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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data visualization software, data processing software, data analysis software, software toolkit, software application, software resource | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF CBET-1351692; NSF IOS-1550994; Human Frontiers Science Program RGY0088 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-02-13 10:57:39 | 3 | ||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | data repository, storage service resource, service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-02-13 10:57:44 | 35 | |||||||||
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PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | software resource, source code, data processing software, software application | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip https://sources.debian.org/src/phylip/ |
SCR_006244 | PHYLogeny Inference Package | 2026-02-13 10:55:48 | 3519 | |||||
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Guppy Project Resource Report Resource Website 1+ mentions |
Guppy Project (RRID:SCR_006255) | Guppy Project | organism-related portal, portal, data or information resource, video resource, topical portal | A project that observes the processes of adaptive evolution in nature, and tests evolutionary hypotheses, by studying populations of guppies on the Caribbean island of Trinidad. Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The National Science Foundation (NSF), through its Integrative Biological Research (FIBR) program, is funding a 5-year study by 13 biologists from colleges, universities, and research institutions throughout the United States and Canada, to study the relationship of adaptive evolution and environmental circumstances. The Trinidadian guppy (Poecilia reticulata) is an excellent species for these purposes because: * It matures rapidly (one generation = 3-4 months) * It inhabits different ecological environments that can be easily manipulated On Trinidad, guppies live in streams, or portions of streams, that can differ in the species of predators that the guppies have to contend with. Some streams are high-predation environments, others low-predation. Different predation environments are often right next to one another, separated by a waterfall (which neither guppies nor predators can cross). Guppies from high-predation environments experience much higher mortality rates than do guppies in low-predation environments. High mortality is associated with the following characteristics, all of which have a genetic basis: * Earlier maturity * Greater investment of resources in reproduction * More and smaller offspring. We have found that mortality rates can be manipulated by: * Transplanting guppies from high-predation localities into sites from which they and their predators had previously been excluded by natural waterfalls, thus lowering mortality rates; * Introducing predators into low-predation sites, thus increasing mortality rates. Such experiments have shown that species evolve as predicted by theory. We have also found that evolution by natural selection can be remarkably fast, on the order of four to seven orders of magnitude faster than had been inferred from the fossil record. | adaption, evolution, adaptive evolution, environment, trinidadian guppy, poecilia reticulata, image, natural selection | has parent organization: University of California at Riverside; California; USA | NSF | nlx_151840 | SCR_006255 | 2026-02-13 10:55:47 | 6 | ||||||||
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crowdLabs Resource Report Resource Website 1+ mentions |
crowdLabs (RRID:SCR_006294) | crowdLabs | storage service resource, community building portal, data analysis service, portal, analysis service resource, data or information resource, production service resource, service resource | A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly. | platform, computation, data sharing |
is listed by: FORCE11 is related to: VisTrails |
NSF | nif-0000-06716 | http://www.force11.org/node/4666 | SCR_006294 | crowd Labs | 2026-02-13 10:55:48 | 1 | ||||||
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Plant Ontology Resource Report Resource Website 10+ mentions |
Plant Ontology (RRID:SCR_006494) | PO | data or information resource, ontology, controlled vocabulary, database | Ontology and database that links plant anatomy, morphology and growth and development to plant genomics data.Plant Ontology Consortium develops, curates and shares controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages, providing semantic framework for meaningful cross species queries across databases. PO is under active development to expand to encompass terms and annotations from all plants. | obo, gene, development, anatomy, morphology, growth, genomics, database |
has parent organization: Oregon State University; Oregon; USA has parent organization: Cornell University; New York; USA |
NSF 0822201; NSF 0321685 |
PMID:18628842 PMID:18194960 |
SCR_006844, nlx_55564 | SCR_006494 | Plant Ontology Browser, PO Browser, Plant Ontology Consortium Database, PO Database, Plant Ontology Database, POC Database | 2026-02-13 10:55:51 | 31 | ||||||
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Integrated Earth Data Applications Resource Report Resource Website 1+ mentions |
Integrated Earth Data Applications (RRID:SCR_006739) | IEDA | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | A community-based data facility to support, sustain, and advance the geosciences by providing data services for observational solid earth data from the Ocean, Earth, and Polar Sciences. IEDA systems enable these data to be discovered and reused by a diverse community now and in the future. Data services include data access, data analysis, data compliance, data publication, DOI search, and web services. Desktop apps GeoMapApp and Virtual Ocean are available to explore, visualize and analyze your own data within the context of hundreds of other earth science data from around the world. IEDA is a partnership between EarthChem and the Marine Geoscience Data System (MGDS). EarthChem and MGDS systems include the geochemical databases PetDB and SedDB, the geochemistry data network EarthChem, the Ridge2000 and MARGINS Data Portals, the Academic Seismic Portal field data collection, the Antarctic and Southern Ocean Data System, the Global Multi Resolution Topography synthesis, and the System for Earth Sample Registration SESAR. | map, ocean, earth, polar, sciences, ocean sciences, earth sciences, polar sciences, doi, global geochemistry, marine geoscience |
has parent organization: Columbia University; New York; USA is parent organization of: Marine Geoscience Data System is parent organization of: Global-Multi Resolution Topography Image Service is parent organization of: Global-Multi Resolution Topography Grid Service |
NSF | The community can contribute to this resource, Free, Open unspecified license | nlx_156096 | SCR_006739 | 2026-02-13 10:55:53 | 1 | |||||||
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Rice Genome Annotation Resource Report Resource Website 1000+ mentions |
Rice Genome Annotation (RRID:SCR_006663) | Osa1 | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes | rice, oryza sativa, maize, corn, zea mays, wheat, triticum aestivum, gene, genome, annotation, FASEB list |
is listed by: OMICtools has parent organization: Michigan State University; Michigan; USA |
NSF DBI-0321538; NSF DBI-0834043 |
PMID:17145706 | Acknowledgement requested | OMICS_01563, nif-0000-31459 | http://rice.tigr.org | http://rice.plantbiology.msu.edu/pseudomolecules/info.shtml | SCR_006663 | Rice Genome Annotation Project, MSU Rice Genome Annotation Project Database and Resource | 2026-02-13 10:55:52 | 1423 | |||
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data repository, storage service resource, data or information resource, service resource, database | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NSF EF0843229; NIGMS U24 GM144232 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-02-13 10:55:56 | 14 | ||||
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Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge https://bio.tools/centrifuge https://sources.debian.org/src/centrifuge/ |
SCR_016665 | 2026-02-13 10:57:49 | 9 | ||||||
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Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | sequence analysis software, data processing software, data analysis software, data analytics software, software application, software resource | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-02-13 10:57:48 | 0 | |||||||
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PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | software resource, simulation software, software application | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | Canadian Institutes of Health Research ; Canada Research Chairs program ; Howard Hughes Medical Institute ; NIDDK P01 DK078669; NHGRI U01 HG004866; NHGRI R01 HG004872; Crohn’s and Colitis Foundation of America ; Sloan Foundation ; NHGRI R01 HG005969; NSF CAREER DBI1053486; ARO W911NF1110473 |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-02-13 10:57:52 | 36 | |||||
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TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | data processing software, data analysis software, software toolkit, software application, software resource | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-02-13 10:57:49 | 10 | ||||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, software resource, data processing software, software application | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-13 10:57:50 | 10 | ||||||
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | data processing software, analysis service resource, production service resource, service resource, software application, software resource, image analysis software | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | 2026-02-13 10:58:04 | 0 | |||||||||
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Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | data analysis software, software resource, data processing software, software application | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-02-13 10:58:03 | 0 | ||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | software resource, simulation software, software application | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2026-02-13 10:57:20 | 13 | |||||||||
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Group Sparse Canonical Correlation Analysis Resource Report Resource Website |
Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) | GSCCA | data analysis software, software resource, data processing software, software application | Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data. | group analysis, correlation analysis | has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) | NSF ; NIH |
Available for download | SCR_014977 | 2026-02-13 10:57:23 | 0 | ||||||||
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ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, software resource, data processing software, software application | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-02-13 10:58:09 | 47 | ||||||
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RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | web service, software application, data access protocol, software resource, simulation software | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | 2026-02-13 10:58:17 | 149 |
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