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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.
https://github.com/bcgsc/NanoSim
Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software.
Proper citation: NanoSim (RRID:SCR_018243) Copy
https://github.com/mrc-ide/PhyDyn
Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST.
Proper citation: PhyDyn (RRID:SCR_018544) Copy
https://github.com/stekhoven/missForest
Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values.
Proper citation: missForest (RRID:SCR_018543) Copy
Web tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request.
Proper citation: Biorender (RRID:SCR_018361) Copy
https://mcguinlu.shinyapps.io/robvis/
Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project.
Proper citation: robvis (RRID:SCR_018755) Copy
Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives.
Proper citation: OpenCOR (RRID:SCR_019001) Copy
http://www.softberry.com/berry.phtml?topic=fgenesh_plus_plus&group=help&subgroup=pipelines
Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.
Proper citation: Fgenesh plus plus (RRID:SCR_018928) Copy
https://www.schrodinger.com/macromodel
Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.
Proper citation: MacroModel (RRID:SCR_016747) Copy
https://www.schrodinger.com/shape-screening
Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder.
Proper citation: Shape screening (RRID:SCR_016750) Copy
https://picrust.github.io/picrust/
Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.
Proper citation: PICRUSt (RRID:SCR_016855) Copy
Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility.
Proper citation: Experimental Design Assistant (RRID:SCR_017019) Copy
https://github.com/SciCrunch/NIF-Ontology/tree/neurons/ttl
An ontology for describing the complex phenotypes of neurons.
Proper citation: Neuron Phenotype Ontology (RRID:SCR_017403) Copy
https://neuron.yale.edu/neuron/
Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software.
Proper citation: NEURON (RRID:SCR_017449) Copy
https://www.toyobo-global.com/
Japanese company that began as a textile manufacturer in 1882 and has expanded to become a global provider of high-function products, including films, functional polymers, industrial materials, and biotechnology products such as enzymes and diagnostic reagents. The company's business is organized around its core technologies in polymerization, modification, processing, and biotechnology, allowing it to contribute to fields like healthcare, environment, and electronics.
Proper citation: TOYOBO (RRID:SCR_027440) Copy
https://github.com/SciCrunch/Antibody-Watch
Text mining antibody specificity from literature. Helps researchers identify potential problems with antibody specificity. By mining the scientific literature and linking findings to Research Resource Identifiers (RRIDs), it provides alerts on antibodies that may yield unreliable results, supporting reproducibility in biomedical research.
Proper citation: Antibody Watch (RRID:SCR_027424) Copy
https://www.revvity.com/product/ivis-spectrum-2-imaging-system-cls158738
In vivo optical imaging system used in preclinical research to non-invasively monitor and quantify biological processes in living animals over time. Designed with innovative camera with patented coating that delivers high sensitivity 2D and 3D bioluminescence and fluorescence imaging capabilities.
Proper citation: Revvity: IVIS Spectrum 2 In Vivo Imaging System (RRID:SCR_027425) Copy
https://biodataai.uth.edu/BRAINCELL-AID
Web service providing annotations for brain cell type–specific marker gene sets derived from single-cell RNA-seq data spanning the entire mouse brain. It uses a multi-agent AI framework that combines fine-tuned large language models with retrieval-augmented generation, producing biologically grounded annotations supported by peer-reviewed literature.
Proper citation: BRAINCELL-AID (RRID:SCR_027398) Copy
https://jaaba.sourceforge.net/
Web application to create variety of automatic behavior classifiers. These classifiers input the animals' trajectories computed by tracking system, and they output time series indicating whether each animal is performing a given behavior in each video frame. Interactive machine learning for automatic annotation of animal behavior. Used to automatically compute interpretable, quantitative statistics describing video of behaving animals.
Proper citation: Janelia Automatic Animal Behavior Annotator (RRID:SCR_027430) Copy
Target-to-Clinic Contract Research Organization (CRO) headquartered in San Diego, CA USA. ChemDiv executes pre-clinical discovery chemistry and biology for drug development and clinical trials for international portfolio of companies across the entire range of targets with small molecule and biotech drugs. The company operates multiple research and development (R&D) subsidiaries in Russia, Ukraine and China as well as business operations around the world.
Proper citation: ChemDiv (RRID:SCR_027402) Copy
https://www.jeol.com/products/scientific/sem/JCM-6000.php
Compact Benchtop Scanning Electron Microscope. Intuitive operation is achieved via touch panel and new operation screens. The high or low vacuum mode is included in the standard configuration, and EDS can be installed, offering truly multi-functional benchtop SEM.
Proper citation: JEOL: JCM-6000 Benchtop Scanning Electron Microscope (RRID:SCR_027403) Copy
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