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Posts tagged ‘informatics’

Weekly reading: NGS technology and inference challenges in review

Summary of Weekly Discussion papers read last semester (Fall 2014) on Next-Generation Sequencing methods and related phylogenomic inference challenges. With a few diversions in between. In chronological sequence.

  1. Barker. 2014. Philosophy of statistical phylogenetic methods.
  2. Witteveen. 2014. Naming and contingency: the type method of biological taxonomy.
  3. Lemmon & Lemmon. 2013. High-throughput genomic data in systematics and phylogenetics.
  4. Mardis. 2013. Next-Generation Sequencing platforms.
  5. Bybee et al. 2011. Targeted Amplicon Sequencing.
  6. Lemmon et al. 2012. Anchored Hybrid Enrichment.
  7. Kumar et al. 2012. Statistics and truth in phylogenomics.
  8. Wright & Hillis. 2014. Bayesian analysis outperforms parsimony for morphological data.
  9. Nguyen et al. 2012. Intermittent evolution and robustness of phylogenetic models.
  10. Schwartz et al. 2014. SISRS – Site Identification from Short Read Sequences.
  11. Narechania et al. 2012. RADICAL – Random Addition Concatenation Analysis.
  12. Philippe et al. 2011. Why more sequences are not enough.

We had some fun discussions. Topic for Spring 2015: Phenotype Ontologies.

New publication: Symbiota software platform

With lead author Corinna Gries of the University of Wisconsin, two Franz Lab members have a new publication in the Biodiversity Data Journal reviewing the Symbiota software platform. Symbiota has become popular with a broad range of North American collections networks and is gaining support in Central America as well.

Citation:

  • Gries, C., E.E. Gilbert & N.M. Franz. 2014. Symbiota – a virtual platform for creating voucher-based biodiversity information communities. Biodiversity Data Journal 2: e1114 (24 Jun 2014). doi: 10.3897/BDJ.2.e1114. Link to Open Access publication.

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ETC and Euler meeting at University of Arizona

Lead members of the Exploring Taxon Concepts (ETC) and Euler projects held a joint workshop at the School of Information Resources and Library Sciences (SIRLS) at the University of Arizona on February 19-20, 2014. On the meeting agenda were mutual updates, project coordination, and the formulation of detailed user scenarios for ETC tools; including: taxon-character matrix generation, matrix review, multi-entry interactive identification key generation, taxon concept similarity comparison, taxonomic revision support, and ETC/Euler interfaces and workflow integration.

Shown on the group photo, from left to right: (sitting) Lorena Endara, Hong Cui (ETC PI), Heather Cole, and Elvis Yu; (standing) Nico Franz, Bertram Ludäscher (Euler PI), James Macklin, Joel Sachs, Robert Morris, Thomas Rodenhausen, and Shizhuo Yu. 

SCAN presentation video at the iDigBio Education & Outreach Workshop

Neil Cobb presents a SCAN progress update at the 2014 iDigBio Education & Outreach Workshop. Watch all of iDigBio’s Vimeo uploads here: https://vimeo.com/idigbio

Southwest Collections of Arthropods Network – Neil Cobb from iDigBio on Vimeo.

TDWG 2013: Crowd sourcing and community management capabilities with Symbiota

Presentation sequence in development for the following TDWG 2013 presentation: Franz, N., C. Gries, T. Nash III & E. Gilbert. 2013. Crowd Sourcing and Community Management Capabilities Available within Symbiota Data Portals.

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A RDF primer for biologists by Steven Baskauf

Steven Baskauf of the TDWG-RDF Task Group has produced an easy to understand and rather artistic primer to understanding RDF (Resource Description Framework), a W3C Standard for describing web-based resources in ways legible to both humans and machines. More on the role of RDF in the greater Semantic Web Architecture “stack” is available here.

Using SCAN to construct a virtual checklist and key

Presentation Notes for the Arthropod Biodiversity Sessions held on September 19, 2013, at the 12th Biennial Conference of Science and Management on the Colorado Plateau, Northern Arizona University.

Using SCAN to Construct an Arthropod Checklist – Preliminary Insights from the “Weevils of North America” Project

Nico Franz, Michael Shillingburg & Sarah Shirota Read more

New Biodiversity Data Journal: Readable by humans and machines

A new, innovative Biodiversity Data Journal has been created in association with Pensoft Publishers, a company whose thematic vision and entrepreneurial and technical savvy jointly represent one of the most significant steps into the future of biodiversity informatics made over the past decade. Read more about the Journal’s agenda and platform in the inaugural paper.