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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-02-14 02:00:53 | 0 | |||||||
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KGGSeq Resource Report Resource Website 50+ mentions |
KGGSeq (RRID:SCR_005311) | KGGSeq | software resource | A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data. | genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Monogenic disorder, Cancer | PMID:22241780 | biotools:kggseq, OMICS_02260 | https://bio.tools/kggseq | SCR_005311 | KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data | 2026-02-14 02:00:52 | 53 | |||||
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Hydra Resource Report Resource Website 100+ mentions |
Hydra (RRID:SCR_005260) | Hydra | software resource | Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process. | structural variation, genome, genomic, breakpoint, c++, cnv, pem, paired-end, segmental duplication, rearrangement |
is listed by: OMICtools is listed by: SoftCite is related to: BEDTools has parent organization: Google Code has parent organization: University of Virginia; Virginia; USA |
OMICS_00318 | SCR_005260 | hydra-sv | 2026-02-14 02:01:05 | 115 | ||||||||
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CpG MPs Resource Report Resource Website |
CpG MPs (RRID:SCR_005441) | CpG_MPs | data analysis service, analysis service resource, production service resource, service resource, software resource | Tool for identification and analysis of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. It may identify the unmethylated and methylated regions for a single sample, the conserved and differential methylation regions with different methylation patterns for paired or multiple samples. It includes four main modules as follows: # Normalization of the sequencing reads of cytosines following guanines; # Identification of the unmethylated (methylated) regions using hotspot extension algorithm; # Identification of conservatively and differentially methylated regionsby combining the combinatorial algorithm for determination of potentially functional regions with the algorithm of analysis of variance (ANOVA) for assess the statistical significance of differentially methylated regions; # Extraction of sequence features and visualization of these potentially functional regions. | genomic methylation pattern, genomic, methylation pattern, java |
is listed by: OMICtools has parent organization: Harbin Medical University; Heilongjiang; China |
OMICS_00596 | SCR_005441 | CpG_MPs: identification of CpG methylation patterns of genomic regions | 2026-02-14 02:00:55 | 0 | ||||||||
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AirPROM Resource Report Resource Website |
AirPROM (RRID:SCR_003827) | AirPROM | data or information resource, organization portal, portal, consortium | Consortium focused on developing computer and physical models of the airway system for patients with asthma and chronic obstructive pulmonary disease (COPD). Developing accurate models will better predict how asthma and COPD develop, since current methods can only assess the severity of disease. They aim to bridge the gaps in clinical management of airways-based disease by providing reliable models that predict disease progression and the response to treatment for each person with asthma or COPD. A data management platform provides a secure and sustainable infrastructure that semantically integrates the clinical, physiological, genetic, and experimental data produced with existing biomedical knowledge from allied consortia and public databases. This resource will be available for analysis and modeling, and will facilitate sharing, collaboration and publication within AirPROM and with the broader community. Currently the AirPROM knowledge portal is only accessible by AirPROM partners. | model, airway system, lung, consortium, clinical, imaging, respiratory system, tissue sample, airway model, genomic, gas diffusion mri, airway development, function, physiological, genetic, computational model, gene-environment interaction |
is listed by: Consortia-pedia has parent organization: European Lung Foundation |
European Union FP7 | nlx_158142 | SCR_003827 | Airway Disease Predicting Outcomes through Patient Specific Computational Modelling | 2026-02-14 02:00:36 | 0 | |||||||
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Comprehensive Biomarker Center Resource Report Resource Website |
Comprehensive Biomarker Center (RRID:SCR_003901) | CBC | commercial organization | Commercial organization that discovers, validates & analyzes genomic biomarkers with a focus on body fluid samples. Take advantage of their proven expertise in biomarker signature development and speed up your biomarker studies. | biomarker, clinical research organization, genomic biomarker, genomic, diagnostic, testing, bodily fluid, clinical, dna, rna, dna extraction, rna extraction, microarray, next-generation sequencing, validation, microrna | is related to: READNA | nlx_158236 | SCR_003901 | febit, febit GmbH, Comprehensive Biomarker Center Gmbh | 2026-02-14 02:00:52 | 0 | ||||||||
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Cohorts for Heart and Aging Research in Genomic Epidemiology Resource Report Resource Website 10+ mentions |
Cohorts for Heart and Aging Research in Genomic Epidemiology (RRID:SCR_004034) | CHARGE Consortium, CHARGE | bibliography, portal, consortium, data or information resource, organization portal | Consortium formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies. A bibliography of CHARGE publications is available. Its founding member cohorts include: * Age, Gene, Environment, Susceptibility Study -- Reykjavik * Atherosclerosis Risk in Communities Study * Cardiovascular Health Study * Framingham Heart Study * Rotterdam Study Additional core cohorts include: * Coronary Artery Risk Development in Young Adults * Family Heart Study * Health, Aging, and Body Composition Study * Jackson Heart Study * Multi-Ethnic Study of Atherosclerosis | genome-wide association study, genomic, epidemiology, phenotype, longitudinal | is related to: International Genomics of Alzheimers Project | Aging, Heart disease | PMID:20031568 | nlx_158460 | SCR_004034 | 2026-02-14 02:00:54 | 17 | |||||||
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iBIOFind Resource Report Resource Website |
iBIOFind (RRID:SCR_001587) | iBIOFind | data or information resource, service resource, software application, software resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles. | workflow, model, prediction, research trend, rare disease, resource discovery, biomedicine, genomic, neural network, visualization, reporting, search engine, genetic, neural, clinical translation science award, biomedical resource, funding, gene, protein, neuron, collaborator, publication, trend, grant, funding opportunity, report |
is related to: ModelMaker is related to: Neural Maestro is related to: eNeoTutor is related to: Cytoscape is related to: Biomedical Resource Ontology is related to: PubMed has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153829 | SCR_001587 | 2026-02-14 02:00:12 | 0 | ||||||||
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PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | data processing software, data analysis software, software toolkit, software application, software resource | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/ https://www.cog-genomics.org/plink/1.9/general_usage#cite https://sources.debian.org/src/plink/ |
http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-02-14 02:00:10 | 15344 | |||||
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ASPGD Resource Report Resource Website 100+ mentions |
ASPGD (RRID:SCR_002047) | ASPGD, ASPGD LOCUS, ASPGD REF | data repository, storage service resource, data or information resource, service resource, database | Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. | function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Candida Genome Database is related to: AmiGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Broad Institute |
NIAID R01 AI077599 | PMID:19773420 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12244, biotools:aspgd | http://www.aspergillusgenome.org/ https://bio.tools/aspgd |
SCR_002047 | Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS | 2026-02-14 02:00:17 | 212 | ||||
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Wellcome Trust Case Control Consortium Resource Report Resource Website 100+ mentions |
Wellcome Trust Case Control Consortium (RRID:SCR_001973) | WTCCC | data or information resource | Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2. | gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, disease |
is related to: Psychiatric Genomics Consortium has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Bipolar disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunction, Diabetes | Wellcome Trust ; Bill and Melinda Gates Foundation ; Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17554300 | Access to summary data and individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. | nif-0000-10551 | SCR_001973 | Wellcome Trust Case-Control Consortium (WTCCC) | 2026-02-14 02:00:12 | 213 | ||||
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University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics Resource Report Resource Website 1+ mentions |
University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics (RRID:SCR_001921) | portal, data or information resource, organization portal, data computation service, database | The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator | expression, functional linkage, gene, biochemical instrumentation, bioenergetic system, bioenergy, bioinformatic, computation, genome, genomic, nmr, organism, protein, protein-protein interaction, proteomic, purification, structural biology, x-ray | nif-0000-10491 | SCR_001921 | UCLA-DOE | 2026-02-14 02:00:11 | 4 | ||||||||||
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Mouse Genome Databases Resource Report Resource Website 1+ mentions |
Mouse Genome Databases (RRID:SCR_007147) | MGD | organism-related portal, portal, data set, data or information resource, database, topical portal | A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes. | gene, genetic, chromosome, genotype, inbred mouse strain, pain, phenotype, polygenic, recombinant, trait, genome, genomic, single nucleotide polymorphism, primer, brain, recombinant inbred mouse strain | has parent organization: University of Tennessee Health Science Center; Tennessee; USA | nif-0000-20982 | SCR_007147 | 2026-02-14 02:01:27 | 2 | |||||||||
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Tetraodon Genome Browser Resource Report Resource Website 1+ mentions |
Tetraodon Genome Browser (RRID:SCR_007079) | data or information resource, portal, database, topical portal | The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute. | duplication, element, euchromatic, evolution, exon, fish, gene, genetic, actinopterygians, aganth, ancestor, cartilaginous, cdna, chromosome, coding, collagen, cytokine, diversity, genome, genomic, heritage, hormone, human, interchromossomal, intergenic, intron, karyotype, lineage, mammal, molecule, mouse, nigroviridis, protein, proteome, pufferfish, receptor, region, selenoprotein, sequence, size, specie, synteny, system, takifugu, tetraodon, transposable, vertebrate | nif-0000-20997 | SCR_007079 | TGB | 2026-02-14 02:01:26 | 8 | ||||||||||
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Broad Institute Resource Report Resource Website 1000+ mentions |
Broad Institute (RRID:SCR_007073) | Broad | institution | Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health. | biomedical, genomic, research, center, nonprofit, organization, human, biology, disease |
is affiliated with: Massachusetts Institute of Technology; Massachusetts; USA; is affiliated with: Harvard University; Cambridge; United States is affiliated with: Integrative Human Microbiome Project is affiliated with: MIT; Cambridge; Massachusetts; United States is related to: LINCS Information Framework is related to: HMS LINCS Database is related to: Cancer Cell Line Encyclopedia is related to: GO2MSIG is parent organization of: ARACHNE is parent organization of: MuTect is parent organization of: SiPhy is parent organization of: ContEst is parent organization of: Broad Minded is parent organization of: JBrowse is parent organization of: Birdseed is parent organization of: VAAL is parent organization of: SomaticCall is parent organization of: BIRDSUITE is parent organization of: GATK is parent organization of: SNAP - SNP Annotation and Proxy Search is parent organization of: SYZYGY is parent organization of: Genetic Maps of the Rat Genome is parent organization of: LINCS Connectivity Map is parent organization of: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes is parent organization of: Haploview is parent organization of: Magnaporthe comparative Database is parent organization of: GeneCruiser is parent organization of: Fungal Genome Initiative is parent organization of: Gene Set Enrichment Analysis is parent organization of: GenePattern is parent organization of: MAGENTA is parent organization of: Multiple Myeloma Genomics Portal is parent organization of: ExAc is parent organization of: Ricopili is parent organization of: UnifiedGenotyper is parent organization of: SomaticIndelDetector is parent organization of: RNA-SeQC is parent organization of: Oncotator is parent organization of: ABSOLUTE is parent organization of: PathSeq is parent organization of: V-Phaser 2 is parent organization of: Indelocator is parent organization of: Scripture is parent organization of: VICUNA is parent organization of: Tuberculosis Database is parent organization of: HaploReg is parent organization of: CellProfiler Image Analysis Software is parent organization of: National Institute of Mental Health (NIMH) Human Genetics Initiative is parent organization of: ChemBank is parent organization of: GeneCluster 2: An Advanced Toolset for Bioarray Analysis is parent organization of: Ultrasome is parent organization of: Diabetes Genetics Initiative is parent organization of: Dog Genome Project is parent organization of: Gene Relationships Across Implicated Loci is parent organization of: InVEx is parent organization of: Broad Genetic Analysis Platform is parent organization of: CellProfiler Analyst is parent organization of: ALLPATHS-LG is parent organization of: MutSig is parent organization of: SegSeq is parent organization of: Argo Genome Browser is parent organization of: Integrative Genomics Viewer is parent organization of: MEDEA is parent organization of: Pathline is parent organization of: ASPGD is parent organization of: DGAP is parent organization of: BARD is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Trinity is parent organization of: Genome Aggregation Database is parent organization of: GenomeSpace is parent organization of: Picard is parent organization of: Connectivity Map 02 is parent organization of: CMap is parent organization of: IndelGenotyper is parent organization of: Discovar assembler is parent organization of: Molecular Signatures Database is parent organization of: GSEA is parent organization of: Eagle is parent organization of: Morpheus by Broad Institute is parent organization of: Cancer Dependency Map Portal is parent organization of: LIGER is parent organization of: Drop-seq tools is parent organization of: scATAC Pipeline is parent organization of: Guide Design Resources is parent organization of: Smart-seq2 Single Sample Pipeline is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: Broad Terra cloud commons for pathogen surveillance is parent organization of: Single Cell Portal is parent organization of: CEMBA MethylC Seq Pipeline is parent organization of: Pegasus is parent organization of: Cumulus is parent organization of: Cirrocumulus is parent organization of: BICCN Anatomy and Morphology Project is parent organization of: Terra is parent organization of: JUMP Cell Painting Consortium is parent organization of: Spectrum Mill is parent organization of: Polysolver is parent organization of: Brain Cell Data Viewer is parent organization of: Eagle is parent organization of: Broad Institute Imaging Platform Core Facility is parent organization of: ATAC Pipeline is parent organization of: ichorCNA is parent organization of: CRISPick is parent organization of: FireBrowse is parent organization of: Cellarium is parent organization of: multiVIB is parent organization of: SlideTags.wdl is parent organization of: Slide-seq Pipeline is parent organization of: BuildIndices |
Eli and Edythe Broad ; individual donors |
nif-0000-31438, grid.66859.34, Wikidata: Q4971893 | https://ror.org/05a0ya142 | SCR_007073 | Broad Institute of MIT and Harvard, Broad Institute Inc. | 2026-02-14 02:01:20 | 1897 | ||||||
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aneurIST Resource Report Resource Website 1+ mentions |
aneurIST (RRID:SCR_007427) | aneurIST | disease-related portal, data or information resource, portal, topical portal | Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis. | gene, genetic, adult, cerebral aneurysm, cerebral brain hemorrhage, cerebral hemorrhage, cerebral parenchymal hemorrhage, cerebral hemorrhage, clinical, genomic, human, intracerebral hemorrhage, intracranial aneurysm, subarachnoid hemorrhage, risk, aneurysm rupture, patient, treatment, infrastructure, platform, genomics, disease, personalized risk assessment, bioinformatics, clinical, data management, data integration, data processing, software tool, cerebrum | has parent organization: Pompeu Fabra University; Barcelona; Spain | Cerebral aneurysm, Subarachnoid hemorrhage, Aging | European Union ; Sixth FPPriority 2 of the Information Society Technologies IST |
nif-0000-00538 | http://www.cilab.upf.edu/aneurist1/ | SCR_007427 | aneurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms, (at)neurIST, (at)neurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms | 2026-02-14 02:01:26 | 3 | |||||
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Allen Human Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Human Brain Atlas (RRID:SCR_007416) | data visualization software, data processing software, data or information resource, atlas, software application, software resource, database | Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D. | atlas, human, brain, anatomic, genomic, data, visualization, mining, tool, MRI, DTI, histology, gene, expression |
is related to: Speech Language Disorders Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Individual private donors ; U.S. Department of Health and Human Services 1C76HF15069; U.S. Department of Health and Human Services 1C76HF19619 |
PMID:23041053 | Free, Available for download, Freely available | nif-0000-00506 | http://humancortex.alleninstitute.org, http://human.brain-map.org/ | SCR_007416 | Human Cortex Study, Allen Institute for Brain Science Human Cortex Study, Allen Brain Atlas - Human Brain | 2026-02-14 02:01:32 | 135 | |||||
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HAP-SAMPLE Resource Report Resource Website 1+ mentions |
HAP-SAMPLE (RRID:SCR_009234) | HAP-SAMPLE | data analysis service, analysis service resource, production service resource, service resource, software application, software resource | Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | nlx_154392 | SCR_009234 | 2026-02-14 02:01:40 | 4 | |||||||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software resource, software library, software toolkit, software application | Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154597, biotools:qtlbim | http://www.ssg.uab.edu/qtlbim/index.jsp https://cran.r-project.org/src/contrib/Archive/qtlbim/ https://bio.tools/qtlbim |
http://www.qtlbim.org/ | SCR_009375 | 2026-02-14 02:01:49 | 2 | ||||||||
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Bio2RDF atlas of post genomic knowledge Resource Report Resource Website 10+ mentions |
Bio2RDF atlas of post genomic knowledge (RRID:SCR_007991) | blog, portal, data or information resource, narrative resource, topical portal | This is a blog about post genomic knowledge. The website''s goal is to make public datasets from the bioinformatics community available in RDF format via standard SPARQL endpoints. | bioinformatic, community, dataset, genomic, knowledge, rdf | nif-0000-10166 | SCR_007991 | Bio2RDF | 2026-02-14 02:01:31 | 41 |
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