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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 | 2025-04-19 06:42:50 | 0 | |||||||
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Jalview Resource Report Resource Website 1000+ mentions |
Jalview (RRID:SCR_006459) | Jalview | software resource | A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. | edit, analysis, annotation, multiple sequence alignment, wysiwyg, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Dundee; Scotland; United Kingdom |
BBSRC BBSB16542 | PMID:19151095 DOI:10.1093/bioinformatics/btp033 |
GNU General Public License, v3, Acknowledgement requested | OMICS_00885, biotools:Jalview | https://bio.tools/Jalview https://sources.debian.org/src/jalview/ |
SCR_006459 | 2025-04-19 06:43:29 | 3334 | |||||
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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. | 2025-04-19 06:41:58 | 0 | |||||||
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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 | 2025-04-19 06:41:59 | 0 | ||||||
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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. | 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 | nlx_158360 | SCR_003959 | Psynova Neurotech Ltd | 2025-04-19 06:42:00 | 9 | |||||||
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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. | 2025-04-19 06:42:08 | 0 | ||||||||
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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 | 2025-04-19 06:42:05 | 1 | |||||||||
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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 | 2025-04-19 06:42:07 | 3 | |||||||
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Vanator Resource Report Resource Website 1+ mentions |
Vanator (RRID:SCR_004370) | Vanator | software resource | A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. | perl, metagenomic, illumina, alignment, assembly, analysis, profile, virus, clinical, environment, next-generation sequencing, taxonomy, read |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:23296970 | OMICS_01505 | SCR_004370 | Vanator-CVR, Vanator-CVR - A metagenomics & virus discovery pipeline, Virus Alignment de Novo Assembly and Taxonomy On Reads, Vanator-CVR: A metagenomics and virus discovery pipeline | 2025-04-19 06:42:18 | 2 | |||||||
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deCODE genetics Resource Report Resource Website 10+ 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 | nif-0000-31959, ISNI: 0000 0004 0618 6889, grid.421812.c, Wikidata: Q493712 | https://ror.org/04dzdm737 | SCR_003334 | Islensk Erfdagreining EHF, Islensk Erfdagreining | 2025-04-19 06:41:40 | 48 | ||||||
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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 | New BSD License, Acknowledgement requested | biotools:bpipe, OMICS_02301 | https://bio.tools/bpipe | SCR_003471 | bpipe - A tool for running and managing bioinformatics pipelines | 2025-04-19 06:41:44 | 13 | |||||
|
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 | 2025-04-19 06:41:51 | 349 | ||||||||
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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 | grid.436973.c, Wikidata: Q30291134, nlx_158133 | https://ror.org/02ca38p84 | SCR_003826 | Quretec Ltd., Quretec Ltd | 2025-04-19 06:41:54 | 2 | |||||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2025-04-19 06:43:02 | 23 | ||||
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Time-series RNA-seq Analysis Package Resource Report Resource Website 1+ mentions |
Time-series RNA-seq Analysis Package (RRID:SCR_002935) | TRAP | software resource | A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. | time-series, rna-seq, analysis |
is listed by: OMICtools has parent organization: Seoul National University; Seoul; South Korea |
PMID:24518221 | OMICS_02590 | SCR_002935 | 2025-04-19 06:41:31 | 3 | ||||||||
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Genetic Analysis Package Resource Report Resource Website 1+ mentions |
Genetic Analysis Package (RRID:SCR_003006) | software resource | GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates. | genetic, analysis, package, data, population, family, calculation, family, disease, aggregation, kinship, environmental, covariate, haplotype, marker | nif-0000-30271 | SCR_003006 | GAP | 2025-04-19 06:41:33 | 1 | ||||||||||
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SASqPCR Resource Report Resource Website 1+ mentions |
SASqPCR (RRID:SCR_003056) | software resource | All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required. | standalone software, computation, analysis, statistics, rt-qpcr, cdna, mrna, gene expression, quantification, reference gene, normalization, sas |
is listed by: OMICtools has parent organization: Google Code |
PMID:22238653 | New BSD License | OMICS_02375 | SCR_003056 | SASqPCR: robust and rapid analysis of RT-qPCR data in SAS | 2025-04-19 06:41:34 | 6 | |||||||
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RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html https://bio.tools/ramigo |
SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2025-04-19 06:43:49 | 11 | |||||
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ARB project Resource Report Resource Website 10+ mentions |
ARB project (RRID:SCR_000515) | ARB | software resource | Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. | rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene |
is listed by: Debian is related to: SILVA is related to: SINA has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:14985472 | Free, Freely available | OMICS_01515 | https://sources.debian.org/src/arb/ | SCR_000515 | The ARB project | 2025-04-19 06:39:52 | 28 | |||||
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ROSTLAB Resource Report Resource Website |
ROSTLAB (RRID:SCR_000792) | group | A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. | protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical |
has parent organization: Columbia University; New York; USA is parent organization of: PredictNLS is parent organization of: SNPdbe |
NLM LM007329; NLM GM50291 |
Publicaly available sources include PredictProtein, the first Internet server for protein structure prediction, and META-PP, as well as more recent databases and resources. | nif-0000-31417 | http://cubic.bioc.columbia.edu/services/disis | SCR_000792 | Rost Group | 2025-04-19 06:40:07 | 0 |
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