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http://www.wwpdb.org/

Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.

Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy   

•   Source: SciCrunch Registry

http://arabidopsis.med.ohio-state.edu

An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB).

Proper citation: Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) Copy   

•   Source: SciCrunch Registry

http://www.agbase.msstate.edu/

A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms.

Proper citation: AgBase (RRID:SCR_007547) Copy   

•   Source: SciCrunch Registry

http://www.biocheminfo.org/klotho/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry.

Proper citation: Klotho: Biochemical Compounds Declarative Database (RRID:SCR_007714) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/nnin-nano-research-facility-wustl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Nano Research Facility (NRF) at Washington University in St. Louis is a NNIN nodal facility supported by the National Science Foundation. It cultivates an open, shared research, and education environment that brings researchers across disciplines together, particularly in the emerging area of nanomaterials with applications in the energy, environment, and biomedical fields. The mission is to be a resource to the scientific and technical community for the advancement of nanoscience and nanotechnology in a safe and environmentally benign manner. NRF includes a micro- and nano-fabrication lab (clean room), surface characterization lab, particle technology lab, and imaging lab with a focus on bio-imaging. NRF provides unique technical expertise in: Knowledge-based synthesis of nanostructured materials Particle instrumentation tools for toxicity studies Non-invasive imaging modalities for biological applications Clean Energy Applications Energy and Environmental nanotechology Environmental Health and Safety As a member of the National Nanotechnology Infrastructure Network (NNIN), supported by the National Science Foundation, NRF is available to both academic and industrial users nation-wide and across the globe.

Proper citation: WUSTL NNIN - Nano Research Facility (RRID:SCR_012674) Copy   

•   Source: SciCrunch Registry

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

A Matlab implementation for efficient permutation testing by using matrix completion.

Proper citation: Efficient Permutation Testing (RRID:SCR_014104) Copy   

•   Source: SciCrunch Registry

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=simplePHENOTYPES

Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy.

Proper citation: simplePHENOTYPES (RRID:SCR_022523) Copy   

•   Source: SciCrunch Registry

https://github.com/plaisier-lab/sygnal

Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.

Proper citation: SYGNAL (RRID:SCR_023080) Copy   

•   Source: SciCrunch Registry

https://yeatmanlab.github.io/pyAFQ/

Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry.

Proper citation: Automated Fiber Quantification in Python (RRID:SCR_023366) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://github.com/virajbdeshpande/AmpliconArchitect

Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.

Proper citation: AmpliconArchitect (RRID:SCR_023150) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/omicsGAN

Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.

Proper citation: OmicsGAN (RRID:SCR_022976) Copy   

•   Source: SciCrunch Registry

http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi

Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs.

Proper citation: VirusDetect (RRID:SCR_023669) Copy   

•   Source: SciCrunch Registry

https://rockd.org/

Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils.

Proper citation: rockd (RRID:SCR_024431) Copy   

•   Source: SciCrunch Registry

http://www.ldeo.columbia.edu/core-repository

Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator.

Proper citation: Lamont-Doherty Core Repository (RRID:SCR_002216) Copy   

•   Source: SciCrunch Registry

http://lrc.geo.umn.edu/laccore/

Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs.

Proper citation: National Lacustrine Core Facility (RRID:SCR_002215) Copy   

•   Source: SciCrunch Registry

https://www.colorado.edu/rc/resources/petalibrary

Provides service to support storage, archival, and sharing of research data. Available at subsidized cost to any researcher affiliated with University of Colorado Boulder.

Proper citation: University of Colorado Boulder High Performance Computing PetaLibrary Core Facility (RRID:SCR_019299) Copy   

•   Source: SciCrunch Registry

https://www.jmu.edu/microscopy/index.shtml

Core provides instrumentation, resources, training, and consultation. Facility offers access to diverse range of light microscope and imaging systems,image analysis software and solutions, practical and theoretical training for faculty, students and classes,consultation on data acquisition, analysis, and presentation.

Proper citation: James Madison University Light Microscopy and Imaging Core Facility (RRID:SCR_021904) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/PTNet

Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression.

Proper citation: PTNet (RRID:SCR_022975) Copy   

•   Source: SciCrunch Registry