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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RIPSeeker Resource Report Resource Website 10+ mentions |
RIPSeeker (RRID:SCR_006810) | RIPSeeker | software resource | A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation. | rip-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_00569 | SCR_006810 | RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments | 2026-08-01 12:03:13 | 10 | |||||||
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BioBricks Foundation Resource Report Resource Website 10+ mentions |
BioBricks Foundation (RRID:SCR_006779) | BBF | institution | The BioBricks Foundation (BBF) is dedicated to advancing synthetic biology to benefit all people and the planet. To achieve this, we must make engineering biology easier, safer, equitable, and more open. We do this in the following ways: by ensuring that the fundamental building blocks of synthetic biology are freely available for open innovation; by creating community, common values and shared standards; and by promoting biotechnology for all constructive interests. We envision a world in which scientists and engineers work together using BioBric parts freely available standardized biological parts to create safe, ethical solutions to the problems facing humanity. We envision synthetic biology as a force for good in the world. We see a future in which architecture, medicine, environmental remediation, agriculture, and many other fields are using the technology of synthetic biology. Our supporters are many and include corporations, individuals, institutions, foundations, government, corporations, and others. Currently, the BBF''s key programs include: * BIOFAB * BioBrick Public Agreement * Technical Standards Framework * Conferences and Workshops * BBF Global Network * OpenWetWare | is parent organization of: OpenWetWare | grid.487833.3, nlx_19572 | https://ror.org/03kqtp318 | SCR_006779 | 2026-08-01 12:03:20 | 35 | |||||||||
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PeproTech Resource Report Resource Website 10000+ mentions |
PeproTech (RRID:SCR_006802) | commercial organization | An Antibody supplier | nlx_152428 | SCR_006802 | 2026-08-01 12:03:21 | 27848 | ||||||||||||
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Life Sciences Discovery Fund Resource Report Resource Website 1+ mentions |
Life Sciences Discovery Fund (RRID:SCR_006845) | LSDF | institution | Funds innovative research and development in Washington state to promote life sciences competitiveness, enhance economic vitality, and improve health and health care. Its grantmaking opportunities are designed to leverage the state''s investment in research and development by achieving three goals: promoting health; making the life sciences sector more competitive; and strengthening Washington''s economy. LSDF currently offers two different types of granting mechanisms for both for-profit and non-profit organizations in Washington: * Proof of Concept grants to enhance the commercial viability of intellectual property developed by non-profit organizations or enhance the competitiveness of early-stage companies for private equity investment. (This grant mechanism combines the Commercialization and PreCede mechanisms offered in prior years.) * Opportunity grants to fund extraordinary research and development proposals having the ability to significantly leverage LSDF dollars against those from other sources. | life science, health, health care, economic well being, grant | nlx_151984, grid.475232.5 | https://ror.org/05tzak412 | SCR_006845 | 2026-08-01 12:03:18 | 3 | |||||||||
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NeuronVisio Resource Report Resource Website 1+ mentions |
NeuronVisio (RRID:SCR_006839) | Neuronvisio | d visualization software | A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB. | 3d visualization, electrophysiological model, hdf storage, matplotlib integration, neuron model, visualization, neuron, visualization, electrophysiology |
is related to: INCF Software Center is related to: NEURON is related to: ModelDB has parent organization: European Bioinformatics Institute |
Wellcome Trust | PMID:22685429 | GNU General Public License, Acknowledgement requested | nlx_156723 | SCR_006839 | Neuron visio | 2026-08-01 12:03:18 | 3 | |||||
|
EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-08-01 12:03:17 | 19 | |||||
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Pel-Freez Biologicals Resource Report Resource Website 100+ mentions |
Pel-Freez Biologicals (RRID:SCR_006827) | commercial organization | An Antibody supplier | nlx_152427 | SCR_006827 | Pel-Freez | 2026-08-01 12:03:21 | 143 | |||||||||||
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BAMStats Resource Report Resource Website 10+ mentions |
BAMStats (RRID:SCR_006973) | BAMStats | software resource | A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API. | matlab, next generation sequencing, java |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_01034 | SCR_006973 | 2026-08-01 12:03:21 | 10 | ||||||||
|
University of Wyoming; Wyoming; USA Resource Report Resource Website 1+ mentions |
University of Wyoming; Wyoming; USA (RRID:SCR_007020) | UW | university | Public land grant research university in Laramie, Wyoming. |
is parent organization of: bamova is parent organization of: TAED - The Adaptive Evolution Database is parent organization of: University of Wyoming School of Pharmacy is parent organization of: University of Wyoming Stable Isotope Core Facility is parent organization of: University of Wyoming Center for Advanced Scientific Instrumentation CASI Core Facility |
Wikidata:Q1326975, ISNI:0000 0001 2109 0381, nlx_97727, Crossref funder ID:100008106, grid.135963.b | https://ror.org/01485tq96 | SCR_007020 | UWYO | 2026-08-01 12:03:21 | 1 | ||||||||
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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 | 2026-08-01 12:03:19 | 11 | |||||
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RazerS Resource Report Resource Website 10+ mentions |
RazerS (RRID:SCR_006889) | RazerS | software resource | A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors. | next-generation sequencing, c++, openmp, linux, mac os x, windows |
is listed by: OMICtools has parent organization: Free University of Berlin; Berlin; Germany |
PMID:22923295 PMID:19592482 |
GNU General Public License | OMICS_00679 | SCR_006889 | 2026-08-01 12:03:19 | 13 | |||||||
|
ArtificialFastqGenerator Resource Report Resource Website 10+ mentions |
ArtificialFastqGenerator (RRID:SCR_006880) | ArtificialFastqGenerator | software resource | Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic. | matlab, java, Next Generation Sequencing, aligns reads, reference genome |
is listed by: OMICtools is listed by: Debian |
PMID:23152858 | GNU GPL v3 | OMICS_00248, SCR_015979 | https://sources.debian.org/src/artfastqgenerator/ | SCR_006880 | Artfastqgenerator - Ouputs artificial FASTQ files derived from a reference genome | 2026-08-01 12:03:14 | 10 | |||||
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BarraCUDA Resource Report Resource Website 1+ mentions |
BarraCUDA (RRID:SCR_006881) | BarraCUDA | software resource | A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: SourceForge |
PMID:22244497 PMID:19451168 |
Acknowledgement requested | OMICS_00650, biotools:barracuda | https://bio.tools/barracuda | SCR_006881 | 2026-08-01 12:03:23 | 4 | ||||||
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CROP Resource Report Resource Website 100+ mentions |
CROP (RRID:SCR_006916) | CROP | software resource | A clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU). By using a Gaussian Mixture model, CROP can automatically determine the best clustering result for 16S rRNA sequences at different phylogenetic levels without setting a hard cutoff threshold as hierarchical clustering does. Yet, at the same time, it is able to manage large datasets and to overcome sequencing errors. | cluster, 16s rrna, otu, gaussian mixture, bayesian, mcmc, metagenomics |
is listed by: OMICtools has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:21233169 | OMICS_01442 | SCR_006916 | CROP: Clustering 16S rRNA For OTU Prediction | 2026-08-01 12:03:14 | 204 | |||||||
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Stanley Medical Research Institute Resource Report Resource Website 1+ mentions |
Stanley Medical Research Institute (RRID:SCR_007047) | SMRI | institution | The Stanley Medical Research Institute (SMRI) is a nonprofit organization supporting research on the causes of, and treatments for, schizophrenia and bipolar disorder. Since it began in 1989, SMRI has supported more than $300 million in research in over 30 countries around the world. It is the largest nongovernmental source of funds for research on these diseases in the United States. Schizophrenia and bipolar disorder are the most important psychiatric disorders in the United States, affecting more than 4 million people at any given time. Until recent years, little research had been done on these diseases, and the treatment of them was unsatisfactory. The neuroscience revolution has brought with it great opportunities for increased understanding of brain diseases such as schizophrenia and bipolar disorder. SMRI is on the leading edge of this exciting research. Approximately 75 percent of SMRI expenditures goes towards the development of new treatments for schizophrenia and bipolar disorder. The remaining funds are used for research on the causes of these diseases. SMRI has a close relationship with and is the supporting organization for the Treatment Advocacy Center (TAC). The Treatment Advocacy Center is a nonprofit organization dedicated to eliminating barriers to the timely and effective treatment of severe psychiatric disorders. TAC promotes laws, policies, and practices for the delivery of psychiatric care and supports the development of innovative treatments for and research into the causes of severe and persistent psychiatric disorders, such as schizophrenia and bipolar disorder. | schizophrenia, bipolar disorder, major depressive disorder, depressive disorder, mental disease |
is parent organization of: Stanley Neuropathology Consortium Integrative Database is parent organization of: Stanley Medical Research Institute Online Genomics Database is parent organization of: Stanley Brain Collection |
grid.453353.7, Crossref funder ID: 100007123, nlx_143934, ISNI: 0000 0004 0473 2858 | https://ror.org/01pj5nn22 | SCR_007047 | 2026-08-01 12:03:22 | 1 | ||||||||
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Diabetes Autoantibody Standardization Program Resource Report Resource Website 10+ mentions |
Diabetes Autoantibody Standardization Program (RRID:SCR_006929) | DASP | knowledge environment | Program that develops materials and methods to improve measurements of autoantibodies that are predictive of type 1 diabetes. These are the most sensitive and meaningful measures for predicting this disease. Historically, autoantibody measures have been variable among laboratories; therefore, this program, in collaboration with the Immunology of Diabetes Society, was established. The goals of DASP are to improve laboratory methods, evaluate laboratory performance, support the development of sensitive and specific measurement technologies, and develop reference methods. Currently, 48 key laboratories from 19 countries participate in DASP. | autoantibody, quality assurance, standardization, standard, laboratory method, laboratory performance, measurement, method |
is related to: NIDDK Information Network (dkNET) has parent organization: Centers for Disease Control and Prevention |
Type 1 diabetes, Diabetes | PMID:12716742 | nlx_152868 | http://www.idsoc.org/committees/antibody/dasphome.html | SCR_006929 | Diabetes Autoantibody Standardization Program (DASP) | 2026-08-01 12:03:24 | 14 | |||||
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MetMap Resource Report Resource Website 1+ mentions |
MetMap (RRID:SCR_006954) | MetMap | software resource | A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00618 | SCR_006954 | 2026-08-01 12:03:15 | 9 | |||||||||
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Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna, https://bio.tools/myrna | SCR_006951 | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-08-01 12:03:20 | 2 | |||||
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Australian Government Bureau of Meteorology Resource Report Resource Website 100+ mentions |
Australian Government Bureau of Meteorology (RRID:SCR_007158) | AU BOM | nonprofit organization | The Bureau of Meteorology is Australia''s national weather, climate and water agency. Its expertise and services assist Australians in dealing with the harsh realities of their natural environment, including drought, floods, fires, storms, tsunami and tropical cyclones. Through regular forecasts, warnings, monitoring and advice spanning the Australian region and Antarctic territory, the Bureau provides one of the most fundamental and widely used services of government. The Bureau contributes to national social, economic, cultural and environmental goals by providing observational, meteorological, hydrological and oceanographic services and by undertaking research into science and environment related issues in support of its operations and services. The Bureau of Meteorology operates under the authority of the Meteorology Act 1955 and the Water Act 2007 which provide the legal basis for its activities, while its operation is continually assessed in accordance with the national need for climatic records, water information, scientific understanding of Australian weather and climate and effective service provision to the Australian community. The Bureau of Meteorology must also fulfill Australia''s international obligations under the Convention of the World Meteorological Organization (WMO) and related international meteorological treaties and agreements. | meteorology, weather, climate, water, natural, environment, flood, fire, strom, tsunami, tropical, cyclone, economic, social, cultural, environmental, oceanographic, research, science, environment | Commonwealth of Australia | nif-0000-30228, ISNI: 000000011086859X, grid.1527.1, Wikidata: Q923429 | https://ror.org/04dkp1p98 | SCR_007158 | AU BOM | 2026-08-01 12:03:24 | 159 | |||||||
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Swami: The Next Generation Biology Workbench Resource Report Resource Website 1+ mentions |
Swami: The Next Generation Biology Workbench (RRID:SCR_007217) | NGBW | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release. | has parent organization: University of California at San Diego; California; USA | IBM Corporation ; Microsoft Research ; NIGMS 5R01GM073931 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_14257 | http://www.ngbw.org/ | SCR_007217 | Next Generation Biology Workbench, Swami | 2026-08-01 12:03:30 | 2 |
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