24.04.2014 BiolDiv

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Meeting 24 April 2014, 10:00 am

Google Hangout

Present: Fabio, Nicolas, Casey, Edward, Anton, Gianpaolo



BiOnym paper

  • Review of various papers collected by Edward and Anton.

In particular Boyle et al. 2013 in BMC Bioinformatics about a taxon nema matching they developed for plants.

Apparently a mix between the GNI parser, and the Tony's Taxamatch. To explore if there are improvements over Taxamatch or if it is only an effect of linking GNI parser + Taxamatch.

  • Finish section 2 and 5 for the next week call (Edward, Nicolas, Fabio).
  • Comparison with same systems in other domain, e.g., vessel names.
  • GP to modify section 3 and 4.
  • Intro of section 3.5: It is the restricted matching running process workflow, not the overall BiOnym conceptual workflow, so can be kept here.
  • Complete the point 5.6 in the discussion about how we evaluated the performance (Edward). But still to evaluate if not better in 4.4.
  • Discussion on details of reporting (to complete if necessary).
  • Section 4: 3 paragraphs as section 3.4 (GP or Edward).
  • Should we move the paragraph on parser comparison to discussion? To be evaluated (Fabio).

User Interface

  • Machine set up in CNR but there is an issue about MySQL 5.6 comparatively to 5.5. Should be running on Friday 25.
  • Is it Apache or TomCat? Casey has to explore what is the best. CNR will install Apache, and explore if TomCat can be also on the same machine.

Next meetings

Friday 02 May 2014, 10:00 am European time.

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