Research Tools and Services Discovery
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| HADDOCK (High Ambiguity Driven protein-protein DOCKing) Online Service HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes. Associated Institutions:Bijvoet Center for Biomolecular Research Related Science Gateway resources:
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| Skyline Online Service Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports All Molecules. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences. Associated Institutions:University of Washington Related Science Gateway resources:
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| Chemical Entities of Biological Interest (ChEBI) Online Service Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. ChEBI incorporates an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI uses nomenclature, symbolism and terminology endorsed by the following international scientific bodies: International Union of Pure and Applied Chemistry (IUPAC) and Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Associated Institutions:European Bioinformatics Institute Related Science Gateway resources:
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| DSpace - open digital repository Online Service DSpace is the software of choice for academic, non-profit, and commercial organizations building open digital repositories. It preserves and enables easy and open access to all types of digital content including text, images, moving images, mpegs and data sets. Associated Institutions:DuraSpace Related Science Gateway resources:
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| NCAR Digital Asset Services Hub (DASH) Online Service It is a centralized system for searching and discovering of digital scientific assets across NCAR and UCAR Community Programs, including datasets, publications, software, and models. The Data Management Plan is required for submitting or depositing your digital assets to be archived at an open repository. Associated Institutions:NCAR,UCAR Related Science Gateway resources:
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| Community Surface Dynamics Modeling System (CSDMS) Online Service CSDMS is an organization that promotes computational modeling of earth-surface processes by providing support for community, computing, and education. The Community Surface Dynamics Modeling System (CSDMS) deals with the Earth's surface - the ever-changing, dynamic interface between lithosphere, hydrosphere, cryosphere, and atmosphere. We are a diverse community of experts promoting the modeling of earth surface processes by developing, supporting, and disseminating integrated software modules that predict the movement of fluids, and the flux (production, erosion, transport, and deposition) of sediment and solutes in landscapes and their sedimentary basins. CSDMS holds over 300 open-source models and tools in it’s repository and offers a suite of services to the earth surface process community. Related Science Gateway resources:
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| NDS Lab Workbench Online Service The Labs Workbench is: 1. An environment for development, integration, and experimentation with research data management and analysis tools and services in support of the NDS vision.. 2. A cloud-based computation and storage resource. 3. A scalable platform for deploying packaged and modular services based on Docker. Related Science Gateway resources:
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| Cyclus Online Service Cyclus is the next-generation agent-based nuclear fuel cycle simulator, providing flexibility to users and developers through a dynamic resource exchange solver and plug-in, user-developed agent framework. The goal of Cyclus is to enable a broad spectrum of fuel cycle simulation while providing a low barrier to entry for new users and agent developers. Cyclus engages with potential module developers and encourages them to join a vibrant community in an expanding ecosystem. Users and developers are always welcome and encouraged to use or contribute to the Cyclus project. Associated Institutions:NCSA Related Science Gateway resources:
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| Bgee Online Service Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species. Related Science Gateway resources:
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| Drupal Online Service Drupal is content management software. It's used to make many of the websites and applications you use every day. Drupal has great standard features, like easy content authoring, reliable performance, and excellent security. But what sets it apart is its flexibility; modularity is one of its core principles. Its tools help you build the versatile, structured content that dynamic web experiences need. Related Science Gateway resources:
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| Jalview Online Service Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Related Science Gateway resources:
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| INTERACTIVE PARALLELIZATION TOOL (IPT) Online Service Interactive Parallelization Tool (IPT) assists domain-experts and students in efficiently parallelizing their existing C/C++ applications using any of the following parallel programming models: Message Passing Interface (MPI), OpenMP, CUDA, and hybrid programming. For assisting in parallelization, IPT uses its knowledgebase of parallel programming expertise (encapsulated as design templates and rules), and specifications (i.e., what to parallelize and where) as provided by users. It parses the user-specifications and accordingly analyses the input source code to reengineer it for generating a parallel version of the code. IPT can be used for self-paced learning of different parallel programming paradigms. It helps in understanding the differences in the structure and performance of the parallel code generated for different specifications while using the same serial application. The current version of IPT has been developed to support explicit parallelization of specific categories of C/C++ applications. We are currently working on (1) extending the capabilities of IPT for parallelizing additional categories of C/C++ applications, (2) provisioning a web-portal for convenient code generation and testing on computational resources of the national CyberInfrastructure (CI), and 35) engaging the community in the development process and the usage of IPT. Related Science Gateway resources:
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| rPredictorDB Online Service rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots. The structures are generated by template-based prediction of RNA secondary structure with experimentally identified structures as templates. RNAs with large secondary structure are visualized using a template-based visualization method allowing for their formatted, clear and readable display. The web also allows for secondary structure template-based prediction for user-uploaded RNA sequences using templates stored in rPredictorDB. Related Science Gateway resources:
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| ValidatorDB Online Service Database of validation results for ligands and non-standard residues in the Protein Data Bank. Related Science Gateway resources:
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| Network for Computational Nanotechnology and nanoHUB Online Service The Network for Computational Nanotechnology (NCN) has a mission to connect theory, experiment, and computation in a way that will transform nanoscience into nanotechnology. While addressing challenges in the field, NCN researchers produce new algorithms, approaches, and software with capabilities not yet available commercially. NCN founding director Mark Lundstrom, the Don and Carol Scifres Distinguished Professor of Electrical and Computer Engineering at Purdue, launched the effort in 2002 with a five-year, $10.5 million NSF grant. The NSF funding was distributed among six partner universities to seed infrastructure creation and develop nanoHUB content. NCN's funding has recently been renewed through the year 2023. The network currently consists of a cyber platform responsible for the support and development of the nanoHUB infrastructure, as well as two content nodes with research and educational directives in the areas of nano-manufacturing (nanoMFG) and nano-bio (Engineered nanoBIO). Led by Gerhard Klimeck, principal investigator and professor of electrical and computer engineering at Purdue University, the NCN cyber platform plans to expand its widely used nanoHUB online science and engineering gateway, developing a virtual society that shares simulation software, data, and other innovative content that provide engineers and scientists with the fundamental knowledge required to advance nanoscience. Annually, more than one million visitors participate in nanoHUB, an online meeting place for simulation, research, collaboration, teaching, learning, and publishing. The nanoHUB provides a library of hundreds of simulation tools, free from the limitations of running software locally. Thousands of users annually run these simulation tools on nanoHUB in the scientific computing cloud. nanoHUB also provides thousands of resources for research and education, including courses, tutorials, seminars, discussions, and facilities to foster nano-research collaboration. The NCN continues to progress. As part of the NSF's infrastructure for the National Nanotechnology Initiative (NNI), NCN engages the community through workshops, seminars, and novel educational resources, implementing new applications on the nanoHUB that are used by experimentalists, theorists and students. The nanoHUB is used extensively in courses and workshops to teach state of the art nanotechnology computer applications. The NCN team has also made a commitment to develop content and applications that would suit a K-12 audience. Associated Institutions:Purdue University,University of Illinois at Urbana-Champaign,Indiana University Related Science Gateway resources:
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| Open OnDemand Online Service Open OnDemand is an NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources, including, but not limited to: Plugin-free web experience Easy file management Command-line shell access Job management and monitoring across different batch servers and resource managers Graphical desktop environments and desktop applications Related Science Gateway resources:
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| GenePattern Online Service GenePattern is a powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. We propose to deploy a GenePattern server on XSEDE infrastructure to provide advanced genomic methods and workflows on high-performance compute architecture. This project will help to commoditize the analysis of very large genomic datasets and disseminate both novel approaches and industry standard methods to a wide audience of researchers. Associated Institutions:UCSD,PSCRelated Science Gateway resources:
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| Microsoft Research Open Data Online Service Microsoft Research Open Data is a data repository that makes available datasets that researchers at Microsoft have created and published in conjunction with their research. You can browse available datasets and either download them or directly copy them to an Azure-based Virtual Machine or Data Science Virtual Machine. To the extent possible, we follow FAIR (findable, accessible, interoperable and reusable) data principles and will continue to push towards the highest standards for data sharing. We recognize that there are dozens of data repositories already in use by researchers and expect that the capabilities of this repository will augment existing efforts. Datasets are categorized by their primary research area. You can find links to research projects or publications with the dataset. Associated Institutions:Microsoft Research Related Science Gateway resources:
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| PredictSNP Online Service Consensus classifiers for prediction of disease-related mutations Related Science Gateway resources:
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| MetaboLights Online Service MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals. Related Science Gateway resources:
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| BioModels Database Online Service BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references. Related Science Gateway resources:
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| BRENDA Online Service BRENDA is the main collection of enzyme functional data available to the scientific community. Related Science Gateway resources:
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| CAZY Online Service The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. Related Science Gateway resources:
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| GraphWeb Online Service GraphWeb is a public web server for graph-based analysis of biological networks that:
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| STRING Online Service STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases. Related Science Gateway resources:
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ACCESS is an advanced computing and data resource supported by the
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and made possible through these lead institutions and their partners:
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University of Illinois at Urbana-Champaign, and
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