The iPlant Collaborative: Cyberinfrastructure for Plant Biology

By S. Goff, M. Vaughn, S. McKay, E. Lyons, A. Stapleton, D. Gessler, Naim Matasci, Liya Wang, M. Hanlon, Andrew Lenards and 55 more. 2011

475 citations recorded by the source corpus.

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

Subfields: Information Systems, Information Systems and Management, Molecular Biology, ML Systems & Hardware, Computational Biology & Bioinformatics

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Citations in the corpus

Finely-grained annotated datasets for image-based plant phenotyping (2016, background): “Implementing in the future such tools in web-based environments would permit the crowd-sourcing of annotations (Kavasidis et al., 2014; Go ﬀ et al., 2011).”
Genome Annotation and Curation Using MAKER and MAKER-P (2014, methodology): “MAKER-P, which is available in massively parallel mode as part of the iPlant project (Goff et al., 2011), is even more powerful.”
Automated Identification of Northern Leaf Blight-Infected Maize Plants from Field Imagery Using Deep Learning. (2017, methodology): “Following this, all visible lesions were marked with a line down the main axis of the lesion using the annotation features of the Bisque image-processing platform hosted on CyVerse (formerly iPlant; Goff et al. 2011) (Figure 1).”
Data access for the 1,000 Plants (1KP) project (2014, background): “Significant in-kind contributions were provided by BGI-Shenzhen in the form of reduced sequencing costs and by the NSF-funded iPlant collaborative [1] in the form of computational informatics support.”
JBrowse: a dynamic web platform for genome visualization and analysis (2016, methodology): “These options can include fetching BAM, VCF, or GFF3 files from other sites; accessing ex-ternal REST APIs such as myvariant.info; or integration with platforms like CoGe or Araport, as implemented by iPlant [21].”
The taxonomic name resolution service: an online tool for automated standardization of plant names (2013, background): “Developed by the iPlant Collaborative [40] as a collaboration between the iPlant Tree of Life project [41] and the Botanical Information and Ecology Network [42], the TNRS standardizes names according to one or more authoritative taxonomic sources.”
Conducting a Microbiome Study (2014, methodology): “Additionally, we officially support use of QIIME on the commercial Amazon Web Services (AWS) Elastic Compute Cloud (EC2) and developers of academic computing clouds including iPlant (Goff et al., 2011) and Magellan (https://www.”
Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. (2015, background): “Successful implementation of a central depository for high-throughput phenotyping will require community input on standard metadata, and the support of existing plant biology infrastructure, such as the Bisque Image Analysis Environment on iPlant [42], since there can be significant diversity in the”
Field-based phenomics for plant genetics research (2012, methodology): “The iPlant Collaborative’s PhytoBisque project seeks to provide a highthroughput platform for image analysis via the iPlant Discovery Environment (Goff et al., 2011).”
ProvDB: A System for Lifecycle Management of Collaborative Analysis Workflows (2016, background): “…been much work on scientiﬁc workﬂow systems over the years, with some of the prominent systems being Kepler [29], Taverna [33], Galaxy [15], iPlant [16], VisTrails [2], Chimera [12], Pegasus [11], to name a few These systems often center around creating, automating, and monitoring a well-deﬁned…”
The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources (2012, background): “One option we are working on is to expose the CSG capabilities within the iPlant Discovery Environment (DE) [28].”