The iPlant Collaborative provides life science research communities access to comprehensive, scalable, and cohesive computational infrastructure for data management; identity management; collaboration tools; and cloud, high-performance, high-throughput computing. iPlant provides training, learning material, and best practice resources to help all researchers make the best use of their data, expand their computational skill set, and effectively manage their data and computation when working as distributed teams. iPlant's platform permits researchers to easily deposit and share their data and deploy new computational tools and analysis workflows, allowing the broader community to easily use and reuse those data and computational analyses.
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http://dx.doi.org/10.1371/journal.pbio.1002342 | DOI Listing |
Trends Plant Sci
February 2017
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA. Electronic address:
Cyberinfrastructure projects (CIPs) are complex, integrated systems that require interaction and organization amongst user, developer, hardware, technical infrastructure, and funding resources. Nevertheless, CIP usability, functionality, and growth do not scale with the sum of these resources. Instead, growth and efficient usage of CIPs require access to 'hidden' resources.
View Article and Find Full Text PDFBMC Bioinformatics
October 2016
Informatics Institute, University of Missouri, Columbia, MO, USA.
Background: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way.
View Article and Find Full Text PDFNat Plants
August 2016
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
Leaf thermoregulation has been documented in a handful of studies, but the generality and origins of this pattern are unclear. We suggest that leaf thermoregulation is widespread in both space and time, and originates from the optimization of leaf traits to maximize leaf carbon gain across and within variable environments. Here we use global data for leaf temperatures, traits and photosynthesis to evaluate predictions from a novel theory of thermoregulation that synthesizes energy budget and carbon economics theories.
View Article and Find Full Text PDFMol Biol Evol
September 2016
Plant Genome Mapping Laboratory, University of Georgia Department of Soil and Crop Sciences, Texas A&M University, College Station
Of central importance in adapting plants of tropical origin to temperate cultivation has been selection of daylength-neutral genotypes that flower early in the temperate summer and take full advantage of its long days. A cross between tropical and temperate sorghums [Sorghum propinquum (Kunth) Hitchc.×S.
View Article and Find Full Text PDFNat Plants
May 2016
Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P.
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