GeneSeqToFamily.zip

Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br

COPO - A Web Platform for "FAIR" Data in Plant Science

Poster on COPO presented at BOSC 2017 (Prague

COPO - Bridging the Gap from Data to Publication in Plant Science

<p>COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories and to facilitate links to data analysis platforms. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces.</p

Additional file 1: of CerealsDB 3.0: expansion of resources and data integration

This file contains an initial web services request to CerealsDB in JSON, with the JSON response from CerealsDB containing a list of the services that the CerealsDB site provides (currently a Contig service and Search service). An example user query is also provided. (DOCX 560 kb

Evaluation of Ebola Virus Inhibitors for Drug Repurposing

A systematic screen of FDA-approved drugs was performed to identify compounds with in vitro antiviral activities against Ebola virus (EBOV). Compounds active (>50% viral inhibition and <30% cellular toxicity) at a single concentration were tested in dose–response assays to quantitate the antiviral activities in replication and viral entry assays as well as cytotoxicity in the Vero cell line used to conduct these assays. On the basis of the approved human dosing, toxicity/tolerability, and pharmacokinetic data, seven of these in vitro hits from different pharmacological classes (chloroquine (CQ), amiodarone, prochlorperazine, benztropine, azithromycin, chlortetracycline, and clomiphene) were evaluated for their in vivo efficacy at a single dose and were administered via either intraperitoneal (ip) or oral route. Initially, azithromycin (100 mg/kg, twice daily, ip), CQ (90 mg/kg, twice daily, ip), and amiodarone (60 mg/kg, twice daily, ip) demonstrated significant increases in survival in the mouse model. After repeat evaluation, only CQ was found to reproducibly give significant efficacy in the mouse model with this dosing regimen. Azithromycin and CQ were also tested in a guinea pig model of EBOV infection over a range of doses, but none of the doses increased survival, and drug-related toxicity was observed at lower doses than in the mouse. These results show the benefits and specific challenges associated with drug repurposing and highlight the need for careful evaluation of approved drugs as rapidly deployable countermeasures against future pandemics

Publications.

Peer-reviewed research citing the use of resources from the iPlant Collaborative (2008–2017) and CyVerse (2017-Present). Also see https://cyverse.org/publications for the latest update. (PDF)</p

Version control.

Public and private version control organizations on GitHub and GitLab for CyVerse Software, Public Container Registry, and Education. (PDF)</p

University of Arizona hardware.

On-premises resources maintained by CyVerse at the University of Arizona. DE = Discovery Environment, VICE = Virtual Interactive Compute Environment. (PDF)</p

DE applications.

How they run, where they run, and popular applications. (PDF)</p

Glossary.

Frequently used abbreviations and acronyms with descriptions. (PDF)</p