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https://ecl.earthchem.org/view.php?id=329

Database contating hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. It can accommodate published historical data as well as legacy and new data that investigators contribute.

Proper citation: VentDB (RRID:SCR_001632) Copy   

•   Source: SciCrunch Registry

http://www.sdsc.edu/

Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale infrastructure for open scientific research. SDSC currently provides advanced user support and expertise for XSEDE (Extreme Science and Engineering Discovery Environment) the five-year NSF-funded program that succeeded TeraGrid in mid-2011.

Proper citation: San Diego Supercomputer Center (RRID:SCR_001856) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/CENlab/software.html

Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.

Proper citation: NeuroRD (RRID:SCR_014769) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gscca_2013/

Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.

Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

http://raptorx.uchicago.edu/

Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.

Proper citation: RaptorX (RRID:SCR_018118) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reprocontainers/

Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.

Proper citation: ReproNim/containers (RRID:SCR_018467) Copy   

•   Source: SciCrunch Registry

http://clavius.bc.edu/~clotelab/DiANNA/

Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification.

Proper citation: DiANNA (RRID:SCR_018529) Copy   

•   Source: SciCrunch Registry

https://github.com/OHDSI/CohortMethod

Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.

Proper citation: CohortMethod (RRID:SCR_018511) Copy   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry

https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) Copy   

•   Source: SciCrunch Registry

https://www.biosimulations.org/

Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.

Proper citation: BioSimulations (RRID:SCR_018733) Copy   

•   Source: SciCrunch Registry

https://github.com/chris-mcginnis-ucsf/DoubletFinder

Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.

Proper citation: DoubletFinder (RRID:SCR_018771) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://grassius.org/

A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.

Proper citation: GRASSIUS (RRID:SCR_012999) Copy   

•   Source: SciCrunch Registry

http://datasets.datalad.org/

DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.

Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy   

•   Source: SciCrunch Registry

https://run.biosimulations.org

Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.

Proper citation: runBioSimulations (RRID:SCR_019110) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hdbig/

A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association.

Proper citation: HDBIG (RRID:SCR_014120) Copy   

•   Source: SciCrunch Registry