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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 Synonyms Record Last Update Mentions Count
deCODE genetics
 
Resource Report
Resource Website
50+ mentions
deCODE genetics (RRID:SCR_003334) deCODE commercial organization A biopharmaceutical company applying its discoveries in human genetics to develop drugs and diagnostics for common diseases. They specialize in gene discovery - their population approach and resources have enabled them to isolate key genes contributing to major public health challenges from cardiovascular disease to cancer. The company's genotyping capacity is now one of the highest in the world. They have a large population-based biobank containing whole blood and DNA samples with extensive relevant phenotypic information from around 120.000 Icelanders. In the company's work in more than 50 disease projects, their statistical and informatics departments have established themselves in data processing and analysis. deCODE genetics is widely recognized as a center of excellence in genetic research. biopharmaceutical, genetics, drug, diagnostic, genotyping, phenotype, data processing, analysis, genetic variant, risk factor, genome, blood, dna, biobank, single nucleotide polymorphism is related to: EU-AIMS
is related to: NEWMEDS
Schizophrenia, Cardiovascular disease, Cancer, Type 2 diabetes, Atrial fibrillation, Heart attack Free, Freely available nif-0000-31959, ISNI: 0000 0004 0618 6889, grid.421812.c, Wikidata: Q493712 https://ror.org/04dzdm737 SCR_003334 Islensk Erfdagreining EHF, Islensk Erfdagreining 2026-09-12 12:55:56 67
Bpipe
 
Resource Report
Resource Website
10+ mentions
Bpipe (RRID:SCR_003471) Bpipe software resource Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. genetics, dna, analysis, cluster, workflow, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Google Code
PMID:22500002 Free, Available for download, Freely available biotools:bpipe, OMICS_02301 https://github.com/ssadedin/bpipe SCR_003471 bpipe - A tool for running and managing bioinformatics pipelines 2026-09-12 12:55:58 13
L-Measure
 
Resource Report
Resource Website
10+ mentions
L-Measure (RRID:SCR_003487) LM data processing software, image analysis software, image processing software, service resource, software application, software resource A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools is listed by: 3DVC
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: bio.tools
has parent organization: Computational Neuroanatomy Group
Human Brain Project ;
NINDS R01 NS39600
PMID:18451794 Public nif-0000-00003, biotools:l-measure http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure SCR_003487 2026-09-12 12:55:59 30
MINC Brain Imaging Toolbox
 
Resource Report
Resource Website
MINC Brain Imaging Toolbox (RRID:SCR_003519) data processing software, image analysis software, software application, software resource, software toolkit THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.Comprised of a large array of sophisticated programs, this comprehensive software package with tools based around the MINC file format. Utilities are provided for conversion, viewing, editing, registering, segmentation, and a wide array of analysis. Many programs are in Perl. MINC software tools for neurological imaging are free. Input format: Analyze, DICOM, Minc mri, neuroimaging, pet, registration, segmentation, analysis, neurological imaging has parent organization: McGill University; Montreal; Canada THIS RESOURCE IS NO LONGER IN SERVICE nlx_10430 http://www.idoimaging.com/cgi-sys/cgiwrap/acrabb/imaging/program.pl?ident=280 SCR_003519 2026-09-12 12:55:59 0
nSolver Analysis Software
 
Resource Report
Resource Website
100+ mentions
nSolver Analysis Software (RRID:SCR_003420) nSolver Analysis Software data processing software, software application, software resource Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages. normalization, analysis, ncounter, os x, windows, quality control is listed by: OMICtools Restricted OMICS_02309 https://nanostring.app.box.com/v/nSolver-AdvancedAnalysis, https://nanostring.com/products/ncounter-analysis-system/ncounter-analysis-solutions/nsolver-data-analysis-support/ SCR_003420 2026-09-12 12:55:58 405
miniTUBA
 
Resource Report
Resource Website
miniTUBA (RRID:SCR_003447) miniTUBA analysis service resource, production service resource, service resource, storage service resource miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring networks of interacting influences that may be predictive of both disease progression and the impact of clinical interventions and probability tables for interpreting results. The DBN analysis that miniTUBA provides is especially good for biomedical experiments or clinical studies in which you collect data different time intervals. Applications of miniTUBA to biomedical problems include analyses of biomarkers and clinical datasets and other cases described on the miniTUBA website. To run a DBN with miniTUBA, you can set a number of parameters and constrain results by modifying structural priors (i.e. forcing or forbidding certain connections so that direction of influence reflects actual biological relationships). You can specify how to group variables into bins for analysis (called discretizing) and set the DBN execution time. You can also set and re-set the time lag to use in the analysis between the start of an event and the observation of its effect, and you can select to analyze only particular subsets of variables. analysis, analyze, bayesian, causation, clinical, linear, medical, structure, temporal, network analysis, network, molecule, information refining, gene expression regulation, bioinformatics, statistical package, interaction network, prediction, pathway, inference, biomedical, intervention is listed by: Biositemaps
has parent organization: National Center for Integrative Biomedical Informatics
has parent organization: University of Michigan; Ann Arbor; USA
Society of University Surgeons Foundation ;
NIDA U54DA021519;
NIAID 1R21AI057875-01;
NIGMS K08 GM074678-01A1
PMID:17644819 Free, Freely available nif-0000-33272 SCR_003447 miniTUBA - Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool, Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool, Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool (miniTUBA), The Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool 2026-09-12 12:55:58 0
Oxford Nanopore Technologies
 
Resource Report
Resource Website
100+ mentions
Oxford Nanopore Technologies (RRID:SCR_003756) Oxford Nanopore commercial organization Commercial organization developing a disruptive, proprietary technology platform for the direct, electronic analysis of single molecules. The instruments GridION and MinION are adaptable for the analysis of DNA, RNA, proteins, small molecules and other types of molecule. Consequently, the platform has a broad range of potential applications, including scientific research, personalized medicine, crop science and security / defence. nanopore technology, dna, rna, protein, small molecule, molecule, analysis, nanopore, nanopore sensing is related to: READNA
is related to: Pychopper
nlx_158233 SCR_003756 Oxford Nanopore Technologies Ltd 2026-09-12 12:56:02 448
Quretec
 
Resource Report
Resource Website
1+ mentions
Quretec (RRID:SCR_003826) Quretec commercial organization Commercial organization that builds software for collection, management, and analysis of complex data, most typical in biomedical domain. The solutions are generic and can be used for multitude of uses and application domains. data capture, data management, analysis, biomedical is related to: AgedBrainSYSBIO Wikidata: Q30291134, grid.436973.c, nlx_158133 https://ror.org/02ca38p84 SCR_003826 Quretec Ltd., Quretec Ltd 2026-09-12 12:56:03 2
Althia
 
Resource Report
Resource Website
Althia (RRID:SCR_003918) Althia commercial organization A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid. oncology, diagnosis, prognosis, solid tumor, hematological tumor, translational, radiation, phenotype, analysis, pathology, hematology, hereditary is related to: PRECISESADS Cancer, Tumor, Solid tumor, Hematological tumor, Precancer nlx_158279 SCR_003918 Althia Health Ltd., Althia Health, Advanced Laboratories of Translational Health, SL, S.L. 2026-09-12 12:56:05 0
Alacris Theranostics
 
Resource Report
Resource Website
Alacris Theranostics (RRID:SCR_003953) Alacris commercial organization Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations. next generation sequencing, computational modeling, clinical trial, somatic tissue, genotyping, genomics, oncogenomics, diagnostics, therapy, disease model, drug, personalized medicine, biomarker, drug development, tumor model, analysis, oncology is related to: OncoTrack Tumor, Cancer nlx_158354, grid.473915.d https://ror.org/04a0gnr15 SCR_003953 Alacris Theranostics GmbH 2026-09-12 12:56:05 0
Psynova Neurotech
 
Resource Report
Resource Website
1+ mentions
Psynova Neurotech (RRID:SCR_003959) Psynova commercial organization Commercial organization focused on the development and exploitation of novel biomarkers for psychiatric illnesses. They provide industrial and academic partners with comprehensive biomarker discovery services in commercial and collaborative projects. They operate in the field of psychiatric disorders and their products and services are designed to excel biomarker research. In 2010, Psynova Neurotech and its partner company Rules-Based-Medicine Inc (now MyriadRBM) conducted a beta launch of a blood test aiding in the diagnosis of schizophrenia (http://www.veripsych.com/). They are now refining the test and have shifted their focus to the development of new blood-based biomarker tests that aid in the diagnosis, prognosis and differential diagnosis of schizophrenia, bipolar disorder and major depression. They offer not only their pre-selceted Multiple Reaction Monitoring (MRM) and Multiplex Immunoassay products, but also custom build panels. If they are provided with a list of analyses to evaluate, they can produce an analytical panel according to individual needs utilizing either MRM or Multiplex Immunoassay technologies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. biomarker, neuropsychiatry, preclinical, model, diagnosis, blood, drug response, immunoassay, brain tissue, mass spectrometry, analysis is related to: University of Cambridge; Cambridge; United Kingdom
is related to: NEWMEDS
Schizophrenia, Psychiatric disorder, Bipolar Disorder, Major Depressive Disorder THIS RESOURCE IS NO LONGER IN SERVICE nlx_158360 SCR_003959 Psynova Neurotech Ltd 2026-09-12 12:56:06 9
Genomedics
 
Resource Report
Resource Website
Genomedics (RRID:SCR_004103) Genomedics commercial organization A commercial company specialized in the field of clinical governance, research and clinical-epidemiological analysis and development of services and software applications for healthcare. Products and Services * Analysis and development software solutions, web, e-learning * Design and Implementation APP for Smartphone and Tablet (iOS, Android, Windows Phone) * Clinical Intelligence & Clinical Decision Support Systems (CDSS) * Data center services and Application Server Provider * Epidemiology, Surveillance and Health Promotion - Development of studies and epidemiological research healthcare, clinical, medicine, health, information service, analysis, software development, web portal, multimedia, e-learning, data center service, application server, business intelligence, epidemiology, surveillance, health promotion, population is related to: EMIF nlx_158578 SCR_004103 Genomedics health care consultants, Genomedics S.r.l. 2026-09-12 12:56:09 0
Sierra Sensors
 
Resource Report
Resource Website
1+ mentions
Sierra Sensors (RRID:SCR_004062) commercial organization In 2018 Bruker acquired Sierra Sensors GmbH, based in Hamburg, Germany. Sierra develops and manufactures innovative analytical biosensors based on Surface Plasmon Resonance (SPR) detection. Driven by patented technologies in the areas of SPR detection and microfluidic sample delivery, Sierra instruments are setting a new standard in high-throughput and high-performance label-free analysis. biosensor, analytical tool, molecule, interaction, label-free analysis, analysis, assay, microfluidic, diagnostic is related to: Kinetics for Drug Discovery nlx_158499 SCR_004062 Sierra Sensors Biosensor Technologies, Sierra Sensors GmbH 2026-09-12 12:56:08 1
Biomol-Informatics
 
Resource Report
Resource Website
1+ mentions
Biomol-Informatics (RRID:SCR_004081) commercial organization THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry. bioinformatics, genome sequencing, genome, sequencing, exome, protein-protein interaction, analysis, molecular dynamics, 3d modeling, evolutive information, training service resource, next generation sequencing, simulation, drug design, computational simulation, macromolecule, molecular dynamics, quantum mechanics, molecular mechanics, dna, protein is related to: European Gram Negative AntiBacterial Engine
has parent organization: Autonomous University of Madrid; Madrid; Spain
THIS RESOURCE IS NO LONGER IN SERVICE nlx_158539, grid.432020.7, Wikidata Q30254873 https://ror.org/057rd1163 SCR_004081 Biomol-Informatics SL 2026-09-12 12:56:08 3
pClamp
 
Resource Report
Resource Website
5000+ mentions
pClamp (RRID:SCR_011323) data acquisition software, data analysis software, data processing software, software application, software resource Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis. electrophysiology, data, acquisition, analysis, Molecular Device, voltage, clamp, is listed by: SoftCite Commercially available rid_000085 https://www.moleculardevices.com/products/axon-patch-clamp-system/acquisition-and-analysis-software/pclamp-software-suite#gref SCR_011323 patch clamp, Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software, patch CLAMP, pCLAMP 11, pCLAMP 10, patch Clamp 2026-09-12 12:57:32 9999
edgeR
 
Resource Report
Resource Website
10000+ mentions
edgeR (RRID:SCR_012802) edgeR data analysis software, data processing software, software application, software resource Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools is used by: Glimma
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: SARTools
is related to: Bioconductor
works with: tximport
Harris and IBS Honours scholarships ;
Independent Research Institutes Infrastructure Support Scheme 361646;
Melbourne International Research Scholarship ;
NHMRC 406657;
Victorian State Government OIS grant
PMID:19910308
DOI:10.1093/bioinformatics/btp616
Free, Available for download, Freely available OMICS_01308, biotools:edger https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ SCR_012802 edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R 2026-09-12 12:57:53 23868
affy
 
Resource Report
Resource Website
1000+ mentions
affy (RRID:SCR_012835) Affy data analysis software, data processing software, software application, software resource Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools is listed by: OMICtools
is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: affydata
is related to: R Project for Statistical Computing
is related to: OMICtools
Danish Biotechnology Instrument Center PMID:14960456 Free, Available for download, Freely available BioTools:affy, OMICS_00740, biotools:affy https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ SCR_012835 Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data 2026-09-12 12:57:53 3073
TopHat
 
Resource Report
Resource Website
5000+ mentions
Rating or validation data
TopHat (RRID:SCR_013035) alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools uses: Bowtie
is used by: CIRCexplorer
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: HISAT2
has parent organization: University of Maryland; Maryland; USA
has parent organization: University of California at Berkeley; Berkeley; USA
has parent organization: Johns Hopkins University; Maryland; USA
has parent organization: University of Washington; Seattle; USA
works with: GeneScissors
NHGRI R01 HG006102;
NHGRI R01 HG006677
PMID:23618408
PMID:19289445
DOI:10.1093/bioinformatics/btp120
Free, Available for download, Freely available biotools:tophat, OMICS_01257 https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ http://tophat.cbcb.umd.edu/ SCR_013035 tophat, TopHat1, Tophat2 2026-09-12 12:57:57 9789
Neuroimaging in Python
 
Resource Report
Resource Website
10+ mentions
Neuroimaging in Python (RRID:SCR_013141) NIPY, community building portal, data or information resource, portal, software application, software development environment, software development tool, software resource Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Python Programming Language
has parent organization: SourceForge
has parent organization: University of California at Berkeley; Berkeley; USA
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
is parent organization of: Dipy
is parent organization of: NiLearn
is parent organization of: NIPY
is parent organization of: NiBabel
is parent organization of: Nipype
is parent organization of: Nitime
NIMH 5R01MH081909-02;
NIBIB 1R03EB008673-01
PMID:21897815 Revised BSD license nlx_149365 http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype SCR_013141 NIPY Community 2026-09-12 12:57:59 27
PlasmoDB
 
Resource Report
Resource Website
1000+ mentions
PlasmoDB (RRID:SCR_013331) analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list uses: SynView
is related to: GeneDB Pfalciparum
has parent organization: Eukaryotic Pathogen Database Resources
has parent organization: Pennsylvania State University
has parent organization: University of Georgia; Georgia; USA
malaria NIAID PMID:18957442 nif-0000-03314, SCR_017665, r3d100011569 SCR_013331 PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource 2026-09-12 12:58:02 1324

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