No specimen (software) left behind

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A short talk at the iEvoBio (Informatics for Phylogenetics, Evolution, and Biodiversity) conference at the The University of Oklahoma, Embassy Suites Hotel and Conference Center, Norman, Oklahoma, USA. June 21-22, 2011.

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No specimen (software) left behind

  1. 1. No specimen left behind A system for mass digitization at the Natural History Museum Vince Smith, Vladimir Blagoderov, Ian Kitching & Thomas Simonsen
  2. 2. Vince Smith No software left behind The Open Source requirement at iEvoBio
  3. 3. Rate of digitisation at the NHM 1400 YEARS to digitize the NHM’s 70 million specimens!
  4. 4. SatScan v.1 (by SmartDrive) 2010 system trials $$$ <ul><li>5 minutes scan time </li></ul><ul><li>5 minutes stitch time (batched) </li></ul><ul><li>Telecentric lens </li></ul>
  5. 5. Digitizing specimens
  6. 6. Report & recommendations http://precedings.nature.com/documents/4486/version/1 <ul><li>Objects >10mm usefully digitized </li></ul><ul><li>85k of 135k ent. draws usefully digitized </li></ul><ul><li>< 8 yrs, 1 person, 1 machine </li></ul><ul><li>Including draw level metadata </li></ul>
  7. 7. <ul><li>Key SatScan v.2 improvements </li></ul><ul><li>Higher resolution, 1,2 &4k dpi </li></ul><ul><li>( 3cm-5mm dpth; 300Mb- 4.8Gb ) </li></ul><ul><li>Z-axis (for image stacking) </li></ul><ul><li>Software setup wizard </li></ul><ul><li>Improved public offer </li></ul><ul><li>Metadata creator tool </li></ul><ul><li>Specimen cropping </li></ul>SatScan v.2 (by SmartDrive)
  8. 8. Resolution examples
  9. 9. The current workflow Not Open Source
  10. 10. The planned workflow Not Open Source
  11. 11. Recent non open-source software
  12. 12. Open source issues raised <ul><li>Is open-source a philosophy, or a pragmatic methodology? </li></ul><ul><li>But open-source does not guarantee the end-product, source-material, blueprints, and documentation available at no cost to the public </li></ul><ul><li>Arguably, open-source provides our informatics provenance </li></ul><ul><li>Open-source does not guarantee the longevity of software </li></ul><ul><li>Open-source is not (on its own) a business model </li></ul>
  13. 13. Questions for “ Birds of a feather ” <ul><li>Is there a case for non-open source software (and hardware) at iEvoBio? </li></ul><ul><li>If there is, how might we do this be done while incentivizing open source? (twin tracks, shorter talks?) </li></ul><ul><li>How to we create sustainable future for biodiversity informatics software? </li></ul>

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