The online home of Cameron Neylon
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.
Image by davemc500hats via Flickr
One thing that has been becoming clearer and clearer to me is the need to an agreed central authority for identify. This is one thing, possibly the one thing, that needs to be absolutely secure and inviolable for Open Science to work. Trust relies on provenance. Attribution, which is at the heart of open practice, relies on provenance. And pulling all of my data together from multiple streams in an automatic way relies on a record of their provenance.
There has been a lot of discussion about Google App Engine but two posts in particular have collided for me. First was the first blog post about an app I saw off the rank which uses a Google account to access an open id. Useful and cool. Secondly was the emphasis in another post from David Recordon about Google Apps as a potential Facebook Killer that the access to Google accounts is a key part of the offering.
Then I realised. Google already probably had the highest penetration as a validator of identities but these only really provide access to Google services. OpenID is great in principle but is not perhaps getting the traction it needs to go global. But all of that now just goes away. If you can write an app to authenticate someone via Google and then link that to OpenID you can do it for anything. Google have just positioned themselves to be the de facto provider of identities. And they may have solved the provenance problem into the bargain.
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And other big words I learnt from mathematicians…
The observant amongst you will have realised that the title of my previous post pushing a boat out into the area of semantics and RDF implied there was more to come. Those of you who followed the reaction [comments in original post, 1, 2, 3] will also be aware that there are much smarter and more knowledgeable people out there thinking about these problems. Nonetheless, in the spirit of thinking aloud I want to explore these ideas a little further because they underpin the way I think about the LaBLog and its organization. As with the last post this comes with the health warning that I don’t really know what I’m talking about. Continue reading “Semantics in the real world? Part II – Probabilistic reasoning on contingent and dynamic vocabularies”
Perimeter Institute by hungryhungrypixels (Picture found by Zemanta).
Sabine Hossenfelder and Michael Nielsen of the Perimeter Institute for Theoretical Physics are organising a conference called ‘Science in the 21st Century‘ which was inspired in part by SciBarCamp. I am honoured, and not a little daunted, to have been asked to speak considering the star studded line up of speakers including, well lots of really interesting people, read the list. The meeting looks to be a really interesting mix of science, tools, and how these interact with people (and scientists). I’m looking forward to it. Continue reading “Science in the 21st Century”
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. Continue reading “Open drug discovery in the undergraduate lab”
As I mentioned a couple of weeks or so ago I’ve been playing around with Friendfeed. This is a ‘lifestreaming’ web service which allows you to aggregate ‘all’ of the content you are generating on the web into one place (see here for mine). This is interesting from my perspective because it maps well onto our ideas about generating multiple data streams from a research lab. This raw data then needs to be pulled together and turned into some sort of narrative description of what happened. Continue reading “Friendfeed, lifestreaming, and workstreaming”
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. 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, University of Bangor, Wales, after meeting up the previous day; Continue reading “Open Science in the Undergraduate Laboratory: Could this be the success story we’re looking for?”
I received the rejection letter late last week but hadn’t got as far as posting about this yet. Given the referee’s comments this was not surprising. We were ranked 20 out of 21 proposals that were considered by the panel. This is not nearly so bad as it sounds. The story as that there were over a hundred proposals so to actually get to the panel wasn’t a bad thing in its own right. The other positive thing to take from this is that the referee’s comments were very clear about what the problems were: too much discussion of the type of things we would like to do, and not enough about how we would get more people involved, or how we would disseminate information. Basically it wasn’t focussed well as a Network application, which is not suprising in light of the fact that I had never been involved in one before so I didn’t really know what is was ‘supposed’ to look like.
We are allowed the resubmit the grant in six months time and I would be inclined to do so. The original proposal document as well as the final submitted version (there are significant differences – I needed to cut a lot to make it fit) is still available for viewing or editing and it ought to be possible to re-jig it over the next six months in light of the referee’s comments.
p.s. Am using Zemanta which looks potentially like a great tool in principle for getting more consistency into the use of tags and linking the information up. Something I am very much in favour of. However it appears to have decided that this post is about Volkswagens. Go figure.
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. 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 (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.
Frank Gibson has continued the discussion that kicked off here and has continued here [1, 2, 3, 4] and in other places [1, 2] along the way. Frank’s exposition on using FuGE as a data model is very clear in what it says and does not say and some of his questions have revealed sloppiness in the way I originally described what I was trying to do. Here I will respond to his responses and try to clarify what it is that I want, and what I want it to achieve. I still feel that we are trying to describe and achieve different things, but that this discussion is a great way of getting to the bottom of this and achieving some clarity in our description and language. Continue reading “Data models for capturing and describing experiments – the discussion continues”