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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Planet Microbe Resource Report Resource Website 1+ mentions |
Planet Microbe (RRID:SCR_024478) | web application, software resource | Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data. | data discovery, curated oceanographic sequencing, biological and physiochemical measurements, water samples, marine microbiology, discover and analyze interconnected 'omics and environmental data, | has parent organization: University of Arizona; Arizona; USA | NSF | PMID:32735679 | Free, Freely available | https://github.com/hurwitzlab/planet-microbe-app | SCR_024478 | 2026-02-15 09:22:43 | 2 | |||||||
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ORION Software Resource Report Resource Website 1+ mentions |
ORION Software (RRID:SCR_004389) | service resource, software resource | ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. | has parent organization: University of Houston; Texas; USA | University of Houston; Texas; USA ; NIA RO1-AG027577; NSF IIS-0431144; NSF IIS-0638875; NSF DMS-0915242 |
nlx_40212 | SCR_004389 | 2026-02-15 09:18:42 | 1 | ||||||||||
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BioSimulations Resource Report Resource Website |
BioSimulations (RRID:SCR_018733) | web application, software resource | Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell. | Sharing, reusing, biomodel, simulation, visualization, simulation result, modeling framework support, simulation tool support, model format support, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA has parent organization: University of Connecticut; Connecticut; USA |
NIBIB P41 EB023912; NSF ; NIGMS |
Restricted | biotools:biosimulations | https://bio.tools/biosimulations | SCR_018733 | 2026-02-15 09:22:23 | 0 | |||||||
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runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | web application, software resource | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NSF ; NIH |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | 2026-02-15 09:22:22 | 3 | |||||||
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PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Kavli Foundation ; General Electric ; Howard Hughes Medical Institute ; Allen Institute for Brain Science ; NSF 0855272; International Neuroinformatics Coordinating Facility ; NIH BRAIN Initiative R24 MH116922 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-02-15 09:22:02 | 4 | ||||||
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OmicsGAN Resource Report Resource Website 1+ mentions |
OmicsGAN (RRID:SCR_022976) | software application, software resource | Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals. | integrate two omics data, interaction network, generate one synthetic data corresponding to each omics profile, phenotype prediction | NSF III1755761; NIGMS R01GM113952; NIDA DK097771 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-02-15 09:23:07 | 1 | ||||||||
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PRECISE Resource Report Resource Website 50+ mentions |
PRECISE (RRID:SCR_007874) | PRECISE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of interactions between amino acid residues of enzyme and its ligands. Provides summary of interactions between amino acid residues of enzyme and its various ligands including substrate and transition state analogues, cofactors, inhibitors, and products., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | enzyme, enzyme and enzyme nomenclature databases, function, align, amino acid, analogue, atom, chain, cofactor, complex, hydrogen bond, inhibitor, interaction, ligand, product, residue, sequence, structure, substrate, transition state | has parent organization: Boston University; Massachusetts; USA | NSF | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21331, SCR_008230 | http://precise.bu.edu/precisedb/ | SCR_007874 | Predicted and Consensus Interaction Sites in Enzymes | 2026-02-16 09:47:03 | 53 | |||||
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iDEP: Integrated Differential Expression and Pathway analysis Resource Report Resource Website 1+ mentions |
iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) | iDEP | web application, software resource | Integrated web application for differential expression and pathway analysis of RNA-Seq data. | differential expression, pathway analysis, RNA-Seq data, | NIGMS GM083226; NSF ; State of South Dakota |
PMID:30567491 | Free, Freely available | SCR_027373 | 2026-02-15 09:24:17 | 8 | ||||||||
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Genes to Cognition: Neuroscience Research Programme Resource Report Resource Website 10+ mentions |
Genes to Cognition: Neuroscience Research Programme (RRID:SCR_007121) | data or information resource, topical portal, portal | A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers. | cognition, gene, neuroscience |
is listed by: 3DVC has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
nif-0000-10235 | SCR_007121 | G2C Neuroscience Research Program, G2C Research Programme, Genes to Cognition: Neuroscience Research Program, Genes to Cognition, G2C, Genes to Cognition - Neuroscience Research Programme, Genes to Cognition-Neuroscience Research Programme, G2C Research Program | 2026-02-16 09:46:53 | 19 | ||||||||
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DelPhi Resource Report Resource Website 1000+ mentions |
DelPhi (RRID:SCR_008669) | software application, software resource, simulation software | DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. Features of DelPhi include solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; and estimation of the best relaxation parameter at run time. | Poisson-Boltzmann equation, electrostatics, simulation software, mixed salt soluton |
has parent organization: Columbia University; New York; USA has parent organization: Howard Hughes Medical Institute |
NSF DBI-9904841 | nif-0000-33392 | SCR_008669 | 2026-02-16 09:47:14 | 1420 | |||||||||
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Human Brain Atlas Resource Report Resource Website 1+ mentions |
Human Brain Atlas (RRID:SCR_006131) | Human Brain Atlas | data or information resource, video resource, atlas | A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp | human, adult, mri, fiber stain, anatomy, normal, neuroanatomy, nissl stain, image, brainstem, cell body, nerve fiber, brain, coronal, sagittal, horizontal, 3d model, montage, weil, hypothalamus |
is used by: NIF Data Federation has parent organization: Michigan State University; Michigan; USA |
NSF IBN 0131267; NSF 0131826; NSF 0131028 |
Copyrighted, Public, Request that you secure their permission, Acknowledgement required | nif-0000-00088 | SCR_006131 | MSU Brain Biodiversity Bank - Human Brain Atlas, Michigan State University Brain Biodiversity Bank - Human Brain Atlas | 2026-02-16 09:46:37 | 3 | ||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | service resource, data repository, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-02-16 09:48:58 | 35 | |||||||||
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CalC Resource Report Resource Website 10+ mentions |
CalC (RRID:SCR_014259) | software application, software resource, simulation software | A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website. | simulation software, modeling tool, intracellular calcium diffusion, intracellular calcium buffering, pde | NSF 0417416; NSF 0817703; NSF 1517085 |
Free, Acknowledgement requested | SCR_014259 | Calcium Calculator | 2026-02-16 09:48:33 | 30 | |||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | software application, software resource, simulation software | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2026-02-16 09:48:37 | 13 | |||||||||
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PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | software application, software resource, simulation software | 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. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | Canadian Institutes of Health Research ; Canada Research Chairs program ; Howard Hughes Medical Institute ; NIDDK P01 DK078669; NHGRI U01 HG004866; NHGRI R01 HG004872; Crohn’s and Colitis Foundation of America ; Sloan Foundation ; NHGRI R01 HG005969; NSF CAREER DBI1053486; ARO W911NF1110473 |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-02-16 09:49:06 | 36 | |||||
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abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | source code, software resource | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596; Harvard University |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-02-15 09:23:06 | 1 | ||||||||
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PTNet Resource Report Resource Website |
PTNet (RRID:SCR_022975) | source code, software resource | Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression. | protein level, protein expression estimation, miRNA-mRNA interactions, mRNA expression, miRNA expression, | NSF III1755761; NIGMS R01GM113952; NIDDK DK097771 |
DOI:10.1093/bib/bbab264 | Free, Available for download, Freely available | SCR_022975 | 2026-02-15 09:22:56 | 0 | |||||||||
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BehaviorDEPOT Resource Report Resource Website 1+ mentions |
BehaviorDEPOT (RRID:SCR_023602) | source code, software resource | Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs. | OpenBehavior, automated behavioral detection, markerless pose tracking, detect frame by frame behavior, video time series, kinematic and postural statistics, |
is listed by: OpenBehavior is related to: SLEAP, LEAP and MotionMapper project works with: DeepLabCut |
NIMH K01MH116264; NIMH K08MH116125; Whitehall Foundation ; Simonsen Foundation ; NSF ; NIMH T32MH073526; Brain Research Foundation ; Brain and Behavior Research Foundation |
PMID:35997072 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/behaviordepot/ | SCR_023602 | 2026-02-15 09:23:13 | 1 | |||||||
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ezBIDS Resource Report Resource Website |
ezBIDS (RRID:SCR_025563) | web application, software resource | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | NINDS UM1NS132207; BRAIN CONNECTS ; NIBIB R01EB029272; NIBIB R01EB030896; NSF ; Kavli Foundation ; Wellcome Trust ; NIMH R01MH133701; Spanish Government |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/ |
SCR_025563 | ez Brain Imaging Data Structure | 2026-02-15 09:23:56 | 0 | |||||||
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ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | source code, software resource | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-02-15 09:19:11 | 5 |
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