Tools   Select Another Resource Report Type

http://portal.ncibi.org/gateway/mimiplugin.html

The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.

Proper citation: MiMI Plugin for Cytoscape (RRID:SCR_003424) Copy   

•   Source: SciCrunch Registry

http://www.findmice.org/index.jsp

Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.

Proper citation: International Mouse Strain Resource (RRID:SCR_001526) Copy   

•   Source: SciCrunch Registry

https://bmrb.io

Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR.

Proper citation: Biological Magnetic Resonance Data Bank (BMRB) (RRID:SCR_002296) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/sim4cc/

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

Proper citation: sim4cc (RRID:SCR_001204) Copy   

•   Source: SciCrunch Registry

http://globin.cse.psu.edu/

Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

Proper citation: Globin Gene Server (RRID:SCR_001480) Copy   

•   Source: SciCrunch Registry

https://glimmpse.samplesizeshop.org/#/

Web based software tool that calculates power and sample size for study designs with normally distributed outcomes.

Proper citation: GLIMMPSE (RRID:SCR_016297) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/about

Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials.

Proper citation: RobotReviewer (RRID:SCR_021064) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/research/umls/

Database of key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records. This set of files and software brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems. Users can use the UMLS to enhance or develop applications, such as electronic health records, classification tools, dictionaries and language translators. The UMLS has three tools, which we call the Knowledge Sources: * Metathesaurus: Terms and codes from many vocabularies, including CPT, ICD-10-CM, LOINC, MeSH, RxNorm, and SNOMED CT * Semantic Network: Broad categories (semantic types) and their relationships (semantic relations) * SPECIALIST Lexicon and Lexical Tools: Natural language processing tools We use the Semantic Network and Lexical Tools to produce the Metathesaurus. Metathesaurus production involves: * Processing the terms and codes using the Lexical Tools * Grouping synonymous terms into concepts * Categorizing concepts by semantic types from the Semantic Network * Incorporating relationships and attributes provided by vocabularies * Releasing the data in a common format Although we integrate these tools for Metathesaurus production, you can access them separately or in any combination according to your needs. The UMLS Terminology Services (UTS) provides three ways to access the UMLS: Web Browsers, Local Installation, and Web Services APIs.

Proper citation: Unified Medical Language System (RRID:SCR_006363) Copy   

•   Source: SciCrunch Registry

https://evidencemodeler.github.io/

Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).

Proper citation: EVidenceModeler (RRID:SCR_014659) Copy   

•   Source: SciCrunch Registry

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi

Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining.

Proper citation: Anne O'Tate (RRID:SCR_023086) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/guide/sitemap/

The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation.

Proper citation: NCBI Resource List (RRID:SCR_005628) Copy   

•   Source: SciCrunch Registry

https://gillisweb.cshl.edu/Primate_MTG_coexp/

We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain.

Proper citation: Gene functional conservation across cell types and species (RRID:SCR_023292) Copy   

•   Source: SciCrunch Registry

https://lincsportal.ccs.miami.edu/signatures/home

Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.

Proper citation: LINCS Data Portal 2.0 (RRID:SCR_022566) Copy   

•   Source: SciCrunch Registry

http://compbio.dfci.harvard.edu/amp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.

Proper citation: Automated Microarray Pipeline (RRID:SCR_001219) Copy   

•   Source: SciCrunch Registry

http://lcg.rit.albany.edu/dp-bind

This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated.

Proper citation: DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins (RRID:SCR_003039) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

•   Source: SciCrunch Registry

http://lussierlab.org/GO-Module/GOModule.cgi

GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool

Proper citation: GO-Module (RRID:SCR_005813) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://snyderome.stanford.edu/

Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions.

Proper citation: iPOP (RRID:SCR_008991) Copy   

•   Source: SciCrunch Registry

https://github.com/nlm-irp-jianglab/SpikeHunter

Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins.

Proper citation: SpikeHunter (RRID:SCR_024831) Copy   

•   Source: SciCrunch Registry