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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Visionary: A Dictionary for the Study of Vision Resource Report Resource Website 1+ mentions |
Visionary: A Dictionary for the Study of Vision (RRID:SCR_008307) | database, data or information resource, data processing software, software application, data acquisition software, software resource | It is a dictionary for terminology used in the study of human and animal vision. It includes terms from the areas of biological and machine vision, visual psychophysics, visual neuroscience and other related fields. Sponsors: Visionary is sponsored by Educational Software for Autism. | animal, biological, dictionary, human, machine, neuroscience, psychophysic, terminology, vision, visual | has parent organization: Boston University; Massachusetts; USA | nif-0000-24678 | SCR_008307 | Visionary | 2026-08-09 09:04:50 | 3 | |||||||||
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BioSig: An Imaging Bioinformatics System for Phenotypic Analysis Resource Report Resource Website 100+ mentions |
BioSig: An Imaging Bioinformatics System for Phenotypic Analysis (RRID:SCR_008428) | BioSig | software library, image processing software, data processing software, software application, software toolkit, software resource | Software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events. | application, autocorrelation, bsd, c, c++, connectivity analysis, correlation, cross-correlation, directed transfer analysis, discriminant analysis, domain independent, eeg, meg, electrocorticography, end event related potential, format conversion, german, gnome, granger causality, information theory, kde, linux, matlab, microsoft, multivariate analysis, partial directed coherence, posix/unix-like, python, regression, spectral analysis, statistical operation, temporal transformation, time domain analysis, win32 (ms windows), windows, electrocorticogram, electrocardiogram, electrooculogram, electromyogram, respiration, signal, processing, biosignal |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Lawrence Berkeley National Laboratory |
DOI:10.1109/MC.2008.407 | Free, Available for download, Freely available | nif-0000-30190 | http://www.nitrc.org/projects/biosig, https://sources.debian.org/src/biosig-tools/ | SCR_008428 | 2026-08-09 09:04:55 | 165 | ||||||
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BiQ Analyzer: A Software Tool for DNA Methylation Analysis Resource Report Resource Website 10+ mentions |
BiQ Analyzer: A Software Tool for DNA Methylation Analysis (RRID:SCR_008423) | data analysis software, data processing software, software application, data visualization software, software resource | BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing. Highlights: - End-to-end support of the analysis process: from raw sequence files to a comprehensive documentation and visualization. - Automatically generate publication-quality lollipop diagrams (show example.) - Integrated 1-click multiple sequence alignment. - Automated CpG highlighting- never spend your time highlighting CpGs by hand anymore. - Open electropherogram files to check for sequencing problems (requires an electropherogram viewer such as Chromas LITE.) - Generate MethDB-compatible DNA methylation files for database submission. - Factor 5 speedup of sequence analysis while at the same time achieving better data quality. Intended users: - Anyone who works with DNA methylation data from bisulfite sequencing. - Occasional users as well as experts (the former will benefit from the help that the program gives in order to achieve a good quality management whereas the latter will save hours and days of tedious work.) Sponsors: This resource is supported by the Max Planck Institute. Keywords: Software, Visualization, DNA, Methylation, Data, Bisulfite, Sequencing, Electropherogram, Analysis, | has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany | nif-0000-30169 | SCR_008423 | BiQ | 2026-08-09 09:04:55 | 18 | ||||||||||
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Bahler Laboratory: Genome Regulation Resource Report Resource Website 1+ mentions |
Bahler Laboratory: Genome Regulation (RRID:SCR_008422) | BahlerLab | organization portal, portal, data or information resource, laboratory portal | The laboratory studies global gene expression programs in fission yeast (S. pombe). They apply a wide range of integrated approaches to analyse regulatory networks during cell proliferation, differentiation and quiescence including genetic and environmental perturbations. They are also interested in genetic diversity, genome evolution, and the complex interactions between genotypes, phenotypes, and the environment. The relative simplicity of the yeast cell promises a deeply satisfying, systems-level understanding of its inner workings within our life time Sponsors: This research is mainly funded by Cancer Research UK and the EC FP7 PhenOxiGEn project. Keywords: Gene, Expression, S.pombe, Yeast, Cell, Proliferation, Differentiation, Environmental, Genetic, Diversity, Genome, Evolution, Genotype, Phenotype, Environment, | has parent organization: University College London; London; United Kingdom | nif-0000-30160 | SCR_008422 | The Bahler Laboratory: Genome Regulation | 2026-08-09 09:04:59 | 9 | |||||||||
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MRIcro Software Resource Report Resource Website 500+ mentions |
MRIcro Software (RRID:SCR_008264) | data analysis software, data processing software, software application, data visualization software, software resource | MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available. | export, fmri, 3d, brain, intensity, lesions, medical, mri, neuroimager, neuropsychologist, pet, platform, region, software, view, volume, image |
is related to: SPM has parent organization: Georgia Institute of Technology; Georgia; USA |
nif-0000-23298 | SCR_008264 | MRIcro | 2026-08-09 09:04:49 | 910 | |||||||||
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Australian Medical Bioinformatics Resource Resource Report Resource Website 1+ mentions |
Australian Medical Bioinformatics Resource (RRID:SCR_008385) | data or information resource, topical portal, portal, disease-related portal, research forum portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AMBeR's aim is to bring together Australia's unique resources for genetic epidemiology and genomics with high level expertise in bioinformatics and statistical science, conduct advanced methodological research, develop new research capacity and competitiveness in cutting-edge techniques, bring them to bear on important medical research problems, train young Australians in bioinformatics and advanced biostatistics, and transfer this expertise to the medical research community. | medical, bioinformatics, statistical, science, genomics, epidemiology, research, methodological, techniques, biostatistics | has parent organization: University of Western Australia; Perth; Australia | Medical Bioinformatics ; National Health ; MRC ; Genomics and Proteomics Program |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30032 | SCR_008385 | AMBeR | 2026-08-09 09:04:59 | 1 | |||||||
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Interventions Testing Program Resource Report Resource Website 10+ mentions |
Interventions Testing Program (RRID:SCR_008266) | data or information resource, topical portal, portal, disease-related portal, research forum portal | NIA''s ITP is a multi-institutional study investigating treatments with the potential to exte nd lifespan and delay disease and dysfunction in mice. Priority consideration will be given to the treatments that are easily obtainable, reasonably priced, and can be delivered in the diet (preferred) or water. Interventions that require labor intensive forms of administration, such as daily injections or gavage, are not feasible within the design of the ITP. Treatments currently under study include: - Pharmaceuticals - Nutraceuticals - Foods - Diets - Dietary supplements - Plant extracts - Hormones - Peptides - Amino acids - Chelators - Redox agents - Other agents or mixtures of agents Although the mice involved in this study will be housed at the University of Michigan, the Jackson Laboratories, and the University of Texas Health Sciences Center at San Antonio, the project is designed to involve collaborations with investigators at any university, institute, or other organization that has ideas about pharmacological interventions that might decelerate aging and wishes to test these in a lifespan study of mice. Sponsors: This program is supported by the National Institute of Aging. | dysfunction, extact, food, gavage, acid, administration, agent, amino, chelator, diet, dietary, disease, hormone, injection, intervention, lifespan, mixture, mouse, nutraceutical, peptide, pharmaceutical, plant, redox, supplement, treatment, water | has parent organization: National Institute on Aging | Aging | nif-0000-23305 | http://www.nia.nih.gov/ResearchInformation/ScientificResources/InterventionsTestingProgram.htm | SCR_008266 | ITP | 2026-08-09 09:04:52 | 32 | |||||||
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Rutgers University Quantitative Neuroscience Laboratory Resource Report Resource Website 1+ mentions |
Rutgers University Quantitative Neuroscience Laboratory (RRID:SCR_008541) | database, organization portal, data or information resource, portal, laboratory portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The brain is made of billions of neurons, which together form the world''s most powerful information-processing machine. Despite decades of research, the fundamental principle by which these cells work together is still unknown. Many theories for brain function have been proposed over the last century. But only in the last few years has it become possible to record simultaneously from large enough numbers of neurons to put these theories to the test experimentally. This is an unprecedented opportunity, but it opens up a new question: how do we go from the gigabytes of experimental data that we now have, to concise conclusions about the function of the brain? The data processing methods traditionally used in neuroscience are not sophisticated enough to exploit this new flood of information. Fortunately, modern statistics and machine learning theory is making great strides in precisely the type of techniques needed to process these large multivariate databases. By applying these methods to neuronal data, we can now test long-standing hypotheses about brain function. The Cell Assembly The main focus of our research is an experimental search for cell assemblies. Before describing what a cell assembly is, it will be useful to describe what it is not. The brain is often thought of as a feed-forward system. In this scheme, sensory information is processed by successive levels of cortical analyzers, each of which transforms the results of previous levels, until sensory information is in a suitable form to guide the animals behavior. In support of this idea, the pattern of connections in the cortex does appear to respect a hierarchical organization, with the output of low-level areas corresponding to a single sensory modality being integrated into high-level multi-modal areas. Responses in higher-level sensory areas appear to have more complex responses to sensory stimuli, in agreement with increased abstraction as the hierarchy is traversed. However, there are several levels at which this feed-forward picture is incomplete. At the circuit diagram level, there more connections projecting across and down the hierarchy, than there are feed-forward projections. What''s more, if information were processed in a strictly feed-forward manner, one would expect a neuron to respond identically to repeated presentations of the same sensory stimulus. Although this is a fairly good approximation in primary sensory areas of cortex, in high-level structures responses are often more variable than expected from strict sensory control. Finally, although feed-forward processing can describe how an animal could perform simple stimulus-response behaviors, it cannot explain more complex top-down behaviors such as memory or thought. An alternative point of view, put forward over 50 years ago by Canadian psychologist Donald Hebb, holds that recurrent and feedback connections play an essential role in brain function. The principal actor in this view is the cell assembly, an anatomically distributed subset of neurons, amongst which mutually excitatory connections have been strengthened by repeated co-activation, allowing the assembly to later maintain its activity through reverberation without direct sensory stimulation. This theory allows for sensory-response behavior, and also behavior resulting purely from internally generated cognitive activity, by the sequential activation of a series of assemblies, leading in turn to the production of motion. In our research, we search for signatures of assembly activity in simultaneous recordings from multiple neurons, and aim to characterize the properties of assembly activity in ways not possible from theory alone. Software for Automatic Clustering KlustaKwik is a program developed in the lab for automatic cluster analysis, specifically designed to run fast on large data sets. In order facilitate open-source development, it is now located at klustakwik.sourceforge.net. This study was supported by NIH grants MH073245 and DC009947; NSF grant SBE-0542013 to the Temporal Dynamics of Learning Center, an NSF Science of Learning Center; a National Institute on Deafness and Other Communication Disorders, NIH, grant DC-005787-01A1; and a Spanish grant FIS 2006-09294. K.D.H. is an Alfred P. Sloan fellow. We would like to dedicate this work to the memory of D. J. Amit. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31389 | SCR_008541 | Rutgers, Quantitative Neuroscience Laboratory | 2026-08-09 09:04:57 | 8 | ||||||||||
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Adverse Childhood Experiences Study Resource Report Resource Website 1+ mentions |
Adverse Childhood Experiences Study (RRID:SCR_008382) | portal, data or information resource, topical portal | A clinical study linking childhood maltreatment and later-life health and well-being. As a collaboration between the Centers for Disease Control and Prevention and Kaiser Permanente''s Health Appraisal Clinic in San Diego, Health Maintenance Organization (HMO) members undergoing a comprehensive physical examination provided detailed information about their childhood experience of abuse, neglect, and family dysfunction. Over 17,000 members chose to participate. To date, over 50 scientific articles have been published and over 100 conference and workshop presentations have been made. Future Directions: The ACE study is now in its 10th year and the prospective phase is currently underway. In this ongoing stage of the study, data are being gathered from various sources including outpatient medical records, pharmacy utilization records, and hospital discharge records to track the subsequent health outcomes and health care use of ACE Study participants. In addition, an examination of National Death Index records will be conducted to establish the relationship between ACE and mortality among the ACE Study population. The ACE Study findings suggest that these experiences are major risk factors for the leading causes of illness and death as well as poor quality of life in the United States. Progress in preventing and recovering from the nation''s worst health and social problems is likely to benefit from the understanding that many of these problems arise as a consequence of adverse childhood experiences. :Sponsors: This resource is supported by the Centers for Disease Control and Prevention and the Kaiser Permanente''s Health Appraisal Clinic in San Diego. | childhood, experience, clinical study, maltreatment, disease, physical abuse, neglect, family dysfunction, young human | Center for Disease Control and Prevention | nif-0000-30022 | SCR_008382 | ACE Study | 2026-08-09 09:04:50 | 2 | |||||||||
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DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition Resource Report Resource Website 1+ mentions |
DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition (RRID:SCR_008262) | training resource, data or information resource, topical portal, portal, meeting resource, challenge | A software development competition, the DIADEM Challenge,to benefit the scientific community by encouraging the development of better software for automating three-dimensional reconstructions of neuronal arbors. The intent of the Sponsors is to ensure that the best software submitted for the competition is made available to the scientific community within a reasonable time and on reasonable terms. No purchase is necessary to enter or win. The competition will have two rounds. As of April 10, 2009, individuals and teams may register to participate in the competition and may download sets of image stacks (Data Sets) of non-human animal brains along with three-dimensional reconstructions for some of these Data Sets for training purposes. Submissions of software, including executable programs, supporting documentation, and reconstruction files for the Data Sets, must be uploaded to the competition website no later than April 9, 2010. In order to be eligible to win the competition, the individuals and at least one member of any teams whose submissions are selected for the Final Round (Finalists) must participate in the Final Round and scientific conference. Personal participation in the Final Round and scientific conference is important for two main reasons: first, because the Finalists software will be tested at the Final Round against additional Data Sets so that the judges can select a winner or winners, and second, because the larger scientific conference, of which the Final Round will be a part, is intended to foster extensive scientific interaction among neuroscientists and computational scientists, including plenary and poster sessions to discuss challenges, solutions, and future directions. There are 5 datasets, all of which have to be reconstructed for the qualifier phase. Once you have registered your group, dataset download information will be sent to you via E-mail. The 5 datasets are: - Cerebellar Climbing Fibers - Hippocampal CA3 Interneuron - Neocortical Layer 6 Axons - Neuromuscular Projection Fibers - Olfactory Projection Fibers Sponsors: The sponsors of this competition are: Allen Institute for Brain Science, Seattle, Washington; Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland; and Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia. | fiber, animal, automating, axon, axonal, brain, cerebellar, challenge, competition, computational, conference, data set, dendritic, development, hippocampal, interneuron, morphology, neocortical, neuromuscular, neuronal, neuroscientist, non-human, olfactory, program, reconstruction, scientific conference, scientist, software, three-dimensional, image | has parent organization: Howard Hughes Medical Institute | nif-0000-23194 | SCR_008262 | DIADAM Challenge | 2026-08-09 09:04:52 | 4 | |||||||||
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BLAST Similarity Search Resource Report Resource Website 10+ mentions |
BLAST Similarity Search (RRID:SCR_008419) | portal, data or information resource, topical portal | The goals of this sequencing effort are to produce and publicly release a whole-genome assembly and auto-annotation of the Aedes genome representing 8X sequence coverage. In collaboration, these centers have delivered the target 8X draft coverage of the disease vector genome. Assembly of the genome was performed using the Broad''s whole genome assembly package ARACHNE (Batzoglou et al., 2002 and Jaffe et al., 2003). The Aedes genome will be annotated in a collaborative effort involving both MSCs and Vectorbase, which is a bioinformatics resource center at the University of Notre Dame. Sponsor: This resource is supported by the National Institute of Allergy and Infectious Diseases. Keywords: Genome, BLAST, Similarity, Search, Engine, Sequence, Bioinformatics, Resource, | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nif-0000-30152 | SCR_008419 | BLAST | 2026-08-09 09:04:55 | 10 | ||||||||||
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Gene Relationships Across Implicated Loci Resource Report Resource Website 50+ mentions |
Gene Relationships Across Implicated Loci (RRID:SCR_008537) | service resource, resource, data analysis service, analysis service resource, production service resource | A tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes. As input, users can upload either (1) SNPs that have emerged from a genome-wide association study or (2) genomic regions that have emerged from a linkage scan or are associated common or rare copy number variants. SNPs should be listed according to their rs#''s and must be listed in HapMap. Genomic Regions are specified by a user-defined identifier, the chromosome that it is located on, and the start and end base-pair positions for the region. Grail can take two sets of inputs - Query regions and Seed regions. Seed regions are definitely associated SNPs or genomic regions, and Query regions are those regions that the user is attempting to evaluate agains them. In many applications the two sets are identical. Based on textual relationships between genes, GRAIL assigns a p-value to each region suggesting its degree of functional connectivity, and picks the best candidate gene. GRAIL is developed by Soumya Raychaudhuri in the labs of David Altshuler and Mark Daly at the Center for Human Genetic Research of Massachusetts General Hospital and Harvard Medical School, and the Broad Institute. GRAIL is described in manuscript, currently in preparation. | software, text mining, genotype, phenotype, snp |
is listed by: 3DVC has parent organization: Broad Institute |
NIAMS 1K08AR055688-01A1; NIAMS AR007530; NHGRI U01HG004171; NIDDK R01DK083759 |
PMID:19557189 | nif-0000-30627 | SCR_008537 | GRAIL | 2026-08-09 09:05:00 | 72 | |||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | data analysis software, data processing software, software application, sequence analysis software, web application, software resource | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-08-09 09:04:59 | 3886 | |||||
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HerpNET Resource Report Resource Website 10+ mentions |
HerpNET (RRID:SCR_008374) | portal, data or information resource, community building portal, database | HerpNET is a collaborative effort by natural history museums to establish a global network of herpetological collections data. Sixty-four institutions are participating in the HerpNET community, with an open ended invitation to institutions who would like to join. Currently 56 institutions are available on the specimen searching portal, with data from over 5.5 million specimens available for searching. VertNet: The Future HerpNET, ORNIS, MaNIS and FishNet2 are taxon-based web portals that now serve georeferenced data on vertebrates from over 90 global institutions. Together these comprise VertNET, a cooperative project working to maintain and expand these distributed database projects. Future plans include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. Sponsors: This resource is supported by the National Science Foundation (NSF No. 0132303) and by a GBIF DIGIT . | frog, curation, herpatology, lizard, museum | nif-0000-25777 | SCR_008374 | HerpNET | 2026-08-09 09:04:58 | 20 | ||||||||||
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Invitrogen Antibodies Resource Report Resource Website 10+ mentions |
Invitrogen Antibodies (RRID:SCR_008410) | reagent supplier, commercial organization, antibody supplier, material resource | Supports research in cellular analysis, genomics, proteomics, and drug discovery. It has merged with Thermo Fisher Scientific. One of several brands under Thermo Fisher Scientific corporation. | supplier, antibody, application, target, primary, search tool, molecular, probe, fluorescence, technology, secondary antibody, primary antibody | has parent organization: Life Technologies | nif-0000-30111 | https://www.thermofisher.com/us/en/home/brands/invitrogen.html?s_kwcid=AL!3652!3!556081813883!e!!g!!invitrogen&cid=bid_cbu_sbu_r01_co_cp1210_pjt0000_bid00000_0se_gaw_bt_pur_con&ef_id=Cj0KCQiArt6PBhCoARIsAMF5wahFgrmXOQkUHVRIZymlTIFFZig0iMe0ulMfxqA7mya8Rvpiv24OAKIaAgR8EALw_wcB:G:s&s_kwcid=AL!3652!3!556081813883!e!!g!!invitrogen&gclid=Cj0KCQiArt6PBhCoARIsAMF5wahFgrmXOQkUHVRIZymlTIFFZig0iMe0ulMfxqA7mya8Rvpiv24OAKIaAgR8EALw_wcB | http://www.caltag.com/ | SCR_008410 | Molecular Probes, Zymed, Invitrogen, Invitrogen Antibodies & Secondary Detection, Life Technologies, Invitrogen Antibodies and Secondary Detection, Invitrogen Antibodies Secondary Detection | 2026-08-09 09:04:55 | 22 | |||||||
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Hardy-Weinberg Equilibrium Calculator Resource Report Resource Website 100+ mentions |
Hardy-Weinberg Equilibrium Calculator (RRID:SCR_008371) | simulation software, software application, software resource | This portal leads to the Chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers (SNPs, indels etc), including analysis for ascertainment bias for dominant/recessive models (due to biological or technical causes.) The purpose of this web program is for estimating possible missingness and an approach to evaluating missingness under different genetic models. Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the missingness of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. Through this tool, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. Sponsors: This resource is supported by an Intermediate Fellowship (grant FS/05/065/19497) from the British Heart Foundation. | gamete, genetic, allele, analysis, biallelic, biological, caluclator, conception, disease, dominant, genotype, hardy-weinberg equilibrium, marker, mendelian, model, randomization, recessive, snp, test, trait | nif-0000-25608 | SCR_008371 | HWE Calculator | 2026-08-09 09:04:58 | 103 | ||||||||||
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ELDERMET Gut microbiota as an indicator and agent of nutritional health in elderly Irish subjects Resource Report Resource Website 10+ mentions |
ELDERMET Gut microbiota as an indicator and agent of nutritional health in elderly Irish subjects (RRID:SCR_008492) | portal, data or information resource, topical portal | Latest publications: ELDERMET research has recently been published in the Proceedings of the National Academy of Sciences (USA). This work focuses on the composition and stability of the intestinal bacteria in older Irish adults. Read the paper here. Would you like to be part of ELDERMET? We are currently looking for people, aged 65 years or older, living in the community. All we ask is that you live in the Cork area, or are willing to travel to Cork, and have recently (within the last two/three weeks) taken any kind of antibiotic. It doesnt matter if you are still taking the antibiotic, as long as the finishing date isnt more than four weeks before your first visit to ELDERMET. ELDERMET Objectives To assess the composition of the faecal microbiota of elderly volunteers in the Irish population, using state-of-the-art molecular techniques. To correlate diversity, composition, and metabolic potential of the faecal microbial metagenome with health, diet and lifestyle indices that are a) likely to be influenced by the microbiota or b) to influence the microbiota. To develop recommendations for specific dietary ingredients, foodstuffs, functional foods and/or dietary supplements, that will improve the health of elderly consumers. To provide evidence-based recommendations for prospective studies to determine the molecular mechanisms for health improvements promoted by specific food ingredients that modulate components of the microbiota. ELDERMET Rationale The human intestinal microbiota is made up of approximately 1000 genetically unique organisms (phylotypes ) [1]. The bacteria present in the intestine make an important contribution to: metabolism executed in the gut [2] health, in diverse activites from pain perception [3] to cognitive function [4]. There is an increasing body of evidence linking alterations in the human gut microbiota with Inflammatory Bowel Disease [5, 6] and Irritable Bowel Syndrome [7]. The changing pattern of the gut microbiota in elderly subjects [8, 9] may be linked to host changes such as immunosenescence, increased susceptibility to disease and potentially systemic effects. The composition of the intestinal microbiota may be modulated by dietary components including prebiotics [10]. ELDERMET will determine the baseline composition of the gut microbiota of several hundred elderly Irish subjects using a combination of traditional culutre and molecular (culture-independent) methodologies. ELDERMET will explore potential correlations between microbiota composition and a range of health indices; cross-referencing data to dietary intake. Data will be analyzed in the context of the related FHRI projects in Nutrigenomics, Food Consumption, Food Safety, and Diet-Health. ELDERMET will provide recommendations to all stakeholders (including health practitioners and the health service, the food industry and the general public) on how to improve health based on defined modifications to dietary intake. Sponsor. This work is supported by the Goverment of Ireland Department of Agriculture Fisheries and Food/Health Research Board Food for Health Research Initiative award to the ELDERMET project as well as by a Science Foundation Ireland award to the Alimentary Pharmabiotic Centre. M.J.C. is now funded by a fellowship from the Health Research Board of Ireland. | Aging | nif-0000-30485 | SCR_008492 | ELDERMET | 2026-08-09 09:04:59 | 12 | ||||||||||
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An Open-Source MATLAB-to-Python Compiler Resource Report Resource Website 1+ mentions |
An Open-Source MATLAB-to-Python Compiler (RRID:SCR_008409) | software development tool, software application, software resource, compiler | OMPC aims to enable reuse of the huge open and free code base of MATLAB on a free and faster growing Python platform. Running Python and MATLAB in a single interpreter avoids issues with running two separate applications. Python adds general purpose programming libraries to the convenient syntax of the language of technical computing. OMPC is not an interpreter, it lets Python to do the work. This means that if Python gets faster OMPC gets faster too. OMPC translates the m-files preserving the structure of the original programs as much as possible. Although OMPC comes with a library that emulates the features of numerical array of MATLAB there is nothing that will stop you from running the translated code the way you like it. This means that you could run the OMPC generated code on IronPython, Jython, PyPy or whatever else if you write your own numerical class. Sponsors: This resource is supported by RIKEN Brain Science Institute. | code, compiler, python, matlab, computng, software, program |
is related to: Python Programming Language is related to: MATLAB |
nif-0000-30104 | SCR_008409 | OMPC | 2026-08-09 09:04:59 | 2 | |||||||||
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Eric H. Chundlers Links Resource Report Resource Website 1+ mentions |
Eric H. Chundlers Links (RRID:SCR_008328) | training resource, data or information resource, topical portal, portal, funding resource | This web site focuses on neuroscience, the study of the nervous system. Links on this page are limited to those Dr. Chundler finds to be the most interesting and useful. | grant, nervous system, neuroscience, research, science | has parent organization: University of Washington; Seattle; USA | nif-0000-24694 | SCR_008328 | Eric H. Chundler''s Links | 2026-08-09 09:04:58 | 1 | |||||||||
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CGEMS Resource Report Resource Website 10+ mentions |
CGEMS (RRID:SCR_008445) | CGEMS | portal, data or information resource, topical portal | The project began as a pilot study to identify inherited genetic susceptibility to prostate and breast cancer. CGEMS has developed into a robust research program involving genome-wide association studies (GWASs) for a number of cancers to identify common genetic variants that affect a person''s risk of developing cancer. In collaboration with extramural scientists, NCI''s Division of Cancer Epidemiology and Genetics (DCEG) has carried out genome-wide scans for breast, prostate, pancreatic, and lung cancers, while a GWAS of bladder cancer is currently underway. By making the data available to both intramural and extramural research scientists, as well as those in the private sector through rapid posting, NIH can leverage its resources to ensure that the dramatic advances in genomics are incorporated into rigorous population-based studies. Ultimately, findings from these studies may yield new preventive, diagnostic, and therapeutic interventions for cancer. Sponsors: This resource is supported by the U.S. National Institues Of Health. | cancer, genetic, marker, prostate, breast, research, genome, association, development, scientist, pancreatic, lung, bladder, science, genomics, population, study, theraphy, diagnosis |
has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
nif-0000-30287 | SCR_008445 | The Cancer Genetic Markers of Susceptibility Project, Cancer Genetic Markers of Susceptibility, The Cancer Genetic Markers of Susceptibility | 2026-08-09 09:04:56 | 28 |
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