Cameron Neylon

...but being straightforward is always the best approach. Since we
published [our
paper](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001164)
in PLoS ONE a few months back I haven't been as happy as I was about the
activity of our Sortase. What this means is that we are now using a
higher concentration of the enzyme to do our ligation reactions. They
seem to be working well and with high yields, but we need to put in more
enzyme. If you don't understand that don't worry -- just imagine you
posted a carefully thought out recipe and then discovered you couldn't
get that same taste again unless you added ten times as much saffron.

None of this prevents the method being useful and doesn't change the
fundamental point of our paper, but if people are following our methods,
particularly if they only go to the paper and don't get in contact, they
may run into trouble. Traditionally this would be a problem, and would
probably lead to our results being regarded as unreliable. However in
our case we can do a simple fix. Because [the
paper](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001164)
is in [PLoS ONE](http://www.plosone.org/home.action) which has some good
commenting features, I can add [a note to the paper
itself](http://www.plosone.org/annotation/listThread.action?inReplyTo=info%3Adoi%2F10.1371%2Fannotation%2F345c1347-af55-4f79-b833-26e2ce4b9948&root=info%3Adoi%2F10.1371%2Fannotation%2F345c1347-af55-4f79-b833-26e2ce4b9948),
right [where we give the concentration of
enzyme](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001164)
(scroll down to note 3 in results) that we used. I can also [add a
note](http://www.plosone.org/annotation/listThread.action?inReplyTo=info%3Adoi%2F10.1371%2Fannotation%2F1b0061f7-c252-4451-864e-fc12549ee9ee&root=info%3Adoi%2F10.1371%2Fannotation%2F1b0061f7-c252-4451-864e-fc12549ee9ee)
to direct people to where we have put [more of our methdology
online](http://openwetware.org/wiki/ISISBio:Protocols/Sortase_mediated_ligation),
at [OpenWetWare](http://openwetware.org). As we get more of this work
into our online lab notebooks we will also be able to point directly
back to example experiments to show how the reaction rate varies, and
hopefully in the longer term sort it out. All easily done on the web,
but impossible on paper, and in an awful lot (but not all!) of the other
journals around.

Or we could just let people find out for themselves...

Note to the PLoS team: Even better would be if I could have a link that
went to a page where the comment was displayedÂ in the context of the
paper (i.e. what youÂ get when you click on the marker when reading the
paper ) Â :-)


…but being straightforward is always the best approach. Since we published our paper in PLoS ONE a few months back I haven’t been as happy as I was about the activity of our Sortase. What this means is that we are now using a higher concentration of the enzyme to do our ligation reactions. They seem to be working well and with high yields, but we need to put in more enzyme.

It’s a little embarrassing…

[![OpenWetWare logo, designed by Jennifer
Cook-Chrysos](http://upload.wikimedia.org/wikipedia/en/a/ad/OWWEmblem.png){decoding="async"}](http://en.wikipedia.org/wiki/Image:OWWEmblem.png)Image
via [Wikipedia](http://en.wikipedia.org/wiki/Image:OWWEmblem.png)

Just a very brief note, which really follows on from the vigorous
discussion in Jennifer Rohn's blog at Nature Networks this week, to say
that the guys at
[OpenWetWare](http://en.wikipedia.org/wiki/OpenWetWare "OpenWetWare"){rel="wikipedia"}
appear to have gone live with some of the new [functionality for
laboratory notebooks](http://openwetware.org/wiki/Help:Notebook) on the
wiki. Check it out from the [OWW main page](http://openwetware.org). I
will have a closer look and make some comments as and when I have a bit
of time but it looks like a good start.

[![](http://img.zemanta.com/pixie.png?x-id=3510c683-4da5-402d-839b-ce34aa3931f1){decoding="async"}](http://www.zemanta.com/ "Zemified by Zemanta")


Image via Wikipedia  Just a very brief note, which really follows on from the vigorous discussion in Jennifer Rohn’s blog at Nature Networks this week, to say that the guys at OpenWetWare appear to have gone live with some of the new functionality for laboratory notebooks on the wiki. Check it out from the OWW main page. I will have a closer look and make some comments as and when I have a bit of time but it looks like a good start.

Another lab notebook framework

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.

Messaggi di Rogue Scholar

It’s a little embarrassing…

Another lab notebook framework

Open Science at BioSysBio – London 20-22 April