Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A database that lists, reviews, and rates resources for teaching neuroscience at the graduate and undergraduate level.
Proper citation: Educational Resources in Neuroscience (RRID:SCR_000169) Copy
National repository for geological materials collected in polar regions housing over 20,000 meters of deep-sea core sediment and over 5,000 kg of dredge, trawl, and grab samples, the largest such Southern Ocean collection in the world. These materials have been acquired from over 90 USAP research vessel cruises. The Facility also houses and curates nearly 3,000 meters of rotary cored geological material acquired by NSF supported drilling programs in the Antarctic. Replacement cost of this core inventory in terms of ship and ice-based drilling is conservatively estimated to be in the range of $150 to $200M. SESAR or the the System for Earth Sample Registration is a service provided by the IDEA. SESAR operates the registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search. Facility services include:
* curation of the existing collections at the facility
* onsite ship and land based curatorial services
* receipt and processing of new cores
* core description and publication of core descriptions
* distribution of samples from the collection to authorized scientists
* hosting of scientific meetings and workshops
* tours, lectures, and student education and training in Antarctic geoscience
* maintenance of:
** a core and sample database
** an Antarctic geology and marine geology reference library and a searchable End Note computer database of the entire collection
** a satellite IODP/MRC for nannofossils and diatoms
Proper citation: Antarctic Marine Geology Research Facility (RRID:SCR_002213) Copy
http://www.cise.ufl.edu/~tichen/ShapeComplexAtlas.zip
A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012
Proper citation: ShapeComplexAtlas (RRID:SCR_002553) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 8, 2017. Service that aggregates altmetrics: diverse impacts from articles, datasets, blog posts, and more, to create a measure of the impact of scholarly output. * view metrics: Point to research products in Slideshare, GitHub, and Dryad. Import items from Google Scholar profiles or a BibTex file and the output is a metrics report that can be viewed and shared. * embed anywhere: Use the full-featured API to add metrics to projects. Or drop the embeddable Javascript widget into a publishing platform''s HTML. * Free - metrics data (and source code). They believe open altmetrics are key for building the coming era of Web-native science.
Proper citation: total impact.org (RRID:SCR_005952) Copy
A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing.
Proper citation: CloVR (RRID:SCR_005290) Copy
Software tools and databases for plant genomics.
Proper citation: PlantGDB (RRID:SCR_013166) Copy
An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers.
Proper citation: Planteome (RRID:SCR_014411) Copy
http://research.bioinformatics.udel.edu/iptmnet/
A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies.
Proper citation: iPTMnet (RRID:SCR_014416) Copy
http://www.algalresourcescollection.com/
Supplier of algae strains that aims to be a resource to both the HAB research community and biotechnological applications. Researchers can order and deposit strains with the ARC.
Proper citation: Algal Resources Collection (RRID:SCR_014942) Copy
Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae.
Proper citation: TheCellMap (RRID:SCR_018728) Copy
A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content.
Proper citation: nanoHUB (RRID:SCR_013963) Copy
Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.
Proper citation: Whole Tale (RRID:SCR_017537) Copy
https://github.com/oushujun/LTR_retriever
Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly.
Proper citation: LTR_retriever (RRID:SCR_017623) Copy
A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages.
Proper citation: PyMVPA (RRID:SCR_006099) Copy
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Proper citation: rMATS (RRID:SCR_023485) Copy
https://github.com/wlloyduw/ContainerProfiler
Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers.
Proper citation: ContainerProfiler (RRID:SCR_023770) Copy
Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins.
Proper citation: PONDR (RRID:SCR_023691) Copy
https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott93302
Project aims to construct comprehensive, dynamic and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data.
Proper citation: Open Tree of Life (RRID:SCR_024603) Copy
https://masst.gnps2.org/microbemasst/
Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.
Proper citation: microbeMASST (RRID:SCR_024713) Copy
https://brains.anatomy.msu.edu/brains/sheep/index.html
Online portal and image database of coronal sections of the sheep brain. Each image contains stained sections of cell bodies and myelinated fibers; nuclei and tracts are labeled.
Proper citation: Sheep Brain Atlas (RRID:SCR_001752) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within NIF that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
