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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Authority Synonyms Record Last Update Mentions Count
Eindhoven University of Technology; North Brabant; Netherlands
 
Resource Report
Resource Website
Eindhoven University of Technology; North Brabant; Netherlands (RRID:SCR_003354) TU/e institution, university is parent organization of: vIST/e
is parent organization of: 4TU.Datacentrum
SCR_003354 SciCrunch Registry Technische Universiteit Eindhoven, TU Eindhoven, Eindhoven University of Technology 2026-09-26 02:19:46 0
Integrated Auto-Extracted Annotation
 
Resource Report
Resource Website
Integrated Auto-Extracted Annotation (RRID:SCR_005892) Integrated AEA, Auto-Extracted Annotation data or information resource, data set A virtual database that indexes both BioNOT for negation data, and the Resource Discovery Pipeline: an automated resource discovery and semi-automated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. This virtual database currently indexes the following resources: * BioNOT, http://snake.ims.uwm.edu/bionot/index.php?searchterm=mecp2+autism&submit=Search * Resource Discovery Pipeline, http://lucene1.neuinfo.org/nif_resource/current/ annotation, negative data is used by: NIF Data Federation
is related to: BioNOT
is related to: NIF Registry Automated Crawl Data
is related to: PubMed
has parent organization: Integrated
NIH Blueprint for Neuroscience Research ;
NIDA Contract HHSN271200577531C
PMID:22434839 Data are licensed by their respective owners. Use and distribution is subject to the Terms of Use by the original resource as well as the, Creative Commons Attribution License nlx_149462 http://neuinfo.org/nif/nifgwt.html?query=nlx_149462 SCR_005892 SciCrunch Registry NIF Integrated Automatically Extracted Annotation, NIF Integrated Auto. Extracted Annotation, NIF Integrated Auto-Extracted Annotation, Integrated Automatically Extracted Annotation, Integrated Auto Extracted Annotation, NIF Auto-Extracted Annotation 2026-09-26 02:19:48 0
Type 1 Diabetes Preclinical Testing Program
 
Resource Report
Resource Website
Type 1 Diabetes Preclinical Testing Program (RRID:SCR_006861) T1D-PTP, NIDDKT1D-PTP resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Investigator access is provided to the established facilities and expertise needed to extend, enhance and validate preclinical studies of promising new therapeutics in cases where additional preclinical testing is needed to validate potential therapies under disease-specific conditions and in multiple animal models before therapeutics can enter the Type 1 Diabetes Rapid Access to Intervention Development (T1D-RAID) development pipeline. The T1D-RAID program provides resources for pre-clinical development of drugs, natural products, and biologics that will be tested as new therapeutics in type 1 diabetes clinical trials. The T1D-RAID program is not currently accepting applications. The T1D-PTP program currently supports two contracts, which are separate from each other and from the T1D-RAID NCI contract resources, to assist in preclinical development of therapeutics for T1D: * Agents to be tested for Preclinical Efficacy in Prevention or Reversal of Type 1 Diabetes in Rodent Models. Type 1 Diabetes Preclinical Testing Program (T1D-PTP) (NOT-DK-09-006) * Needs for Preclinical Efficacy Testing of Promising Agents to Prevent or Reverse Diabetic Complications (NOT-DK-09-009) The T1D-RAID and T1D-PTP are programs intended to remove the most common barriers to progress in identification and development of new therapies for Type 1 Diabetes. The common goal of these programs is to support and provide for the preclinical work necessary to obtain proof of principle establishing that a new molecule or novel approach will be a viable candidate for expanded clinical evaluation. testing, therapeutic, clinical, drug, preclinical, therapy, drug development, high-throughput screening, animal model, formulation, pharmacology, toxicology is related to: Type 1 Diabetes - Rapid Access to Intervention Development
is related to: NIDDK Information Network (dkNET)
has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
Type 1 diabetes, Diabetes NIDDK THIS RESOURCE IS NO LONGER IN SERVICE nlx_152741 SCR_006861 SciCrunch Registry Type 1 Diabetes Preclinical Testing Program (T1D-PtP), NIDDKType 1 Diabetes Preclinical Testing Program 2026-09-26 02:19:49 0
rsync
 
Resource Report
Resource Website
1+ mentions
rsync (RRID:SCR_003113) software resource, source code Software that provides rapid incremental file transfer. file transfer is used by: studyforrest.org
has parent organization: Samba
Free, Available for download, Freely available nlx_156711 SCR_003113 SciCrunch Registry 2026-09-26 02:19:46 7
Network-based Prediction of Human Tissue-specific Metabolism
 
Resource Report
Resource Website
1+ mentions
Network-based Prediction of Human Tissue-specific Metabolism (RRID:SCR_007392) data or information resource, data set THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Network visualizations in which the expression and predicted flux data are projected over the global human network. These network visualizations are accessible through the supplemental website using the publicly available Cytoscape software (Cline, Smoot et al. 2007). Since many high degree nodes exist in the network, special layouts are required to produce network visualizations that are readily interpretable. To this end we produced network visualizations in which hub nodes are repeated multiple times and hence layouts with a small number of edge crossings can be generated. Contains entries for brain compartments and brain pathways. molecular neuroanatomy resource, brain, pathway, tissue-specific metabolism, human, network-based prediction, cytoscape 2.5, tissue-specific metabolic behavior, network visualization, high degree nodes, hub nodes, currency metabolites, cellular-compartments, cellular compartment, metabolite, cytoplasm, extracellular, lysosome, mitochondrion, nucleus, endoplasmic, peroxisome, metabolic flux is related to: Cytoscape
has parent organization: Tel Aviv University; Ramat Aviv; Israel
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00431 SCR_007392 SciCrunch Registry Network-based Prediction of Human Tissue-specific Metabolism 2026-09-26 02:19:49 1
HSPH Trace Metals Laboratory
 
Resource Report
Resource Website
1+ mentions
HSPH Trace Metals Laboratory (RRID:SCR_002819) HSPS Trace Metals Laboratory access service resource, core facility, service resource Core facility that provides metals analytical capabilities to biomedical and non-biomedical researchers and serves as a source for study design consultation and sample QA/QC requirements. The transport, fate, exposure, and toxic effects of heavy metals is a primary focus of research at the Center. It operates as a modified fee-for-service laboratory. Researchers have the option of having the samples run by the Service staff, or of receiving instruction (for themselves or a doctoral or post doctoral trainee) on how to operate the analytical equipment and analyze their own samples. Both options have associated fees and, as with other services, facility access funds can be requested internal or external services when individual grant support is not yet available. transport, fate, exposure, toxicity, heavy metal is listed by: Eagle I
has parent organization: Harvard T.H. Chan School of Public Health
Restricted nlx_156296 http://www.hsph.harvard.edu/niehs/member-resources-2/ihfsc/metals-service/, http://search.sph.harvard.edu/research/niehs/facility-cores/trace-metals-lab/ https://apps.sph.harvard.edu/publisher/upload/research/niehs/facility-cores/trace-metals-lab/ SCR_002819 SciCrunch Registry Harvard NIEHS Center for Environmental Health Trace Metals Lab, Trace Metals Laboratory (HSPH) 2026-09-26 02:19:46 1
HS3D - Homo Sapiens Splice Sites Dataset
 
Resource Report
Resource Website
1+ mentions
HS3D - Homo Sapiens Splice Sites Dataset (RRID:SCR_002939) HS3D data or information resource, data set Data set of Homo Sapiens Exons, Introns and Splice regions extracted from GenBank Rel.123 with an aim of giving standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation). 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GTAG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows. Finally, there are 271,937 + 332,296 windows of false splice sites, selected by searching canonical GTAG pairs in not splicing positions. The false sites in a range of +/- 60 from a true splice site are marked as proximal. human genome, splice, exon, intron, region, gene, dna, nucleotide, splice region is related to: GenBank Free, Available for download, Freely available nif-0000-02988 SCR_002939 SciCrunch Registry Homo Sapiens Splice Sites Dataset, HS3D (Homo Sapiens Splice Sites Dataset) 2026-09-26 02:19:46 7
University of Pisa; Pisa; Italy
 
Resource Report
Resource Website
University of Pisa; Pisa; Italy (RRID:SCR_006616) institution, university is related to: IMIDIA
is related to: EMIF
is parent organization of: NEuronMOrphological analysis tool
SCR_006616 SciCrunch Registry Universita di Pisa, Università degli Studi di Pisa, Universita degli Studi di Pisa, University of Pisa, Università di Pisa 2026-09-26 02:19:49 0
Yeast Resource Center
 
Resource Report
Resource Website
1+ mentions
Yeast Resource Center (RRID:SCR_007942) YRC biomedical technology research center, training resource Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping has parent organization: University of Washington; Seattle; USA NCRR ;
NIGMS P41 GM103533
nif-0000-03650 SCR_007942 SciCrunch Registry YRC 2026-09-26 02:19:50 6
Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra
 
Resource Report
Resource Website
Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra (RRID:SCR_004315) software resource, source code Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra. has parent organization: University of Washington; Seattle; USA PMID:16447975 nlx_32529 SCR_004315 SciCrunch Registry ChargeCzar, Charge Czar 2026-09-26 02:19:47 0
Sleep-EDF Database
 
Resource Report
Resource Website
1+ mentions
Sleep-EDF Database (RRID:SCR_006976) Sleep-EDF Database data or information resource, data set Sleep EEG dataset from 8 subjects in European Data Format (EDF) including original recordings and their hypnograms as described in B Kemp, AH Zwinderman, B Tuk, HAC Kamphuisen, JJL Obery��. Analysis of a sleep-dependent neuronal feedback loop: the slow-wave microcontinuity of the EEG. IEEE-BME 47(9):1185-1194 (2000). The recordings were obtained from Caucasian males and females (21 - 35 years old) without any medication; they contain horizontal EOG, FpzCz and PzOz EEG, each sampled at 100 Hz. The sc* recordings also contain the submental-EMG envelope, oro-nasal airflow, rectal body temperature and an event marker, all sampled at 1 Hz. The st* recordings contain submental EMG sampled at 100 Hz and an event marker sampled at 1 Hz. The 4 sc* recordings were obtained in 1989 from ambulatory healthy volunteers during 24 hours in their normal daily life, using a modified cassette tape recorder. The 4 st* recordings were obtained in 1994 from subjects who had mild difficulty falling asleep but were otherwise healthy, during a night in the hospital, using a miniature telemetry system with very good signal quality. eeg, sleep, male, female, hypnogram, european data format, early adult human, caucasian, recording has parent organization: PhysioNet Difficulty falling asleep, Healthy PMID:11008419 Acknowledgement requested nlx_153823 SCR_006976 SciCrunch Registry Sleep Recordings and Hypnograms in European Data Format (EDF), Sleep Recordings and Hypnograms in European Data Format 2026-09-26 02:19:49 1
Mouse Genome Informatics Transgenes
 
Resource Report
Resource Website
1+ mentions
Mouse Genome Informatics Transgenes (RRID:SCR_003468) MGI Transgene data or information resource, data set Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available.
Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.
transgene, allele, phenotype is used by: NIF Data Federation
is related to: Integrated Manually Extracted Annotation
has parent organization: Mouse Genome Informatics (MGI)
Acknowledgement requested, Non-commercial, Commercial with permission, Copyrighted nif-0000-34000 SCR_003468 SciCrunch Registry 2026-09-26 02:19:46 3
ALLBUS - German General Social Survey
 
Resource Report
Resource Website
ALLBUS - German General Social Survey (RRID:SCR_003588) ALLBUS data or information resource, data set Data set of up-to-date data on attitudes, behavior, and social structure in Germany. Every two years since 1980 a representative cross section of the population is surveyed using both constant and variable questions. The ALLBUS data become available to interested parties for research and teaching as soon as they are processed and documented. social sciences, attitude, behavior, social structure, germany is listed by: re3data.org nlx_157750 SCR_003588 SciCrunch Registry ALLBUS (Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften) (German General Social Survey), German General Social Survey, Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften 2026-09-26 02:19:46 0
ALCHEMY
 
Resource Report
Resource Website
1+ mentions
ALCHEMY (RRID:SCR_005761) ALCHEMY software resource, source code 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 SciCrunch Registry ALCHEMY - An automated population genetic model driven SNP genotype calling method 2026-09-26 02:19:48 5
English Longitudinal Study of Ageing
 
Resource Report
Resource Website
10+ mentions
English Longitudinal Study of Ageing (RRID:SCR_006727) ELSA data or information resource, data set An interdisciplinary data resource on health, economic position and quality of life as people age. Longitudinal multidisciplinary data from a representative sample of the English population aged 50 and older have been collected. Both objective and subjective data are collected relating to health and disability, biological markers of disease, economic circumstance, social participation, networks and well-being. Participants are surveyed every two years to see how people''s health, economic and social circumstances may change over time. One of the study''s aims is to determine the relationships between functioning and health, social networks, resources and economic position as people plan for, move into and progress beyond retirement. It is patterned after the Health and Retirement Study, a similar study based in the United States. ELSA''s method of data collection includes face-to-face interview with respondents aged 50+; self-completion; and clinical, physical, and performance measurements (e.g., timed walk). Wave 2 added questions about quality of health care, literacy, and household consumption, and a visit by a nurse to obtain anthropometric, blood pressure, and lung function measurements, as well as saliva and blood samples, and to record results from tests of balance and muscle strength. Another new aspect of Wave 2 is the ''Exit Interview'' carried out with proxy informants to collect data about respondents who have died since Wave 1. This interview includes questions about the respondents'' physical and psychological health, the care and support they received, their memory and mood in the last year of their life, and details of what has happened to their finances after their death. Wave 3 data added questions related to mortgages and pensions. The intention is to conduct interviews every 2 years, and to have a nurse visit every 4 years. It also is envisioned that the ELSA data will ultimately be linked to available administrative data, such as death registry data, a cancer register, NHS hospital episodes data, National Insurance contributions, benefits, and tax credit records. The survey data are designed to be used for the investigation of a broad set of topics relevant to understanding the aging process. These include: * health trajectories, disability and healthy life expectancy; * the determinants of economic position in older age; * the links between economic position, physical health, cognition and mental health; * the nature and timing of retirement and post-retirement labour market activity; * household and family structure, social networks and social supports; * patterns, determinants and consequences of social, civic and cultural participation; * predictors of well-being. Current funding for ELSA will extend the panel to 12 years of study, giving significant potential for longitudinal analyses to examine causal processes. * Dates of Study: 2002-2007 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: ** 2000-2003 (Wave 1): 12,100 ** 2004-2005 (Wave 2): 9,433 ** 2006-2007 (Wave 3): 9,771 ** 2008-2009 (Wave 4): underway Links * Economic and Social Data Service (ESDS): http://www.esds.ac.uk/longitudinal/about/overview.asp * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00139#scope-of-study middle adult human, late adult human, adult human, biological marker, direct assessment, physical impairment, interview, clinical, physical, performance, health care, literacy, household consumption, anthropometric, blood pressure, lung function, measurement, saliva, blood, balance, muscle strength, psychological health, care, support, memory, mood, longitudinal, international, health, disability, economic circumstance, social participation, well-being, behavior, family life, health care, health status, household income, income, marriage, retirement, social network is listed by: Inter-university Consortium for Political and Social Research (ICPSR)
has parent organization: University College London; London; United Kingdom
Aging NIA ;
UK Department of Health ;
UK Department of Social Security ;
other UK government departments
Public for the first 3 waves through the University of Essex Economic and Social Data Service (ESDS) website. Greater restrictions may apply for researchers seeking to access more sensitive data (e.g., Geographical classificatory variables and DNA). nlx_151823 SCR_006727 SciCrunch Registry English Longitudinal Study of Ageing (ELSA), ELSA - English Longitudinal Study of Ageing, English Longitudinal Study of Aging 2026-09-26 02:19:49 16
BreakDB
 
Resource Report
Resource Website
BreakDB (RRID:SCR_003134) BreakDB data or information resource, data set Data set developed to store, annotate and dsplay structural variant (SV) breakpoint events identified by PEMer and from other sources. structural variant, breakpoint is related to: PEMer
has parent organization: European Molecular Biology Laboratory
PMID:19236709 Free, Freely available nlx_156789 SCR_003134 SciCrunch Registry Break DB 2026-09-26 02:19:46 0
Kumamoto University; Kumamoto; Japan
 
Resource Report
Resource Website
Kumamoto University; Kumamoto; Japan (RRID:SCR_004102) institution, university is related to: Center for Animal Resources and Development
is parent organization of: Cytokine Family Database
SCR_004102 SciCrunch Registry 2026-09-26 02:19:47 0
University of Salerno; Salerno; Italy
 
Resource Report
Resource Website
University of Salerno; Salerno; Italy (RRID:SCR_007853) UNISA institution, university is parent organization of: University of Salerno Laboratory of Molecular Medicine and Genomics SCR_007853 SciCrunch Registry University of Salerno, Universita degli Studi di Salerno, Università degli Studi di Salerno 2026-09-26 02:19:50 0
University of Sciences in Philadelphia; Pennsylvania; USA
 
Resource Report
Resource Website
University of Sciences in Philadelphia; Pennsylvania; USA (RRID:SCR_008023) institution, university is parent organization of: University of the Sciences in Philadelphia College of Pharmacy SCR_008023 SciCrunch Registry 2026-09-26 02:19:50 0
Cognitive Electrophysiology Data Portal
 
Resource Report
Resource Website
10+ mentions
Cognitive Electrophysiology Data Portal (RRID:SCR_003129) Cognitive Electrophysiology Data Portal data or information resource, data set Multiple data sets, and associated publications, of electrophysiological data from the Computational Memory Lab, University of Pennsylvania. Separate requests must be made for each dataset. A collection of behavioral testing data is also available. cognitive, electrophysiology, behavior, cognitive electrophysiology data has parent organization: University of Pennsylvania; Philadelphia; USA Free, Available for download, Freely available nlx_156800 SCR_003129 SciCrunch Registry 2026-09-26 02:19:46 21

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