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Posts tagged ‘software’

Weekly reading: Practical introduction to ontologies and OWL

This week we will try out Protégé and pizza ontologies. We will work through an updated version of this tutorial.

Weekly reading: RADICAL – Random Addition Concatenation Analysis

An interesting paper and powerful tool that cuts empirically through the longstanding and somewhat dispiriting total evidence ‘versus’ partitions discussion thread in our field.

Narechania, A., R.H. Baker, R. Sit, S.O. Kolokotronis, R. DeSalle & P.J. Planet. 2012. Random Addition Concatenation Analysis: A novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the Cyanobacteria. Genome Biology and Evolution 4(1): 30-43. Available on-line here.

Weekly reading: SISRS – Site Identification from Short Read Sequences

This week’s discussion will focus on a novel method to identify and separate signal from noise for Next-Generation sequencing datasets – SISRS.

Schwartz, R.S., K. Harkins, A.C. Stone & R.A. Cartwright. 2014. A composite genome approach to identify phylogenetically informative data from Next-Generation Sequencing. http://arxiv.org/abs/1305.3665

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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