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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Proteome Commons Resource Report Resource Website 10+ mentions |
Proteome Commons (RRID:SCR_006234) | Proteome Commons | portal, service resource, data or information resource, database, software resource, data repository, community building portal, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. | proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome |
is listed by: re3data.org has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Proteome Commons Tranche repository |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:20356086 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151800 | SCR_006234 | ProteomeCommons.org, ProteomeCommons | 2026-08-12 10:49:22 | 12 | |||||
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XNAT Central Resource Report Resource Website 10+ mentions |
XNAT Central (RRID:SCR_006235) | XNAT Central | service resource, data or information resource, image repository, database, data repository, storage service resource | Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface. | magnetic resonance, pet, computed tomography, neuroimaging, mri, computer axial tomography imaging protocol, freesurfer aparc, freesurfer aseg, clinical assessment, atlas scaling factor, fast segmentation, image collection, clinical |
is used by: NITRC-IR is used by: NIF Data Federation is used by: Integrated Datasets is listed by: re3data.org is related to: Morphometry BIRN is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Free, Freely available | nif-0000-04375, r3d100010874 | https://doi.org/10.17616/R3533H | SCR_006235 | Extensible Neuroimaging Archive Toolkit CENTRAL | 2026-08-12 10:49:22 | 48 | ||||||
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PartiGene ARTHROPODA Database Resource Report Resource Website 1+ mentions |
PartiGene ARTHROPODA Database (RRID:SCR_006071) | ARTHROPODA PartiGene Databases | portal, organism-related portal, data or information resource, database, topical portal | As part of our effort in PhyloGenomics, we have developed the PartiGene ARTHROPODA Database. In these databases, we have analyzed the EST datasets for sixty different arthropod species. To aid searching we have split the interface between four class-based views: Chelicerata, Hexapoda, Crustacea, Myriapoda. Amongst other analyses, we have included Alfried Vogler's lab's PartiGene analysis of ~30 different arthropod species ESTs. A separate access point for that dataset is also available. | expressed sequence tag, cluster, arthropod | has parent organization: nematodes.org | nlx_151477 | SCR_006071 | 2026-08-12 10:49:19 | 1 | |||||||||
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Newtomics Resource Report Resource Website 1+ mentions |
Newtomics (RRID:SCR_006073) | Newt-Omics | service resource, data or information resource, production service resource, database, analysis service resource, data analysis service | Newt-omics is a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centered database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise. The newt Notopthalmus viridescens is the master of regeneration. This organism is known for more than 200 years for its exceptional regenerative capabilities. Newts can completely replace lost appendages like limb and tail, lens and retina and parts of the central nervous system. Moreover, after cardiac injury newts can rebuild the functional myocardium with no scar formation. To date only very limited information from public databases is available. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publicly available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt, that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians. * Number of contigs: 26594 * Number of est in contigs: 48537 * Number of transcripts with verified peptide: 5291 * Number of peptides: 15169 | gene expression, regeneration, annotation, expression data, peptide sequence, gene sequence, tissue regeneration, newt, pathway, mammal, blast, contigs, peptide, tissue, microarray, heart, lens, dorsal, ventral, transcript, functional annotation, molecular process, model organism, expressed sequence tag, sequence, mass spectrometry, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute for Heart and Lung Research; Bad Nauheim; Germany |
Hessian Ministry for Science and Art | PMID:22039101 | To be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of the MPI for heart and lung research. | nlx_151479, biotools:newt-omics | https://bio.tools/newt-omics | SCR_006073 | newt db, Newt database | 2026-08-12 10:49:20 | 1 | ||||
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NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | service resource, data or information resource, production service resource, database, analysis service resource, data analysis service | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-08-12 10:49:20 | 25 | ||||
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NHMRC Australian PhenomeBank Resource Report Resource Website 1+ mentions |
NHMRC Australian PhenomeBank (RRID:SCR_006149) | APB | biomaterial supply resource, cell repository, organism supplier, material resource | The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. | RIN, Resource Information Network, murine, mutation, gene, strain, transgenic, alteration, phenotype, live mouse, sperm, embryo, transgene, database, allele, chromosome, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network has parent organization: Australian Phenomics Network works with: International Mouse Strain Resource |
Public | nlx_151640 | http://pb.apf.edu.au/phenbank/foreignPageImport.html?page=http://pbstatic.apf.edu.au:80/phenbank/home.htm | SCR_006149 | Australian Phenome Bank, Phenome Bank, Australian PhenomeBank, NHMRC Australian Phenome Bank, PhenomeBank | 2026-08-12 10:49:22 | 3 | ||||||
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NEuronMOrphological analysis tool Resource Report Resource Website 1+ mentions |
NEuronMOrphological analysis tool (RRID:SCR_006304) | NEMO | image analysis software, image processing software, software application, data processing software, software resource | Software to handle and process large numbers of optical microscopy image files of neurons in culture or slices in order to automatically run batch routines, store data and apply multivariate classification and feature extraction using 3-way principal component analysis (PCA). This freeware for semi automated quantitative and dynamic analysis of neuron morphometry incorporates the most important microstructural quantification methods, such as fractal and sholl analysis with statistical and classification tools to provide an integrated image processing environment which enables fast and easy feature identification. It includes: * Friendly interactive graphical user interface * Image pre-processing * Morphological analysis * Topological analysis * Cell counting * 3-way PCA analysis (also available as an ImageJ plugin) * Plot of variables Sequential images of labeled or unlabelled neurons or tissue slices can be uploaded batch-wise in order to create a 3 axis (time, image coordinate) data base and a datamatrix of variables for 3-way Principal Component Analysis*. | morphometric analysis, neuron, morphology, principal component analysis, image pre-processing, neuron reconstruction, morphological analysis, neuron counting, neuron morphology, image processing, morphometrics, 3-way principal component analysis, topological analysis | has parent organization: University of Pisa; Pisa; Italy | Open-source | nlx_151981 | SCR_006304 | NEuronMOrphological analysis tool NEMO, NEMO (NEuron MOrphological analysis tool) | 2026-08-12 10:49:24 | 5 | |||||||
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Computerized Anatomical Reconstruction and Editing Toolkit Resource Report Resource Website 50+ mentions |
Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) | CARET | data visualization software, image processing software, software application, data processing software, software resource | Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems. | reconstruction, visualization, cerebral cortex, surface, brain, dataset, cerebellar cortex, atlas application, mesh generation, quantitative shape analysis, segmentation, shape analysis, intersubject, image-to-template, gaussian curvature, mean curvature, animation, three dimensional display, two dimensional display, surface rendering, cortical flat map, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SumsDB has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIMH R01 MH60974; NEI EY02091 |
PMID:11522765 | Free, Available for download, Freely available | nif-0000-00279 | http://www.nitrc.org/projects/caret, https://sources.debian.org/src/caret/ | SCR_006260 | Computerized Anatomical Reconstruction Editing Toolkit | 2026-08-12 10:49:23 | 59 | ||||
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TED-Ed Resource Report Resource Website 1+ mentions |
TED-Ed (RRID:SCR_006138) | TED-Ed, TED Ed | training material, video resource, narrative resource, data or information resource | Video library of curated educational videos, many of which represent collaborations between talented educators and animators nominated through the TED-Ed platform. This platform also allows users to take any useful educational video, not just TED''s, and easily create a customized lesson around the video. Users can distribute the lessons, publicly or privately, and track their impact on the world, a class, or an individual student. TED-Ed''s videos aim to capture and amplify the voices of the world''s greatest educators. | education, educator, student, lesson, think, learn, social studies, psychology, philosophy, religion, mathematics, literature, language, health, design, engineering, technology, business, economics, art | has parent organization: TED | The community can contribute to this resource | nlx_151629 | SCR_006138 | TED Ed - Lessons Worth Sharing, TED-Ed: Lessons Worth Sharing | 2026-08-12 10:49:20 | 1 | |||||||
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BrainImage Software Resource Report Resource Website 1+ mentions |
BrainImage Software (RRID:SCR_006139) | BrainImage | image analysis software, image processing software, software application, data processing software, software resource | A multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can: * Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes. * Create and display triangular mesh surfaces from MRI volumes. * Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display. * Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit. This 3D image processing and analysis program for the Apple Macintosh PowerPC is based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. The last version of the software included multiplatform capability, volume visualization and advanced image analysis tools. | mri, segmentation, visualization, volume, neuroimaging, analyze, anatomic, application, artifact removal, image display, java, labeling, macos, mesh generation, microsoft, modeling, magnetic resonance, quantification, region of interest, rendering, spatial transformation, three dimensional display, volume measurement, volumetric analysis, volumetric analysis, windows, platform |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: NIH Image has parent organization: Stanford University School of Medicine; California; USA |
Human Brain Project | GNU General Public License | nif-0000-00272 | http://spnl.stanford.edu/tools/brainimage.htm | SCR_006139 | Brain Image, BrainImageJ, BrainImageJava | 2026-08-12 10:49:20 | 8 | |||||
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Guppy Project Resource Report Resource Website 1+ mentions |
Guppy Project (RRID:SCR_006255) | Guppy Project | video resource, portal, organism-related portal, data or information 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 | 2026-08-12 10:49:23 | 6 | ||||||||
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Federation of International Mouse Resources Resource Report Resource Website 1+ mentions |
Federation of International Mouse Resources (RRID:SCR_006137) | FIMRe | data or information resource, topical portal, community building portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources | embryo, gamete, embryonic stem cell, embryonic stem cell line, live breeding stock, live mouse, resource center, international network, mouse model, human disease, gene, genome, biomaterial supply resource, cell repository, organism supplier, biospecimen repository, mutation, cryopreserved |
is related to: Jackson Laboratory is related to: Mutant Mouse Resource and Research Center is related to: European Mouse Mutant Archive is related to: RIKEN BioResource Center has parent organization: Mouse Genome Informatics (MGI) |
PMID:16688526 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_151627 | SCR_006137 | Federation of International Mouse Resources (FIMRe) | 2026-08-12 10:49:21 | 4 | ||||||
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SpliceDisease Resource Report Resource Website 1+ mentions |
SpliceDisease (RRID:SCR_006130) | SpliceDisease | service resource, data or information resource, database, data repository, storage service resource | Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser. | rna splicing, mutation, disease, gene, genomic sequence, nucleotide substitution, deletion, insertion, mutation location, splicing mutation, nucleotide, disease association, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 81001481 | PMID:22139928 | The community can contribute to this resource | biotools:splicedisease_db, nlx_151614 | https://bio.tools/splicedisease_db | SCR_006130 | Splice Disease, SpliceDisease Database Site, Splice Disease Database, SpliceDisease Database | 2026-08-12 10:49:20 | 2 | ||||
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StemBase Resource Report Resource Website 1+ mentions |
StemBase (RRID:SCR_006252) | StemBase | service resource, data or information resource, production service resource, database, analysis service resource, data analysis service | A publicly accessible database containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives to facilitate the discovery of gene functions relevant to stem cell control and differentiation. It has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. There is currently more than 210 stem cell samples in 60 different experiments, with more being added regularly. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell in the frame of the Stem Cell Genomics Project. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Center for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase. | stem cell, gene expression, dna microarray, correlation tool, serial analysis of gene expression, correlation |
is used by: BloodExpress has parent organization: University of Ottawa; Ontario; Canada |
Genome Canada ; Canadian Stem Cell Network ; Canadian Institutes of Health Research ; Canada Research Chairs |
PMID:19284540 PMID:18453254 PMID:15763554 |
Publicly accessible. Please cite. | nlx_151919 | SCR_006252 | Stem Cell Genomics database | 2026-08-12 10:49:22 | 4 | |||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | image analysis software, image processing software, software application, data processing software, software resource | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-08-12 10:49:21 | 1 | ||||||||
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PredictSNP Resource Report Resource Website 100+ mentions |
PredictSNP (RRID:SCR_006327) | PredictSNP | service resource, production service resource, analysis service resource, software resource, data analysis service | Consensus classifier tool that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database. A stand-alone version is also available. | single nucleotide polymorphism, classifier, prediction, mutation, protein function, FASEB list |
is listed by: OMICtools is related to: Protein Mutant Database is related to: UniProt |
PMID:24453961 | Free for academic use | OMICS_02218 | SCR_006327 | PredictSNP - Consensus classifier for prediction of disease-related mutations | 2026-08-12 10:49:24 | 148 | ||||||
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Bentham OPEN Resource Report Resource Website 1+ mentions |
Bentham OPEN (RRID:SCR_006202) | Bentham OPEN | portal, journal article, data or information resource, service resource, organization portal | Publish over 230 plus peer-reviewed open access journals. These free-to-view online journals cover all major disciplines of science, technology, medicine and social sciences. Bentham OPEN offers its ''Complimentary Membership'' to International R & D organizations, institutes and universities. This opportunity will entitle authors from different member institutes to a special discount of 30% in the open access publication fee for submission of articles to Bentham OPEN journals. Additionally, input and contributions from associate institutes would also be recognized and a link to their respective Website would be displayed on the Bentham OPEN membership page. The member institution''s logo will also be published on the same page. Bentham Open Membership provides the following advantages: * Possibility to explore 73 distinct disciplines by means of publishing in 239 open access journals. * Free access to all provides prospects of higher citations. * Author(s) own the copyrights to their published articles. * High standard criteria for peer-review. * Unbound right to read, download or print open access articles. * Access to a range of articles in printed form such as short communications, full length research articles, reviews or conference proceedings. * Simple steps from submission to publication, leading to fast turn-around. * Possibility of archiving published articles. The complimentary membership is valid for a span of one year and upon completion of the prescribed period, it is renewed by mutual interest and agreement. If you find the above mentioned details relevant, then kindly contact us via e-mail at membership_at_benthamscience.org or oa_at_benthamscience.org. | publisher, publish, addiction, agriculture sciences, astronomy, biochemistry, biological sciences, biotechnology, cell biology, structural biology, chemistry, computer science, dentistry, earth science, energy, fuel, engineering, environmental science, ethics, food and nutrition, forest science, genomics, imaging, informatics, marine science, materials science, mathematics, medicine and health, microbiology, nanoscience, pharmaceutical sciences, physics, plant science, proteomics, psychiatry and psychology, social sciences, toxicology, transportation, veterinary sciences | Creative Commons Attribution-NonCommercial License | nlx_151746 | SCR_006202 | Bentham Open Access | 2026-08-12 10:49:23 | 1 | ||||||||
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PDFX Resource Report Resource Website 1+ mentions |
PDFX (RRID:SCR_006163) | PDFX | service resource, production service resource, software application, text extraction software, software resource | A fully-automated PDF-to-XML converter service for scientific articles. It takes a full-text PDF article as input and outputs the hierarchy of its distinct logical elements in an XML format. The elements that PDFX can currently extract are: * Front Matter ** title, abstract, author, author footnote * Body Matter ** body text, h1, h2, h3, image, table, figure/table caption, figure/table reference, bibliographic item, bibliographic reference (citation) * Extras ** header, footer, side note, page number, email, URI Note: This system has been designed for processing scientific articles. While virtually any PDF file is acceptable input, quality of the processing output might be degraded e.g. for entire books, slide presentations or spreadsheet/strictly tabular data. There are two ways in which you can use PDFX: * via a web browser * via any other HTTP client, such as the curl command-line tool | semantic mark up, text extraction, pdf, xml, html |
is listed by: FORCE11 has parent organization: Utopia Docs |
Free | nlx_151665 | SCR_006163 | 2026-08-12 10:49:21 | 2 | ||||||||
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Knime Resource Report Resource Website 500+ mentions |
Knime (RRID:SCR_006164) | KNIME | software toolkit, text-mining software, software application, data processing software, software resource, workflow software | KNIME (Konstanz Information Miner) is a user-friendly and comprehensive Open-Source data integration, processing, analysis, and exploration platform. KNIME (naim) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualization and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME can be downloaded onto the desktop and used free of charge. KNIME products include additional functionalities such as shared repositories, authentication, remote execution, scheduling, SOA integration and a web user interface as well as world-class support. Robust big data extensions are available for distributed frameworks such as Hadoop. KNIME is used by over 3000 organizations in more than 60 countries. The modular data exploration platform, initially developed at the University of Konstanz, Germany, enables the user to visually create data flows, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for tools of numerous vendors due to its open and modular API. The KNIME.com product pipeline includes an Enterprise Server, Cluster Execution, Reporting solutions, and professional KNIME support subscriptions. KNIME.com also offer services such as data analysis, hands-on training and the development of customized components for KNIME. | platform, next-generation sequencing, data analysis, visualization, selection, analysis, high-throughput screening, data mining, drug discovery | has parent organization: University of Konstanz; Baden-Wurttemberg; Germany | PMID:23110532 PMID:22644661 PMID:22607449 PMID:21984761 PMID:21873641 |
nlx_151666 | SCR_006164 | Konstanz Information Miner | 2026-08-12 10:49:20 | 770 | |||||||
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Impress Resource Report Resource Website 50+ mentions |
Impress (RRID:SCR_006160) | IMPReSS | data or information resource, narrative resource, experimental protocol, standard specification, data access protocol, software resource, international standard specification, web service | Contains standardized phenotyping protocols essential for the characterization of mouse phenotypes. IMPReSS holds definitions of the phenotyping Pipelines and mandatory and optional Procedures and Parameters carried out and data collected by international mouse clinics following the protocols defined. This allows data to be comparable and shareable and ontological annotations permit interspecies comparison which may help in the identification of phenotypic mouse-models of human diseases. The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. IMPReSS has a SOAP web service machine interface. The WSDL can be accessed here: http://www.mousephenotype.org/impress/soap/server?wsdl | phenotype, phenotyping, adult, embryonic, ontology, enu-induced gene knockout, gene, knockout mouse, ethylnitrosourea |
is related to: European Mouse Phenotyping Resource of Standardised Screens has parent organization: International Mouse Phenotyping Consortium (IMPC) |
nlx_151661 | SCR_006160 | International Mouse Phenotyping Resource of Standardised Screens, IMPReSS - International Mouse Phenotyping Resource of Standardised Screens | 2026-08-12 10:49:20 | 66 |
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