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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.
http://hmpdacc.org/resources/tools_protocols.php
A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files.
Proper citation: Core Gene Evaluation Script (RRID:SCR_014604) Copy
https://sourceforge.net/projects/invue/
An API and software suite for large scale data visualization and analysis.
Proper citation: inVUE (RRID:SCR_014608) Copy
A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.
Proper citation: RAST Server (RRID:SCR_014606) Copy
http://www.med-associates.com/product-category/video-software/
Automation software used to analyze fear behavior in rodents. Freezing is represented in the data file in several different ways, including the total time the subject spends motionless during the session, the percent of time motionless, the number of freezing episodes or occurrences, or as an average index of motion.
Proper citation: Med Associates Video Freeze Software (RRID:SCR_014574) Copy
https://www.deshawresearch.com/resources_desmond.html
Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer.
Proper citation: Desmond (RRID:SCR_014575) Copy
http://www.brainsimagebank.ac.uk
A searchable collection of anonymised images and associated clinical data. It includes normal individuals at all ages (from prenatal to old age). The image bank contains integrated data sets already collected as part of research studies which include control subjects. New data is added as they become available.
Proper citation: BRAINS Imagebank (RRID:SCR_014576) Copy
https://www.licor.com/bio/products/imaging_systems/odyssey/
A data analysis software developed to simplify and record data from fluorescent related assays such as Western Blots, EMSAs, and Western Assays. This software will consolidate all of the resulting data into one easy-to-track image, and thus removes the need for multiple exposures, as well as standardizing the resulting fluorescent bands without image saturation, blowout, or removed sensitivity. Odyssey CLx is capable of scanning multiple mini-blots, microplates, or slides at the same time.
Proper citation: Odyssey CLx (RRID:SCR_014579) Copy
https://cran.r-project.org/web/packages/HMP/index.html
An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments.
Proper citation: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP (RRID:SCR_014612) Copy
http://biocore.github.io/SitePainter/
An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context.
Proper citation: SitePainter (RRID:SCR_014618) Copy
http://aem.asm.org/content/71/12/8228.full
THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.
Proper citation: Unifrac (RRID:SCR_014616) Copy
http://www.imb.sinica.edu.tw/core/publicfacilities/pdf/LAS-1000plus_om_e_ver2.pdf
A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned.
Proper citation: Image Reader LAS-1000 (RRID:SCR_014585) Copy
https://www.edaq.com/ES280_PowerChrom-Software
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. A software which collects, displays, and analyzes chromatographic signals. This software doesn't require any programming, and collects signals from one or two detectors. PowerChrom is supplied as part of the PowerChrom system, or separately for use with e-corder recording systems.
Proper citation: PowerChrom (RRID:SCR_014588) Copy
http://www.cbcb.umd.edu/software/metapath
A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG.
Proper citation: Metapath (RRID:SCR_014621) Copy
A programming library that uses standard graphics cards to produce 2D and 3D visual stimuli for vision research experiments.
Proper citation: Vision Egg (RRID:SCR_014589) Copy
A public–private initiative that supports research that provides evidence on the biological validity of therapeutic targets and that gain insight into the effectiveness of pharmacological intervention. It aims to provide a research and development framework that applies human disease. It shares its information openly.
Proper citation: Open Targets (RRID:SCR_014622) Copy
http://sea.rice.edu/sites/g/files/bxs231/f/Using%20the%20Axioskop%20Details%20Guide%20061413_0.pdf
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 19, 2022. Software used to control the Zeiss Axioskop microscope.
Proper citation: Zeiss Axioskop Software (RRID:SCR_014587) Copy
http://huttenhower.sph.harvard.edu/humann
A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities.
Proper citation: HUMAnN (RRID:SCR_014620) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub.
Proper citation: HDD Access (RRID:SCR_014581) Copy
http://www.proteinsimple.com/fluorchem_q.html
A software used for quantitative Western blot imaging and analysis. This software is compatible with several dyes and kits, providing extra flexibility for application. This software is designed to be able to look at multiple proteins simultaneously on a single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated isoforms.
Proper citation: FluorChem Q Imager (RRID:SCR_014549) Copy
Ratings or validation data are available for this resource
http://www.olympus-lifescience.com/en/software/cellsens/
Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.
Proper citation: Olympus cellSens Software (RRID:SCR_014551) Copy
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