Duncan Hull

Graffiti artist or blogger? - Duncan Hull

He's not without his critics: http://news.bbc.co.uk/1... - Neil Swainston

@Neil its those pesky graffiti "artists" getting their revenge - Duncan Hull

Computerworld - The meet-up in San Francisco last month had a whiff of revolution about it, like a latter-day techie version of the American Patriots planning the Boston Tea Party. The inaugural get-together of the burgeoning NoSQL community crammed 150 attendees into a meeting room at CBS Interactive. Like the Patriots, who rebelled against Britain's heavy taxes, NoSQLers came to share how they had overthrown the tyranny of slow, expensive relational databases in favor of more efficient and cheaper ways of managing data. - Duncan Hull

Biocatalogue.org, a centralised registry of curated life science Web Services, is being officially launched today (Wednesday 1 July) at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology conference (ISMB-ECCB 2009) in Stockholm. This type of systematic access has the potential to significantly accelerate the work of researchers in the medical, agronomical and pharmaceutical fields. The service allows researchers to discover, annotate, register and use biological web-based services. Biocatalogue.org already has around 1,000 biological Web Services – and more and more will be registered and annotated by services providers, curators and users on a daily basis. - Duncan Hull

A very simple little hierarchy view that filters out the top level deprecated classes using a set of extensions to Protege that make it easier for OBO ontology developers to find their way around and edit OBO ontologies in OWL. In the OBO2OWL translation obsoleted terms have no parents and are marked with an annotation to say that they have been deprecated. This means they can get in the way when tools don't take them into account. - Duncan Hull

It's much better to go for the thing that's exciting. But the question of how you know what's worth working on and what's not separates someone who's going to be really good at research and someone who's not. There's no prescription. It comes from your own intuition and judgment. - Duncan Hull

Well, it turns out I'm not descended from Genghis Khan. I'm sure that's as surprising to you as it is to me. I mean, according to what we hear from people who use genomics to track human migrations, a huge percentage of the human race is actually descended from Genghis Khan. But not me. - Duncan Hull

quote "Science is a gift economy; value is defined as the degree to which one's ideas have freely contributed to knowledge and impacted the thinking of others. " - Duncan Hull

Summary: The Systems Biology Markup Language (SBML) is an established community XML format for the markup of biochemical models (Hucka et al., 2003). With the introduction of SBML level 2 version 3, specific model entities, such as species or reactions, can now be annotated using ontological terms. These annotations, which are encoded using the resource description framework (RDF), provide the facility to specify definite terms to individual components, allowing software to unambiguously identify such components and thus link the models to existing data resources (Kell & Mendes, 2008). libSBML (Bornstein et al., 2008) is an application programming interface library for the manipulation of SBML files. While libSBML provides the facilities for reading and writing such annotations from and to models, it is beyond the scope of libSBML to provide interpretation of these terms. The libAnnotationSBML library introduced here acts as a layer on top of libSBML linking SBML annotations to the... more... - Duncan Hull

MOTIVATION: In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customized for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex... more... - Duncan Hull