Research Tools and Services Discovery
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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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| Rfam Online Service The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). Related Science Gateway resources:
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| Protein Crystallisation Construct Designer (ProteinCCD) Online Service The Protein Crystallisation Construct Designer (ProteinCCD) is a tool to help deciding how to choose promising constructs for protein expression and crystallisation. A specific feature of CCD is that since it starts from the DNA sequence, it keeps track of the protein-DNA relationship. Thus, although all the analysis and construct choice is being done in the protein level, CCD can be used to suggest primers for PCR amplification of the chosen constructs, since it also knows the DNA sequence. Related Science Gateway resources:
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| Globus: Research data management simplified Online Service Globus is a secure, reliable research data management service. With Globus, you can move, share, publish & discover data via a single interface. Whether your files live on a supercomputer, lab cluster, tape archive, public cloud or your laptop, you can manage them from anywhere, using your existing identities, via just a web browser. Globus also provides a platform for application integration and gateway development leveraging advanced identity management, single sign-on, search and authorization capabilities. Globus’s Transfer service is a hosted service (software-as-a-service or SaaS) that allows you to manage your data wherever it’s stored and move it to where it needs to be. Globus Connect, available in multi-user and personal versions, is downloadable software for Mac, Windows, and Linux that makes your data manageable using the Transfer service. Globus’s Auth service is a hosted authentication service that provides secure user authentication for your applications using existing IDs from thousands of academic and research organizations, including campuses, ORCID, XSEDE, NERSC, and Google. Globus Data Publication is a Web application that allows you and your research colleagues to publish and manage data collections. You can create and manage your own communities and collections, enabling you and your colleagues to submit datasets subject policies that you configure. Associated Institutions:University of Chicago,Argonne National Laboratory Related Science Gateway resources:
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| MultiPLX Online Service About the program: MultiPLX 2.1 is a tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution. It uses state-of-the-art nearest neighbour DNA binding thermodynamics to estimate possible unwanted pairings between PCR samples. This thermodynamic data is then used to distribute primers into groups that satisfy user defined set of constraints. Related Science Gateway resources:
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| European Variation Archive Online Service The European Variation Archive is an open-access database of all types of genetic variation data from all species. 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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