13.06.2014 BiolDiv

From IMarine Wiki

(Difference between revisions)
Jump to: navigation, search
(Created page with "'''Meeting Friday 13 June 2014''' Present: Fabio (until 10:40), GP, Nicolas, Casey, Edward. ==Notes== ===WPS=== * OGC protocol: specifications for processing. Used by Terradue...")
 
Line 10: Line 10:
* Developed for BiOnym asking to Taverna staff to check for coherence. Some adjustment were necessary but works now for Taverna workflow.
* Developed for BiOnym asking to Taverna staff to check for coherence. Some adjustment were necessary but works now for Taverna workflow.
* To be used by FishBase in August 2014 version. To be compared with the call of API in the Statistical Manager.
* To be used by FishBase in August 2014 version. To be compared with the call of API in the Statistical Manager.
-
* Catalogue of WPS services available in the infrastructure: [[http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities]http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities] which is read by WPS indexing engines.
+
* Catalogue of WPS services available in the infrastructure: [[http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities]http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities] which is read by WPS indexing engines. More information on the syntax in http://wps.statistical.d4science.org/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&Identifier=org.gcube.dataanalysis.statistical_manager_wps_algorithms.generated.Bionym_local
* Index BiOnym in MyExperiment for Taverna users after one week to let Anton, Edward and Nicolas checking the political issues to be indexed in MyExperiment.
* Index BiOnym in MyExperiment for Taverna users after one week to let Anton, Edward and Nicolas checking the political issues to be indexed in MyExperiment.
-
* Ask Tony Rees, Yde de Jong, GBIF people, more? to check the interface (Nicolas, Edward).
+
* Ask Tony Rees, Yde de Jong, GBIF people, more? to check the interface (Nicolas, Edward; 'more' could include Dima, Rod Page, BioVel).
Line 29: Line 29:
* Discussion on most likely journals (expensive options like PLosOne discarded):
* Discussion on most likely journals (expensive options like PLosOne discarded):
** Biological paper: target Biodiversity Informatics (Nicolas to check BioMed journals).
** Biological paper: target Biodiversity Informatics (Nicolas to check BioMed journals).
-
** Informatics paper: target Ecological modelling (less Ecography).
+
*** More spin-off papers are possible targeted at specific sub-communities; e.g. a paper demonstrating the use of BiOnym in Ecology/Biogeography for  Ecological Informatics (http://www.journals.elsevier.com/ecological-informatics/) or Ecography (http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291600-0587); or a paper demonstrating the use of BiOnym for BioInformatics/sequence analysis
 +
** Informatics paper: not clear what such a paper would describe apart from the GCube infrastructure; needs some thinking.

Latest revision as of 13:55, 13 June 2014

Meeting Friday 13 June 2014

Present: Fabio (until 10:40), GP, Nicolas, Casey, Edward.

Contents

Notes

WPS


BiOnym Interface

  • Ticket sent by Fabio.
  • Casey replied Friday morning and uploaded the corrections as version 5 (another subversion to be sent by Casey after integration of 2 matchers by default, see below).
  • Just an issue on double quotes around scientific names to be fixed.
  • Decision on matchers by default: GSAy first, TriGrams second. Let's start with that default and test.
  • Computing capacity for BiOnym: 16 synchronous requests are possible. Should be enough even if there are heavy requests (big files, several TAFs).


Paper

  • Integration of latest corrections.
  • Submission to day.
  • Few days for light review by CNR publishers and then published.
  • Discussion on most likely journals (expensive options like PLosOne discarded):


Next meeting

Friday 20th June 2014, 10 am, changed from Thursday due to Holiday (again!) in the Philippines on 19th.

Personal tools