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Allyson Lister
Works at University of Manchester
Attended Newcastle University
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Allyson Lister

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Paper submission for the 10th Annual International Symposium on Integrative Bioinformatics has been extended until 3rd March 2014.

Please note that full papers will appear in a special edition of the Journal of Integrative Bioinformatics: http://journal.imbio.de/.
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Allyson Lister

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Deadline to apply for our PhD position on "Systems Pharmacology Models of Druggable Targets and Disease Mechanisms"
is Friday http://lenoverelab.org/jobs Funding is a BBSRC CASE fellowship with GSK
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Allyson Lister

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Have you ever wanted to play with a properly large graph database? How about one which scales linearly for writing new entities, even over millions of such entities?

In a previous post (http://themindwobbles.wordpress.com/2013/02/20/epigenomic-data-integration-with-graphs-a-beginning/), I talked about what kind of visualizations would make sense for large-scale epigenomic and related data. In today's post, I introduce the kind of data structures we’re developing in the Newcastle ARIES project to support the creation of such visualizations.
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Allyson Lister's profile photoTrish Whetzel's profile photo
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Just in general and then how this might relate to other prjects like Bio2RDF, NIF, etc.
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Allyson Lister

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The article says a version of #Ubuntu suitable for #Android phones will come out next month. At work, I use Ubuntu exclusively, but am both excited and not so sure of its use in a phone. Still, it's a groovy home screen :-) Anyone have any inside information?
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Michal Galdzicki's profile photoAllyson Lister's profile photo
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I think they were saying any android phone - so the same price as most phones, I guess? :)
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Allyson Lister

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So glad that FiveThirtyEight (http://fivethirtyeight.blogs.nytimes.com) has done well since the last election, going from a self-run blog to a NY Times blog. He has some fanatastic graphics there, visible at-a-glance on the right side, and more in-depth in the blog posts themselves.
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Madelaine Gogol's profile photoPeter Billing's profile photo
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I just started his book, and it sounds interesting so far... http://www.amazon.com/The-Signal-Noise-Predictions-Fail-but/dp/159420411X
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Have her in circles
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Allyson Lister

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Join us at the 10th Annual International Symposium on Integrative Bioinformatics, 12th - 14th May 2014 at Newcastle University http://www.imbio.de/ib2014/
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Mykola Aleshchanov's profile photoAllyson Lister's profile photoDaniel Swan's profile photo
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Ah yes hadn't noticed that! :)
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Allyson Lister

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"Two clichés of science journalism have now played out around the ENCODE project. ENCODE’s publicity first presented a misleading “all the textbooks are wrong” narrative about noncoding human DNA. Now several critiques of ENCODE’s narrative have been published, and one was so vitriolic that it fueled “undignified academic squabble” stories that focused on tone more than substance. Neither story line does justice to our actual understanding of genomes, to ENCODE’s results, or to the role of big science in biology."
HT +Eamonn Maguire

I suppose it shouldn't be surprising that these projects, which are very useful in themselves, fall over a bit on the spin doctoring. Are scientists really very adept at such things anyway? I suppose people spin their work because they feel it is necessary to continue funding - so, is it possible for funding agencies to understand the inherent worth of big experiments like ENCODE without requiring a "change in human understanding" to go along with it?
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I call this the "poverty of storicism" (sorry for butchering English) - a belief that  the  ultimate product of a scientific study is a "story" - something that gives us that a-ha moment, something that can be published in  Nature and be quoted by NYT, something we can relate to. The truth is these stories are becoming increasingly sparse as we dwell further into the clockwork of the cell. You would not expect to get exciting stories that everyone can relate to out of reverse engineering a cpu, why do we expect it from a cell? It does not mean that profiling and reconstructing a model of it is useless -- data is the product in that case not the story. But that's not how grant agencies, old-school reductionist biologists and general public perceives it. And stories are what the heads of these large projects try to deliver - in sometimes what looks like a desperate heroic effort often at the cost of integrity of the project they are leading.
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Allyson Lister

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If you are planning on traveling to ICBO/DILS/CSWS, you may want to consider submitting to and attending the Workshop on Semantic Systems Biology organized by the amazing +Dagmar Waltemath and +Michel Dumontier 
All submission are due on Monday, April 15 2013.
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Allyson Lister

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I've been working on some interesting ideas surrounding graph (i.e. nodes and edges) data integration for epigenomic and related data: http://wp.me/p1luY-mt . This overlaps in some ways with my (research) love of ontologies (a node-and-edge structure is one way to view OWL ontologies, for example).

We've been playing around with various visualization libraries such as the Gephi toolkit (https://gephi.org, they have a GUI and a STK) and D3JS (http://d3js.org/, a javascript library that looks super shiny). I'd love to hear your views on visualization of this kind of data!
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Jim Procter's profile photoAdam Leadbetter's profile photoWilliam Longabaugh's profile photoAllyson Lister's profile photo
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OK thanks - will try that :)
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Allyson Lister

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Does +Darren Wilkinson have a comment on this? :-)
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Incidentally, you might be interested in this criticism of the cartoon from a Bayesian: http://andrewgelman.com/2012/11/16808/ and possibly also this response from a frequentist: http://normaldeviate.wordpress.com/2012/11/09/anti-xkcd/ 
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Over the summer I spent 3 months working with the Software Ontology (SWO) with Robert Stevens and +Duncan Hull. It was great fun, and I hope I can continue the work at some point in the future. We updated it, and began the merging procedure with EDAM. EDAM and SWO are two really useful ontologies which share a reasonable amount of concepts, and could (I believe) be even better once they're aligned.

Merging/aligning ontologies is tough, especially when the majority of the overlap is near, but not complete matches. However, it is really rewarding as ultimately, I think that many ontologies in the bioinformatics community contain a decent amount of overlap. Sure, efforts such as the OBO Foundry try to limit such overlap, but in practice it occurs.
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Good to hear about this work
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People
Have her in circles
7,805 people
Work
Occupation
Ontologist
Employment
  • University of Manchester
    Ontologist, 2012 - present
    Part time work modifying the Software Ontology.
  • Newcastle University
    Research Asssociate, 2012 - 2014
  • Newcastle University
    PhD Student, 2006 - 2012
  • CISBAN, Newcastle University
    Research Associate, PhD Student, 2006 - 2011
  • European Bioinformatics Institute
    Senior Programmer, 1999 - 2006
Basic Information
Gender
Female
Story
Introduction
Interests include ontologies, data integration, systems biology, bioinformatics in general, and science news.

You can find more information about my research and my work interests at http://themindwobbles.wordpress.com

Help me to circle you correctly!
Education
  • Newcastle University
    Systems Biology / Computing Science, PhD, 2006 - 2012
  • University of York
    Biological Computation, MSc, 1998 - 1999
  • Rice University
    Biology / Ancient Mediterranean Civilizations, B.A., 1993 - 1997