Research Tools and Services Discovery
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| EPIC Modeling and Simulations Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Explicit Planetary Isentropic-Coordinate (EPIC) Atmospheric Model Based on Ubuntu 14.04.3 Development Patched up to date as of 1/2/17 Base Ubuntu 14.04.3 + Xfce + Xfce-goodies, firefox, icon sets and themes EPIC 3v9Related Jetstream resources:
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| EDGE_v1 Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 EDGE bioinformatics websiteRelated Jetstream resources:
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| Photoscan_Centos7 Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Centos7 GUI development with Agisoft's photoscan preinstalled and configuredRelated Jetstream resources:
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| bcbio-nextgen Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.Related Jetstream resources:
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| VJC_R341_Bioc3_6_HSOS_admDec28 Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 updates Bioc packages and includes HSOS infrastructure of Dec 2017Related Jetstream resources:
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| pna-agent-tacc Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Anaconda python 3.6, OpenMMRelated Jetstream resources:
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| VJC_R3_4_1_BiocHSOS_HDFS v_1_1 Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Adding infrastructure to support running hdf server.Related Jetstream resources:
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| VJC_R3.4.1_BiocHSOS v.1.1 Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Includes sufficient infrastructure to run rhdf5client + HSOSRelated Jetstream resources:
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| VJC_R3.4.1_Bioconductor Cloud Image urn:ogf:glue2:info.xsede.org:resource:rdr:resource.organizations:561 Includes sufficient infrastructure to run rhdf5clientRelated Jetstream resources:
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| ROSIE, The Rosetta Online Server that Includes Everyone Online Service ROSIE, the Rosetta Online Server that Includes Everyone, provides a web-based interface to applications in the Rosetta biomolecular structure prediction and design project. Current apps include protein-protein docking, RNA de novo folding, ERRASER, antibody homology modeling, sequence tolerance predictions, supercharged surface designs, beta peptide designs, non-canonical backbone design, and VIP design. The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. With this Gateway, we provide a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. The first nine ROSIE applications, by six separate developer teams, are Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. ROSIE is available at http://rosie.rosettacommons.org. Associated Institutions:Johns Hopkins University,Stanford University,The University of North Carolina at Chapel Hill Related Science Gateway resources:
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| m+m: movement + meaning Online Service m+m: movement + meaning is developing a software framework that, broadly speaking, enables researchers to construct meaningful semantic models of movement data. The acquisition, processing, and rendering of movement data can be local or distributed, real-time or off-line. Examples of systems that can be built with m+m as the internal communication middleware include those for the semantic interpretation of human movement data, machine-learning models for movement recognition and movement analytics, the representation of semantic properties of movement data in virtual characters, and the mapping of movement data as a controller for online navigation, collaboration, distributed performance. Associated Institutions:Simon Fraser University Related Science Gateway resources:
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| GenSAS Online Service The Genome Sequence Annotation Server (GenSAS) is an online platform that provides a pipeline for whole genome structural and functional annotation. Users can upload genome sequences and select from a variety of tools for repeat masking, prediction of gene models and other structural features as well as functional annotation tools. GenSAS integrates with JBrowse and Apollo to provide visualization and editing. Associated Institutions:Washington State University,University of Connecticut,University of California Davis Related Science Gateway resources:
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| ORCA(Quantum Chemistry Program) Online Service The program ORCA is a modern electronic structure program package. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Associated Institutions:Max-Planck-Institut für Kohlenforschung Related Science Gateway resources:
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| Flotilla: An Open-Source Toolkit for Single-Cell RNA-Seq Data Analysis Online Service flotilla is a Python package for visualizing transcriptome (RNA expression) data from hundreds of samples. Associated Institutions:University of California, San Diego Related Science Gateway resources:
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| NGSEP (Next Generation Sequencing Eclipse Plugin) Online Service NGSEP (Next Generation Sequencing Eclipse Plugin), an integrated framework for analysis of high throughput sequencing reads. The main functionality of NGSEP is the variants detector, which allows to make simultaneous discovery of SNVs, indels, and CNVs. NGSEP also provides a user interface for bowtie2 to perform mapping to the reference genome and other utilities such as alignments sorting, merging of variants from different samples, and functional annotation of variants. NGSEP is based on Eclipse which is one of the leading development environments for Java. Note: Since we offer different distribution alternatives for different kinds of users, the quick download (green) button may not lead you to the version of the product that you need. Please visit the web page to choose the distribution of NGSEP that better suits your data analysis environment. Associated Institutions:International Center for Tropical Agriculture (CIAT), Cali, Colombia Related Science Gateway resources:
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| PharmaHUB Online Service pharmaHUB deals with collaboration and sharing of information on processes and products of pharmaceutical products. Related Science Gateway resources:
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| Innovations in Scholarly Communication Online Service We are interested in the way information is created, shared, and processed in academia. This is reflected in a number of related activities aimed at charting the changing scholarly landscape. We created an overview of current and expected developments and models to get a grip on the abundance and variety of research tools used. Associated Institutions:Utrecht University Library Related Science Gateway resources:
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| GenomeSpace Online Service GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. Associated Institutions:University of California, San Diego,Stanford University,Pennsylvania State University,Weizmann Institute of Science,University of California, Santa Cruz Related Science Gateway resources:
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| CLEERhub Online Service CLEERhub is a digital habitat with the mission to address the continued need for developing engineering education researchers by leveraging the success of past NSF-funded programs such as RREE, ISEE and CAEE and the expertise gained by various project team members. CLEERhub is part of a NSF-funded project called Expanding and sustaining research capacity in engineering and technology education: building on successful programs for faculty and graduate students (DUE-0817461). Related Science Gateway resources:
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| Decision Theater Network Online Service The Decision Theater Network actively engages researchers and leaders to visualize solutions to complex problems. The Network provides the latest expertise in collaborative, computing and display technologies for data visualization, modeling, and simulation. The Network addresses cross-disciplinary local, national and international issues by drawing on Arizona State University’s diverse academic and research capabilities. Associated Institutions:Arizona State University Related Science Gateway resources:
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| The Arabidopsis Informational Portal (Araport) Online Service The Arabidopsis Information Portal is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation including gene structure, gene expression, protein function, and interaction networks. Associated Institutions:J. Craig Venter Institute,TACC,University of Cambridge Related Science Gateway resources:
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| CyberSKA Online Service CyberSKA is a project aimed at exploring and implementing the cyberinfrastructure that will be required to address the evolving data intensive science needs of future radio telescopes such as the Square Kilometre Array. Related Science Gateway resources:
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| CloudLaunch Online Service CloudLaunch is an extensible application that can be used to launch virtual appliances of your choice on a public or private cloud. A virtual appliance is a virtual machine that packages a ready-to-run application(s), eliminating the need to install and configure complex stacks of software. (e.g. Galaxy, Genomics Virtual Lab, SLURM) CloudLaunch has a simple plugin system that can be extended to support additional appliances, and can target not only clouds, but potentially container infrastructure or any other kind of deployment platform. Related Science Gateway resources:
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| TopPIC Gateway Online Service TopPIC Suite gateway provides software for top-down mass spectrometry data analysis for public use. TopPIC Suite consists of four software tools for the interpretation of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.
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| CoRIS Portal Online Service CoRIS is the Coral Reef Conservation Program's (CRCP) information portal that provides access to NOAA coral reef information and data products with emphasis on the U.S. states, territories and remote island areas. NOAA Coral Reef activities include coral reef mapping, monitoring and assessment; natural and socioeconomic research and modeling; outreach and education; and management and stewardship. Associated Institutions:NOAARelated Science Gateway resources:
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ACCESS is an advanced computing and data resource supported by the
National Science Foundation
and made possible through these lead institutions and their partners:
Carnegie Mellon University,
University of Colorado Boulder,
University of Illinois at Urbana-Champaign, and
State University of New York at Buffalo .
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