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Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community.
Proper citation: Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) Copy
https://bioconductor.org/packages/release/bioc/html/Glimma.html
Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.
Proper citation: Glimma (RRID:SCR_017389) Copy
https://github.com/JosephCrispell/homoplasyFinder/wiki
Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R.
Proper citation: HomoplasyFinder (RRID:SCR_017300) Copy
https://github.com/Sethupathy-Lab/miRquant
Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications.
Proper citation: miRquant (RRID:SCR_017261) Copy
https://icsd.products.fiz-karlsruhe.de/
Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research.
Proper citation: Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) Copy
https://github.com/ISUgenomics/SequelQC
Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.
Proper citation: SequelQC (RRID:SCR_017279) Copy
Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data.
Proper citation: Human Neocortical Neurosolver (RRID:SCR_017437) Copy
Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.
Proper citation: SCÅTTER (RRID:SCR_017271) Copy
Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com.
Proper citation: NIH Figshare Archive (RRID:SCR_017580) Copy
https://amp.pharm.mssm.edu/geneshot/
Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.
Proper citation: Geneshot (RRID:SCR_017582) Copy
Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Proper citation: Mousebytes (RRID:SCR_017904) Copy
https://clowder.ncsa.illinois.edu/
Web based data management system that allows users to share, annotate, organize and analyze large collections of datasets. Software tool for creating some metadata about software tools automatically. Open source data management for long tail data. Provides support for extensible metadata annotation and distributed analytics for automatic curation of uploaded data. Open source software that can be customized and deployed on your own cloud.
Proper citation: Clowder (RRID:SCR_017599) Copy
Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform.
Proper citation: iBright Analysis Software (RRID:SCR_017632) Copy
http://www.informatics.jax.org/batch_data.shtml
Software tool to access various mouse genome information in batch format. Batch data and analysis tools.
Proper citation: Batch Data and Analysis Tool (RRID:SCR_017515) Copy
http://taylor0.biology.ucla.edu/structureHarvester/
Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Structure Harvester (RRID:SCR_017636) Copy
https://github.com/nci/drishti
Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc.
Proper citation: Drishti (RRID:SCR_017999) Copy
https://www.volumegraphics.com/de/produkte/vgstudio.html
Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data.
Proper citation: VG Studio MAX (RRID:SCR_017997) Copy
Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.
Proper citation: AmoebaDB (RRID:SCR_017592) Copy
https://github.com/XSLiuLab/tumor-immunogenicity-score
Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in.
Proper citation: TIGS (RRID:SCR_017565) Copy
https://CRAN.R-project.org/package=webchem
Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information.
Proper citation: webchem (RRID:SCR_017684) 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.
