Research Tools and Services Discovery
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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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| Whole Tale Online Service Merging Science and Cyberinfrastructure Pathway Whole Tale is an NSF-funded Data Infrastructure Building Block (DIBBS) initiative to build a scalable, open source, web-based, multi-user platform for reproducible research enabling the creation, publication, and execution of tales - executable research objects that capture data, code, and the complete software environment used to produce research findings. A beta version of the system is available at https://dashboard.wholetale.org. A tale is an executable research object that combines data (references), code (computational methods), computational environment, and narrative (traditional science story). Associated Institutions:NCSA,UIUCRelated Science Gateway resources:
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| Purdue Community Hub Online Service Purdue's ITaP Research Computing division collaborates with many research groups across campus and endeavors to provide access to leading-edge computational and data storage systems. Related Science Gateway resources:
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| CLIPC: Constructing Europe's Climate Information Portal Online Service CLIPC provides access to climate information of direct relevance to a wide variety of users, catering for consultant advisers, policy makers, private sector decision makers and scientists, but also interested members of the general public. This one-stop-shop platform allows you to find answers to questions related to climate and climate impact. Related Science Gateway resources:
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| EVER-EST Online Service The EVER-EST project (European Virtual Environment for Research – Earth Science Themes: a solution ) will create a virtual research environment (VRE) focussed on the requirements of the Earth Science community. Within the earth sciences there are major challenges such as climate change research and ensuring the secure and sustainable availability of natural resources and understanding natural hazards which require inter-disciplinary working and sharing of large amounts of data across diverse geographic locations and science disciplines to work towards a solution. Associated Institutions:ESA – European Space Agency /ESRIN Related Science Gateway resources:
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| WHISPers Online Service The Wildlife Health Information Sharing Partnership event reporting system (WHISPers) is a partner-driven, web-based repository for sharing information about historic and ongoing wildlife mortality and morbidity events. The primary goal of the system is to provide natural resource management partners and the public with timely, accurate information on where wildlife disease events are occurring or have occurred for better preparation and decision making. WHISPers is one of the core databases used by the USGS National Wildlife Health Center (NWHC), which is the only national center dedicated to wildlife disease detection, control, and prevention. In the future, data in WHISPers will likely be populated by hundreds, if not thousands, of natural resource management professionals who seek services from the NWHC or want to collaborate and easily share information across political boundaries. Data in WHISPers are used by the Department of Homeland Security’s National Biosurveillance Integration Center, the World Organisation for Animal Health, and will soon be set up to alert the top echelon of the U.S. Department of the Interior regarding wildlife health events on federal lands; it is likely that more national and international surveillance and research organizations will use WHISPers alerts in the future to increase situational awareness of diseases in wildlife. Related Science Gateway resources:
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| Allen Institute for Cell Science Online Service The Allen Cell Explorer is the data portal for the Allen Institute for Cell Science, where you can explore our publicly available data, tools and models. The portal provides an unprecedented view into the organizational diversity of human stem cells by combining large-scale 3D imaging data, predictive models, observations of cells, detailed methods, and cell lines available for use in labs around the world. Associated Institutions:Allen Institute Related Science Gateway resources:
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| Unidata Science Gateway Online Service The Unidata Science Gateway is a collection of technologies, resources, and Unidata expertise to assist educators, researchers and students in atmospheric science arrive at their scientific objectives faster and more easily. Contact us at support-gateway@unidata.ucar.edu to start the conversation. Associated Institutions:UCARRelated Science Gateway resources:
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| CPORT Online Service CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor. Related Science Gateway resources:
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| BIOVIA Pipeline Pilot Online Service Pipeline Pilot gives you the building blocks to create data science solutions and make them available to be used strategically. Users of any programming level can quickly create custom protocols for a variety of applications, including data processing, data and application integration, analytics, machine learning and dashboards, web service creation and deployment. Associated Institutions:Dassault Systemes BIOVIA Related Science Gateway resources:
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| Earth Life Consortium (ELC) Online Service The Earth-Life Consortium (ELC) seeks to make all paleobiological data easily discoverable, accessible, and analyzable, with the larger goal of understanding the interactions between the Earth's biological and geophysical systems across all timescales of the Earth's history. Initial efforts are focusing on building a common search interface for paleobiological and paleoecological data stored in the Paleobiology Database and Neotoma Paleoecology Database. Related Science Gateway resources:
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| MyProxy Online Service MyProxy is open source software for managing X.509 Public Key Infrastructure (PKI) security credentials (certificates and private keys). MyProxy combines an online credential repository with an online certificate authority to allow users to securely obtain credentials when and where needed. Users run myproxy-logon to authenticate and obtain credentials, including trusted CA certificates and Certificate Revocation Lists (CRLs). Associated Institutions:NCSA Related Science Gateway resources:
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| COSMIC2 Science Gateway Online Service Structural biology is in the midst of a revolution. Instrumentation and software improvements have allowed for the full realization of cryo-electron microscopy (cryo-EM) as a tool capable of determining atomic structures of protein and macromolecular samples. These advances open the door to solving new structures that were previously unattainable, which will soon make cryo-EM a ubiquitous tool for structural biology worldwide, serving both academic and commercial purposes. However, despite its power, new users to cryo-EM face significant obstacles. One major barrier consists of the handling of large datasets (10+ terabytes), where new cryo-EM users must learn how to interface with the Linux command line while also dealing with managing and submitting jobs to high performance computing resources. To address this barrier, we are developing the COSMIC2 Science Gateway as an easy, web-based, science gateway to simplify cryo-EM data analysis using a standardized workflow. Specifically, we have adapted the successful and mature Cyberinfrastructure for Phylogenetic Research (CIPRES) Workbench [8] and integrated Globus Auth [6] and Globus Transfer [7] to enable federated user identity management and large dataset transfers to Extreme Science and Engineering Discovery Environment’s (XSEDE) [1] high performance computing (HPC) systems. With the support of XSEDE’s Extended Collaborative Support Services (ECSS) [16] and the Science Gateway Community Institute’s (SGCI) Extended Developer Support (EDS), this gateway will lower the barrier to high performance computing tools and facilitate the growth of cryo-EM to become a routine tool for structural biology. Associated Institutions:UCSD,SDSC Related Science Gateway resources:
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| MATIN - Materials Innovation Network Online Service MATerials Innovation Network (MATIN) is an advanced cloud-based platform developed with a mission to accelerate materials innovation. MATIN is the product of the initiative and related efforts by the Institute for Materials (IMat) at Georgia Institute of Technology (Georgia Tech) in alignment with and toward implementation of the U.S. Materials Genome Initiative. Related Science Gateway resources:
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| Eukaryotic Promoter Database (EPD) Online Service This resource allows the access to several databases of experimentally validated promoters: EPD and EPDnew databases. They differ by the validation technique used and the coverage. EPD is a collection of eukaryotic promoters derived from published articles. Instead, the EPDnew databases (HT-EPD) are the result of merging EPD promoters whith in-house analysis of promoter-specific high-throughput data for selected organisms only. This process gives EPDnew high precision and high coverage. Related Science Gateway resources:
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| ROBETTA - Full-chain Protein Structure Prediction Server Online Service Robetta provides both ab initio and comparative models of protein domains. Domains without a detectable PDB homolog are modeled with the Rosetta de novo protocol (Simons et al. (1997) J Mol Biol. 268:209-225, Bradley et al. (2005) Science 309 (5742), 1868-71). Comparative models are built from template PDBs detected and aligned using locally installed versions of HHSEARCH/HHpred, RaptorX, and Sparks-X. Alignments are clustered and comparative models are generated using the RosettaCM protocol. The procedure is fully automated. Associated Institutions:University of Washington Related Science Gateway resources:
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| Thematic Real-time Environmental Distributed Data Services (THREDDS) Data Server Online Service The goal of Unidata's Thematic Real-time Environmental Distributed Data Services (THREDDS) is to provide students, educators and researchers with coherent access to a large collection of real-time and archived datasets from a variety of environmental data sources at a number of distributed server sites. The THREDDS Data Server (TDS) is a web server that provides metadata and data access for scientific datasets, using a variety of remote data access protocols. Associated Institutions:UCAR,Unidata Related Science Gateway resources:
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| SwissDrugDesign Online Service SwissDrugDesign provides a collection of web-based tools covering all aspects of computer-aided drug design. Related Science Gateway resources:
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| Data Wolf Online Service Data Wolf is designed to facilitate the documentation and dissemination of scientific work with a system that makes it easy to create and share workflows while separating the science from the logistics of execution. This allows scientists to focus on research without concerning themselves with the details of where the workflow will execute, how will the data be stored, how do I share my results, etc. Models, algorithms, and data are kept in open formats so they are accessible outside the scientific workflow system and models that are encapsulated by a workflow can be exposed as a RESTful web service. Data Wolf has 3 main components: 1) Editor (DataWolf JS), 2) Service layer (RESTful service) and 3) Engine. Associated Institutions:NCSA Related Science Gateway resources:
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| The Kepler Project Online Service The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scientists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging "R" scripts with compiled "C" code, or facilitating remote, distributed execution of models. Using Kepler's graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a "scientific workflow"—an executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and components developed by the scientific community to address common needs. Associated Institutions:SDSC Related Science Gateway resources:
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| Cactus Code Online Service Cactus provides computational scientists and engineers with a collaborative, modular and portable programming environment for parallel high performance computing. Cactus can make use of many other technologies for HPC, such as Samrai, HDF5, PETSc and PAPI, and several application domains such as numerical relativity, computational fluid dynamics and quantum gravity are developing open community toolkits for Cactus. Associated Institutions:NCSA Related 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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