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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Neural Systems and Graphics Computing Laboratory: Micro3D Software Resource Report Resource Website |
Neural Systems and Graphics Computing Laboratory: Micro3D Software (RRID:SCR_001811) | data analysis software, data processing software, data visualization software, software application, software resource | The Micro3D 2004 is a software for 3-D reconstruction, visualization, and analysis of neuronal populations and brain regions. Micro3D generates geometric models from line and point coded data sets, representing labeled objects such as cell bodies or axonal plexuses, and boundaries of brain regions in serial sections. Data are typically imported from image-combining computerized microscopy systems, such as Neurolucida (MicroBrightField, Colchester, VT). The models may be rotated and zoomed in real-time. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the model. Flattening of sheets of points in curved layers (e.g., neurons in a cortical lamina) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps, and allows production of mpeg videos. Micro3D 2004 runs on LINUX PCs equipped with Open Inventor. It performs operations similar to the Silicon Graphics based version that has been used in more than 25 investigations and in various species, ranging from insects to monkeys, at the LM- and EM-level. Sponsors:Micro 3D was developed with support from The Research Council of Norway and The Oslo Research Park / FORNY. | 3-d reconstruction, analysis, axonal plexus, brain, cell body, computerized, contour line, density map, geometric, insect, microscopy, model, monkey, neuronal, object, population, region, serial section, software, specie, visualization, image | PMID:16596747 | Free, Available for download, Freely available | nif-0000-10375 | SCR_001811 | SciCrunch Registry | NeSys Micro3D | 2026-11-14 11:21:51 | 0 | ||||||||
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Kindai University; Osaka; Japan Resource Report Resource Website 1+ mentions |
Kindai University; Osaka; Japan (RRID:SCR_001814) | university | Private non-sectarian and coeducational university based in Higashiosaka, Osaka, Japan. | private, university, osaka, japan | is parent organization of: Kindai University School of Medicine; Osaka; Japan | Free | ISNI:0000 0004 1936 9967, nlx_149308, grid.258622.9, Wikidata:Q912329 | https://ror.org/05kt9ap64 | SCR_001814 | SciCrunch Registry | Kinki University | 2026-11-14 11:21:51 | 1 | |||||||
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AStalavista Resource Report Resource Website 50+ mentions |
AStalavista (RRID:SCR_001815) | AStalavista | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc. | alternative splicing event, alternative splicing, visualization, genome, transcript |
is listed by: OMICtools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:17485470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01943 | http://genome.imim.es/astalavista, http://genome.crg.es/astalavista/ | SCR_001815 | SciCrunch Registry | Alternative Splicing transcriptional landscape visualization tool | 2026-11-14 11:21:53 | 86 | |||||
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PSGInfer Resource Report Resource Website |
PSGInfer (RRID:SCR_000243) | PSGInfer | software resource | Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. | alternative splicing, rna-seq, probabilistic splice graph |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23846746 | Free, Available for download, Freely available | OMICS_01967 | SCR_000243 | SciCrunch Registry | PSGInfer: Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs | 2026-11-14 11:21:27 | 0 | ||||||
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Cascleave Resource Report Resource Website |
Cascleave (RRID:SCR_000197) | Cascleave | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates. | matlab |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24149049 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01670 | SCR_000197 | SciCrunch Registry | Cascleave 2.0 - Caspase substrate cleavage site prediction, Cascleave 2.0 | 2026-11-14 11:21:26 | 0 | ||||||
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HEM Resource Report Resource Website |
HEM (RRID:SCR_000194) | HEM | software resource | Software package that fits heterogeneous error models for analysis of microarray data | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Virginia; Virginia; USA |
PMID:15044230 | Free, Available for download, Freely available | OMICS_01970 | SCR_000194 | SciCrunch Registry | HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions | 2026-11-14 11:21:26 | 0 | ||||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | consortium, data or information resource, organization portal, portal | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | SciCrunch Registry | 2026-11-14 11:21:28 | 3 | |||||||
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Molegro Virtual Docker Resource Report Resource Website 1+ mentions |
Molegro Virtual Docker (RRID:SCR_000190) | Molegro Virtual Docker | software resource | An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets. | protein ligand, protein target, visualization, integrated platform | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01603 | SCR_000190 | SciCrunch Registry | 2026-11-14 11:21:26 | 9 | ||||||||
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Zhejiang University; Zhejiang; China Resource Report Resource Website 1+ mentions |
Zhejiang University; Zhejiang; China (RRID:SCR_000224) | ZJU | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A public research university with twelve main academic disciplines that include science, engineering, agriculture and medicine. The university has campuses across China in locations such as Yuquan, Zhijiang and Zhoushan. It has studies available in undergraduate, graduate and post-doctorate degrees. | china, undergraduate, graduate, post doctorate, research university |
uses: ReadCube is parent organization of: DaTo is parent organization of: PlantNATsDB - Plant Natural Antisense Transcripts DataBase |
THIS RESOURCE IS NO LONGER IN SERVICE | grid.13402.34, Wikidata:Q197543, Crossref funder ID:501100004835, nlx_149178, ISNI:0000 0004 1759 700X | https://ror.org/00a2xv884 | SCR_000224 | SciCrunch Registry | Zhejiang University | 2026-11-14 11:21:28 | 1 | ||||||
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MRNet Resource Report Resource Website 1+ mentions |
MRNet (RRID:SCR_000225) | MRNet | software resource | A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication. | is listed by: OMICtools | DOI:10.1145/1048935.1050172 | Free, Available for download, Freely available | OMICS_01686 | SCR_000225 | SciCrunch Registry | MRNet: A Multicast/Reduction Network | 2026-11-14 11:21:27 | 1 | |||||||
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RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software application, software resource | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | SciCrunch Registry | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-11-14 11:21:28 | 115 | ||||||
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Trinity College Dublin; Dublin; Ireland Resource Report Resource Website 1+ mentions |
Trinity College Dublin; Dublin; Ireland (RRID:SCR_000261) | TCD | university | A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level. | arts, humanities, social sciences, mathematics, engineering, health sciences, Dublin, Ireland |
is related to: Pharma-Planta Consortium is related to: Biomedical Diagnostics Institute is parent organization of: ExplorEnz is parent organization of: CASBAH is parent organization of: Trinity Biobank is parent organization of: Random.org |
nlx_87233 | SCR_000261 | SciCrunch Registry | College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin, Trinity, Trinity College Dublin, Trinity College, Trinity College Dublin - University of Dublin, University of Dublin | 2026-11-14 11:21:27 | 1 | ||||||||
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MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | SciCrunch Registry | Mass Spectrometry Analysis Software | 2026-11-14 11:21:28 | 2 | ||||||||
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Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina Resource Report Resource Website |
Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina (RRID:SCR_000264) | School of Medical Sciences - UCA | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. Private medical school in Buenos Aires that offers degree programs in the medical sciences. Resource is in Spanish. | buenos aires, medicine, graduate, private, medical school |
has parent organization: Pontifical Catholic University of Argentina; Buenos Aires; Argentina is parent organization of: Biomedical Research Program UCA |
THIS RESOURCE IS NO LONGER IN SERVICE. | https://ror.org/0422kzb24 | http://www.uca.edu.ar/index.php/home/index/es/universidad/facultades/buenos-aires/cs-medicas | SCR_000264 | SciCrunch Registry | UCA School of Medical Sciences, UCA Facultad de Ciencias M�dicas, Pontificia Universidad Cat�lica Argentina Facultad de Ciencias M�dicas, Pontifical Catholic University of Argentina School of Medical Sciences | 2026-11-14 11:21:27 | 0 | ||||||
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M(at)CBETH Resource Report Resource Website |
M(at)CBETH (RRID:SCR_000265) | M(at)CBETH | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset. | microarray, classification, performing microarray classification, |
is listed by: OMICtools has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
PMID:15890742 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02292 | SCR_000265 | SciCrunch Registry | MicroArray Classification BEnchmarking Tool on Host server | 2026-11-14 11:21:27 | 0 | ||||||
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Polish Ministry of Science and Higher Education Resource Report Resource Website 1+ mentions |
Polish Ministry of Science and Higher Education (RRID:SCR_000251) | institution | Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research. | funding, government, agency, higher education, scientific research, public, poland | ISNI: 0000 0001 0684 6072, Wikidata: Q4294468, Crossref funder ID: 501100004569, grid.425823.a, nlx_149369 | https://ror.org/05dwvd537 | http://www.nauka.gov.pl/en/ | SCR_000251 | SciCrunch Registry | Ministry of Science and Higher Education - Republic of Poland, Polish Ministry of Science Higher Education, Ministry of Science and Higher Education (Poland) | 2026-11-14 11:21:27 | 9 | ||||||||
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Polytechnic University of Catalonia; Barcelona; Spain Resource Report Resource Website 1+ mentions |
Polytechnic University of Catalonia; Barcelona; Spain (RRID:SCR_000252) | UPC | university | A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER). | public, architecture, engineering, technology, catalan, internationalization, architecture | is parent organization of: TaxoAssignement | nlx_158613 | SCR_000252 | SciCrunch Registry | Universitat Politècnica de Catalunya, Universitat Politècnica de Catalunya BarcelonaTech, UPC BarcelonaTech, Universitat Politecnica de Catalunya, Universitat Politecnica de Catalunya BarcelonaTech, BarcelonaTech, Polytechnic University of Catalonia | 2026-11-14 11:21:28 | 1 | ||||||||
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Polytechnic University of Valencia; Valencia; Spain Resource Report Resource Website |
Polytechnic University of Valencia; Valencia; Spain (RRID:SCR_000255) | UPV | university | A technical university in Spain which offers degree programs in 14 different faculties, including business administration, computer science and industrial engineering at the undergraduate, graduate and postdoctoral level. The school has five different campuses. | technical, polytechnic, business administration, computer science, architecture, industrial engineering, design, cartography, fine arts, management | is parent organization of: DTI denoising | nlx_157969 | SCR_000255 | SciCrunch Registry | Polytechnic University of Valencia, Technical University of Valencia, Universidad Politécnica de Valencia, Universitat Politecnica de Valencia, Universitat Politècnica de València | 2026-11-14 11:21:27 | 0 | ||||||||
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Pompeu Fabra University; Barcelona; Spain Resource Report Resource Website |
Pompeu Fabra University; Barcelona; Spain (RRID:SCR_000256) | UPF | university | Public university in Spain that offers programs in social sciences and humanities, health and life sciences, international training in communication and communication sciences. Has colleges based on topics such as law, translation and interpretation, and engineering. Research is organized into economics and business, experimental sciences and health, law. | University, public, Spain, Barcelona |
is related to: EMIF is related to: Centre for Genomic Regulation; Barcelona; Spain is parent organization of: EEG time series Data Sets is parent organization of: Bern-Barcelona EEG database is parent organization of: Reliable detection of directional couplings using rank statistics is parent organization of: Characterizing unidirectional couplings between point processes and flows is parent organization of: Detecting event-related time-dependent directional couplings is parent organization of: Nonlinear time series analysis in a nutshell is parent organization of: Time-resolved and time-scale adaptive measures of spike train synchrony is parent organization of: Gene-Disease Association Type Ontology is parent organization of: DisGeNET is parent organization of: aneurIST is parent organization of: Functional Coverage of the Proteome is parent organization of: Cellular Biology of Addiction is parent organization of: GIMIAS is parent organization of: TransFIC is parent organization of: BioMoby |
Wikidata:Q24543, nlx_52215, grid.5612.0, ISNI:0000 0001 2172 2676 | https://ror.org/04n0g0b29 | SCR_000256 | SciCrunch Registry | Universitat Pompeu Fabra, Pompeu Fabra University, UPF Barcelona | 2026-11-14 11:21:28 | 0 | |||||||
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Sorbonne University; Paris; France Resource Report Resource Website |
Sorbonne University; Paris; France (RRID:SCR_000246) | UPMC | university | A public research university in France that emphasizes medical and scientific research centered on four themes: life and health, the living earth and environment, matter and new materials and modeling and engineering. It is a member of the Sorbonne Universities alliance. | public, engineering, modeling, environment, france, public research university, living earth |
is related to: EMIF is parent organization of: Parseq is parent organization of: Cordelier Research Center is parent organization of: XNBC |
, Wikidata: Q41497113, GRID: grid.462844.8, Crossref Funder ID: 501100019125, ISNI: 0000 0001 2308 1657, nlx_17035 | https://ror.org/02en5vm52 | SCR_000246 | SciCrunch Registry | , University Pierre and Marie Curie, Pierre and Marie Curie University, University Pierre et Marie Curie, Sorbonne Université; Pierre and Marie Curie University, Paris; Universite Pierre et Marie Curie | 2026-11-14 11:21:28 | 0 |
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