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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core Resource Report Resource Website 1+ mentions |
Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core (RRID:SCR_007342) | Tulane Tissue Culture Core | biomaterial supply resource, cell repository, material resource | The Stem Cell Research and Regenerative Medicine''s Tissue Culture Core provides cells for research use within the department, as well as for distribution to other facilities. The core obtains hMSCs from bone marrow donor samples and expands these cells for research use. The hMSC''s are also characterized for bone, fat and cartilage differentiation, and are stored on site for use. The Tissue Culture Core also handles the expansion and characterization of mouse and rat MSC''s. The animal cells are cultured in a separate area, and never interact with human derived cells. We also have a supply of hMSC''s marked with GFP+, Mito Red and Mito Blue available. | stem cell, mesenchymal stem cell, marrow stromal cell, frozen, adult, bone marrow, adipose tissue, bone, fat, cartilage |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Tulane University School of Medicine; Louisiana; USA |
United States Department of DefenseBlueprint for Neuroscience Research ; NSF ; NIH |
Public: The Tissue Culture Core provides cells for research use within the department, As well as for distribution to other facilities. | nif-0000-00246 | http://www.som.tulane.edu/gene_therapy/distribute.shtml | SCR_007342 | Tulane Stem Cell Research Regenerative Medicine Tissue Culture Core | 2026-09-12 01:00:57 | 1 | |||||
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Academic Seismic Portal at UTIG Resource Report Resource Website |
Academic Seismic Portal at UTIG (RRID:SCR_000403) | ASP at UTIG, ASP_UTIG | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links. | seismic, metadata, image, reflection, refraction, marine geology, geophysics |
is listed by: re3data.org is listed by: CINERGI is related to: Academic Seismic Portal at LDEO has parent organization: University of Texas at Austin; Texas; USA |
NSF | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154745, r3d100010631 | https://doi.org/10.17616/R3CP6C | SCR_000403 | Academic Seismic Portal (ASP) at UTIG | 2026-09-12 01:02:23 | 0 | |||||
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Honey Bee Brain EST Project Resource Report Resource Website 1+ mentions |
Honey Bee Brain EST Project (RRID:SCR_002389) | Bee-ESTdb | biomaterial supply resource, material resource | A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu. | expressed sequence tag, brain, behavior, cdna, blast, gene, annotation, microarray, gene expression, comparative genomics, cdna clone, resource:genbank |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NSF ; University of Illinois Critical Research Initiatives Program ; Burroughs Wellcome Fund |
PMID:11932240 | Free | nif-0000-00118 | SCR_002389 | Honeybee EST Project | 2026-09-12 01:02:27 | 5 | |||||
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CGSC Resource Report Resource Website 10+ mentions |
CGSC (RRID:SCR_002303) | CGSC | biomaterial supply resource, material resource | The CGSC Collection contains only non-pathogenic BSL-1 laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies, but a few B strains. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. The collection includes cultures of wild-type contributed from a number of laboratories and a few thousand derivatives carrying one or up to 29 mutations from among 3500 mutations in (or included in deletions spanning) more than 1300 different loci. Some combinations were constructed particularly for mapping purposes and are still used for teaching and for rapid localization, some for manifestation of a particular phenotype, some strains for transferring a particular region or for complementation analysis. Some plasmids, e.g., the Clarke and Carbon collection, F-primes, a number of toolkit plasmids, and a few classic plasmids are included, but it is not a comprehensive collection of plasmids. Additionally, we have recently acquired most of the strains from the Keio Collection of systematic individual gene knockout (deletion/kan insertion) strains. | e. coli. escherichia coli, chromosome, culture, genotype, interval, k-12, linkage map, locus, mutation, non-pathogenic, phenotype, plasmid, prokaryote, strain, wild-type, auxotrophic, amino acids, wanner lambda red, gene disruption, keio knockout |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Yale University; Connecticut; USA |
NSF DBI-0742708; User fees |
nif-0000-21083 | SCR_002303 | The Coli Genetic Stock Center, E. coli Genetic Stock Center, CGSC - The Coli Genetic Stock Center, Coli Genetic Stock Center | 2026-09-12 01:02:27 | 27 | |||||||
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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 | 2026-09-12 01:02:33 | 1 | ||||||||||
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ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software application, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-09-12 01:01:05 | 1 | ||||||
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FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | data processing software, software application, software resource | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NDSEG Fellowship ; NIAID R21 AI115014; NSF Graduate Research Fellowship DGE 0940902; NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; Welch Foundation |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-09-12 01:01:07 | 6 | |||||
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CloudReg Resource Report Resource Website |
CloudReg (RRID:SCR_022795) | data processing software, image analysis software, software application, software resource | Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration. | brain volume, nonlinear registration, automatic terabyte scale, cross modal brain volume registration, image analysis pipeline, volumetric datasets with artifacts | is used by: BICCN | AP Giannini Foundation ; Johns Hopkins University Kavli Neuroscience Discovery Institute Postdoctoral Fellowship ; Karen Toffler Charitable Trust ; Kavli Neuroscience Discovery Institute ; Microsoft Research ; NIA P01AG009973; NIA R01 AG066184; NIDA 1K99DA050662; NIMH K08MH113039; NIMH R01 MH099647; NIMH U19MH114821; NINDS K99 NS116122; NSF EEC 1707298 |
PMID:34253927 | Free, Available for download, Freely available | https://github.com/neurodata/CloudReg/ | SCR_022795 | 2026-09-12 01:01:11 | 0 | |||||||
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Kourami Resource Report Resource Website 1+ mentions |
Kourami (RRID:SCR_022280) | data processing software, software application, software resource | Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X. | graph guided assembly, novel human leukocyte antigen allele discovery, HLA alleles, HLA alleles assembly | Gordon and Betty Moore Foundation ; NHGRI R01HG007104; NSF CCF1256087; NSF CCF1319998 |
PMID:29415772 | Free, Available for download, Freely available | SCR_022280 | 2026-09-12 01:01:11 | 4 | |||||||||
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iSamples Resource Report Resource Website 1+ mentions |
iSamples (RRID:SCR_021750) | data or information resource, portal, project portal | Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications. | Align physical sample identifiers, physical sample identifiers, align identifiers | NSF 2004562; NSF 2004642; NSF 2004815; NSF 2004839 |
DOI:10.1093/gigascience/giab028 | Free, Freely available | https://zenodo.org/communities/isamples?page=1&size=20 | SCR_021750 | internet of Samples | 2026-09-12 01:01:10 | 1 | |||||||
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Rascaf Resource Report Resource Website 1+ mentions |
Rascaf (RRID:SCR_022014) | data processing software, software application, software resource | Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data. | Scaffolding, RNA-seq data, scaffolding with RNAseq read alignments, improving genome assembly, RNA sequencing data | NSF IOS1339134 | DOI:10.3835/plantgenome2016.03.0027 | Free, Available for download, Freely available | SCR_022014 | 2026-09-12 01:01:10 | 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 listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Allen Institute for Brain Science ; General Electric ; Howard Hughes Medical Institute ; International Neuroinformatics Coordinating Facility ; Kavli Foundation ; NIH BRAIN Initiative R24 MH116922; NSF 0855272 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-09-12 01:02:55 | 4 | ||||||
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CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software resource, software toolkit | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | Howard Hughes Medical Institute ; LEO Foundation ; NIGMS R01 GM123731; NIH P30 AR07504; NIH U01 AR073159; NSF DMS1763272; Pew Charitable Trust ; Simons Foundation ; UC Irvine |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-09-12 01:02:59 | 753 | ||||||||
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simplePHENOTYPES Resource Report Resource Website 1+ mentions |
simplePHENOTYPES (RRID:SCR_022523) | software resource, software toolkit | Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy. | Multiple traits simulation, pleiotropy, partial pleiotropy, spurious pleiotropy, causal mutations affecting multiple traits |
is related to: CRAN is related to: R Project for Statistical Computing |
NSF 1733606 | PMID:33129253 | Free, Available for download, Freely available | https://github.com/samuelbfernandes/simplePHENOTYPES | SCR_022523 | Simulation of Pleiotropic, Linked and Epistatic Phenotypes | 2026-09-12 01:03:01 | 2 | ||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | American Cancer Society Research Scholar Grant ; NCI U24CA143835; NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950 |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-09-12 01:03:03 | 1 | ||||||||
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Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software resource, software toolkit | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | Alfred P. Sloan Foundation ; Gordon and Betty Moore Foundation ; NIBIB R01EB027585; NIMH 1RF1MH121868; NSF 1551330; The BRAIN Initiative |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-09-12 01:03:04 | 12 | ||||||||
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MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software resource, software toolkit | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NHGRI R01HG005220; NIAID U19AI110820; NIDDK R24DK110499; NIDDK U54DK102557; NSF DEB-2028280 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-09-12 01:03:04 | 212 | ||||||||
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AmpliconArchitect Resource Report Resource Website 50+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software resource, software toolkit | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NHGRI HG010149; NIGMS R01GM114362; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-09-12 01:03:03 | 53 | ||||||||||
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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 | NIDA DK097771; NIGMS R01GM113952; NSF III1755761 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-09-12 01:03:02 | 1 | ||||||||
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VirusDetect Resource Report Resource Website 10+ mentions |
VirusDetect (RRID:SCR_023669) | software resource, software toolkit | Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs. | Virus discovery, analyze large scale sRNA datasets, virus identification, deep sequencing of small RNAs, sequencing, small RNAs | NSF | PMID:27825033 | Free, Available for download, Freely available | https://github.com/kentnf/VirusDetect | SCR_023669 | 2026-09-12 01:03:05 | 18 |
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