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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Molecular Signatures Database Resource Report Resource Website 1000+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NCI CA295532; NIGMS ; NIH |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-09-12 01:02:17 | 1702 | ||||||
|
Open Babel Resource Report Resource Website 100+ mentions |
Open Babel (RRID:SCR_014920) | data analytics software, data processing software, software application, software resource | Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats. | toolbox, conversion, analysis, molecular model, chemistry, biochemistry, chemical file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:open_babel | https://bio.tools/open_babel | SCR_014920 | 2026-09-12 01:01:03 | 100 | ||||||||
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BZ-H3A analyzer software Resource Report Resource Website 10+ mentions |
BZ-H3A analyzer software (RRID:SCR_017375) | data processing software, image analysis software, software application, software resource | Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series. | Analysis, Keyence, Japan, fluorescence, microscope, BZ-X | SCR_017375 | 2026-09-12 01:01:05 | 13 | ||||||||||||
|
Center for Computational Biology at JHU Resource Report Resource Website 1+ mentions |
Center for Computational Biology at JHU (RRID:SCR_016680) | CCB at JHU | data or information resource, organization portal, portal | Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis. | center, computational, biology, genomics, genetics, DNA, RNA, sequence, technology, analysis |
has parent organization: Johns Hopkins University; Maryland; USA is parent organization of: Centrifuge Classifier |
SCR_016680 | CCB at Johns Hopkins University, CCB at JHU, Center for Computational Biology at JHU, Center for Computational Biology at Johns Hopkins University | 2026-09-12 01:01:04 | 1 | |||||||||
|
ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | data or information resource, organization portal, portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-09-12 01:01:04 | 16 | ||||||
|
Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, image analysis software, software application, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-09-12 01:01:04 | 15 | ||||||
|
UN-SCAN-IT Gel Analysis Software Resource Report Resource Website 10+ mentions |
UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) | data processing software, image analysis software, software application, software resource | Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC. | electrophoresis, gel, image, analysis, density, quantification, Silk Scientific Inc | Restricted | SCR_017291 | 2026-09-12 01:01:05 | 10 | |||||||||||
|
SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | data processing software, image analysis software, software application, software resource | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | LHNCBC HHSN276201500692P; NIH ; NLM |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-09-12 01:01:04 | 4 | |||||||||
|
IncuCyte® Chemotaxis Software Resource Report Resource Website 10+ mentions |
IncuCyte® Chemotaxis Software (RRID:SCR_017316) | data processing software, image analysis software, software application, software resource | IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate. | Add-on, module, IncuCyte ZOOM, live-cell, analysis, system, ClearView, Chemotaxis, Plate, Essen Bioscience, Sartorius | is provided by: Sartorius | Restricted | SCR_017316 | IncuCyte Chemotaxis Software | 2026-09-12 01:01:05 | 12 | |||||||||
|
cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | data processing software, image analysis software, software application, software resource | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-09-12 01:01:04 | 2939 | |||||||||
|
Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | data or information resource, portal, project portal | Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility. | Reproducible, data, merging, science, cyberinfrastructure, pathway, tale, capture, code, finding, analysis | NSF 1541450 | DOI:10.1016/j.future.2017.12.029 | Free, Freely available | https://github.com/whole-tale/wt-design-docs//blob/stable/README.rst | SCR_017537 | 2026-09-12 01:01:06 | 1 | ||||||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | data processing software, software application, software resource | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-09-12 01:01:06 | 76 | ||||||
|
Broad Terra cloud commons for pathogen surveillance Resource Report Resource Website 10+ mentions |
Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) | data or information resource, portal | Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics. | COVID-19, COVID-19 data, analysis, collaborate, genomic data, sequencing data, NCBI SRA, genome assembly workflow, quality control, metagenomic classification |
is listed by: Data and Computational Resources to Address COVID-19 is listed by: Terra has parent organization: Broad Institute |
COVID-19 | Free, Freely available | SCR_018278 | Terra | 2026-09-12 01:01:07 | 39 | ||||||||
|
Image Quant TL Resource Report Resource Website 100+ mentions |
Image Quant TL (RRID:SCR_018374) | data processing software, image analysis software, software application, software resource | Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting. | Image analysis, Cytiva, image, electrophoresis gel image, blot image, array, colony count image, analysis | SCR_018374 | , Image Quant TL array analysis, ImageQuant TL 8.2 | 2026-09-12 01:01:07 | 381 | |||||||||||
|
Stereo Investigator - Whole Slide Edition Resource Report Resource Website 1+ mentions |
Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) | data processing software, image analysis software, software application, software resource | Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses. | Quantitative, analysis, stereology, whole, slide, image, MBF Bioscience | Restricted | SCR_017667 | 2026-09-12 01:01:06 | 3 | |||||||||||
|
HALO Resource Report Resource Website 100+ mentions |
HALO (RRID:SCR_018350) | HALO | data processing software, image analysis software, software application, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-09-12 01:01:07 | 108 | ||||||||
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Conrad Prebys Center for Chemical Genomics Resource Report Resource Website |
Conrad Prebys Center for Chemical Genomics (RRID:SCR_001687) | data or information resource, organization portal, portal | The Conrad Prebys Center for Chemical Genomics (CPCCG) uses advanced screening technologies to identify high level chemical probes that interact with proteins involved in cellular processes. Optimization of these probes using medicinal chemistry and informatics will form the basis of a new generation of medicines. CPCCG is 1 of 4 Comprehensive Centers chosen nationally to be a part of the Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that allow research into health and disease on the cellular level. CPCCG core services span a range of biochemical and cell-based screens for obtaining hits and provide chemistry resources for optimizing hits into probes or drug development. - Full scale screening capabilities and technology which can provide rapid screening on a broad diversity of assays and detection platforms - Several fully-integrated industrial-scale high-throughput screening (HTS) workstations - HTS microscopy/HCS and novel algorithm development for image analysis - Full hit-to-probe chemistry and exploratory pharmacology - Powerful NMR based Chemical Fragment Screening - Highly integrated informatics infrastructure and efficient data mining capabilities - Protein production facility - Cell production facility for scale-up tissue culture The CPCCG Screening Core can screen 96, 384 or 1536 well formats using either biochemical or cell-based assays, and can process over 300,000 wells per day. Total throughput capacity will climb to over 2 million compounds per day following the opening of Burnhams east coast campus in Lake Nona, Florida. | drug, algorithm, analysis, assay, biochemical, cell, cellular, chemical, culture, development, disease, genomic, hcs, health, hts microscopy, keywords: chemical, medicinal, microscopy, molecular, molecule, probe, process, production, protein, technology, tissue, image | Free, Freely Available | nif-0000-10180 | http://sdccg.burnham.org | SCR_001687 | CPCCG | 2026-09-12 01:00:52 | 0 | ||||||||
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Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology Resource Report Resource Website 1+ mentions |
Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology (RRID:SCR_001724) | data or information resource, organization portal, portal | ENFIN is a virtual institute to enable systems-level integration of experimental results. It is committed to provide a Europe-wide integration of computational approaches in systems biology. Its objectives are: - To develop a shared approach between traditionally dry and traditionally wet researchers in the area of systems-level interpretation of experimental results - To develop a distributed computational platform this integration and analysis of experimental data - To directly prove that such an approach has scientific value - To encourage and participate in the critical assessment of systems-level approaches - To disseminate knowledge and techniques to other academic researchers worldwide - To disseminate knowledge and techniques to commercial researchers, in particular European SMEs - To train young European researchers from a variety of backgrounds in system-level informatics techniques. The ENFIN Network runs four major platforms: A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling, a Provision of Analysis Tools - EnSUITE, a Platform for Data Integration - EnCORE, and training Courses and Workshops on Systems Biology. Sponsors: The ENFIN project is funded by the European Commission within its FP6 Programme, under the thematic area Life sciences, genomics and biotechnology for health,contract number LSHG-CT-2005-518254. | european, experimental, function, academic, analysis, computational, integration, modeling, network, platform, prediction, reconstruction, research, researcher, result, scientific, systems biology | has parent organization: European Bioinformatics Institute | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10224 | http://www.enfin.org/page.php?page=home | SCR_001724 | ENFIN | 2026-09-12 01:00:52 | 7 | |||||||
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SoftBerry Resource Report Resource Website 100+ mentions |
SoftBerry (RRID:SCR_000902) | data or information resource, portal, software resource | Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services. | genomic, analysis, computation, biomedical, data analysis, rnaseq, sna, snp, transcriptome | Restricted | nlx_156881 | http://linux1.softberry.com/ | SCR_000902 | Linux SoftBerry, Soft berry | 2026-09-12 01:00:52 | 356 | ||||||||
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Net Station API Resource Report Resource Website |
Net Station API (RRID:SCR_000867) | Net Station API | application programming interface, commercial organization, data access protocol, software resource | APIs for Net Station data files. APIs are available for C++, C#, and Java. | eeg, meg, electrocorticography, c++, java, visualization, analysis, presentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Net Station EEG Software |
Free, Available for download, Freely available | nlx_155824 | http://www.nitrc.org/projects/netstation_api | SCR_000867 | Net Station Software for EEG Acquisition and Physician and Review | 2026-09-12 01:00:51 | 0 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
