24.04.2014 BiolDiv

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==BiOnym paper==
==BiOnym paper==
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*Review
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* 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==
==User Interface==
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* Casey succeeded to make it work on her own computer.
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* Machine set up in CNR but there is an issue about MySQL 5.6 comparatively to 5.5. Should be running on Friday 25.
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* However, she encountered difficulties to compile it in one of the FB/SLB mirror server in UBC, Vancouver, Canada ([[http://fishbase.ca/imarine/BionymPortlet.html]]). So we can see the interface and select the options, but we cannot submit.
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* It seems that there was a confusion about this installation on .ca: FIN used that server for testing, but the interface was never thought to be installed outside the D4Science/iMarine infrastructure. Since the beginning, the goal was to develop a portlet that would be incorporated in the Biodiversity Research VRE, to complement the two data exploration tools on species and point data, and to serve the alert workflow between TAFs and various aggregators.
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* Is it Apache or TomCat? Casey has to explore what is the best. CNR install Apache, and explore if TomCat can be also.
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* Casey developed the application as a tool for the infrastructure, with the technologies recommended by CNR, not as an application for FIN servers. Indeed, the first developments were made on FishBase website but it was merely for [prototyping, and develop the GSAy approach.At the beginning, the collaboration with Fabio using his environment was not planned.
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* After discussion posterior to the meeting, having the interface outside would allow it to be accessible without registration in the BR VRE.
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* However, Leo stressed the point that having a dedicated BiOnym VRE would make the activity and product more visible, and would not prevent to use the same portlet in the BR VRE. It could be made available without registration then? (I suppose in that case, people will have to save the result on their own computer).
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* GP proposed the plan for implementation.
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** 3 phases for the application implementation>
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** Phase 1
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*** Create a virtual server in CNR (?) where the application could be deployed as it is.
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*** Start with one word entry, then uploading a csv file.
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** Phase 2
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*** Embed the interface of that server in the infrastructure.
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*** But as far as possible FIN would like to skip that one. Only if there is urgency for presentations or else.
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** Phase 3
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*** Develop the interface as a portlet.
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*** Create the BiOnym VRE (can be done asap).
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*** Put the portlet in production in BiOnym and BR VREs.
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=Next meetings=
=Next meetings=
Thursday 17 April 2014, 11:00 am European time for discussion on the paper.
Thursday 17 April 2014, 11:00 am European time for discussion on the paper.

Revision as of 08:55, 24 April 2014

Meeting 24 April 2014, 10:00 am

Google Hangout

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


Contents

Notes

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 install Apache, and explore if TomCat can be also.

Next meetings

Thursday 17 April 2014, 11:00 am European time for discussion on the paper.

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