26 Works

Enhancing sUAS Data with Semantic Technologies

Jane Wyngaard, andrea thomer, Lindsay Barbieri, Beth Huffer & Sarah Swanz
ESIP sponsored Laboratories project Jan -July 2018 First steps in engaging with the community to build a draft Minimal Information Framework (MIF) See Gdoc proposal for more details

\"Don’t Go It Alone: Collaborating Across Institutions to Provide Bioinformatics Instruction\"

Alexander Carroll, Barrie Hayes & Danica Lewis
Poster presented at the 2017 MAC-MLA Annual Meeting on Oct. 23 in Staunton, VA.

Data from: Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons

Elizabeth A. Miller, Joshua A. Livermore, Susan C. Alberts, Jenny Tung & Elizabeth A. Archie
Background: The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals. Results: We used Illumina sequencing of the bacterial 16S rRNA gene to investigate...

Container Strategies for Data and Software Preservation Workshop

Michael Hildreth, Natalie Meyers, Sandra Gesing, Richard Johnson, Elisabeth Long, Jaroslaw Nabrzyski, Douglas Thain, Mark Suhovecky, Vicky Rampin, Ian Taylor, Charles Vardeman, Alexander Vyushkov, Reid Boehm, daniel brake, Donald Brower, Lincoln Bryant, Ryan Chamberlain, Euan Cochrane, Anita de Waard, Mandy Havert, Lukas Heinrich, Kolin Hodgson, Cole Hudson, Greg Janée, Maciej Malawski … & Charles Williams
A workshop organized by the DASPOS project, to be held 19-20 May 2016.


Margaret Berta, Marya Lieberman, Laura Salazar, Bonnie Hall, Corbin Zea, Nicholas Myers, Martin St. Clair, Toni Barstis, Sarah Bliese, Stephen Mang & Rusty Speidel
Distributed Pharmaceutical Analysis Lab

Intro Entrez Workshop

Alexander Carroll, Barrie Hayes & Danica Lewis
Instructional materials for Introduction to NCBI and Entrez Searching Workshop taught at UNC-CH and NCSU. First offered in March 2017.

Data from: Group living and male dispersal predict the core gut microbiome in wild baboons

Laura E. Grieneisen, Josh Livermore, Susan Alberts, Jenny Tung & Elizabeth A. Archie
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer...

Open Science Framework Interoperability

Natalie Meyers
An introductory talk at ESIP Summer Meeting 2017 on topic of Open Science Framework Interoperability to introduce the RMap Project

Data from: Environmental context and contaminant biotransport by Pacific salmon interact to mediate the bioaccumulation of contaminants by stream-resident fish

Brandon S. Gerig, Dominic T. Chaloner, David J. Janetski, Ashley H. Moerke, Richard R. Rediske, James P. O'Keefe, Dilkushi A. De Alwis Pitts & Gary A. Lamberti
1.The extent to which environmental context mediates the bioaccumulation of biotransported contaminants by stream-resident organisms is poorly understood. For example, it is unclear the extent to which contaminant type, instream characteristics, or resident fish identity interact to influence the uptake of contaminants deposited by Pacific salmon (Oncorhynchus spp.) during their spawning runs. 2.To address this uncertainty, we sampled four stream-resident fish species from 13 watersheds of the Laurentian Great Lakes in locations with and without...

Preservation of Corporate Information

Considering preservation before there is a need for preservation may be the next wave of corporate interest. While corporate interests often have to do with keeping up with Jones Co, preservation, I hope, will not suffer the same fate as other fads. Preservation of corporate information has multiple challenges: legal, real estate, bottom-line and out of date equipment required to access superseded formats. It does, however, also offer an element of content management that can...

Data from: Tales from the crypt: a parasitoid manipulates the behaviour of its parasite host

Kelly L. Weinersmith, Sean M. Liu, Andrew A. Forbes & Scott P. Egan
There are many examples of apparent manipulation of host phenotype by parasites, yet few examples of hypermanipulation—where a phenotype-manipulating parasite is itself manipulated by a parasite. Moreover, few studies confirm manipulation is occurring by quantifying whether the host's changed phenotype increases parasite fitness. Here we describe a novel case of hypermanipulation, in which the crypt gall wasp Bassettia pallida (a phenotypic manipulator of its tree host) is manipulated by the parasitoid crypt-keeper wasp Euderus set,...


Richard Hoffmann, Natalie Meyers & chelsea hoffmann

Data from: Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex

Marco Pombi, Pierre Kengne, Geoffrey Gimonneau, Billy Tene-Fossog, Diego Ayala, Colince Kamdem, Federica Santalomazza, Wamdaogo Moussa Guelbeogo, N'Falé Sagnon, Vincenzo Petrarca, Didier Fontenille, Nora J. Besansky, Christophe Antonio-Nkondjio, Roch K. Dabire, Alessandra Della Torre, Frederic Simard & Carlo Costantini
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms....

Center for Open Science: Response to ASAPbio RFA for a Preprint Service

Brian Nosek, Melanie Benjamin, Sara Bowman, Michael Haselton, David Litherland, Natalie Meyers, Nicole Pfeiffer, Andrew Sallans, Rusty Speidel, Jeffrey Spies & Matthew Spitzer
The Center for Open Science (COS) and technical partners propose to extend its open infrastructure to support ASAPbio's call for a central service. COS's approach is community based and is accompanied by letters of support from 12 preprint services (e.g., arXiv, bioRxiv, SocArXiv), 15 data repositories (e.g., Dryad, Protein Data Bank, figshare), and 5 other stakeholders (e.g., HHMI, Health Research Alliance, GBSI).

Reproducibility and the Open Science Framework

Natalie Meyers
Reproducibility and the Open Science Framework presentation for DataONE User Group Meeting July 25, 2017 in Bloomington, Indiana.

BLAST Workshop

Alexander Carroll, Barrie Hayes & Danica Lewis
Instructional materials for BLAST Workshop taught at UNC-CH and NCSU. First offered in November 2017.

Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...

Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Sean F. Ryan, Michaël C. Fontaine, J. Mark Scriber, Michael E. Pfrender, Shawn T. O'Neil & Jessica J. Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate...

OSF and Fedora

Richard Johnson, Sayeed Choudhury, David Wilcox, Jeffrey Spies, Aaron Birkland & Elliot Metsger
Johns Hopkins University, the University of Notre Dame, Duraspace, and the Center for Open Science have collaborated to create an integration between the OSF and Fedora to bring preservation into the active research lifecycle.

Data from: Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA

Kristy Deiner, Mark A. Renshaw, Yiyuan Li, Brett P. Olds, David M. Lodge & Michael E. Pfrender
As environmental DNA (eDNA) from macro-organisms is often assumed to be highly degraded, current eDNA assays target small DNA fragments to estimate species richness by metabarcoding. A limitation of this approach is the inherent lack of unique species-specific single-nucleotide polymorphisms available for unequivocal species identification. We designed a novel primer pair capable of amplifying whole mitochondrial genomes and evaluated it in silico for a wide range of ray-finned fishes (Class: Actinopterygii). We tested the primer...

Data from: Suitability of Laurentian Great Lakes for invasive species based on global species distribution models and local habitat

Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng & John M. Drake
Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model...

Reducing the curatorial bottleneck of data reuse: A role for cognitive computing?

Natalie Meyers
Reducing the curatorial bottleneck of data reuse: A role for cognitive computing? a lightning talk at ESIP Summer Mtg July 27 2017

Data from: Widespread position-specific conservation of synonymous rare codons within coding sequences

Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott J. Emrich, Patricia L. Clark & Scott Emrich
Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5’ terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare codons farther within coding sequences has not yet been established, several recent reports have identified rare-to-common synonymous codon...

NCSU Libraries and UNC-CH HSL Bioinformatics Workshops

Alexander Carroll, Barrie Hayes & Danica Lewis

Supporting Research Computing with Library Services

Natalie Meyers
ARL CNI Fall Forum 2017 Lightning Talk

Registration Year

  • 2017

Resource Types

  • Text
  • Dataset


  • University of Notre Dame
  • Notre Dame University
  • Center For Open Science
  • University of North Carolina at Chapel Hill
  • Rice University
  • University of Florida
  • Grand Valley State University
  • Binghamton University
  • Utah State University
  • University of Michigan-Ann Arbor