About

Yes, it is a weak pun on “the mind boggles”… And also a reference/homage to the Weebles (weebles wobble but they won’t fall down): the mind wobbles, but it won’t fall down.

You can also find me on Google+, FriendFeed, Twitter, and SlideShare.

Short Version: My name is Allyson Lister and I’m currently working part time with Newcastle University. I completed my PhD from Newcastle University in early 2012. You can read my PhD thesis on this blog, as I’ve converted the Latex to a WordPress-friendly format.

In 2012 I spent a few months working part time on the Software Ontology as an ontologist with the University of Manchester. Until March 2011, I was also a Research Associate with CISBAN, also at Newcastle University. Before that, I spent 6 1/2 years at the EBI working on UniProt. Prior to the EBI, I received my undergraduate degree in Biology (with a second major in Ancient Mediterranean Civilizations) at Rice University, and received a MSc in Bioinformatics from the University of York.

Long Version:

Having originally left WordPress in 2007 for the short-lived Vox platform, I’ve now moved my posts and myself back.

Here’s some information about the sort of thing I post about here:

  • data integration: It is the main focus of my research, and one of the biggest challenges facing bioinformatics and the life sciences in general. So many formats, so little time! Reconciling these using brute force, standardisation, semantics, and sneakiness are what it’s all about.
  • ontologies: I like ontologies for many reasons, not the least their potential for reconciling the many different ways of defining and naming things in our lives. We need a common ground from which to perform successful integration and analysis, and I think a well-written ontology (or set of them) is a beautiful thing. They are a major tool in my research bag of tricks. Not only that, but I have also helped develop a community-driven ontology for describing life-science experiments (OBI). I have consulted on or helped develop a number of other ontologies in the bioinformatics community such as the Software Ontology.
  • workshops: my method of remembering what goes on in workshops and conferences is to take notes, and I can be a pretty fast typist. I enjoy blogging on each lecture at such an event as they happen, and you’ll notice a lot of workshop and conference posts on this site. They are mainly written while the speaker is speaking, with a minimum (if any) of later editing. However, if any speaker reads my notes and would like to suggest areas where I made a mistake, I am more than happy to make those sorts of changes. One of my favourite ways of blogging.
  • systems biology: that’s the field in which my bioinformatics research is applied, which makes it an immediately-applicable tag for this blog. But try to define it and, as with so many things in this world, you could get as many definitions as there are people. (OK, perhaps a slight exaggeration for dramatic effect.) So, I’ll not try to define it today, and just say that my posts often deal with work in this field.
  • science outreach: My Mom is a teacher, my Dad was a teacher and remains working in Education. If it wasn’t so much hard work, I’d consider it as a career myself. :) However, I do enjoy trying to pass on my enjoyment of and interest in the sciences. Some of my posts talk about the work I did doing with the Teacher Scientist Network. More recently, I’ve become a STEM Ambassador. Outreach is just fantastic, especially when explaining science to kids, and it’s something I like to talk about in this site, when the opportunity arises.
  • standards: Perhaps it’s because I spent years working at the EBI, where they provide databases and services in specific syntaxes. Perhaps it’s just the way my personality is. Whatever the reason, I really enjoy working with data standards. I’ve been involved with a few efforts (including FuGE, OBI, SBML, SBO, and MIGS) to varying degrees. I’m a bit of a standards fiend, and try to remind myself that not everyone finds them as interesting (though everyone should at least find them relevant!).

Please note that this blog, unless otherwise stated, reflects only my opinions. In any case, any errors in these pages are all my own!

Creative Commons License
The Mind Wobbles Blog by Allyson Lister is licensed under a Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License.

I also contribute to Ontogenesis, and write for biosharing.org and the ISCB blog.

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