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Services for the long-term preservation and curation of America's digital data - data of any type or size, with minimal requirements on the data provider. It has the capacity to preserve hundreds of terabytes of digital data and comprises several partner organizations that provide a wide range of services. The project leverages high-speed networks, mass-scale storage capabilities, and the expertise of the partners in order to provide a geographically distributed, heterogeneous, and highly redundant archive system. Features of the project include: * Three geographically distributed copies of the data * Curatorial audit reporting * Development of best practices for data packaging and sharing Chronopolis is available to anyone who wants to have their data preserved. Storage is based on a yearly, per-terabyte charge. The smallest unit available is one terabyte; collections smaller than this will be charged the one terabyte rate.
Proper citation: chronopolis (RRID:SCR_003116) Copy
https://www.fitzgerald-fii.com
Commercial organization that supplies antibodies, proteins, ELISA kits, serum, and plasma to the research community.
Proper citation: Fitzgerald Industries International (RRID:SCR_003237) Copy
http://cran.r-project.org/web/packages/pairheatmap/
A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.
Proper citation: pairheatmap (RRID:SCR_003109) Copy
Set of plugins for the Eclipse platform which facilities note-taking and annotation of web-based works and non-web-based works.
Proper citation: Pliny (RRID:SCR_003107) Copy
http://www.cuny.edu/index.html
University system in New York City, New York. It is made up of 11 senior colleges, seven community colleges, The Macaulay Honors College, and five graduate and professional schools.
Proper citation: City University of New York; New York; USA (RRID:SCR_003106) Copy
A Mozilla project to teach and enable users on how to create on the web. Their tools, events and teaching guides allow webmakers to create the content that makes the web great and understand how the web works. They've built everything so you can see how it works, take it apart and remix it
Proper citation: Webmaker (RRID:SCR_003227) Copy
http://gemdock.life.nctu.edu.tw/3D-Interologs
Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.
Proper citation: 3D-Interologs (RRID:SCR_003101) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.
Proper citation: MAGE-TAB (RRID:SCR_003222) Copy
http://www.fged.org/projects/minseqe/
The Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research. The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows: # The description of the biological system, samples, and the experimental variables being studied # The sequence read data for each assay # The "final" processed (or summary) data for the set of assays in the study # General information about the experiment and sample-data relationships # Essential experimental and data processing protocols
Proper citation: MINSEQE (RRID:SCR_003221) Copy
http://senselab.med.yale.edu/neurondb
Database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
Proper citation: NeuronDB (RRID:SCR_003105) Copy
http://www.w3.org/community/openannotation/
Community group working towards a common, RDF-based, specification for annotating digital resources. The effort began by trying to reconcile two proposals: the Annotation Ontology (http://code.google.com/p/annotation-ontology/) and the Open Annotation Model (http://www.openannotation.org/spec/beta/ ). Initially, editors of these proposals collaborated to devise a common draft specification that addresses requirements and use cases that were identified in the course of their respective efforts. This draft became available for public feedback and experimentation in the second quarter of 2012. The final deliverable is a specification, published under an appropriate open license, that is informed by the existing proposals, the common draft specification, and the community feedback.
Proper citation: W3C Open Annotation Community Group (RRID:SCR_003226) Copy
Generate, archive, and distribute world-wide up to 12.000 conditional mutations across the mouse genome in mouse embryonic stem (ES) cells and Establish a limited number of mouse mutants from this resource. EUCOMM contributes the largest fraction of conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the IKMC. EUCOMM vectors, mutant ES cells and mutant mice are distributed worldwide, enabling functional genomics research in a standardized and cost-effective manner by a much wider biomedical research community than has been possible previously. EUCOMM mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMM mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Mutagenesis Strategies * Conditional gene trapping - random approach for expressed genes * Conditional targeted trapping - directed approach, used for expressed genes * Conditional gene targeting - directed approach, used for non-expressed genes
Proper citation: European Conditional Mouse Mutagenesis Program (RRID:SCR_003104) Copy
Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.
Proper citation: SobekCM (RRID:SCR_003225) Copy
https://github.com/timflutre/eqtlbma/wiki
Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes).
Proper citation: eQtlBma (RRID:SCR_003102) Copy
Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.
Proper citation: ResearchCompendia (RRID:SCR_003223) Copy
http://www.ncbi.nlm.nih.gov/dbvar/
Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.
Proper citation: dbVar (RRID:SCR_003219) Copy
National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor.
Proper citation: NIH NeuroBioBank (RRID:SCR_003131) Copy
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
Proper citation: RNAhybrid (RRID:SCR_003252) Copy
http://cal.tongji.edu.cn/PlantLoc/index.jsp
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.
Proper citation: PlantLoc (RRID:SCR_003138) Copy
http://www.stereologyresourcecenter.com/
A company of professionally trained stereologists, bioscientists, computer engineers, educators, and support personnel that provides comprehensive neurostereology products and services to the global bioscience community. These products and services include: stereology and image analysis software, digital imaging technology, turnkey stereologer solutions, comprehensive stereology and image analysis/image processing software, professional contract services, neurostereology workshops, basic stereology courses, and online stereology webinars. The Center also offers tissue processing (sectioning, staining, slide preparation) and stereology data collection services. Researchers may use equipment and facilities to complete projects with full confidentiality and according to Good Laboratory Practices guidelines.
Proper citation: Stereology Resource Center (RRID:SCR_003137) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
