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Posts from the ‘Member News’ Category

Future of taxonbytes, introducing BioKIC

An announcement. The taxonbytes website has seen minimal new content in the past 6-8 months. We now have an official successor for the blog, and effectively for much of the content presented here. taxonbytes will soon become dormant, but not taken off-line. Our new, more social, and more formally branded content will be presented here:

BioKIC – Biodiversity Knowledge Integration Center @ ASU

We hope that taxonbytes has been a source of valuable information to some, and thank everybody very profoundly for contributing and reading along. Nico Franz

Spring 2015 Collecting

In the desert, there doesn’t seem to ever be a bad time to collect. This spring has been no exception for the taxonbytes lab members!

Most entomological collecting in the southwest seems to be planned in accordance with the amazing monsoon activity that the area is known for. Even though there is still much to be discovered in the fauna that emerges after our summer rains, there is also a large fauna which is not associated with rains; in fact there are many species which exhibit late spring-early summer emergences which seems to be oddly uncommon in collections.

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New publication: Provenance for explaining taxonomy alignments

A short paper related to the Euler/X toolkit and concept taxonomy alignment project has been published. It deals with the issue of diagnosing inconsistent input constraints in an attempted pairwise taxonomy alignment, analyzing and visualizing their logical provenance so that the user can localize the inconsistencies and proceed towards repairing them. These logic services are already implemented in the toolkit.

Abstract. Derivations and proofs are a form of provenance in automated deduction that can assist users in understanding how reasoners derive logical consequences from premises. However, system-generated proofs are often overly complex or detailed, and making sense of them is non-trivial. Conversely, without any form of provenance, it is just as hard to know why a certain fact was derived. We study provenance in the application of Euler/X, a logic-based toolkit for aligning multiple biological taxonomies. We propose a combination of approaches to explain both, logical inconsistencies in the input alignment, and the derivation of new facts in the output taxonomies.

Chen, M., S. Yu, P. Kianmajd, N. Franz, S. Bowers & B. Ludäscher. 2015. Provenance for explaining taxonomy alignments. In: Ludäscher, B. & B. Plale (Editors), Provenance and Annotation of Data and Processes. Revised Selected Papers of the 5th International Provenance and Annotation Workshop, IPAW 2014, Cologne, Germany, June 9-13, 2014. Lecture Notes in Computer Science 8628: 258-260. Available on-line here.

Announcing the Sixth Annual Lepidoptera Course, 16–25 August, 2015

Held at the Southwestern Research Station (SWRS) in the Chiricahua Mountains in SE Arizona (a 2.5 hour drive from Tucson), the focus of the Lep Course 2015 (August 16-25, 2015) is to train graduate students, postdocs, faculty, state and federal employees, and citizen-scientists in the classification and identification of adult Lepidoptera and their larvae. Topics to be covered include the biology and systematics of major families of Lepidoptera, an introduction to adult and larval morphology with a focus on taxonomically important traits, extensive field work that concentrates on  both collecting and photographing adults and larvae, collecting and curatorial techniques, genitalic dissection, larval classification, use (and abuse) of DNA barcoding, and general topics in Lepidoptera systematics, ecology, and evolution.

With its extensive series of Sky Island mountain ranges, SE Arizona has the highest Lepidoptera diversity in the United States. With low desert scrub, oak and mixed oak-pine woodland, lush riparian, juniper, Douglas fir, and mountain meadow habitats – all within a 40 minute drive from the station – the SWRS is an ideal location from which to sample this diversity of both habitats and species.

If you want to interact with other Lepidoptera enthusiasts, see a spectacular Dysschema, identify the Organ of vom Rath, sort through trap samples with hundreds of species, learn about diversity of Lepidoptera, and enjoy the vistas of the SE Arizona, then this course will provide a unique experience.

Partial list of invited instructors (subject to change):

  • Richard Brown (Mississippi Entomological Museum)
  • Jennifer Bundy (RD4AG)
  • Chris Grinter (Illinois Natural History Survey)
  • Don Harvey (Smithsonian Institution)
  • Sangmi Lee (Arizona State University Hasbrouck Insect Collection)
  • Chris Schmidt (Canadian National Collection)
  • Bruce Walsh (University of Arizona)

For more information, see http://research.amnh.org/swrs/education/lepidoptera-course or www.lepcourse.org or contact Bruce Walsh at jbwalsh@u.arizona.edu. You can also see photos and comments from students in the 2011 course at their facebook site, “2011 Lep Course, SWRS SEAZ”.

New publication: Finding our way through phenotypes

Three members of the taxonbytes lab (Sal Anzaldo, Nico Franz, and former postdoc Aaron Smith) are co-authors of a new paper published in PLoS Biology: Finding Our Way through Phenotypes. Lead authors (in a large community effort) are Andrew Deans, Paula Mabee, and members of the Phenotype Research Coordination Network.

Deans, A.R. et al. (73 co-authors, including S.S. Anzaldo, N.M. Franz & A.D. Smith). 2015. Finding our way through phenotypes. PLoS Biol 13(1): e1002033. Link to publication

Abstract. Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today’s data barriers and facilitate analytical reproducibility.

EntSoc14 Twitter pride and joy


ECN 2014 and ESA 2014 in Portland have come and gone. Great meeting, and dare I say a new sense of togetherness via social media that can improve science communication, science itself.

Knowledge Representation in Systematic Biology – Edited book proposal seeking comments, contributions

I have an opportunity to edit a new book in the series “Species and Systematics” (originally UC Press; now CRC Press). The draft outline is below, but is subject to change and expansion as deemed appropriate.

I am looking for suggestions, and for potential contributors (naturally, while reserving standard/common sense rights to kindly accept or decline). The book will to collect a number of strong, diverse chapters on various projects and directions in this still very young field. Lead authors of chapters will coordinate with co-authors as preferred. I also intend to give authors much freedom to do and say things they maybe could not express using different publication outlets (while keeping things fair and high-minded).

Another key issue is (of course) – who may have time and motivation to contribute an original and impactful chapter in the coming six months? Either way, I am open to suggestions, contact me on- or off-line.

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Les Landrum Retirement Celebration at Alameda

On Friday, October 3rd, 2014, we celebrated the official retirement of ASU Vascular Plant Herbarium Curator Dr. Les Landrum. The event took place at the just inaugurated Alameda Building. Attendance of colleagues and students, and spirits, were high – a true and fitting celebration of Les’ broad impact on the Herbarium, Southwestern United States floristics, mentoring and collaboration, and plant systematics (Myrtaceae) and biodiversity informatics (SEINet) more generally.

DarwinGuavasLiz Makings led the excellent organization of the event and, by giving an entertaining and insightful overview of the honoree’s personality and career (up to now), expressed a depth of appreciation for Les and his work that was felt by all.

Needless to say, “retirement” is a relative term for Les, and we will be fortunate to rely on his presence and dedication to the Herbarium and collections group for years to come.

Some photos of the party and its diverse and inspired food offerings are posted here.

Thank you, Les.

LandrumRetirement2

Dr. Les Landrum surrounded by friends, colleagues, and students. October 3rd, 2014.