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Allyson Lister
Works at University of Oxford
Attended Newcastle University
7,861 followers|178,060 views
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Very interesting user experience when trying to browse a few entries from the NAR database issue. As I've just started at BioSharing.org, it makes me think - just what would you all want in a standards and database registry? What would make you give full points to any particular entry? Yes, working URLs are a big thing, but what would the killer feature be for you? Examples, high numbers of cross references, contact points for owners of the entries? Please let me know! HT +Alejandra Gonzalez-Beltran 
Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened?  Did people quit making databases?  No.  This year, the “dead” databases (links no longer valid) outnumber the new ones. To celebrate Digital World Biology’s release of Molecule World I’ll discuss some of the new structure databases…
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Allyson Lister

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University of Oxford Job Opportunity: Research Software Engineer - Java, Python, Web-app, Database, Semantic-web

In this varied, interesting and challenging role the successful candidate will provide technical knowledge, software engineering and leadership ability for (i) a growing portfolio of data and knowledge management projects - including the ISA software suite (http://isacommons.org), the BioSharing registry (http://biosharing.org) - funded by UK, EU and NIH Big Data to Knowledge Initiative, and (i) activities for the ELIXIR UK node (http://elixir-uk.org) of the ELIXIR programme.

Job title: Research Software Engineer
Location: University of Oxford, Oxford e-Research Centre, 7 Keble Road, Oxford, OX1 3QG, UK
Contract type: 3 years fixed term, in the first instance (salary range £30-40k, or according to experience)

Details on how to apply, link to application form and detailed job description at: http://tinyurl.com/myxa7ux
The website for isacommons.org can be found by clicking here. isacommons.org is registered through Easily.co.uk - get web site hosting or domain name registration here.
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We're organizing a biological data visualization course in November 2015. So please spread the word, and register for updates at http://bit.ly/datavizcourseleuven
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Segway's entry into SWO - +Michael Hoffman , please let me know if you wish a more precise assertion for any of the axioms present below...
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Updated all except output files - will post a new pic once I've included those tomorrow-ish. All in SVN though if you were interested ;) https://sourceforge.net/p/theswo/code/HEAD/tree/trunk/dev/ontologydev/
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What bioinformatics software would you consider a "must have" for a software ontology? Tell me and if it's not already in, I'll add it this week! :) http://softwareontology.wordpress.com/
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It's added in the latest development version, without a reference to the owning organization, as I wasn't sure what you wanted that to be? The Hoffman lab? A particular organization or group? To look at your software in OWL, you need to download *.owl from https://sourceforge.net/p/theswo/code/HEAD/tree/trunk/dev/ontologydev/ (It'll be in a nicer format with the next point release in the next week or two.
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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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Just started working with +Susanna-Assunta Sansone and her group on http://www.biosharing.org. As always, happy to chat about biological data standards - and now I'm back working in them too! https://themindwobbles.wordpress.com/2015/02/03/back-into-data-standards-with-biosharing/
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Welcome Allyson!
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Good morning all! I've been taking a look at ImpactStory (http://impactstory.org) and wondering if it's worth paying for. What do I get there that I don't get currently through 1) google scholar, 2) (the slightly odd) microsoft academic search, 3) linked in 4) research gate etc., all of which I get for free and to which I am already subscribed.

This of course leads to the bigger question of how many places do we need to maintain our research identity? Via my work persona, I do like to be available to other researchers interested in the same area of work, and therefore I am willing to maintain a number of social media outlets such as those above. However, where do we stop signing up for such things, and how do we know what's working best for us with respect to reaching out to the community of like-minded researchers?

Your thoughts would be most appreciated - thanks!

1. http://scholar.google.co.uk/citations?user=3gIIMLsAAAAJ&hl=en
2. http://academic.research.microsoft.com/Author/3762141
3. http://www.linkedin.com/profile/view?id=3123595
4. https://www.researchgate.net/profile/Allyson_Lister
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Updated Segway 1.2 ontology entry in the #softwareontology. +Michael Hoffman , I've added all we discussed. I'm using "genome annotation" at the moment rather than "semi-automated genome annotation" - I'll add the latter once I've received an updated EDAM ontology from the EDAM folks - EDAM and SWO are merged, and that term is something more appropriate to their part of the hierarchy. Enjoy!
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+Stian Soiland-Reyes We will fix this in the New Year.
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Do you have what it takes? :)
 
SBML Editor nominations are now open! Submit your nominations by Dec. 8.
Drive
Nominating a new SBML Editor for 2015-2017This is a call for nominations for a new SBML Editor to replace one outgoing editor, Nicolas Le Novère, beginning in January 2015. The SBML Editor election process is described on the page at http://sbml.org/Documents/SBML_Development_Process/Election_of_SBML_Editors The SBML Editors play a key role in writing and developing SBML specifications. SBML Editors have to be willing to invest time and effort into evaluating proposals for changes, rese...
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Registration for HARMONY 2015 is open
The registration for HARMONY 2015 is now open. It will take place Mon. 20- Fri. 24 April 2015 at the Leucorea in Wittenberg, Germany.

HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. 
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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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Ah yes hadn't noticed that! :)
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People
Have her in circles
7,861 people
Jeremy McMillan's profile photo
David Hidding's profile photo
Matt Mullins's profile photo
Jinath Premaratne's profile photo
Dennis Humble's profile photo
STEFF EVANS's profile photo
Molly  Parker's profile photo
manoj kumar Krishnapillai's profile photo
Văn Thùy Liên's profile photo
Work
Occupation
Ontologist etc.
Skills
Biological data standards, semantic data, biological databases, ontologies
Employment
  • University of Oxford
    Knowledge Engineer, 2015 - present
    Development of the BioSharing.org project. http://www.biosharing.org
  • University of Manchester
    Ontologist, 2012 - 2014
    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, data standards, 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