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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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splitneuron Resource Report Resource Website |
splitneuron (RRID:SCR_005001) | software application, software resource | A database-based neuron simulation tool. An innovative approach to large-scale, biologically plausible, neural-network simulation library. Based on data structures and methods directly coded into database, information flow implying separation of data representing neurons, conceived to share load on multiple machines and calibrating operational load on each machine. | nlx_95900 | SCR_005001 | splitneuron library | 2026-08-09 09:04:01 | 0 | |||||||||||
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DISCO Resource Report Resource Website 100+ mentions |
DISCO (RRID:SCR_004586) | DISCO | service resource, software resource | DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to harvest the information and keep those sets of information up-to-date. How is this accomplished? By using a series of files and/or scripts which are then placed in the root directory of the resource developer''s resource. (NIF can also host the files on its servers and crawl for changes there.) Once the files of the resource providers are in place, and DISCO is notified, the DISCO server can then recognize and consume the information shared, providing machine understandable information to NIF Integrator Servers (also known as Aggregators) about your resource. What can DISCO do for my resource? * Inform search engines about your resource and keep your NIF Registry resource description up-to-date. * Expose your data (semi-structured datasets or fields within your structured database) through NIF''s Data Federation you choose what data will be shared. * Create links from an NCBI database (e.g., PubMed, Protein, Nucleotide, etc.) to your data records in NIF using Entrez LinkOut. * Advertise your terminology or ontological information. * Share your resource''s news with the NIF community., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | interoperation, sitemap, linkout, news, harvest, aggregate, FASEB list |
is used by: NIF Data Federation has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NIH | PMID:20387131 PMID:18975149 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143827 | SCR_004586 | registration and interoperation framework, DISCO: Extensible Web resource DISCOvery | 2026-08-09 09:03:55 | 332 | |||||
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MAKER Resource Report Resource Website 1000+ mentions |
MAKER (RRID:SCR_005309) | software toolkit, software resource | Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values. | gene prediction, genome annotation, identifies repeats, aligns ESTs and proteins to genome, data management, genome annotation, annotation, curation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: MAKER Web Annotation Service has parent organization: University of Utah; Utah; USA |
PMID:25501943 | SCR_023883, nlx_144363, biotools:maker | https://bio.tools/maker, https://github.com/Yandell-Lab/maker | SCR_005309 | Maker2, maker | 2026-08-09 09:04:13 | 1519 | |||||||
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Alien hunter Resource Report Resource Website 1+ mentions |
Alien hunter (RRID:SCR_004575) | software application, software resource | Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer. |
is listed by: SoftCite has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:16837528 | nlx_56835 | SCR_004575 | Alien_hunter: Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA | 2026-08-09 09:04:07 | 3 | |||||||||
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TDTPOWER Resource Report Resource Website |
TDTPOWER (RRID:SCR_005021) | TDTPOWER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software) | gene, genetic, genomic, sas macro | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154678 | SCR_005021 | 2026-08-09 09:04:01 | 0 | ||||||||
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FSST - Functional Similarity Search Tool Resource Report Resource Website |
FSST - Functional Similarity Search Tool (RRID:SCR_005819) | FSST | software application, software resource | The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | other analysis, functional similarity search, annotation, ontology, java, training tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GOTaxExplorer has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
BMBF 016R0453; DFG KFO 129/1-1; European Union F6 contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149320 | SCR_005819 | Functional Similarity Search Tool (FSST), Functional Similarity Search Tool | 2026-08-09 09:04:16 | 0 | |||||
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Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software toolkit, software resource | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene, https://sources.debian.org/src/ugene/ | SCR_005579 | 2026-08-09 09:04:08 | 183 | ||||||
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DONE: Detection of Outlier NEurons Resource Report Resource Website |
DONE: Detection of Outlier NEurons (RRID:SCR_005299) | DONE | software application, software resource | Software that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface. | neuron, feature-space, archetype, outlier, matlab, neuromorphometry, computational neuroscience |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NeuroMorpho.Org has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
FAPESP 05/00587-5; CNPq 301303/06-1; CNPq 573583/2008-0; FAPESP sponsorship 2010/01994-1; FAPESP sponsorship 2010/16310-0; EPSRC EP/G03950X/1; EPSRC EP/E002331/1; National Research Foundation of Korea R32-10142 |
PMID:22615032 | GNU General Public License | nlx_144348 | http://www.nitrc.org/projects/done | SCR_005299 | Detection of Outlier NEurons | 2026-08-09 09:04:13 | 0 | ||||
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Kickstarter Resource Report Resource Website 10+ mentions |
Kickstarter (RRID:SCR_004246) | Kickstarter | service resource, funding resource | Kickstarter is the world''s largest funding platform for creative projects. Every week, tens of thousands of amazing people pledge millions of dollars to projects from the worlds of music, film, art, technology, design, food, publishing and other creative fields. A new form of commerce and patronage. This is not about investment or lending. Project creators keep 100% ownership and control over their work. Instead, they offer products and experiences that are unique to each project. All or nothing funding. On Kickstarter, a project must reach its funding goal before time runs out or no money changes hands. Why? It protects everyone involved. Creators aren''t expected to develop their project without necessary funds, and it allows anyone to test concepts without risk. Each and every project is the independent creation of someone like you. Projects are big and small, serious and whimsical, traditional and experimental. They''re inspiring, entertaining and unbelievably diverse. We hope you agree... Welcome to Kickstarter! | nlx_143647 | SCR_004246 | 2026-08-09 09:04:04 | 19 | |||||||||||
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POPDIST Resource Report Resource Website |
POPDIST (RRID:SCR_004904) | POPDIST | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, (aix/irix/decalpha), linux, macos, ms-dos, ms-windows, (95) | is listed by: Genetic Analysis Software | PMID:21564908 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154542 | SCR_004904 | 2026-08-09 09:04:00 | 0 | |||||||
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ORION Software Resource Report Resource Website 1+ mentions |
ORION Software (RRID:SCR_004389) | service resource, software resource | ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. | has parent organization: University of Houston; Texas; USA | University of Houston; Texas; USA ; NIA RO1-AG027577; NSF IIS-0431144; NSF IIS-0638875; NSF DMS-0915242 |
nlx_40212 | SCR_004389 | 2026-08-09 09:03:55 | 1 | ||||||||||
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Yabi Resource Report Resource Website |
Yabi (RRID:SCR_005359) | Yabi | service resource, software resource | A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. | grid computing, high performance computing, cloud computing, bioinformatics, pipeline, workflow, command line, python, linux, storage, compute, genomics, transcriptomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Murdoch University; Perth; Australia |
PMID:22333270 | GNU General Public License, v3 | OMICS_01148, biotools:yabi | https://bio.tools/yabi | SCR_005359 | 2026-08-09 09:04:05 | 0 | ||||||
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CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness Resource Report Resource Website |
CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness (RRID:SCR_005615) | CATIE, CATIE Schizophrenia, Clinical Antipsychotic Trials in Intervention Effectiveness | clinical trial | The NIMH-funded Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) Study was a nationwide public health-focused clinical trial that compared the effectiveness of older (first available in the 1950s) and newer (available since the 1990s) antipsychotic medications used to treat schizophrenia. These newer medications, known as atypical antipsychotics, cost roughly 10 times as much as the older medications. CATIE is the largest, longest, and most comprehensive independent trial ever done to examine existing therapies for this disease. Schizophrenia is a brain disorder characterized by hallucinations, delusions, and disordered thinking. The course of schizophrenia is variable, but usually is recurrent and chronic, often causing severe disability. Previous studies have shown that taking antipsychotic medications consistently is far more effective than taking no medicine and that the drugs are necessary to manage the disease. The aim of the CATIE study was to determine which medications provide the best treatment for schizophrenia. Additional information may be found by following the links, http://www.nimh.nih.gov/trials/practical/catie/index.shtml, http://www.clinicaltrials.gov/ct/show/NCT00014001?order=1 | schizophrenia, clinical trial, treatment, outcome, antipsychotic |
is used by: Limited Access Datasets From NIMH Clinical Trials is listed by: ClinicalTrials.gov is related to: CATIE - Alzheimers Disease is related to: NIMH Repository and Genomics Resources has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Schizophrenia | NIMH | SCR_005512, nlx_146233, nlx_146234 | http://www.nimh.nih.gov/health/trials/practical/catie/phase1results.shtml | http://www.nimh.nih.gov/health/trials/practical/catie/index.shtml | SCR_005615 | CATIE Schizophrenia Study, Clinical Antipsychotic Trials in Intervention Effectiveness, Clinical Antipsychotic Trials in Intervention Effectiveness - Schizophrenia | 2026-08-09 09:04:16 | 0 | ||||
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Centre for Neuro Skills Resource Report Resource Website |
Centre for Neuro Skills (RRID:SCR_006106) | CNS | assessment test provider, material resource | A topical portal and providers of brain injury rehabilitation services. Resources * Pharmacology Guide * Glossary of Brain Injury Terms * Brain Injury Research Articles * Common Brain Injury Assessment Tools / Rating Scale * Certified Continuing Education Courses * Links to Resource Sites | brain, rehabilitation, therapy | Traumatic brain injury, Brain injury | nlx_151579 | SCR_006106 | CNS - Centre for Neuro Skills, Center for Neuro Skills | 2026-08-09 09:04:22 | 0 | ||||||||
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LDSUPPORT Resource Report Resource Website |
LDSUPPORT (RRID:SCR_007036) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux | is listed by: Genetic Analysis Software | nlx_154427 | SCR_007036 | 2026-08-09 09:04:36 | 0 | ||||||||||
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LINKAGE Resource Report Resource Website |
LINKAGE (RRID:SCR_007033) | software application, software resource | Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes. | Genetic linkage analysis, map genes, find location, disease, genes |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: FASTLINK |
nlx_154346, biotools:linkage | https://bio.tools/linkage, https://gaow.github.io/genetic-analysis-software/l/lcp/, https://gaow.github.io/genetic-analysis-software/l/linkage-general-pedigrees/ | http://www.jurgott.org/linkage/LinkagePC | SCR_007033 | , Linkage Control Program | 2026-08-09 09:04:36 | 0 | |||||||
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PhenoTips Resource Report Resource Website 10+ mentions |
PhenoTips (RRID:SCR_006340) | PhenoTips | software application, software resource | A software tool providing a Web interface and a database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. The main goals of this software are * To allow for collecting patient data in standard formats, enabling effortless data exchange and automated search in annotated gene and disease databases, and * To provide advanced functionalities and a friendly user interface that help reduce the clinician''''s workload, permitting seamless use of this application within the clinician''''s routine. PhenoTips uses the Human Phenotype Ontology (HPO) to express clinical phenotypes, and provides a friendly interface with error-tolerant, predictive search of phenotypic descriptions. PhenoTips closely mirrors clinician workflows: observations can be recorded directly during the patient encounter, and the interface is compatible with any device that runs a modern Web browser. The clinician can record demographic information, family history, medical history, various standard measurements, phenotypic abnormalities detected in the patient, pertinent indications that were not observed and that can be helpful for differential diagnosis, relevant images depicting manifestations of the patient''''s disorders, and additional notes for each of these categories. The software automatically plots growth curves, selects phenotypes reflecting abnormal measurements, instantly finds OMIM disorders matching the phenotypic description and suggests other symptoms to investigate in order to reach a more accurate diagnosis. | clinical symptom, physical finding, clinical, phenotype, demographic information, family history, medical history, standard measurement, indication, image, note, growth curve |
is related to: Human Phenotype Ontology is related to: OMIM has parent organization: University of Toronto; Ontario; Canada |
Genetic disorder | Free | nlx_152049 | SCR_006340 | PhenoTips: phenotyping made easy | 2026-08-09 09:04:27 | 24 | ||||||
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Graphical Overview of Linkage Disequilibrium Resource Report Resource Website 1000+ mentions |
Graphical Overview of Linkage Disequilibrium (RRID:SCR_007151) | GOLD | software application, software resource | Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:10842743 | nlx_154363 | SCR_007151 | 2026-08-09 09:04:38 | 2212 | ||||||||
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BMAPBUILDER Resource Report Resource Website 1+ mentions |
BMAPBUILDER (RRID:SCR_007264) | BMAPBUILDER | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, macos, unix, linux | is listed by: Genetic Analysis Software | nlx_154084 | SCR_007264 | 2026-08-09 09:04:47 | 1 | |||||||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software application, software resource | An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomics |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Principe Felipe Research Centre; Valencia; Spain |
MCyT GEN 2001 - 4885-C05-03; eTumour Project FP6-2002-LIFESCIHEALTH 503094 |
PMID:16081474 | Free for academic use | OMICS_01475, nlx_149335 | SCR_005828 | Blast2GO (B2G) | 2026-08-09 09:04:18 | 8620 |
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