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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Science Dynamics Resource Report Resource Website 1+ mentions |
Science Dynamics (RRID:SCR_016958) | data or information resource, data set, numeric dataset, portal, project portal | Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks. | Science, Dynamics, project, dataset, code, framework, optimization, academic, publishing, metric, observing, Goodhart, Law, action, journal, network | has parent organization: University of Washington; Seattle; USA | Microsoft Azure Research Award ; e Washington Re-search Foundation Fund for Innovation in Data-Intensive Discovery ; Moore/Sloan Data Science Environments Project at the University of Washington |
Free, Freely available | https://www.ise.bgu.ac.il/labs/fire/sciencedynamics/index.html | SCR_016958 | 2026-08-21 12:41:13 | 1 | ||||||||
|
Illuminating the Druggable Genome Resource Report Resource Website 50+ mentions |
Illuminating the Druggable Genome (RRID:SCR_016924) | IDG | consortium, data or information resource, data repository, organization portal, portal, service resource, storage service resource | Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). | understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools |
is recommended by: National Library of Medicine is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian |
NIH Common Fund | biotools:pharos | https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about | https://druggablegenome.net | SCR_016924 | Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome | 2026-08-21 12:41:12 | 64 | |||||
|
Prevention of Lower Urinary Tract Symptoms Resource Report Resource Website |
Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) | PLUS | consortium, data or information resource, organization portal, portal | Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women. | plan, perform, analyze, data, prevent, lower, urinary, track, symptom, women |
is listed by: NIDDK Information Network (dkNET) is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: University of Minnesota Medical School; Minnesota; USA |
NIDDK | SCR_016923 | Prevention of Lower Urinary Tract Symptoms, Prevention LUTS, PLUS | 2026-08-21 12:41:02 | 0 | ||||||||
|
The Human BioMolecular Atlas Program Resource Report Resource Website 10+ mentions |
The Human BioMolecular Atlas Program (RRID:SCR_016922) | HuBMAP | data or information resource, funding resource, portal, project portal | Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows. | organism, cell, tissue, data, generation, technology, organization, functional, mapping, human, body |
uses: Azimuth is listed by: NIDDK Information Network (dkNET) is related to: HuBMAP Data Portal |
NIH | https://humanatlas.io/omap, https://avr.hubmapconsortium.org/, https://commonfund.nih.gov/HuBMAP, https://zenodo.org/records/5244551 | SCR_016922 | Human BioMolecular Atlas Program, HuBMAP, The Human BioMolecular Atlas Program, NIH HuBMAP | 2026-08-21 12:41:12 | 26 | |||||||
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Digital Expression Explorer 2 Project Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Project (RRID:SCR_016929) | DEE2 | data or information resource, data repository, database, portal, project portal, service resource, storage service resource | Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes. | transcriptome, database, RNA-seq, sequencing, processed, data |
is related to: Digital Expression Explorer 2 Source Code is related to: Digital Expression Explorer 2 Docker Image |
DOI:10.5281/zenodo.1561840 | Free, Freely available | SCR_016929 | DEE2 Project | 2026-08-21 12:41:02 | 4 | |||||||
|
ALGGEN-PROMO Resource Report Resource Website 100+ mentions |
ALGGEN-PROMO (RRID:SCR_016926) | data analysis software, data or information resource, data processing software, laboratory portal, organization portal, portal, sequence analysis software, service resource, software application, software resource | Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches. | identify, transcription, factor, binding, site, DNA, sequence, species, regulatory, element, search | PMID:11847087 PMID:12824386 |
Free, Available for download, Freely available | SCR_016926 | PROMO, ALGorithmics and GENetics PROMO, ALGGEN, ALGGEN-PROMO | 2026-08-21 12:41:12 | 434 | |||||||||
|
FibrilTool Resource Report Resource Website 1+ mentions |
FibrilTool (RRID:SCR_016773) | data analysis software, data analytics software, data processing software, image analysis software, software application, software resource | ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image. | quantify, fibrillar, structure, raw, image, microscopy | is listed by: BISE | Agence Nationale de la Recherche ; Institut National de la Recherche Agronomique (INRA) ; France ; Ministry of Science and Higher Education ; Poland ; National Science Centre ; Poland |
PMID:24481272 | Free, Available for download, Freely available to the scientific community | SCR_016773 | 2026-08-21 12:41:10 | 5 | ||||||||
|
NZYTech Resource Report Resource Website 10+ mentions |
NZYTech (RRID:SCR_016772) | organization | Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins. | biomaterial, analysis, service, production, supplier, molecular, biology, diagnostics, enzyme, protein | grid.436825.e, Wikidata: Q30291029 | https://ror.org/00rtryt44 | SCR_016772 | Lda. � Genes and Enzymes, NZYTech | 2026-08-21 12:41:00 | 13 | |||||||||
|
smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | data analysis software, data processing software, software application, software resource | Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. | nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence | requires: SAMTOOLS | Free, Available for download, Freely available | SCR_016892 | single molecule Molecular Inversion Probesfil, smMIPfil | 2026-08-21 12:41:02 | 2 | |||||||||
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Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging. | automated, processing, analysis, visualization, data, acquired, single, molecule, localization, microscopy, SMLM, imaging, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: ImageJ |
Charles University ; Czech Science Foundation ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-08-21 12:41:02 | 48 | |||||
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CCTop Resource Report Resource Website 100+ mentions |
CCTop (RRID:SCR_016890) | data analysis software, data processing software, service resource, software application, software resource, web application | Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. | CRISPR, Cas9, target, prediction, sgRNA, site, data | is related to: Python Programming Language | European Research Council ; German Research Foundation |
PMID:25909470 | SCR_016890 | 2026-08-21 12:40:58 | 130 | |||||||||
|
Culture Collection of Algae at the University of Texas Resource Report Resource Website 10+ mentions |
Culture Collection of Algae at the University of Texas (RRID:SCR_016782) | UTEX | biospecimen repository, data or information resource, database, material storage repository, organization portal, portal, service resource, storage service resource | The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world. | culture, collection, algae | has parent organization: University of Texas at Austin; Texas; USA | College of Natural Sciences of The University of Texas at Austin ; U.S. National Science Foundation |
Commercially available | SCR_016782 | The UTEX Culture Collection of Algae, Culture Collection of Algae at the University of Texas, UTEX | 2026-08-21 12:41:10 | 33 | |||||||
|
CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Fundamental Research Funds for the Central Universities ; National Basic Research Program of China ; Program for New Century Excellent Talents in University |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-08-21 12:41:03 | 42 | |||||
|
MacroModel Resource Report Resource Website 100+ mentions |
MacroModel (RRID:SCR_016747) | simulation software, software application, software resource | Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex. | molecular, modeling, free, energy, changes, perturbation, method, conformation, motion, interaction, ligand, receptor, complex | has parent organization: Schrodinger | Commercially available, Free version available | https://en.freedownloadmanager.org/Windows-PC/MacroModel.html | SCR_016747 | 2026-08-21 12:40:56 | 138 | |||||||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, data processing software, software application, software resource | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-08-21 12:41:11 | 42 | |||||
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EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-08-21 12:40:58 | 107 | |||
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Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data analysis software, data processing software, software application, software resource | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-08-21 12:41:11 | 46 | ||||||||
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Shape screening Resource Report Resource Website 1+ mentions |
Shape screening (RRID:SCR_016750) | simulation software, software application, software resource | Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder. | shape, based, superposition, search, new, compound | has parent organization: Schrodinger | Commercially available | SCR_016750 | 2026-08-21 12:41:00 | 3 | ||||||||||
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Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a metabolomic data processing pipeline in R codes. | metabolomic, data, processing, pipeline, analysis, datasets | Health Research Council of New Zealand | DOI:10.1093/bioinformatics | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/Metab.html | SCR_016877 | Metabolome, Metab 1.0 | 2026-08-21 12:40:58 | 1 | ||||||
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OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | 2026-08-21 12:41:01 | 5 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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