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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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flyPAD Resource Report Resource Website 1+ mentions |
flyPAD (RRID:SCR_021522) | software resource, source code | FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software. | FPGA code, running main board of flyPAD, VHDL, Quartus 2, OpenBehavior |
is listed by: OpenBehavior is related to: flyPAD project |
DOI:10.1038/ncomms5560 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/optopad-and-flypad/ | SCR_021522 | 2026-08-12 10:52:37 | 1 | ||||||||
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sepsis3-amsterdamumcdb Resource Report Resource Website 1+ mentions |
sepsis3-amsterdamumcdb (RRID:SCR_022042) | software resource, source code | Repository contains files for implementing the Sepsis-3 definition in the freely-accessible Amsterdam University Medical Centers Database. | Sepsis-3 criteria, Amsterdam University Medical Centers Database | Restricted | SCR_022042 | Sepsis-3 in AmsterdamUMCdb | 2026-08-12 10:52:39 | 2 | ||||||||||
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Meta-Prism Resource Report Resource Website 1+ mentions |
Meta-Prism (RRID:SCR_021836) | software resource, source code | Software tool as microbial community sample search method based on smart pair wise sample comparison without compromising accuracy. Used as microbial communities similarites calculation and comparison tool. | microbial community sample search, sample comparison, microbial communities similarites calculation | Free, Available for download, Freely available | SCR_021836 | Meta-Prism 2.0 | 2026-08-12 10:52:24 | 3 | ||||||||||
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naturalsounds analysis Resource Report Resource Website |
naturalsounds analysis (RRID:SCR_021793) | software resource, source code | Software tool as source code for analyzing functional ultrasound data. | analyzing functional ultrasound data | Free, Available for download, Freely available | https://zenodo.org/record/5493682#.YYCTbp7MJPY | SCR_021793 | naturalsounds_analysis | 2026-08-12 10:52:24 | 0 | |||||||||
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Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | data analysis software, data processing software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | Parallel META, Parallel Meta | 2026-08-13 09:26:07 | 4 | |||||||
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Adaptively Sampled Particle Fluids Resource Report Resource Website |
Adaptively Sampled Particle Fluids (RRID:SCR_000083) | ASPF | simulation software, software resource, source code, software application | Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux. | fluid simulation, lagrangian particle fluid, linux |
is listed by: Biositemaps is listed by: Simtk.org |
Free, Available for download, Freely available | nif-0000-23328 | SCR_000083 | 2026-08-13 09:26:07 | 0 | ||||||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | organization portal, data or information resource, consortium, 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 | 2026-08-13 09:26:08 | 3 | |||||||
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National MS Society Resource Report Resource Website 10+ mentions |
National MS Society (RRID:SCR_000104) | National MS Society | topical portal, data or information resource, disease-related portal, funding resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward. | multiple sclerosis, award, grant, postdoctoral fellowship | Multiple Sclerosis | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143693 | SCR_000104 | National Multiple Sclerosis Society | 2026-08-13 09:26:07 | 34 | |||||||
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Ludwig Boltzmann Cluster Translationale Onkologie Resource Report Resource Website |
Ludwig Boltzmann Cluster Translationale Onkologie (RRID:SCR_000020) | Ludwig Boltzmann Cluster Translational Oncology | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project. | cancer, tumor, clinical, oncology, photodynamic therapy, gynecology, gynecologic oncology, stem cell transplantation, surgical oncology, tumor cell | is parent organization of: Ludwig Boltzman Tumour Bank | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143958 | SCR_000020 | 2026-08-13 09:26:06 | 0 | ||||||||
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RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software resource, software application | 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 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-08-13 09:26:08 | 115 | ||||||
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TEDDY Resource Report Resource Website 1+ mentions |
TEDDY (RRID:SCR_000383) | TEDDY | data or information resource, organization portal, clinical trial, database, consortium, portal | International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. | consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization |
is listed by: One Mind Biospecimen Bank Listing is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository is related to: Teddy study IA prediction has parent organization: University of South Florida; Florida; USA |
Type 1 diabetes, Diabetes | NIDDK 2UC4DK063829 | PMID:21564455 | nlx_152857 | SCR_000383 | The Environmental Determinants of Diabetes in the Young, TEDDY study | 2026-08-13 09:26:10 | 3 | |||||
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Trans-Institute Angiogenesis Research Program Resource Report Resource Website |
Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) | TARP | topical portal, data or information resource, resource, portal | Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests. | blood vessel, growth, development, target, therapeutic, vascularization, angiogenesis, lymphangiogenesis |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Institutes of Health |
Angiogenesis, Lymphangiogenesis | JDRF ; NEI ; NHLBI ; NCI ; NICHD ; NIDDK ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152866 | SCR_000384 | Trans-Institute Angiogenesis Research Program (TARP) | 2026-08-13 09:26:10 | 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 | MicroArray Classification BEnchmarking Tool on Host server | 2026-08-13 09:26:08 | 0 | ||||||
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Local Binary Pattern Analysis Tools for MR Brain Images Resource Report Resource Website 1+ mentions |
Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) | LBP Analysis Tools for MR Brain Images | data processing software, software application, image analysis software, software resource, image processing software | The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology. | free for non-commercial use only, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155652 | SCR_000412 | 2026-08-13 09:26:10 | 1 | ||||||||
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PSCBS Resource Report Resource Website |
PSCBS (RRID:SCR_000417) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. | abnormal copy number regions detection, allele specific DNA copy number data segmentation, |
is listed by: OMICtools is listed by: Debian is related to: CRAN has parent organization: University of California at San Francisco; California; USA |
PMID:21666266 DOI:10.1093/bioinformatics/btr329 |
Free, Available for download, Freely available | OMICS_05545 | https://sources.debian.org/src/r-cran-pscbs/ | SCR_000417 | PSCBS: Analysis of Parent-Specific DNA Copy Numbers | 2026-08-13 09:26:10 | 0 | ||||||
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Open Colleges Resource Report Resource Website |
Open Colleges (RRID:SCR_000418) | Open Colleges | training resource, online course | A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia. | open source, accredited, accounting, beauty, animal care, writing, journalism, education, business, building, real estate |
is parent organization of: Open Colleges Interactive Brain is parent organization of: Open Colleges Group |
nlx_155866 | SCR_000418 | 2026-08-13 09:26:10 | 0 | |||||||||
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uManager Resource Report Resource Website 100+ mentions |
uManager (RRID:SCR_000415) | data processing software, software application, software toolkit, data acquisition software, software resource | Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. | microscopy, plugin, data acquisition, automated microscope control, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ImageJ has parent organization: University of California at San Francisco; California; USA |
Free, Available for download, Freely available | SCR_016865, nlx_155812 | https://micro-manager.org/wiki/Download_Micro-Manager_Latest_Release, https://sources.debian.org/src/micromanager/, http://www.nitrc.org/projects/micromanager | SCR_000415 | Micro-Manager, Micro Manager | 2026-08-13 09:26:10 | 285 | |||||||
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NICHD Developmental Neuroethology - Laboratory of Comparative Ethology Resource Report Resource Website |
NICHD Developmental Neuroethology - Laboratory of Comparative Ethology (RRID:SCR_000416) | NICHD Laboratory of Comparative Ethology | data or information resource, organization portal, laboratory portal, portal | Understanding the mechanisms underlying the expression and perception of auditory communication in nonhuman primates provides important insights for understanding the neural systems that mediate nonverbal auditory communication in humans. Our research is devoted to understanding the changes in vocal behavior that are associated with maturation and social experience under normative conditions, and to investigating neural systems to define their roles in auditory communication. The anterior cingulate gyrus, in the frontal cerebral cortex, is an essential neural system for the expression of the primate isolation call, a structural and functional equivalent of the cry sounds of humans. Bilateral removal of this structure in adult squirrel monkeys resulted in a long-lasting inability to emit isolation calls. Partial recovery, often over many weeks, initially took the form of production of short, faint and uninflected versions of the typical isolation call. Humans suffering infarct damage to this region likewise show an initial recovery in the form of short, faint, monosyllabic sounds, suggesting that the anterior cingulate gyrus of nonhuman primates is the evolutionary precursor of a neural structure involved in human affective expression and speech. Our working model of isolation call production is that the anterior cingulate gyrus is the site where the command to produce this vocalization is initiated. Since the anterior cingulate region also has reciprocal connections with temporal lobe auditory cortex, a presumptive feedback pathway exists for registering commands to initiate vocalization with the temporal lobe cortex, which plays a major role in perceiving and decoding the acoustic details of species-specific vocalizations. At present, we do not know the role of the anterior cingulate gyrus in the production of infant vocalizations. However, we have found that neonatal removal of the amygdala, an important forebrain component of the limbic system, or portions of the inferotemporal gyrus, which sends projections to the amygdala, result in significant changes in the vocal behavior of infant rhesus macaques. Vocal development is a dynamic process, and a pattern shared by several nonhuman primates has emerged regarding the nature of this process. Infants are highly vocal during periods of brief separation from their caregiver, and we take advantage of this to document the range of vocalizations produced by infants of different ages. In the neonatal period, infants of 3 species of nonhuman primate (rhesus macaque, squirrel monkey and common marmoset) all produce sounds that vary widely in their acoustic structure. Many of these bear a striking similarity to sounds used in a variety of social settings by adults, suggesting that neural systems responsible for generating adult vocalizations are already in place during early infancy. As infants mature, their vocal behavior during brief periods of social separation becomes much more stereotyped. It isn't until much later in development, as individuals engage in a variety of social interactions with peers and adults, that the sounds expressed in early infancy begin to re-appear in adult contexts. The role of individual experience during development is currently being explored to determine the mechanisms leading to the acquisition of adult vocal skills. | behavior, ethology, development, auditory communication, nonverbal auditory communication, vocal behavior, maturation, social experience, neural system, vocal development, vocal skill, development, infant, amygdala, anterior cingulate gyrus, voice, sound, adult, neuroethology, primate behavior, functional neuroanatomy, atlas |
has parent organization: National Institute of Child Health and Human Development is parent organization of: Brain atlas of the common marmoset |
NICHD | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00398 | SCR_000416 | Developmental Neuroethology - Laboratory of Comparative Ethology | 2026-08-13 09:26:10 | 0 | ||||||
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Neuroscience Link List Resource Report Resource Website |
Neuroscience Link List (RRID:SCR_000130) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A website that provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program home-pages. | link list, links, neuroscience resources, topical portal | has parent organization: Weill Cornell Medical College; New York; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00083 | SCR_000130 | World-Wide Web Virtual Library:Neuroscience, World-Wide Web Virtual Library:Neuroscience (Biosciences), The World-Wide Web Virtual Library:Neurosciences | 2026-08-13 09:26:07 | 0 | ||||||||
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Computational Neuroscience on the Web Resource Report Resource Website 1+ mentions |
Computational Neuroscience on the Web (RRID:SCR_000010) | topical portal, data or information resource, portal | Annotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology. | computational, neuroscience, compartmental, modeling, simulation, biological, neural, system, neuroinformatics, index | Free, Freely available | nif-0000-00107 | http://home.earthlink.net/~perlewitz/ | SCR_000010 | 2026-08-13 09:26:06 | 1 |
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