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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Berkeley Drosophila Genome Project Resource Report Resource Website 100+ mentions |
Berkeley Drosophila Genome Project (RRID:SCR_013094) | BDGP, BDGP EST, BDGP INS | data or information resource, database | Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs. | drosophila genome, cdna, est, transposon insertions, genomic sequencing, gene, FASEB list |
is related to: Bgee: dataBase for Gene Expression Evolution is related to: OpenFlyData.org has parent organization: University of California at Berkeley; Berkeley; USA is parent organization of: Patterns of Gene Expression in Drosophila Embryogenesis |
NHGRI ; NIGMS |
PMID:21177961 | nif-0000-02867, r3d100010624 | http://www.bdgp.org/ | SCR_013094 | SciCrunch Registry | 2026-09-26 02:19:22 | 478 | ||||||
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Duke Human Heart Repository Resource Report Resource Website 50+ mentions |
Duke Human Heart Repository (RRID:SCR_013980) | biomaterial supply resource, material resource | A biomaterial supply resource which collects and disseminates human heart tissue. Samples include both failing and non-failing hearts, RNA/DNA analysis, tissue staining and immunofluorescence samples.The tissue that has been flash frozen and stored at -80˚C is acquired from distinct regions of the heart such as the LV free wall, septum, and valve leaflets. Individual sample sizes are typically 100-300mg for flash frozen tissues. The DHHR also serves as a resource for assay development, target identification, and sponsored research, capable of isolating cardiomyocytes from hearts and using them for in-vitro assays such as calcium handling, enzyme activity, signalling pathways and other biochemical research activities | biomaterial supply resource, human heart, human heart tissue, cardiovascular, tissue, tissue sample |
lists: American Heart Association lists: ASPET lists: Duke Biobank lists: International Society for Biological and Environmental Repositories lists: American Society for Cell Biology is listed by: Connected Researchers is related to: Connected Researchers has parent organization: Duke University; North Carolina; USA |
Free, Available to the research community | SCR_013980 | SciCrunch Registry | 2026-09-26 02:19:23 | 89 | ||||||||||
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Brain Health Registry Resource Report Resource Website 10+ mentions |
Brain Health Registry (RRID:SCR_010230) | Brain Health Registry | patient registry, people resource | A website aimed at recruiting and assessing subjects for all types of neuroscience studies with the internet. The hope is to accelerate various types of observational studies and clinical trials, and also reduce costs. They are interested in having people, including healthy subjects of all ages, join the registry. Joining only takes a few minutes. The web-based project is designed to speed up cures for Alzheimer's, Parkinson's and other brain disorders. It uses online questionnaires and online neuropsychological tests (which are very much like online brain games). | questionnaire, brain test, brain, health, neuropsycholgoical test, game, clinical trial | has parent organization: University of California at San Francisco; California; USA | Alzheimer's disease, Parkinson's disease, Depressive Disorder, Traumatic brain injury, Brain disorder, Post-Traumatic Stress Disorder, Aging | Free, The community can contribute to this resource | nlx_156798 | SCR_010230 | SciCrunch Registry | 2026-09-26 02:19:20 | 14 | |||||||
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Dexy Resource Report Resource Website |
Dexy (RRID:SCR_013982) | software application, software resource | A multi-purpose project automation tool written in Python which helps create technical documents. Dexy is a free-form literate documentation tool for writing any kind of technical document incorporating code. It provides a consistent interface to tools and scripts and keeps track of what to run, in which order, and with what parameters. | software application, Python, technical document, documentation tool, live code |
is listed by: Connected Researchers is related to: Connected Researchers |
OpenGamma | Open source | SCR_013982 | SciCrunch Registry | dexy | 2026-09-26 02:19:23 | 0 | ||||||||
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CDE Tool Resource Report Resource Website |
CDE Tool (RRID:SCR_013981) | software application, software resource, systems interoperability software | A software application which automatically packages up the code, data, and environment required to deploy and run Linux programs on other machines without any installation or configuration. Users can prepend any set of Linux commands with the "cde" binary, and CDE will run them and automatically package up all files accessed during execution. A package is a directory that can be compressed and delivered to any x86-Linux machine and contains all the files and environment variables required to run the original commands. After receiving the package, the user can run those same commands from within the package on any modern x86-Linux distro., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | software application, CDE, Linux, systems interoperability software |
is listed by: Connected Researchers is related to: Connected Researchers |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/pgbovine/CDE/ | SCR_013981 | SciCrunch Registry | CDEpack | 2026-09-26 02:19:23 | 0 | ||||||||
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NEMO Analysis Toolkit Resource Report Resource Website |
NEMO Analysis Toolkit (RRID:SCR_013624) | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. The NEMO ERP Analysis Toolkit includes tools for EEG/ERP and MEG data decomposition, and ontology-based mark-up, annotation, and labeling of patterns in EEG and MEG data. These tools have been implemented in MATLAB by Robert Frank, a mathematician and data analyst for NEMO. The current NEMO analysis pipeline has been designed with the aim to support cross-lab, cross-experiment meta-analysis of EEG and MEG data. The current proposed processing pipeline consists of the following steps: * Step 1: Decomposing ERP data (continuous data are transformed into discrete patterns for analysis) o PCA/ ICA/Microstate * Step 2: Marking up the analysis results o Each pattern is annotated with labels that relate pattern attributes to NEMO ontology concepts * Step 3: Clustering the observed patterns within and across experimental groups * Step 4: Labeling the cross-experiment clusters Each item in the above list is a step/phase in the processing pipeline and is associated with a set of matlab scripts in our NEMO ERP Analysis Toolkit, which is implemented by a collection of MATLAB scripts. |
is related to: NEMO Ontology has parent organization: University of Oregon; Oregon; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32929 | SCR_013624 | SciCrunch Registry | NEMO ERP Analysis Toolkit | 2026-09-26 02:19:23 | 0 | |||||||||
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Cellosaurus Resource Report Resource Website 100+ mentions |
Cellosaurus (RRID:SCR_013869) | data or information resource, database | Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples. | RIN, Resource Information Network, cell lines, thesaurus, controlled vocabularies, ontologies, RRID Community Authority, |
is used by: ExPASy Bioinformatics Resource Portal is listed by: Resource Information Network is related to: CLASTR has parent organization: SIB Swiss Institute of Bioinformatics works with: ATCC works with: Taiwan Bioresource Collection and Research Center works with: Rio de Janeiro Cell Bank works with: CellBank Australia works with: Collection of Cell Lines in Veterinary Medicine works with: Cell Lines Service works with: Coriell Cell Repositories works with: Drosophila Genomics Resource Center works with: German Collection of Microorganisms and Cell Cultures works with: EBiSC works with: European Collection of Cell Cultures works with: Interlab Cell Line Collection works with: IZSLER Biobank works with: Japanese Collection of Research Bioresources Cell Bank works with: Kunming Wild Animal Cell Bank works with: Korean Cell Line Bank works with: Millipore works with: National Cancer Institute Developmental Therapeutics Program works with: The NINDS Human Cell and Data Repository (NHCDR) works with: NIH AIDS Reagent Program works with: RIKEN BioResource Center works with: Tohoku University Cell Resource Center for Biomedical Research Cell Bank works with: Ximbio |
Swiss Institute of Bioinformatics | PMID:29805321 | Free, Freely available | nif-0000-30108, r3d100010875 | https://doi.org/10.17616/R31906 | SCR_013869 | SciCrunch Registry | 2026-09-26 02:19:23 | 178 | ||||||
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Cluster Resource Report Resource Website 5000+ mentions |
Cluster (RRID:SCR_013505) | Cluster | software resource, software toolkit | Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets. | Cluster analysis, processing on large microarray datasets |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:14871861 | Free, Available for download, Freely available | OMICS_01571 | http://www.eisenlab.org/eisen/?page_id=42, https://sources.debian.org/src/cluster3/ | SCR_013505 | SciCrunch Registry | Cluster 3.0 | 2026-09-26 02:19:23 | 5814 | |||||
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Kitware Resource Report Resource Website 10+ mentions |
Kitware (RRID:SCR_013989) | service resource, software repository, software resource | A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training. | software repository, open source, visualization, computer vision, medical imaging, data publishing, quality software process solutions |
is listed by: Connected Researchers is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VTK CISG Registration Toolkit is related to: Connected Researchers is parent organization of: Midas Platform is parent organization of: ParaView is parent organization of: VolView is parent organization of: VTK |
PASCAL network of excellence ; Max-Planck Society ; Fraunhofer Society |
Open source | SCR_013989 | SciCrunch Registry | 2026-09-26 02:19:23 | 12 | |||||||||
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SFMProject Resource Report Resource Website |
SFMProject (RRID:SCR_014166) | software repository, software resource | Structure from motion algorithms repository. Common interface for various sfm algorithms. | motion algorithm, repository, sfm algorithm | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014166 | SciCrunch Registry | 2026-09-26 02:19:25 | 0 | ||||||||||
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machine learning open source software Resource Report Resource Website 10+ mentions |
machine learning open source software (RRID:SCR_013990) | mloss | software repository, software resource | A software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of mloss.org is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source solutions. | software repository, machine learning, machine learning software |
is listed by: Connected Researchers is related to: Connected Researchers |
Open source, The community can contribute to this resource | SCR_013990 | SciCrunch Registry | mloss.org | 2026-09-26 02:19:23 | 14 | ||||||||
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MVZ Collections Resource Report Resource Website 1+ mentions |
MVZ Collections (RRID:SCR_010608) | MVZ Collections | biomaterial supply resource, material resource | A collection of over 640,000 specimens of amphibians, reptiles, birds, bird eggs or nests, and mammals, as well as over 50,000 tissue samples from these vertebrate groups. These research collections are ranked as one of the largest in the United States, and the largest of any university museum. In addition, the Museum has numerous special collections that include archived field notes and photographs, historical annotated maps and correspondence, avian sound recordings, chromosome and histology preparations, Milton Hildebrand anatomical and film collections, artwork related to terrestrial vertebrate natural history, and a library of books, reprints, and journals for curation and research activities. Specimen data are accessible online, and the Museum is working to improve data access to the other collections. Museum Collections * Mammal Collection * Herpetological Collection * Bird Collection * Egg & Nest Collection * Tissue Collection * Fieldnotes, Photos, & Map Collection * Other Collections The Museum of Vertebrate Zoology (MVZ) welcomes donations of amphibians, reptiles, birds, bird eggs and nests, mammals and related materials. Acceptance of a donation is at the discretion of MVZ Curators. * Specimens -- May include preserved specimens and/or parts (e.g., tissue samples) as well as unpreserved material (e.g., frozen carcasses, live animals) that will be prepared by Museum Curators, curatorial staff, or students. * Related Materials -- Donations of images (digital or printed photographs or slides), sound recordings, field notes, and other natural history archival material. Materials must be connected to specimens or research projects. Donated material and associated data will be made available for research, education, or public exhibit according to the mission and policies of the Museum and Regents, except by prior signed agreement between the donor and the Museum. | tissue, dna, egg, nest, tissue, blood, protein extract, skin, skeleton |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Museum of Vertebrate Zoology |
Will provide limited grants of tissue from its collections to qualified researchers | nlx_51505 | SCR_010608 | SciCrunch Registry | Museum of Vertebrate Zoology Collections | 2026-09-26 02:19:21 | 1 | |||||||
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Rayburst Open-Source Code Resource Report Resource Website |
Rayburst Open-Source Code (RRID:SCR_013799) | software application, software resource | A software application which provides the source code for the Rayburst Algorithm. The fully automated algorithm casts rays in a 2D/3D dataset without the use of pre-generated ray tables. It is implemented in ANSI C as a single module. The most current version is Version 1.1, last updated on Aug. 15, 2006. | software application, Rayburst Algorithm, ANSI C |
is listed by: Computational Neurobiology and Imaging Center is related to: Computational Neurobiology and Imaging Center has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Free, Public | SCR_013799 | SciCrunch Registry | 2026-09-26 02:19:23 | 0 | ||||||||||
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Mayo Clinic Biobank Resource Report Resource Website |
Mayo Clinic Biobank (RRID:SCR_010723) | Mayo Clinic Biobank | biomaterial supply resource, material resource | A collection of blood samples and health information donated by volunteers, not focusing on any specific disease. Unlike many biobanks already in existence at Mayo Clinic and elsewhere, the Mayo Clinic Biobank is NOT focused on any particular disease. Rather, this biobank will collect samples and health information on patients and volunteers regardless of their health history. The only requirement is that they be 18 years of age or older, have a Mayo Clinic number, and be able to give informed consent. Once a participant becomes a part of the Biobank, they will be a part of ongoing health research conducted at Mayo Clinic indefinitely. The Biobank was established at Mayo Clinic, Rochester, and recruitment began in April of 2009. The goal of this project is to enroll 20,000 Mayo Clinic patients over the course of a three-year period in an effort to support a wide array of health-related research studies throughout the Institution. | blood, clinical data |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
All 18 years of age or older, Aging | nlx_91152 | SCR_010723 | SciCrunch Registry | 2026-09-26 02:19:21 | 0 | ||||||||
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dcm2nii Resource Report Resource Website 100+ mentions |
dcm2nii (RRID:SCR_014099) | software application, software resource, systems interoperability software | A tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the NIfTI format used by various scientific tools. dcm2nii works for all modalities (CT, MRI, PET, SPECT) and sequence types. | image converter, nifti format, systems interoperability software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of South Carolina; South Carolina; USA |
NIDCD R01DC009571; NIDCD U01DC011739 |
Available for download | http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage | SCR_014099 | SciCrunch Registry | 2026-09-26 02:19:23 | 205 | ||||||||
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WEIGHTED FDR Resource Report Resource Website |
WEIGHTED FDR (RRID:SCR_013442) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154604, SCR_000848, nlx_154690, biotools:weighted_fdr | https://bio.tools/weighted_fdr | SCR_013442 | SciCrunch Registry | R/WEIGHTED_FDR | 2026-09-26 02:19:23 | 0 | ||||||||
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iso2mesh Resource Report Resource Website 10+ mentions |
iso2mesh (RRID:SCR_013202) | iso2mesh | software application, software resource, software toolkit | A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling. | matlab, mesh generation, modeling, magnetic resonance, optical imaging, os independent, mri, computed tomography, octave |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155855 | http://www.nitrc.org/projects/iso2mesh | SCR_013202 | SciCrunch Registry | 2026-09-26 02:19:22 | 28 | |||||||
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GenGen Resource Report Resource Website 10+ mentions |
GenGen (RRID:SCR_013447) | GenGen | software application, software resource | A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. | genomic analysis, imaging genomics, pathway, network, snp, gene, genetics, genomics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: OpenBioinformatics.org |
Free | nlx_155766 | http://www.nitrc.org/projects/gengen | SCR_013447 | SciCrunch Registry | GenGen: Genetic Genomics Analysis of Complex Data | 2026-09-26 02:19:22 | 26 | ||||||
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Lifelines Biobank Resource Report Resource Website 10+ mentions |
Lifelines Biobank (RRID:SCR_010730) | Lifelines Biobank | biomaterial supply resource, material resource | Overall aim of the LifeLines Study is to unravel the interaction between genetic and environmental factors in the development of multifactorial diseases, their concurrent development in individuals and their complications as a complex trait. The LifeLines database contains questionnaire data, physical measurements and biological samples from different health examinations. Collaboration is encouraged as it helps to maximize the scientific value of the wealth of epidemiologic data made possible by the participation of more than 165,000 individuals in the LifeLines Cohort Study. Primary objectives of the LifeLines Cohort Study are: a. Which are the disease overriding risk factors which predict the development of a multifactorial disease during lifetime? b. How are these universal risk factors modified, or what determines the effect of a universal risk factor in an individual? Specific research questions will focus on risk factors and modifiers (genetic, environmental and combined or complex factors) for single and multiple diseases. In addition to co-morbidity, LifeLines focuses on co-determinants. The primary endpoints include measures of aging, metabolic and endocrine diseases, cardiovascular and renal diseases, pulmonary and musculoskeletal diseases, and psychopathology. Secondary aims include the assessment of the prevalence and incidence of multifactorial diseases, their risk factors and their treatment in individuals as well as in families. The burden of disease for the society will be quantified in terms of care needed, and total costs of care. Until November 3, 2011, almost 68,000 subjects have been included in the study. The 60,000th participant was screened in the beginning of September 2011. Recruitment rate at present is between 700 and 800 subjects per week. The laboratory measurements which are performed has changed. As of October 2011, LifeLines will continue to measure: hematologic parameters, including hemoglobin, white blood cells, platelets, WBC differentiation, blood glucose, cholesterol, HDL-cholesterol, triglycerides, serum creatinin and sodium/potassium. Liver enzymes, thyroid hormones, calcium, phosphate, albumin, uric acid and microalbuminuria will not be measured routinely. The samples that are available for almost all participants, are: # serum (taken either with or without gel separator) # EDTA plasma # citrate plasma # DNA # early morning urine sample # urine samples of 24-hour urine collection Any researcher who is member of an internationally recognized academic institution and who is interested in utilizing the research possibilities, data and materials of LifeLines may apply for access. The applicant who is acting as Principal Investigator must be connected to a department or institution with the competence to carry out the research project to term. A contract will give the right to use the data for a pre-determined period of time. This contract also comprises the costs for the LifeLines Biobank which the investigator needs to reimburse. To apply for access, refer to the electronic application process. | blood, urine, plasma, serum, dna, edta plasma, citrate plasma, general population, clinical data, epidemiologic data, genetic factor, environmental factor, complex factor, multifactorial disease, risk factor, metabolic disease, endocrine disease, cardiovascular disease, renal disease, pulmonary disease, musculoskeletal disease, psychopathology, disease, nutrition, lifestyle, genetic epidemiology | is listed by: One Mind Biospecimen Bank Listing | General population, Aging | Public: Any researcher who is member of an internationally recognized academic institution and who is interested in utilizing the research possibilities, Data and materials of LifeLines may apply for access. A LifeLines Scientific Project is a project which uses data or results of biological examinations and measurements in materials from LifeLines (when both are used, The term LifeLines materials will be used). | nlx_93394 | SCR_010730 | SciCrunch Registry | LifeLines Cohort and Biobank, LifeLines Cohort Biobank, LifeLines Cohort & Biobank | 2026-09-26 02:19:21 | 30 | ||||||
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Paradigm Resource Report Resource Website 50+ mentions |
Paradigm (RRID:SCR_009634) | Paradigm | software resource | Software application for millisecond accurate experimental control for cognitive neuroscience, psychology and linguistics research. Presents text, images, sounds, movies, self-paced reading trials and rating scales. An integrated Python scripting API is available. Joystick and microphone response are available. Supports button boxes from PST, Cedrus, fORP and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, experimental control, eye tracking, hardware, microsoft, magnetic resonance, physiological recording, python, scanner, win32 (ms windows), experiment, experimental design, fmri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155918 | SCR_009634 | SciCrunch Registry | Paradigm Experiment Builder | 2026-09-26 02:19:20 | 62 |
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