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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Evidence-Based Health Care Search Strategies Resource Report Resource Website |
Evidence-Based Health Care Search Strategies (RRID:SCR_010606) | narrative resource, data or information resource, wiki | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. This wiki focuses on the process, techniques and tools of high quality searching in the context of evidence-based health care. Information collected in the wiki is primarily intended for medical librarians, but may be of interest to others. Please keep in mind that search strategies and tools here are intended for use by trained professionals in the course of their professional duties, and are not intended for use by the general public. If they are helpful or useful to others that is a plus, but not the primary purpose of the site. | ebhc, ebm, evidence-based, health, healthcare, medicine, medline, pubmed searching | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_51340 | SCR_010606 | EBHC Search Strategies Wiki, EBHC Search Strategies | 2026-08-01 12:04:16 | 0 | |||||||||
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vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-08-01 12:04:16 | 58 | ||||||||||
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American Society for Cell Biology Resource Report Resource Website 1+ mentions |
American Society for Cell Biology (RRID:SCR_010600) | ASCB | data or information resource, portal, narrative resource, meeting resource, community building portal, training resource | The American Society for Cell Biology (ASCB) was founded in 1960 to bring the varied facets of cell biology together. The Society''s purpose is to promote and develop the field of cell biology. Its objectives are achieved through the scholarly dissemination of research at its Annual Meeting and Summer Meetings and in its publications. The ASCB strives to ensure the future of basic scientific research by providing training and development opportunities for students and young investigators, and also by keeping Congress and the American public informed about the importance of biological research. Since its founding, the ASCB has grown to approximately 10,000 members in the United States and more than 65 countries around the world. About 25% of ASCB members are international. Current members come from universities, colleges, professional schools, government, industry, and public and private research institutions. Membership in the ASCB is open to all research scientists, students, educators (high school, undergraduate, and graduate level), and technicians who have education or research experience in cell biology or an allied field. |
is listed by: Duke Human Heart Repository is parent organization of: Cell Image Library (CIL) is parent organization of: iBioSeminars |
nlx_50636 | SCR_010600 | The American Society for Cell Biology | 2026-08-01 12:03:54 | 8 | |||||||||
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IFOMIS Resource Report Resource Website |
IFOMIS (RRID:SCR_010604) | IFOMIS | knowledge environment, narrative resource, data or information resource, standard specification | The Institute for Formal Ontology and Medical Information Science (IFOMIS) comprehends an interdisciplinary research group, with members from Philosophy, Computer and Information Science, Logic, Medicine, and Medical Informatics, focusing on theoretically grounded research in both formal and applied ontology. Its goal is to develop a formal ontology that will be applied and tested in the domain of medical and biomedical information science. |
has parent organization: Saarland University; Saarbrucken; Germany is parent organization of: BFO |
Alexander von Humboldt-Stiftung | nlx_51151 | SCR_010604 | Institute for Formal Ontology and Medical Information Science | 2026-08-01 12:03:54 | 0 | ||||||||
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MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-08-01 12:03:55 | 463 | |||||||
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Boston University Alzheimer's Disease Center Resource Report Resource Website 1+ mentions |
Boston University Alzheimer's Disease Center (RRID:SCR_010692) | BU ADC | data or information resource, portal, topical portal, disease-related portal, training resource | The goal of the Alzheimers Disease Center is to help reduce the human and economic costs associated with Alzheimers disease through the advancement of knowledge. The primary missions of the Center are to: conduct and facilitate cutting-edge Alzheimers disease research; enhance clinical care for Alzheimers disease patients and their families; and provide education regarding Alzheimers disease to both professional and lay audiences. The Center is made up of a multidisciplinary group of professionals dedicated to research, clinical care, and education. | alzheimers, research, patient, family, education, disease related portal, training resource |
has parent organization: Boston University School of Medicine; Massachusetts; USA is parent organization of: Boston University Alzheimer's Disease Center Neuropathology Core Facility |
Alzheimer's disease | NIA | Public | nlx_80502 | SCR_010692 | BU Alzheimers Disease Center | 2026-08-01 12:04:15 | 1 | |||||
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Life Extension Foundation Resource Report Resource Website |
Life Extension Foundation (RRID:SCR_010574) | institution | Established in 1980, the Life Extension Foundation is a nonprofit organization, whose long-range goal is to radically extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. The largest organization of its kind in the world, the Life Extension Foundation has always been at the forefront of discovering new scientific breakthroughs for use in developing novel disease prevention and treatment protocols to improve the quality and length of human life. Through its private funding of research programs aimed at identifying and developing new therapies to slow and even reverse the aging process, the Life Extension Foundation seeks to reduce, and ultimately eliminate, such age-related killers as heart disease, stroke, cancer and Alzheimer''s disease. Long-time members are keenly aware of the scientific research that Life Extension Foundation funds to develop validated methods to slow and reverse the aging process. Less known is Life Extension''s multi-prong program to develop safer and more effective cancer therapies. One reason we focus so heavily on cancer research is that this dreaded disease represents a roadblock in our ability to develop effective means to combat aging. | is parent organization of: Life Extension | Aging | ISNI: 0000 0001 0300 2958, nlx_41735, grid.490868.b | https://ror.org/02vzd2x77 | SCR_010574 | 2026-08-01 12:04:14 | 0 | |||||||||
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Gossamer Resource Report Resource Website 1+ mentions |
Gossamer (RRID:SCR_010612) | Gossamer | software resource | A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. | is listed by: OMICtools | OMICS_00017 | SCR_010612 | Gossamer: A Space-Efficient Genome Assembler | 2026-08-01 12:04:16 | 1 | |||||||||
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NeuroLOG Resource Report Resource Website 500+ mentions |
NeuroLOG (RRID:SCR_010582) | knowledge environment, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The NeuroLOG consortium is addressing: *Management and access of partly structured data, heterogeneous and distributed in an open environment. *Access control and protection of private medical data. *Control of workflows implied in complex computing process on grid infrastructures. *Extraction and quantification of relevant parameters for different pathologies: Multiple sclerosis, Brain Vascular Stroke, Brain tumors Four application pipelines have been proposed in the context of the project. The pipelines are formalized using the Scufl data flow language. *Multiple Sclerosis image analysis pipelines *Brain Stroke application pipeline (from GIN) *Stroke / tumours Anacom application pipeline (from IFR49) Different softwares developed and/or used in this project are presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is related to: OntoNeuroLOG has parent organization: University of Nice Sophia Antipolis; Nice; France |
French National Research Agency contract ANR-06-TLOG-024 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44086 | SCR_010582 | NeuroLOG Project, NeuroLOG | 2026-08-01 12:03:53 | 546 | ||||||||
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Biodatomics Resource Report Resource Website |
Biodatomics (RRID:SCR_010464) | data processing software, data analysis software, software application, software resource | An open source commercial platform for genomic analysis. Included is a home brewed workflow engine and code provenance tracking, no data provenance tracking. Multiple tools like HMMR and Blast are included in the platform with an architecture that allows others to be plugged in and the code to be modified. Data storage is handled by hadoop clusters. | nlx_157693 | SCR_010464 | BioDT | 2026-08-01 12:04:13 | 0 | |||||||||||
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Pathema Resource Report Resource Website 1+ mentions |
Pathema (RRID:SCR_010585) | Pathema | data analysis service, data or information resource, database, service resource, production service resource, analysis service resource | Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. | bacillus anthracis, clostridium botulinum, burkholderia mallei, burkholderia pseudomallei, clostridium perfringens, entamoeba histolytica, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
NIAID contract HHSN266200400038C | PMID:19843611 | biotools:pathema, nlx_45829 | https://bio.tools/pathema | SCR_010585 | Pathema Genome Resource, Pathema Bioinformatics Resource Center | 2026-08-01 12:04:14 | 6 | |||||
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HUPO - Human Proteome Organisation Resource Report Resource Website 10+ mentions |
HUPO - Human Proteome Organisation (RRID:SCR_010707) | HUPO | data or information resource, portal, meeting resource, knowledge environment, training resource, organization portal, journal article | The Human Proteome Organisation (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training. |
is parent organization of: HUPO Proteomics Standards Initiative is parent organization of: HUPO Antibody Initiative is parent organization of: HUPO Brain Proteome Project |
nlx_85721 | SCR_010707 | Human Proteome Organisation | 2026-08-01 12:03:55 | 36 | |||||||||
|
ABySS Resource Report Resource Website 500+ mentions |
ABySS (RRID:SCR_010709) | ABySS | data analysis software, software application, software resource, sequence analysis software, data processing software | Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements. | paired-end sequence assembler, short reads, assembling human genome, large genomes, bloom filter, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; NHGRI R01HG007182 |
PMID:19251739 DOI:10.1101/068338 DOI:10.1101/gr.214346.116 |
Free, Available for download, Freely available | biotools:abyss, OMICS_00006 | https://github.com/bcgsc/abyss, https://sources.debian.org/src/abyss/, https://bio.tools/abyss, | SCR_010709 | ABySS 1.0, ABySS 2.0 | 2026-08-01 12:04:15 | 761 | ||||
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Alfresco - FRont-End for Sequence COmparison Resource Report Resource Website |
Alfresco - FRont-End for Sequence COmparison (RRID:SCR_010544) | data visualization software, source code, software application, data processing software, software resource | The aim is to develop a new visualization tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualized and used to find corresponding sequence domains. The program functions as an stand-alone application and also over the World Wide Web. With this in mind it is being developed using the Java programming language. A key feature of the program is to use available analysis programs relevant to comparative genome sequence analysis, combine the results of these, and graphically present them in an intuitive way, thereby facilitating the analysis of large genomic regions. We''ve decided to call this program Alfresco. We originally wanted to call it Fresco (FRont-End for Sequence COmparison) but that name was already taken. To run Alfresco you need to have jdk1.1 installed. Alfresco has only been tested on Solaris 2.5, Dec OSF 4.0D and Linux, but should run on any machine with jdk1.1. New: Alfresco now runs on Mac and Windows as well. | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | nlx_28281 | SCR_010544 | 2026-08-01 12:04:14 | 0 | |||||||||||
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Medical Imaging Resource Report Resource Website 50+ mentions |
Medical Imaging (RRID:SCR_010665) | narrative resource, data or information resource, wiki | A wiki all about medical imaging. Anyone may contribute who registers. Popular pages include Optical Imaging, Imaging brain function with optical topography, Optical mammography, Introduction to optical imaging, Comparison of time domain and frequency domain systems, Forward problem in diffuse optical imaging, Optical molecular imaging. | radiology | nlx_71965 | SCR_010665 | 2026-08-01 12:04:16 | 65 | |||||||||||
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Meraculous Resource Report Resource Website 10+ mentions |
Meraculous (RRID:SCR_010700) | Meraculous | software resource | An algorithm for de novo genome assembly with short paired-end reads. | is listed by: OMICtools | OMICS_00021 | SCR_010700 | Meraculous: De Novo Genome Assembly with Short Paired-End Reads | 2026-08-01 12:03:55 | 39 | |||||||||
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MIRIAM: Minimal Information Required In the Annotation of Models Resource Report Resource Website 1+ mentions |
MIRIAM: Minimal Information Required In the Annotation of Models (RRID:SCR_010547) | MIRIAM | topical portal, data or information resource, portal | MIRIAM is an effort to standardise the Minimal Information Required In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology. The goal of the project, initiated by the BioModels.net effort is to produce a set of guidelines suitable for use with any structured format for computational models. MIRIAM is a registered project of the MIBBI (Minimum Information for Biological and Biomedical Investigations). If you are looking for the online resources providing support to MIRIAM Standard, please go to: MIRIAM Resources. |
is related to: bioDBcore has parent organization: BioModels.net |
nlx_31750 | SCR_010547 | 2026-08-01 12:04:15 | 2 | ||||||||||
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UBERON Resource Report Resource Website 50+ mentions |
UBERON (RRID:SCR_010668) | UBERON | ontology, controlled vocabulary, data or information resource | An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human. | anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, obo |
is used by: Neuroscience Information Framework is listed by: BioPortal is related to: Gene Ontology has parent organization: OBO |
ARRA ; NSF ; NHGRI 5R01HG004838; NHGRI P41HG002273; DOE DE-AC02-05CH11231; NCRR 1U24RR029825-01; NHGRI P41HG002273-09S1 |
PMID:22293552 | nlx_74404 | SCR_010668 | Uber anatomy ontology, Uber-anatomy ontology | 2026-08-01 12:03:54 | 59 | ||||||
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dictyBase - Teaching Tools Using Dictyostelium discoideum Resource Report Resource Website 1+ mentions |
dictyBase - Teaching Tools Using Dictyostelium discoideum (RRID:SCR_010701) | data or information resource, narrative resource, training material | Dictyostelium discoideum is a great organism to use to teach cellular biology. It exhibits very interesting behaviors, such as chemotaxis and phagocytosis, that can readily be studied in standard laboratories without the need for expensive equipment. Lists of labs being used in real courses settings and all necessary information for performing those experiments are provided. Major headings: * Dictyostelium cell biology course, by Dr. David Knecht, University of Connecticut * Dictyostelium cell biology, by Dr. Derrick Brazill, Hunter College, New York * Report on the number of cells in a slug, contributed by John Bonner * Practical on chemotaxis, by Dr. Thierry Soldati, University of Geneva * Comments from Researchers * References suggested by contributors | has parent organization: Dictyostelium discoideum genome database | nlx_83913 | SCR_010701 | Teaching Tools Using Dictyostelium discoideum | 2026-08-01 12:04:15 | 5 | ||||||||||
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Matrix2png Resource Report Resource Website 100+ mentions |
Matrix2png (RRID:SCR_010669) | software resource | An open visualization tool for the display of matrix data. It is available for download or interactive web use. It is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data. | dna microarray, matrix | has parent organization: University of British Columbia; British Columbia; Canada | nlx_74565 | SCR_010669 | 2026-08-01 12:04:15 | 126 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
