Cameron Neylon

[![The Queen\'s Tower, Imperial
College](http://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/Queen%27s_Tower.jpg/202px-Queen%27s_Tower.jpg){decoding="async"}](http://commons.wikipedia.org/wiki/Image:Queen%27s_Tower.jpg)Image
via
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This has taken me longer than expected to write up. Julius Lucks, John
Cumbers, and myself lead a workshop on Open Science on Monday 21^st^ at
the BioSysBio meeting at [Imperial College
London](http://www.imperial.ac.uk/ "Imperial College London"){rel="homepage"}.Â 
I had hoped to record screencast, audio, and possibly video as well but
in the end the laptop I am working off couldn't cope with both running
the projector and Camtasia at the same time with reasonable response
rates (its a long story but in theory I get my 'proper' laptop back
tomorrow so hopefully better luck next time). We had somewhere between
25 and 35 people throughout most of the workshop and the feedback was
all pretty positive. What I found particularly exciting was that,
although the usual issues of scooping, attribution, and the general
dishonestly of the scientific community were raised, they were only in
passing, with a lot more of the discussion focussing on practical
issues.

I spoke on Open Science in general, and gave examples of groups blogging
in a general way about their research, open notebooks, open grant
proposal writing and some of my thoughts about how we should take
scientific information management forward. Julius Lucks presented an
introduction to
[OpenWetWare](http://en.wikipedia.org/wiki/OpenWetWare "OpenWetWare"){rel="wikipedia"}
with a particular focus on some of his recent experiences on using
online systems to complement and expand the remit of the traditional
journal article.

John Cumbers then spoke at the end trying to define the important issues
and identify the priorities to be tackled in the future. The pictures
are of the notes he wrote on the whiteboard. In retrospect we should
have moved faster into this part of the workshop. While the earlier
conversation was good and productive, it was less focussed, and if we
had pushed on quicker (and if Iâ€™d spoken less!) we might have pinned
some of the issues down more.

![Whiteboard photo
\#2](http://farm4.static.flickr.com/3140/2433395153_b8533fa20f.jpg?v=0){decoding="async"
loading="lazy" height="375" width="500"}

Having said that, I think we got a pretty clear and strong steer on what
the issues are and what people felt was important. The pictures were
taken of the whiteboard after the workshop. The concept of a charter or
protocol and standards for Open Science got very strong support. While
there wasnâ€™t any agreement on exactly what form that would take there
was a very strong sense that by providing clear guidelines, both on what
qualifies as â€˜Open Scienceâ€™ and on code(s) of conduct to be
followed, would provide a clarity that doesnâ€™t currently exist; a
framework that people can sign up to and reasonably expect that other
people will recognise and follow. In a sense it doesnâ€™t matter that
much what such codes actually are. Simply having such things will make a
big difference.

![Whiteboard
photo](http://farm4.static.flickr.com/3039/2433362021_4eca708828.jpg?v=0){decoding="async"
loading="lazy" height="375" width="500"}

Associated with the ideas of a code of conduct is the need for legally
enforceable licenses for data. There was a strong sense that if it were
possible to enforce attribution, and possibly protect some rights to a
slice of any future return on exploitation that there would be much
wider adoption of Open Practice. The work of [Science
Commons](http://sciencecommons.org/ "Science Commons"){rel="homepage"},
[Open Knowledge
Foundation](http://en.wikipedia.org/wiki/Open_Knowledge_Foundation "Open Knowledge Foundation"){rel="wikipedia"}
and others in this space is clearly very important. The idea of Open
Science within a closed community as a way of achieving was raised.
While I can see the appeal for solving these practical issues of
enforceable licences, to me, it defeats the purpose of the exercise. But
I think this idea is likely to keep coming back around, so it deserves
consideration and discussion.

We will take the discussion forward on charters, licences, recognition,
and all the issues raised looking forward to the workshop at the
[Pacific Symposium on
Biocomputing](http://en.wikipedia.org/wiki/Pacific_Symposium_on_Biocomputing "Pacific Symposium on Biocomputing"){rel="wikipedia"}
in January next year. I would suggest a way forward is for people to
blog their ideas and suggestions and that we aim to try and capture and
integrate those ideas over the next few months. I would suggest using
the tag â€˜open-science-charterâ€™ for aggregation. Anyone who doesnâ€™t
have or doesnâ€™t want to bother with their own blog is more than
welcome to send me their ideas and I can publish them here.

Overall the workshop was a very positive experience. If there was one
take home message for me it was that, for this group at least, the
discussion has moved on from â€˜Iâ€™m too scared to do thisâ€™ to â€˜I
donâ€™t think I can do this for these specific set of reasons; get them
sorted and then we will see where we go from there.

[![](http://img.zemanta.com/pixie.png?x-id=6b0abe31-5e37-43b4-b419-ed5437df93bf){decoding="async"}](http://www.zemanta.com/ "Zemified by Zemanta")


Image via Wikipedia  This has taken me longer than expected to write up. Julius Lucks, John Cumbers, and myself lead a workshop on Open Science on Monday 21
<sup>
 st
</sup>
at the BioSysBio meeting at Imperial College London.Â

Somewhat more complete report on BioSysBio workshop

Tomorrow myself and a few of the usual suspects, who I have finally met
in person are giving a workshop on 'Open Science' as part of [BioSysBio
2008](http://conferences.theiet.org/biosysbio/). If anyone else who I
haven't met yet is about at the meeting then feel free to introduce
yourself, even if you can't make it to the workshop. The [workshop
abstract](http://openwetware.org/wiki/User:Cameron_Neylon/BioSysBioabstract)
is up on [OpenWetWare](http://openwetware.org) if you want to have a
look. I hope to be able to record screencast and video of the session to
make it available to all of you who can't make it. If you want to make
comments in advance or raise any issues then drop a comment here or in
the usual places.


Tomorrow myself and a few of the usual suspects, who I have finally met in person are giving a workshop on ‘Open Science’ as part of BioSysBio 2008. If anyone else who I haven’t met yet is about at the meeting then feel free to introduce yourself, even if you can’t make it to the workshop. The workshop abstract is up on OpenWetWare if you want to have a look.

BioSysBio conference and workshop

[Frank Gibson](http://peanutbutter.wordpress.com) has [posted
again](http://peanutbutter.wordpress.com/2008/04/14/modeling-experiments-and-presenting-the-information/)
in our ongoing conversation about using FUGE as a data model for
laboratory notebooks. We have also been discussing things by email and I
think we are both agreed that we need to see what actually doing this
would look like. Frank is looking at putting some of my experiments into
a FUGE framework and we will see how that looks. I think that will be
the point where we can really make some progress. However here I wanted
to pick up on a couple of points he has made in his last post.

> From Frank: However, this is no denying that FuGE is a datamodel and
> does not come with a high degree of tool support or nice user
> interfaces, which Cameron is crying out for, as are most lab
> scientists from a usability point of view.

Certainly to implement FUGE we will need to provide a set of tools that
provide interfaces that work. To a certain extent it is certainly true
that Frank is talking about data models while I am talking about
interfaces. Nonetheless any data model will influence and indeed limit
the possibilities of user interfaces. My concern with any data model is
that it will limit user interface design in a way that makes it
inappropriate for use in a research laboratory.

> > Me: I got off to a very bad start here. I should have used the word
> > â€˜captureâ€™ here. This to me is about capturing the data streams
> > that come out of lab work.

> Frank: This seems to be a change of tact :) The original post was
> about a data model for lab notebooks .

This is part of the semantic problem (pardon the pun). To me, the
primary use of a lab book is to capture the processes that occur in the
lab, as far as is practicable. Data stream here should be understood to
mean streams from instruments, monitors, and the stream of descriptive
information that comes from the scientist.

My central problem with implementing a data model for an experiment is
that we do not necessarily know in advance what the boundaries of the
experiment are. But the key question will be how can FuGE work as a data
model in practice. This is why we need to actually try it out and see
how it fits. In a sense the question of â€˜what is the experimentâ€™ is
similar to the one we have developed at a practical level in deciding
what element of our record justifies its own post.

Frank divides the issues into four different stages or issues and is
correct in saying that we have to a large extent conflated these issues
together.

> Frank again: Summary
>
> So I will start with re-pointing what I believe to be the areas of
> conflation within these discussions
>
> 1\. the representation of experiments -- the data model
>
> 2\. the presentation or level of abstraction to the user (probably
> some what dependent on 3.)
>
> 3\. the implementation of the data model
>
> 4\. the publication of the data (Notification, RSS etc.)

I donâ€™t disagree with this, but I think there is another phase or
stage. A Stage 0 where the stuff that happens in the real world is
mapped onto the data model. This is the part that worries me the most.
It is also an important question to deal with in a general sense. Where
do we impose our data model? Before the experiment, when we are planning
it, or after it has been done and we have an understanding of what we
have one and what it mean. So this is where we need to see how it works
in practice and go from there.

Posting this from BioSysBio 2008 at Imperial College London.


Frank Gibson has posted again in our ongoing conversation about using FUGE as a data model for laboratory notebooks. We have also been discussing things by email and I think we are both agreed that we need to see what actually doing this would look like. Frank is looking at putting some of my experiments into a FUGE framework and we will see how that looks. I think that will be the point where we can really make some progress.

More on FuGE and data models for lab notebooks

As part of the [BioSysBio
meeting](http://conferences.theiet.org/biosysbio/) being held in London
20-22 of April, [Mattias
Rantalainen](http://openwetware.org/wiki/User:Mattias_Rantalainen)
kindly asked me to contribute to a workshop on Open Science being held
on the Wednesday. A number of [OpenWetWare](http://openwetware.org)
people including [Julius
Lucks](http://www.openwetware.org/wiki/User:Julius_B._Lucks) and [John
Cumbers](http://openwetware.org/wiki/User:John_Cumbers) have agreed to
come on board to help. You can see the draft abstract which is [up at
OpenWetWare](http://openwetware.org/wiki/User:Cameron_Neylon/BioSysBioabstract).
If you are the meeting do come along either to cheer us along in our
quest to enthuse the next generation of scientists about Open Stuff or
to argue with us about the details of how to do it. I wanted to flag two
things up here. One is that we propose to start thrashing out a
'Protocol for Open Science'; a charter of rights and responsibilities
that we hope we can agree as a community to adopt as a standard, or
perhaps set of standards.

I don't imagine this will be an easy process but the aim is to start to
define the issues with the aim of taking this forward over the next
12-18 months. An initial draft will be put forward at the workshop and
will be made available for community discussion.

More practically Julius has set up an openscience email list based at
OpenWetWare. You can sign up just by adding your OWW username to the
[wiki List page](http://openwetware.org/wiki/List:OpenScience) (you do
have to be a member of OWW but this is just a matter of signing up).
This will be useful for carrying on the conversation not just about
standards but also about the all the issue surrounding being open.

I propose the tag osci-protocol to capture the blog based discussion and
other discussion.


As part of the BioSysBio meeting being held in London 20-22 of April, Mattias Rantalainen kindly asked me to contribute to a workshop on Open Science being held on the Wednesday. A number of OpenWetWare people including Julius Lucks and John Cumbers have agreed to come on board to help. You can see the draft abstract which is up at OpenWetWare.

Open Science at BioSysBio &#8211; London 20-22 April

Shirley has already [posted a quick
notice](http://onebiglab.blogspot.com/2008/03/psb-proposal-accepted-for.html)
on this but I thought I would follow up. Our
[proposal](http://precedings.nature.com/documents/1633/version/1) for a
session at the [Pacific Symposium on
Biocomputing](http://psb.stanford.edu/) on Open Science was successful
and we have been asked to put together a workshop session to run on
January 5 next year in Hawaii.

This is a slight departure for PSB. The workshop sessions are slightly
shorter than the traditional sessions and full papers will not feature
in the proceedings. However as [one of the
concerns](http://blog.openwetware.org/scienceintheopen/2008/03/08/what-to-use-as-a-the-primary-key-for-chemicals/#comment-1005)
was that getting full papers in six months before the meeting would be
difficult, that it might be a challenge to get people to submit
conference papers, and they would be out of date by the meeting, this
looks like a win-win situation. Also we have more or less complete
freedom to structure the session as we see fit.

The current idea is a series of talks followed by a panel discussion but
the details are negotiable. We will be putting out a call for
submissions soon, and we will be directly contacting some of you to
solicit submissions for a talk. Those giving a talk will have to
register (and pay) for the meeting by September 19. While there is
likely to be [some support
available](http://psb.stanford.edu/keydates.html) from the PSB
organizers there are no guarantees. We realise that this will make it
difficult for some people but at the moment we don't have any additional
sources of funding available. We are of course very happy to write
letters of support for local funding applications to support travel and
registration for the meeting.

In addition to this we need to put together a five page introduction
discussing the aims and background to the workshop. This is due on
September 22. Naturally we will be aiming to write this in the open and
will hopefully make a start on that soon. All assistance will be
gratefully received and we will almost certainly make significant use of
pre-existing material that is available. It might be appropriate to
start a discussion on how we manage authorship of such documents for the
future before we get too far down that road.

Finally on PSB another question: do people want to try and organise an
'extra' session for ourselves around the PSB meeting? How many people
think they can make it? This could be as simple as an evening in a bar
or restaurant or as formal as seeing if we can get a lecture theatre for
an extra half or full day. Obviously that would cost money -- which we'd
need to find from somewhere but if there is a strong desire for this
then we can look into it.

And finally, finally; there are moves afoot to organise an Open Science
workshop at the [BioSysBio
meeting](http://conferences.theiet.org/biosysbio/) in London (April
20-22, workshop would be on Monday 21st). Could people who are planning
to be at the meeting get in touch either in the comments or by email \[C
doit Neylon blat rl.ac.uk\] so we can look at what could be organised
for that? Again the thinking is a couple of talks followed by a panel
discussion. People from publishers (open access or not) and with
contrary views are particularly welcome. Lets have a good and vigorous
discussion!


Shirley has already posted a quick notice on this but I thought I would follow up. Our proposal for a session at the Pacific Symposium on Biocomputing on Open Science was successful and we have been asked to put together a workshop session to run on January 5 next year in Hawaii.  This is a slight departure for PSB. The workshop sessions are slightly shorter than the traditional sessions and full papers will not feature in the proceedings.

Rogue Scholar Beiträge

Somewhat more complete report on BioSysBio workshop

BioSysBio conference and workshop

More on FuGE and data models for lab notebooks

Open Science at BioSysBio – London 20-22 April

Open Science at Pacific Symposium on Biocomputing (and BioSysBio)