bjorn-Brembs-and-Peter-Binfield-How-to-get-rid-of/)Â and
some video available atÂ [Mogulus](http://mogulus.com/cameron_neylon)
via video on demand) as well as theÂ [article in PloS Computational
Biology](http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000247)Â by
Phil Bourne and Lynn Fink the issue of unique researcher identifiers has
really emerged as absolutely central to making traditional publication
work better, effectively building a real data web that works, and making
it possible to aggregate the full list of how people contribute to the
community automatically.

Good citation practice lies at the core of good science. The value of
research data is not so much in the data itself but its context, its
connection with other data and ideas. How then is it that we have no way
of citing a person? We need a single, unique way, of identifying
researchers. This will help traditional publishers and the existing
ecosystem of services by making it possible to uniquely identify authors
and referees. It will make it easier for researchers to be clear about
who they are and what they have done. And finally it is a critical step
in making it possible to automatically track all the contributions that
people make. We've all seen CVs where people say they have refereed for
Nature or the NIH or served on this or that panel. We can talk about
micro credits but until there are validated ways of pulling that
information and linking it to an identity that follows the person, not
who they work for, we won't make much progress.

On the other hand most of us do not want to be locked into one system,
particularly if it is controlled by one commercialÂ organization.
Â Thomson ISI'sÂ [ResearcherID](http://www.researcherid.com/)Â is
positioned as a solution to this problem, but I for one am not happy
with being tied into using one particular service, regardless of who
runs it.

In the PLoS Comp Biol article Bourne and Fink argue that one solution to
this isÂ [OpenID](http://openid.net/). OpenID isn't a service, it is a
standard. This means that an identity can be hosted by a range of
services and people can choose between them based on the service
provided, personal philosophy, or any other reason. The central idea is
that you have a single identity which you can use to sign on to a wide
range of sites. In principle you sign into your OpenID and then you
never see another login screen. In practice you often end up typing in
your ID but at least it reduces the pain in setting up new accounts. It
also provides in most cases a "home page". If you go
toÂ <http://cameron.neylon.myopenid.com>Â you will see a (pretty
limited) page with some basic information.

OpenID is becoming more popular with a wide range of webservices
providing it as a login option
includingÂ [Dopplr](http://dopplr.com),Â [Blogger](http://blogger.com),
and research sites includingÂ [MyExperiment](http://myexperiment.org).
Enabling OpenID is also on the list for a wide range of other services,
although not always high up the priority list. As a starting point it
could be very easy for researchers with an OpenID simply to add it to
their address when publishing papers, thus providing a unique, and
easily trackable identifier that is carried through the journal,
abstracting services, and the whole ecosystem services built around
them.

There are two major problems with OpenID. The first is that it is poorly
supported by big players such as Google and Yahoo. Google and Yahoo will
let you use your account with them as an OpenID but they don't accept
other OpenID providers. More importantly,Â [people just don't seem to
get OpenID](http://electronicmuseum.org.uk/2008/07/16/openid-fail/). It
seems unnatural for some reason for a person's identity marker to be a
URL rather than a number, a name, or an email address. Compounded with
the limited options provided by OpenID service providers this makes the
practical use of such identifiers for researchers very much a minority
activity.

So what about building an OpenID service specifically for researchers?
Imagine a setup screen that asks sensible questions about where you work
and what field you are in. Imagine that on the second screen, having
done a search through literature databases it presents you with a list
of publications to check through, remove any mistakes, allow you to add
any that have been missed. And then imagine that the default homepage
format is similar to an academic CV.

Problem 1: People already have multiple IDs and sometimes multiple
OpenIDs. So we make at least part of the back end file format, and much
of what is exposed on the
homepageÂ [FOAF](http://www.foaf-project.org/), making it possible to at
least assert that you are the same person as, say
cameronneylon@yahoo.com.

Problem 2: Aren't we just locking people into a specific service again?
Well no, if people don't want to use it they can use any OpenID
provider, even set one up themselves. It is an open standard.

Problem 3: What is there to make people sign up? This is the tough one
really. It falls into two parts. Firstly, for those of us who already
have OpenIDs or other accounts on other systems, isn't this just (yet)
another "me too" service. So, in accordance with the five rules I have
proposed for successful researcher web services, there has to be a
compelling case for using it.

For me the answer to this comes in part from the question. One of the
things that comes up again and again as a complaint from researchers is
the need to re-format their CV (seeÂ [Schleyer et al,
2008](http://www.jmir.org/2008/3/e24/)Â for a study of this). Remember
that the aim here is to automaticallyÂ aggregate most of the information
you would put in a CV. Papers should be (relatively) easy, grants might
be possible. Because we are doing this for researchersÂ we know what the
main categories are and what they look like. That is we have
semantically structured data.

Ok so great I can re-format my CV easier and I don't need to worry about
whether it is up to date with all my papers but what about all these
other sites where I need to put the same information? For this we need
to provide functionality that lets all of this be carried easily to
other services. Simple embed functionality like that you see
onÂ [YouTube](http://youtube.com), and most other good file hosting
services, which generates a little fragment of code that can easily be
put in place on other services (obviously this requires other services
to allow that -- which could be a problem in some cases). But imagine
the relief if all the poor people who try to manage university
department websites could just throw in some embed codes to
automatically keep their staff pages up to date? Anyone seeing a
business model here yet?

But for this to work the real problem to be solved is the vast majority
of researchers for whom this concept is totally alien. How do we get
them to be bothered to sign up for this thing which apparently solves a
problem they don't have? The best approach would be if journals and
grant awarding bodies used OpenIDs as identifiers. This would be a dream
result but doesn't seem likely. It would require significant work on
changing many existing systems and frankly what is in it for them? Well
one answer is that it would provide a mechanism for journals and grant
bodies toÂ publiclyÂ acknowledgeÂ the people who referee for them. An
authenticated RSS feed from each journal or funder could be parsed and
displayed on each researcher's home page. The feed would expose a record
of how many grants or papers that each person has reviewed (probably
with some delay to prevent people linking that to the publication of
specific papers). Of course such a feed could be used for lot of other
interesting things as well, but none of them will work without a unique
person identifier.

I don't think this is compelling enough in itself, for the moment, but a
simpler answer is what was proposed above -- just encouraging people to
include an OpenID as part of their address. Researchers will bend over
backwards to make people happy if theyÂ believeÂ those people have an
impact on their chances of being published or getting a grant. A little
thing could provide a lot of impetus and that might bring into play the
kind of effects that could result from acknowledgement and ultimately
make the case that shifting to OpenID as the login system is worth the
effort. This would particularly the case for funders who really want to
be able to aggregate information about the people they fund effectively.

There are many details to think about here. Can I use my own domain name
(yes, re-directs should be possible). Will people who use another
service be at a disadvantage (probably, otherwise any business model
won't really work). Â Is there a business model that holds water (I
think there is but the devil is in the details). Should it be non-profit
or for profit or run by a respected body (I would argue that for-profit
is possible and should be pursued to make sure the service keeps
improving -- but then we're back with a commercial provider).

There are many good questions that need to be thought through but I
think the principle of this could work, and if such an approach is to be
successful it needs to get off the ground soon and fast.

*Note:Â I am aware that a number of people are working behind the scenes
on components of this and on similar ideas. Some of what is written
above is derived from private conversations with these people and as
soon as I know that their work has gone public I will add references and
citations as appropriate at the bottom of this post.Â *


Following on fromÂ Science Online 09Â and particularly discussions on Impact Factors and researcher incentivesÂ (also onÂ FriendfeedÂ and some video available atÂ Mogulus via video on demand) as well as theÂ article in PloS Computational BiologyÂ by Phil Bourne and Lynn Fink the issue of unique researcher identifiers has really emerged as absolutely central to making traditional publication work better,

A specialist OpenID service to provide unique researcher IDs?

[![Sydney Harbour Bridge NYE
fireworks](http://farm4.static.flickr.com/3105/3154292974_782e84087f.jpg?v=0){decoding="async"
loading="lazy" align="left" width="378"
height="254"}](http://flickr.com/photos/27038548@N00/3154292974/)All
good traditions require someone to make an arbitrary decision to do
something again. Last year I threw up a few New Year's resolutions in
the hours before NYE in the UK. Last night I was out on the shore of
Sydney Harbour. I had the laptop -- I thought about writing something --
and then I thought -- nah I can just lie here and look at the pretty
lights. However I did want to follow up the successes and failures of
last year's resolutions and maybe make a few more for this year.

So [last year's
resolutions](http://blog.openwetware.org/scienceintheopen/2007/12/31/some-new-years-resolutions/)
were, roughly speaking, 1) to adopt the principles of the NIH Open
Access mandate when choosing journals for publications, 2) to get more
of the existing data within my group online and available, 3) to take
the whole research group fully open notebook, 4) to mention Open
Notebooks in every talk I gave, and 5) attempt to get explicit funding
for developing open notebook approaches.

So successes -- the research group at RAL is now (technically) working
on an Open Notebook basis. This has taken a lot longer than we expected
and the guys are still really getting a feel for what that means both in
terms of how the record things and how they feel about it. I think it
will improve over time and it just reinforces the message that none of
this is easy.Â  I also made a point about talking about the Open
Notebook approach is every talk I gave -- mostly this was well received
-- often there was some scepticism but the message is getting out there.

However we didn't do so well on picking journals -- most of the papers I
was on this year were driven by other people or were directed requests
for special issues, or both. The papers that I had in mind I still
haven't got written, some drafts exist, but they're definitely not
finished. I also haven't done any real work on getting older data online
-- it has been enough work just trying to manage the stuff we already
have.

Funding is a mixed bag -- [the network
proposal](http://blog.openwetware.org/scienceintheopen/category/research-network-proposal-for-open-science/)
that was in last New Year's was rejected. A few proposals have gone in
-- more haven't gone in but exist in draft form -- and a group of us
went close to getting a tender to do some research into the uptake of
Web 2. tools in science (more on that later but [Gavin
Baker](http://www.gavinbaker.com) has [written about
it](http://www.gavinbaker.com/2008/12/23/opening-research-proposals-thoughts-on-virtual-collaboration/)
and our [tender document itself is
available](http://www.scribd.com/doc/9402283/Tender-Use-and-relevance-of-web-20-resources-for-researchers)).
The success of the year was the funding that [Jean-Claude
Bradley](http://usefulchem.blogspot.com) obtained from
[Submeta](http://www.submeta.org/) (as well as support from Aldrich
Chemicals and Nature Publishing Group) to support the [Open Notebook
Science Challenge](http://onschallenge.wikispaces.com/). I can't take
any credit for this but I think it is a good sign that we may have more
luck this coming year.

So for this year -- there are some follow ons -- and some new ones:

1.  I *will* re-write the network application (and will be asking for
    help) and re-submit it to a UK funder
2.  I will clean up the "Personal View of Open Science" series of blog
    posts and see if I can get it published as a perspectives article in
    a high ranking journal
3.  I will get some of those damn papers finished -- and decide which
    ones are never going to be written and give up on them. Papers I
    have full control over will go by first preference to Gold OA
    journals.
4.  I will pull together the pieces needed to take action on the ideas
    that came out of the Southampton Open Science workshop, specifically
    the idea of a letter signed by a wide range of scientists and
    interested people to a high ranking journal stating the importance
    of working towards published papers being fully supported by data
    and methodological detail that is fully available
5.  I will focus on doing less things and doing them better -- or at
    least making sure the resources are available to do more of the
    things I take on...

I think five is enough things to be going on with. Hope you all have a
happy new year, whenever it may start, and that it takes you further in
the direction you want to go (whether you know what that is now or not)
than you thought was possible.

p.s. I noticed in the comments to [last year's
post](http://blog.openwetware.org/scienceintheopen/2007/12/31/some-new-years-resolutions/)
a comment from one [Shirley Wu](http://shirleywho.wordpress.com)
suggesting the idea of running a session at the [2009 Pacific Symposium
on Biocomputing](http://psb.stanford.edu) -- a proposal that resulted in
the [session we are holding in a few
days](http://psb09openscience.wordpress.com) (again more later on -- we
hope -- streaming video, micro blogging etc). Just thinking about how
much has changed in the way such an idea would be raised and explored in
the last twelve months is food for thought.


All good traditions require someone to make an arbitrary decision to do something again. Last year I threw up a few New Year’s resolutions in the hours before NYE in the UK. Last night I was out on the shore of Sydney Harbour. I had the laptop – I thought about writing something – and then I thought – nah I can just lie here and look at the pretty lights.

New Year’s Resolutions 2009

This is the second in a series of posts (first one
[here](http://cameronneylon.net/blog/re-inventing-the-wheel-again-what-the-open-science-movement-can-learn-from-the-history-of-the-pdb/))
in which I am trying to process and collect ideas that came out of
Scifoo. This post arises out of a discussion I had with [Michael
Eisen](http://mcb.berkeley.edu/faculty/GEN/eisenm.html) (UC Berkely) and
[Sean Eddy](http://www.hhmi.org/research/groupleaders/eddy_bio.html)
(HHMI Janelia Farm) at lunch on the Saturday. We had drifted from a
discussion of the problem of attribution stacking and citing datasets
(and datasets made up of datasets) into the problem of academic credit.
I had trotted out the usual spiel about the need for giving credit for
data sets and for tool development.

Michael made two interesting points. The first was that he felt people
got too much credit for datasets already and that making them more
widely citeable would actually devalue the contribution. The example he
cited was genome sequences. This is a case where, for historical
reasons, the publication of a dataset as a paper in a high ranking
journal is considered appropriate.

In a sense I agree with this case. The problem here is that for this
specific case it is allowable to push a dataset sized peg into a paper
sized hole. This has arguably led to an over valuing of the sequence
data itself and an undervaluing of the science it enables. Small
molecule crystallography is similar in some regards with the publication
of crystal structures in paper form bulking out the publication lists of
many scientists. There is a real sense in which having a publication
stream for data, making the data itself directly citeable, would lead to
a devaluation of these contributions. On the other hand it would lead to
a situation where you would cite what you used, rather than the paper in
which it was, perhaps peripherally described. I think more broadly that
the publication of data will lead to greater efficiency in research
generally and more diversity in the streams to which people can
contribute.

Michaelâ€™s comment on tool development was more telling though. As
people at the bottom of the research tree (and I count myself amongst
this group) it is easy to say â€˜if only I got credit for developing
this toolâ€™, or â€˜I ought to get more credit for writing my blogâ€™,
or anyone of a thousand other things we feel â€˜ought to countâ€™. The
problem is that there is no such thing as â€˜creditâ€™. Hiring decisions
and promotion decisions are made on the basis of perceived need. And the
primary needs of any academic department are income and prestige. If we
believe that people who develop tools should be more highly valued then
there is little point in giving them â€˜creditâ€™ unless that
â€˜creditâ€™ will be taken seriously in hiring decisions. We have this
almost precisely backwards. If a department wanted tool developers then
it would say so, and would look at CVs for evidence of this kind of
work. If we believe that tool developers should get more support then we
should be saying that at a higher, strategic level, not just trying to
get it added as a standard section in academic CVs.

More widely there is a question as to why we might think that blogs, or
public lectures, or code development, or more open sharing of protocols
are something for which people should be given credit. There is often a
case to be made for the contribution of a specific person in a
non-traditional medium, but that doesnâ€™t mean that every blog written
by a scientists is a valuable contribution. In my view it isnâ€™t the
medium that is important, but the diversity of media and the concomitant
diversity of contributions that they enable. In arguing for these
contributions being significant what we are actually arguing for is
diversity in the academic community.

So is diversity a good thing? The tightening and concentration of
funding has, in my view, led to a decrease in diversity, both
geographical and social, in the academy. In particular there is a
tendency to large groups clustered together in major institutions,
generally led by very smart people. There is a strong argument that
these groups can be more productive, more effective, and crucially offer
better value for money. Scifoo is a place where those of us who are less
successful come face to face with the fact that there are many people a
lot smarter than us and that these people are probably more successful
for a reason. And you have to question whether your own small
contribution with a small research group is worth the taxpayerâ€™s
money. In my view this is something you should question anyway as an
academic researcher â€" there is far too much comfortable complacency
and sense of entitlement, but thatâ€™s a story for another post.

So the question is; do I make a valid contribution? And does that
provide value for money? And again for me Scifoo provides something of
an answer. I donâ€™t think I spoke to any person over the weekend
without at least giving them something new to think about, a slightly
different view on a situation, or just an introduction to something that
hadnâ€™t heard of before. These contributions were in very narrow areas,
ones small enough for me to be expert, but my background and experience
provided a different view. What does this mean for me? Probably that I
should focus more on what makes my background and experience unique â€"
that I should build out from that in the directions most likely to
provide a complementary view.

But what does it mean more generally? I think that it means that a
diverse set of experiences, contributions, and abilities will improve
the quality of the research effort. At one session of Scifoo, on how to
support ground breaking science, I made the tongue in cheek comment that
I thought we needed more incremental science, more filling in of tables,
of laying the foundations properly. The more I think about this the more
I think it is important. If we donâ€™t have proper foundations, filled
out with good data and thought through in detail, then there are real
risks in building new skyscrapers. Diversity adds reinforcement by
providing better tools, better datasets, and different views from which
to examine the current state of opinion and knowledge. There is an
obvious tension between delivering radical new technologies and
knowledge and the incremental process of filling in, backing up, and
checking over the details. But too often the discussion is purely about
how to achieve the first, with no attention given to the importance of
the second. This is about balance not absolutes.

So to come back around to the original point, the value of different
forms of contribution is not due to the fact that they are
non-traditional or because of the medium *per se*, it is because they
are different. If we value diversity at hiring committees, and I think
we should, then looking at a diverse set of contributions, and the
contribution that a given person is likely to make in the future based
on their CVs, we can assess more effectively how they will differ from
the people we already have. The tendency of â€˜the academyâ€™ to hire
people in its own image is well established. No monoculture can ever be
healthy; certainly not in a rapidly changing environment. So diversity
is something we should value for its own sake, something we should try
to encourage, and something that we should search CVs for evidence of.
Then the credit for these activities will flow of its own accord.


This is the second in a series of posts (first one here) in which I am trying to process and collect ideas that came out of Scifoo. This post arises out of a discussion I had with Michael Eisen (UC Berkely) and Sean Eddy (HHMI Janelia Farm) at lunch on the Saturday. We had drifted from a discussion of the problem of attribution stacking and citing datasets (and datasets made up of datasets) into the problem of academic credit.

The problem of academic credit and the value of diversity in the research community

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

Open drug discovery in the undergraduate lab

A whole series of things have converged in the last couple of days for
me. First was [Jean-Claude's](http://usefulchem.blogspot.com)
description of the work
\[[1](http://usefulchem.blogspot.com/2008/03/expanding-usefulchem-collaboration-to.html),
[2](http://usefulchem.blogspot.com/2008/04/were-gonna-ugi-all-night.html)\]
he and [Brent Friesen](http://ochemonline.wordpress.com/) of the
[Dominican
University](http://www.dom.edu "Dominican University"){rel="homepage"}
are doing putting the [combi-Ugi
project](http://usefulchem.wikispaces.com/combiugi) into an
undergraduate laboratory setting. The students will make new compounds
which will then be sent for testing as antimalarial agents by [Phil
Rosenthal](http://www.ucsf.edu/bms/faculty/rosenthal.html) at
[UCSF](http://www.ucsf.edu "University of California, San Francisco"){rel="homepage"}.
This is a great story and a testament in particular to Brent's work to
make the laboratory practical more relevant and exciting for his
students.

At the same time I get an email from [Anna
Croft](http://www.chemistry.bangor.ac.uk/akc/), University of [Bangor,
Wales](http://en.wikipedia.org/wiki/Bangor%2C_Gwynedd "Bangor, Gwynedd"){rel="wikipedia"},
after meeting up the previous day;

> \[...\] I discussed the idea of blog-labbooks with my student/PDRAs on
> the way back and we were all keen to trial your stuff. I have also
> taken the liberty of talking to a couple of my colleagues over morning
> tea, and they were also very interested in the project and the idea of
> open science -- I expect when a couple of my other colleagues are back
> next week they will also be keen.
>
> **We thought it might be particularly valuable as a teaching resource
> in the first instance -- ie making the undergrads use it as** \[CN --
> my emphasis\]  1. it is more like the technology they are used to and
> 2. transparancy might improve the quality of their record keeping. It
> may come in very handy for undergrad practicals even, because it will
> be obvious to anyone who has copied each other. So I'm sure we could
> provide you with more than enough trouble shooting and commentary on
> the practice of open science to support your thesis that it is better
> for all ;)

I think this is emerging as a theme. If we can get these systems into
the undergraduate laboratory we can do two things. We can help to engage
the students by providing tools that, to them, may seem more relevant to
their everyday lives. We can improve the educational experience by using
the social networking and commenting tools available to help the
students learn from each other. Perhaps most exciting, if as Jean-Claude
and Brent are doing this is embedded in a real science project,
particularly one with clear social significance, the students will be
*directly involved with the science.* We talk a lot about 'research led
teaching' in the UK but I've seen little evidence of people really doing
it. Here is a real chance to make that happen, and because it's [Open
Notebook
Science](http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html)
they will be able to track the results from their own computers, at
home, perhaps even while uploading the results to their facebook page
(all right maybe not...).

But let's think bigger again. What if it were possible to spread this
out globally, using a coherent information tracking system. Chemistry
undergraduates all over the world could be making thousands of
characterised drug like molecules. Perhaps the screening could be done
in undergraduate biochemistry laboratories with well defined screening
assays for a wide range of targets: malaria, cancer cell lines, *S.
aureus*, HIV protease. You could expand this into physical
chemistry/biophysics with undergraduates looking at docking of the new
or proposed compounds against the available targets. A global programme
could link all of this together generating a massive library of
compounds screened against a wide range of targets.

And all of this would be open. [Deepak](http://mndoci.com) asked the
question the other day, '[What if the result of every docking result was
published online?](http://mndoci.com/blog/2008/03/28/what-if/)' and I
have previously imagined a '[Genbank of SAR
data](http://blog.openwetware.org/scienceintheopen/2008/01/27/picture-this/)'.
A programme like this could actually provide the impetus for such
repositories, while simultaneously adding value with characterisation
data for new compounds to existing initiatives like
[ChemSpider](http://www.chemspider.com/). Whether or not we actually
found hits the SAR data would be immensely valuable for future data
mining. Whether or not the SAR was useful to impetus towards building
these databases would be immensely valuable.

So -- what about the challenges. Converting research chemistry into
undergraduate labs is not straightforward. Jean-Claude's Ugi reactions
are a particularly good example for this because you can just mix three
compounds in methanol and in many cases the product precipitates. But
even here it's not trivial -- one component is usually smelly; the
compounds may not dissolve in methanol; the product may not precipitate.
Getting the fundamentals of a particular reaction right will take person
hours and quite a lot of them. In UK language this could be done with a
final year undergraduate project student to get one type of reaction
working in a three to six month project.

Screening can be just as hard. The reactions are not necessarily
straightforward, the reagents (and positive and negative controls) can
be expensive, and the equipment required to do it efficiently may not be
available. But again many reasonably straightforward assays are
available, and the rest just require time, expertise, and money. This
could be tracked down from a range of sources.

So, resources are required which really means money. Which is where the
third co-incidental strand comes in. [Via Pawel Szczesny on
FriendFeed](http://friendfeed.com/e/681654ce-7129-127e-03ff-27e15eec5eae)
I got a link to the following
[pos](http://phylogenomics.blogspot.com/2008/04/bill-and-melinda-gates-that-is-ask-for.html)[t](http://phylogenomics.blogspot.com/2008/04/bill-and-melinda-gates-that-is-ask-for.html)
about a [call from the Bill and Melinda Gates
foundation](http://www.gcgh.org/explorations/Pages/Introduction.aspx).
The problem with this call is that it really needs a drug resistance
angle to fly and while that is possible it complicates the whole idea
significantly. But between the B&MG foundation, Google, and others all
looking for projects that are both socially significant, make them look
good, and co-incidentally generate lots of data in the health arena that
they can process, this ought to be fundable. In particular this looks to
me like a great fit for Google. For us, it's great education, great
publicity, great science, and it demonstrates the benefits of openness.

A small scale project funding a development round for 12 months to try
and sort out appropriate reactions and assays, while trying to agree and
implement a data framework that will work for us would probably cost
around \$200-300k total costs. This would be followed by a larger scale
implementation phase, heading towards a few million probably, as it gets
rolled out. As it embeds in the education system the costs would
probably drop over time to eventually be absorbed in the programme
costs.

What do people think?

Further Reading: Jean-Claude's proposal on '[Crowdsourcing
Chemistry](http://usefulchem.blogspot.com/2008/01/chemistry-crowdsourcing-pre-proposal.html)'

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A whole series of things have converged in the last couple of days for me. First was Jean-Claude’s description of the work [1, 2] he and Brent Friesen of the Dominican University are doing putting the combi-Ugi project into an undergraduate laboratory setting. The students will make new compounds which will then be sent for testing as antimalarial agents by Phil Rosenthal at UCSF.

Messaggi di Rogue Scholar

A specialist OpenID service to provide unique researcher IDs?

New Year’s Resolutions 2009

The problem of academic credit and the value of diversity in the research community

Open drug discovery in the undergraduate lab

Open Science in the Undergraduate Laboratory: Could this be the success story we’re looking for?