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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneChip Operating Software Resource Report Resource Website 500+ mentions |
GeneChip Operating Software (RRID:SCR_003408) | GCOS | data processing software, data analysis software, software resource, sequence analysis software, software application | Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request. | gene expression, snp mapping, resequencing, analysis, genotyping, platform, software, comparison, analysis |
is listed by: Biositemaps is listed by: SoftCite has parent organization: Scripps Research Institute |
Free, Available for download, Freely available | nif-0000-33019 | https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/genechip-operating-software-service-pack-2-software-update.html | SCR_003408 | GeneChip Operating Software (GCOS), DNA Array Core Facility GeneChip Operating Software, DNA Array Core Facility GeneChip Operating Software (GCOS) | 2026-08-04 09:40:54 | 649 | ||||||
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Scripps Research Institute Resource Report Resource Website 1+ mentions |
Scripps Research Institute (RRID:SCR_001907) | TSRI | institution | Nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute has laboratories employing scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. | institution, American, medical, research, education, biomedical, private, organization |
uses: DIRECT2experts is related to: Clinical and Translational Science Awards Consortium is related to: The Pancreatic Beta-Cell Consortium is parent organization of: piCALL is parent organization of: GeneChip Operating Software is parent organization of: TSRI-Yates Lab is parent organization of: BioGPS: The Gene Portal Hub is parent organization of: METLIN is parent organization of: AutoDock Vina is parent organization of: ViReMa is parent organization of: Autopack is parent organization of: Integrative Neuroscience Initiative on Alcoholism is parent organization of: Joint Center for Structural Genomics is parent organization of: Functional Glycomics Research is parent organization of: VIPERdb is parent organization of: GOEx - Gene Ontology Explorer is parent organization of: VIPERdb is parent organization of: Zinc Finger Tools is parent organization of: XCMS is parent organization of: Chemoproteomic identification and therapeutic validation of proteins of metabolic significance is parent organization of: Leginon is parent organization of: outbreak.info is parent organization of: Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | grid.214007.0, ISNI: 122199231, Wikidata: Q793867, nif-0000-10475 | https://ror.org/02dxx6824 | SCR_001907 | The Scripps Research Institute, Scripps Research | 2026-08-01 12:01:54 | 1 | |||||
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SoftCite Resource Report Resource Website |
SoftCite (RRID:SCR_024411) | portal, software resource, knowledge base, project portal, data or information resource | Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale. | Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature, |
lists: ProteinPilot lists: ROCit lists: survivalROC lists: GIFT lists: PyWavelets lists: pRRophetic lists: GOplot lists: Rgdal lists: riskRegression lists: RNAfold lists: RNALocate lists: pyPCcazip lists: ScanProsite lists: RapGreen lists: ABySS lists: AMBER lists: ANNOVAR lists: ASAP lists: ASPicDB lists: AStalavista lists: ATSAS lists: Alien hunter lists: Adobe Photoshop lists: Affymetrix lists: Augustus lists: Argus lists: Adobe Illustrator lists: ART lists: AutoDock Vina lists: AutoDock lists: ANALYZE lists: BLASTClust lists: arrayQualityMetrics lists: BLASTN lists: BLASTX lists: BLASTP lists: Bowtie lists: Autogrid lists: BRB-ArrayTools lists: BEDTools lists: BWA lists: BioEdit lists: BRASS lists: Bioconductor lists: BioExtract lists: BaCelLo lists: BioMoby lists: Brain Extraction Tool lists: Bowtie 2 lists: BoxPlotR lists: biomaRt lists: BioPerl lists: CANGS lists: CFX Manager lists: CEAS lists: BlobFinder lists: CLC Genomics Workbench lists: BREAKDANCER lists: CASAVA lists: CLC Main Workbench lists: ClustalW lists: Clustal W2 lists: ComBat lists: CCP4 lists: Blender lists: Coot lists: CGView lists: COMSOL Multiphysics lists: CTFFIND lists: CalcuSyn lists: ChIPpeakAnno lists: Chimera lists: CVODE lists: DAVID lists: Cufflinks lists: caret lists: ClueGO lists: Cluster lists: Clocklab lists: DIANA-mirPath lists: Cytoscape lists: EMAN lists: E-Prime lists: DESeq2 lists: Definiens Developer XD lists: Eigensoft lists: EMBOSS lists: Ensembl lists: DIALIGN lists: Design-Expert lists: EndNote lists: CMAP lists: EEGLAB lists: CMap lists: Epi Info lists: FASTA lists: Ensembl Genome Browser lists: Epik lists: FACS lists: FCS Express lists: Flowlogic lists: FSL lists: FLASH lists: FATCAT lists: FastQC lists: G*Power lists: GOLD lists: FGENESH lists: FreeSurfer lists: FlowJo lists: GeneTools lists: Galaxy lists: GATK lists: ELDA lists: GraphPad lists: GRADEpro lists: Fiji lists: Gblocks lists: FigTree lists: GENIE lists: GBrowse lists: Gemma lists: GeneChip Operating Software lists: GeneMapper lists: GeneMarker lists: GenABEL lists: GenePattern lists: GraphPad Prism lists: GenePix Pro lists: Google lists: Genesis lists: Hologic lists: GeneSpring GX lists: GeneVenn lists: HaploReg lists: Google Scholar lists: HALO lists: Gwyddion lists: IMAGIC lists: HKL-2000 lists: Glide lists: Glimmer lists: I-TASSER lists: GenomeStudio lists: IMOD lists: Haploview lists: Hmmer lists: Hydra lists: IUPRED lists: HomeCageScan lists: Geneious lists: IGOR Pro lists: IMPUTE lists: Infernal lists: Image-Pro Plus lists: JASP lists: LSM Image Examiner lists: Imaris lists: Image Pro Plus lists: ImageQuant lists: ImageJ lists: Integrative Genomics Viewer lists: jcvi lists: InterProScan lists: KaleidaGraph lists: Ligprep lists: Heidelberg Eye Explorer lists: JMP lists: Ingenuity Pathways Knowledge Base lists: Leica QWin lists: JCB DataViewer lists: Jalview lists: LigandScout lists: Ingenuity Pathway Analysis lists: LabView lists: Kepler lists: MAFFT lists: Jmol lists: ImageScope lists: MACS lists: Maq lists: MUMmer lists: MATLAB lists: Mimics lists: MACH lists: MCODE lists: Mascot lists: Maestro lists: MSQuant lists: MediaWiki lists: MINC lists: MRIcron lists: MOE lists: ModFit LT lists: LIMMA lists: MassLynx lists: mitopred lists: MrBayes lists: MolProbity lists: MUSCLE lists: MutationAssessor lists: MaxQuant lists: Minitab lists: MODELLER lists: MetaboAnalyst lists: MedCalc lists: Origin lists: MPlus lists: MutationTaster lists: MuTect lists: Multi Gauge lists: NIA Array Analysis lists: NIH Image lists: Phenix lists: MycoBank lists: OpenClinica lists: Nexus lists: OMTools lists: NIS-Elements lists: PAST lists: NVivo lists: PRISM (Stanford database) lists: Metscape lists: PROCHECK lists: oligo lists: OpenEpi lists: Pathway Commons lists: Nanoparticle Tracking Analysis lists: Openlab lists: PLINK lists: PAUP lists: NONMEM lists: PREFAB lists: NetworkX lists: PeptideProphet lists: Primer Designer lists: PhyML lists: PASS lists: PyMOL lists: PSIPRED lists: PROFILER lists: PHYLIP lists: Phobius lists: Prime lists: Phyutility lists: Picard lists: ProteinProphet lists: Phaser lists: ProSAS lists: PostgreSQL lists: Primer-BLAST lists: ProteinLynx Global Server lists: QUANTO lists: Primer Express lists: Primer3Plus lists: ProtTest lists: ProbCons lists: Primer3 lists: Poretools lists: Protein preparation Wizard lists: QmRLFS-finder lists: PicTar lists: RevMan lists: Pipeline Pilot lists: QIIME lists: PRISMA lists: REDCap lists: RAxML lists: Proteome Discoverer lists: Research Randomizer lists: SPARTAN lists: SPSS lists: RNAstructure lists: Refmac lists: QuantPrime lists: Prodigal lists: RepeatModeler lists: Ringo lists: SQLite lists: SAGE lists: Rhinoceros lists: SAMTOOLS lists: SPAdes lists: RepeatMasker lists: SEDFIT lists: STATISTICA lists: RNAhybrid lists: SlideBook lists: STRUCTURE lists: SABmark lists: SPM lists: Stata lists: RStudio lists: SciPy lists: Scion Image lists: Simulink lists: TAGGER lists: TopHat lists: SAM lists: ShortRead lists: SIFT lists: SCAN lists: SignalP lists: Scopus lists: Strelka2 lists: Trans-ABySS lists: Statgraphics Centurion lists: T-Coffee lists: Statistical Analysis System lists: TargetScan lists: UCHIME lists: Sequencher lists: SigmaStat lists: UCSC Genome Browser lists: affy lists: Taverna lists: MBF BioScience: Stereo Investigator lists: Trimmomatic lists: Vmatch lists: WFU PickAtlas lists: SigmaPlot lists: X!Tandem lists: STAR lists: TASSEL lists: SyStat lists: WEBLOGO lists: UCSF Chimera lists: TreeView lists: pheatmap lists: WinWCP lists: microRNA.org lists: glmnet lists: Phenix.refine lists: BASE lists: beadarray lists: RMS lists: lumi lists: Web of Science lists: minfi lists: geNORM lists: WU-BLAST lists: WinBUGS lists: SPP lists: tRNAscan-SE lists: WebPlotDigitizer lists: qBasePLUS lists: Matplotlib lists: TreeBASE lists: pClamp lists: TBLASTN lists: igraph lists: V3D lists: survival lists: miRanda lists: piRNABank lists: topGO lists: NGmerge lists: OMNISEC lists: NOTUNG lists: OpenBUGS lists: Optimization Toolbox lists: ProgRes Capture Pro lists: Ocular lists: Umediation lists: Nano Measurer lists: PHYLDOG lists: VSEARCH lists: WinNonlin lists: WHONET lists: ToposPro lists: Treerecs lists: Agilent Seahorse Wave lists: SimPhy lists: TomoStudio lists: Mutation Assessor lists: Stem lists: SRAMP lists: CRISPResso2 lists: geepack lists: Evalue lists: DAGitty lists: FastMulRFS lists: ggridges lists: gamm4 lists: AutoRT lists: CopyKAT lists: Inference of CRISPR Edits lists: classInt lists: ASTRAL-Pro lists: maftools lists: mitml lists: CMplot lists: MetaPSICOV lists: LaCyTools lists: MADOKA lists: Kaplan Meier Plotter lists: IntFOLD lists: ModFOLD lists: lDDT has parent organization: University of Texas at Austin; Texas; USA |
Sloan Foundation | DOI:10.1002/asi.24454 | Free, Available for download, Freely available | https://github.com/softcite/softcite_dataset_v2, https://zenodo.org/record/7995565 | SCR_024411 | Software Citation | 2026-08-04 09:45:30 | 0 | ||||||
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Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | software resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites. | broadcast, data federation, defined rdf schema, infrastructure, meta-data, rdf, retrieve, biomedical, biositemap, sitemap |
lists: Adaptively Sampled Particle Fluids lists: DicomWorks lists: MEDx lists: Medical Image Processing and Visualization lists: Surface-Based Atlases lists: RESNET lists: SurfRelax lists: FEATURE lists: Cardiovascular Model Repository lists: Simtk.org lists: ConTrack lists: Allopathfinder lists: Molecular Simulation Trajectories Archive of a Villin Variant lists: BioPortal lists: SumsDB lists: NeuronDB lists: BrainInfo lists: Protege lists: i2b2 Cross-Institutional Clinical Translational Research project lists: GeneChip Operating Software lists: Honig Lab lists: Proteomics Identifications (PRIDE) lists: ASAP: the Alternative Splicing Annotation Project lists: MiMI Plugin for Cytoscape lists: Substructure Index-based Approximate Graph Alignment lists: Proteome Commons Tranche repository lists: caTIES - Cancer Text Information Extraction System lists: REDCap lists: miniTUBA lists: Einstein-Montefiore ICTR Research Informatics Core lists: T-profiler lists: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse lists: GCG/SeqWeb lists: Solstice lists: California National Primate Research Center lists: BioGPS: The Gene Portal Hub lists: Blox lists: Subcellular Location Image Finder lists: PeptideAtlas lists: Clair library lists: Lyngby lists: SimTKCore lists: Velos lists: Ingenuity Pathway Analysis lists: Philips lists: Talktech lists: SUN Interface Engine lists: Quadramed - Medicus, Quantim lists: Wisconsin National Primate Research Center lists: i2b2 Research Data Warehouse lists: Merge Healthcare Incorporated lists: Clinical Trial Management Application lists: Cerner Millenium lists: Open Clinical Report Repository lists: Quovadx, Inc. lists: VectorValuedHistogramNormalizer lists: Morphometry BIRN lists: Talairach Daemon lists: LONI Visualization Tool lists: LONI Debabeler lists: LONI Pipeline Processing Environment lists: Brede Wiki lists: medInria lists: FreeSurfer lists: ITK-SNAP lists: VoxBo lists: Ensembl lists: MRIcron lists: Synchronized Histological Image Viewing Architecture lists: LONI ShapeViewer lists: LONI ShapeTools lists: FFT Library lists: NUTMEG lists: bioDBcore lists: Mutant Mouse Resource and Research Center lists: Brainscape lists: MindSeer lists: University of Southern California LONI Software lists: Statistics Online Computational Resource lists: NIH MRI Study of Normal Brain Development lists: Ontology Development and Information Extraction lists: Mindtouch DekiWiki lists: National Mesothelioma Virtual Bank lists: MGH-USC Human Connectome Project lists: Fusion ICA Toolbox lists: Biomedical Resource Ontology lists: Biomedical Informatics Research Network lists: 3D Slicer lists: Analysis of Functional NeuroImages lists: Automated Image Registration lists: TOADS-CRUISE Brain Segmentation Tools lists: BrainImage Software lists: Brede Toolbox lists: Whole Brain Catalog lists: Low Resolution Electromagnetic Tomography lists: Cambridge Brain Activation lists: ModelDB lists: fMRI Data Center lists: EEGLAB lists: 3DViewnix lists: MIPAV: Medical Image Processing and Visualization lists: NeuroLens lists: WFU PickAtlas lists: Protein Subcellular Location Image Database lists: STRIDE Virtual Biospecimen Bank lists: BrainVoyager is related to: Biomedical Resource Ontology is related to: Software Distribution Sets is related to: REX is related to: Rat Genome Database (RGD) has parent organization: National Centers for Biomedical Computing has parent organization: National Institutes of Health is parent organization of: Resource Discovery System |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10583 | SCR_001976 | 2026-08-04 09:40:31 | 1 |
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