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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CONTRAfold Resource Report Resource Website 1+ mentions |
CONTRAfold (RRID:SCR_023994) | CONTRAfold | simulation software, software application, software resource | Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction. | sequence prediction, | is listed by: Debian | PMID:16873527 | Free, Available for download, Freely available | OMICS_03452 | https://sources.debian.org/src/CONTRAfold/ | SCR_023994 | CONditional TRAining for RNA Secondary Structure Prediction, contrafold | 2026-08-09 09:08:44 | 2 | |||||
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toppred Resource Report Resource Website 1+ mentions |
toppred (RRID:SCR_024385) | simulation software, software application, software resource | Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins. | Membrane protein structure prediction, transmembrane topology prediction, predicting topology, bacterial inner membrane proteins topology prediction, | is listed by: Debian | PMID:1593632 | Free, Available for download, Freely available, | OMICS_07268 | https://sources.debian.org/src/toppred/ | SCR_024385 | 2026-08-09 09:08:53 | 3 | |||||||
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pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | simulation software, software application, software resource | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | 2026-08-09 09:09:03 | 33 | ||||||||
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Metastudent Resource Report Resource Website |
Metastudent (RRID:SCR_024110) | simulation software, software application, software resource | Software tool to predict gene ontology terms for protein sequences through homology. | predict gene ontology terms, protein sequences, through homology, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20187 | https://sources.debian.org/src/metastudent/, https://sources.debian.org/src/metastudent-data/ | SCR_024110 | metastudent-data, metastudent | 2026-08-09 09:08:46 | 0 | |||||||
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Yanosim Resource Report Resource Website |
Yanosim (RRID:SCR_024363) | Yanosim | simulation software, software application, software resource | Software tool as read simulator for nanopore DRS datasets. | read simulator for nanopore DRS datasets, read simulator, nanopore DRS datasets, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanosim/ | SCR_024363 | yanosim, yet another nanopore simulator | 2026-08-09 09:08:27 | 0 | |||||||
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CTSim Resource Report Resource Website |
CTSim (RRID:SCR_024004) | simulation software, software application, software resource | Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions. | Computed tomography simulator, reconstruct original phantom image from projections, reconstruct image, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctsim/ | SCR_024004 | ctsim, Open Source Computed Tomography Simulator | 2026-08-09 09:08:44 | 0 | ||||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-08-09 09:02:54 | 108 | |||
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DrugSim2DR Resource Report Resource Website 1+ mentions |
DrugSim2DR (RRID:SCR_024564) | simulation software, software application, software resource | Software R package to predict drug functional similarity to drug repurposing. | predict drug functional similarity, similarity to drug repurposing, | is listed by: CRAN | Free, Available for download, Freely available | SCR_024564 | 2026-08-09 09:08:30 | 1 | ||||||||||
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Japan Society for the Promotion of Science Resource Report Resource Website 10+ mentions |
Japan Society for the Promotion of Science (RRID:SCR_001085) | JSPS | regional funding resource, group, funding resource | Research and outreach organization dedicated to promoting science, research and education. The society has four main objectives, including building international cooperative networks, enhancing education and research at universities, building evidence-based science-promotion systems and creating diverse world level knowledge. | research, science, promotion, japan, education | nlx_151882 | SCR_001085 | 2026-08-09 09:03:08 | 49 | ||||||||||
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ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | simulation software, software application, software resource | Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy. | species tree reconstruction, reconstruction from multi-copy gene family trees | is listed by: SoftCite | PMID:32886770 | Free, Available for download, Freely available | SCR_024520 | ASTRAL for PaRalogs and Orthologs, ASTRAL-Pro 2 | 2026-08-09 09:09:04 | 3 | ||||||||
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Mindboggle-101 atlases Resource Report Resource Website 10+ mentions |
Mindboggle-101 atlases (RRID:SCR_002439) | Mindboggle-101 | data or information resource, atlas | Complete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world! http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full | clinical neuroinformatics, computational neuroscience, mgh/mgz, magnetic resonance, nifti, image collection | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIMH MH084029 | PMID:23227001 | Free, Freely available | nlx_155814 | http://www.nitrc.org/projects/mindboggle101 | SCR_002439 | Mindboggle-101 manually labeled brains | 2026-08-09 09:03:35 | 14 | ||||
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OpenLink Software Resource Report Resource Website |
OpenLink Software (RRID:SCR_003662) | OpenLink | commercial organization, service resource, software resource | An technology innovator in database and application server software that has been a long time developer of database and semantic repository technologies on both single servers and clusters. This, combined with OpenLink's experience with SQL, gives an all round view of performance across many environments and workload profiles, from transactions to decision support or search. OpenLink also has extensive experience in developing scale-out parallel database technology. The cross-platform product portfolio addresses challenges such as: Universal Data Access, Data Virtualization & Management, Personal & Enterprise Data Spaces, and Implementation & Support. | standards compliant, data access, integration, management, technology, linked data |
is related to: Open PHACTS is parent organization of: DBpedia |
nlx_157816 | SCR_003662 | OpenLink Group Limited | 2026-08-09 09:03:46 | 0 | ||||||||
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UNC Primate Brain Atlas Resource Report Resource Website 1+ mentions |
UNC Primate Brain Atlas (RRID:SCR_002570) | UNC Primate Brain Atlas | data or information resource, atlas | Symmetric atlas of the primate brain created using 18 cases of rhesus macaques aged 16-34 months. It includes the T1-weighted image (with and without skull), and also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures segmentation (amygdala, caudate, hippocampus, pallidus, putamen), and a lobar parcellation map. You can find more details about the creation of this atlas in the following paper : M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8 | atlas data, magnetic resonance, nrrd |
is used by: UNC-Wisconsin Neurodevelopment Rhesus MRI Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Creative Commons Attribution-ShareAlike License | nlx_155972 | SCR_002570 | 2026-08-09 09:03:36 | 3 | ||||||||
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UNC Infant 0-1-2 Atlases Resource Report Resource Website 1+ mentions |
UNC Infant 0-1-2 Atlases (RRID:SCR_002569) | UNC Infant 0-1-2 Atlases | data or information resource, atlas | 3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old. | analyze, atlas application, linux, macos, microsoft, magnetic resonance, posix/unix-like, infant, pediatric, template, longitudinal, neonate, male, female, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
Normal | NIH ; NIBIB EB006733; NIBIB EB008760; NIBIB EB008374; NIBIB EB009634; NIMH MH088520; NIMH MH070890; NIMH MH064065; NINDS NS055754; NICHD HD053000 |
PMID:21533194 | Free, Available for download, Freely available | nlx_155971 | http://www.nitrc.org/projects/pediatricatlas | SCR_002569 | UNC 0-1-2 Infant Atlases | 2026-08-09 09:03:31 | 2 | |||
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Gnubila Resource Report Resource Website |
Gnubila (RRID:SCR_004109) | Gnubila | commercial organization, service resource, software resource | A commercial software and service company operating in Spain, France and Colombia whose main stakeholder is Indra and its main product is the G platform, on top of which they have developed several vertical applications for various industry sectors like banking, healthcare, government and SMB. Since its constitution, gn??bila has constituted an international reference in the development and deployment of Network Service Infrastructures and Platforms for Businesses, Organizations and Individuals, facilitating communication, collaboration and the coordination of applications, data and information. gn??bila Products: * Cloud Application Platform * Cloud TP Platform * Platform as a Service * Development Platform | cloud computing, gaming platform as a service, application platform as a service, application services, middleware, grid infrastructure | is related to: EMIF | nlx_158585 | SCR_004109 | Gn??bila, Gnubila Technology | 2026-08-09 09:04:01 | 0 | ||||||||
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Stereoscopic Atlas of Intrinsic Brain Networks Resource Report Resource Website 1+ mentions |
Stereoscopic Atlas of Intrinsic Brain Networks (RRID:SCR_002568) | SAIBN | data or information resource, atlas | A 3D stereoscopic (anaglyph method) full brain functional connectivity atlas created using a parcellation atlas published by Craddock et al. (2012). Using 3D Slicer 3.6.3 and the two hundred Region of Interest (ROI) version of the Craddock atlas, 200 grayscale surface models were created using a z-stat threshold > 2.3, and each surface model was processed with a surface decimation algorithm, smoothed with the Taubin algorithm and without surface normals. For improved visualization of the functional connectivity networks and their relative anatomical position, the surface model of five subcortical anatomical structures (corpus callosum, bilateral caudate, pallidum, putamen, thalamus, amygdala and hippocampus) were included in SAIBN. These surfaces were created with 3D Slicer using the segmentation computed with Freesurfer v. 5.1. The viewer should use red-cyan glasses to see the 3D stereoscopic effect using 3D Slicer (version 3.6.3, http://www.slicer.org/pages/Special:SlicerDownloads). | magnetic resonance, corpus callosum, bilateral caudate, pallidum, putamen, thalamus, amygdala, hippocampus |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer |
Free | nlx_155970 | SCR_002568 | Stereoscopic Atlas of Intrinsic Brain Networks (SAIBN) | 2026-08-09 09:03:29 | 1 | |||||||
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Retina Project Resource Report Resource Website 1+ mentions |
Retina Project (RRID:SCR_002884) | Retina Project | data or information resource, spatially referenced dataset, atlas | Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project. | electrophysiology, protein expression, fluorescent, gene, amacrine cell, astrocyte, bipolar cell, blood vessel, brain, cell, ganglion cell layer, central nervous system, circuit, horizontal cell, hybridization, microglia, adult mouse, muller cell, neocortex, neuronal, photoreceptor, protein, recombinase, retina, spinal cord, mutant mouse strain, bac, retinal cell, cell type, night vision, direction, neuronal circuitry, connectivity, image collection |
is used by: NIF Data Federation has parent organization: GENSAT at NCBI - Gene Expression Nervous System Atlas |
Department Of Health And Human Services ; NINDS N01 NS02331 |
PMID:19648912 | Free, Freely available | nif-0000-25587 | SCR_002884 | GENSAT Retina Project, Retina Project from GENSAT, The Retina Project, The Retina Project from GENSAT, GENSAT - Retina Project | 2026-08-09 09:03:36 | 2 | |||||
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eScholarship Resource Report Resource Website 500+ mentions |
eScholarship (RRID:SCR_002624) | eScholarship | data or information resource, service resource, bibliography | Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide. | California Digital Library, publication, scholarly communication, publish, book, journal, working paper, conference, scholarship, publishing service, |
is listed by: FORCE11 is listed by: DataCite has parent organization: California Digital Library has parent organization: University of California; California; USA |
Free, Freely available | nlx_156042 | https://api.datacite.org/dois?prefix=10.34940 | SCR_002624 | CDL eScholarship | 2026-08-09 09:03:30 | 531 | ||||||
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Zebrafinch Brain Architecture Project Resource Report Resource Website 1+ mentions |
Zebrafinch Brain Architecture Project (RRID:SCR_004277) | Zebrafinch Brain Architecture Project | data or information resource, atlas | Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies. | nissl stain, sagittal, horizontal plane, transverse plane, myelin stain, brain | has parent organization: Brain Architecture Project | W. M. Keck Foundation ; Crick-Clay Professorship ; NINDS NS50436; NIGMS R24 GM092842 |
nlx_143663 | SCR_004277 | 2026-08-09 09:03:53 | 5 | ||||||||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software, https://bio.tools/ancestrymap | http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-08-09 09:03:52 | 12 |
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