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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | software application, data visualization software, database, software resource, data processing software, web application, data or information resource | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-02-15 09:21:22 | 3 | |||||||
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NeuroExpresso Resource Report Resource Website 10+ mentions |
NeuroExpresso (RRID:SCR_015724) | web application, data or information resource, database, software resource | Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. | mouse brain, marker gene, tissue expression, microarray, gene expression, rna sequencing | NeuroDevNet ; CAMH ; NIMH MH077159; NIMH MH111099; NIGMS 719GM076990; NSERC Discovery Grant |
Freely available | https://github.com/oganm/neuroexpresso | SCR_015724 | 2026-02-15 09:21:37 | 24 | |||||||||
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Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | software application, simulation software, software toolkit, software resource | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NSF Graduate Research Fellowship ; Simons Foundation ; NIGMS GM078221; NIGMS GM73141; NIGMS GM114961; NIGMS GM084453; NIGMS GM111819; NSF BMAT 1507736; NCI F32 CA189246; NIGMS GM092802; NIGMS GM110089; NIGMS GM117189 |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | Rosetta modeling software | 2026-02-15 09:21:24 | 212 | |||||||
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ASHLAR Resource Report Resource Website 1+ mentions |
ASHLAR (RRID:SCR_016266) | Ashlar | software application, image processing software, data processing software, software resource | Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration. | cycif, registration, software, python, cyclic, immunofluorescence, fluorescence, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM107618 | Free, Available for download | biotools:ASHLAR | https://bio.tools/ASHLAR | SCR_016266 | ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration | 2026-02-15 09:21:50 | 5 | |||||
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fermi-lite Resource Report Resource Website 1+ mentions |
fermi-lite (RRID:SCR_016112) | software application, data processing software, algorithm resource, software resource, alignment software, standalone software, image analysis software | Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling. | assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, calling | is related to: Illumina | NHGRI U54 HG003037; NIGMS GM100233 |
PMID:26220959 | Free, Available for download | SCR_016112 | FermiKit, Fml-asm | 2026-02-15 09:21:47 | 4 | |||||||
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Glam2 Resource Report Resource Website 50+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-02-15 09:21:02 | 72 | |||||
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Edtsurf Resource Report Resource Website 1+ mentions |
Edtsurf (RRID:SCR_016083) | software application, data visualization software, source code, data processing software, software resource | Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening. | construct, triangulate, surface, macromolecule, van der Waals, solvent, accessible, molecular, cavities, program |
is listed by: Debian is listed by: OMICtools |
the Alfred P. Sloan Foundation ; NIGMS GM083107; NIGMS GM084222; NSF 0746198 |
PMID:19956577 | Free, Available for download, Freely available | OMICS_16795 | https://sources.debian.org/src/edtsurf/ | SCR_016083 | EDTSurf: Quick and accurate construction of macromolecular surfaces | 2026-02-15 09:21:46 | 4 | |||||
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Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | software application, data visualization software, database, software resource, data processing software, web application, data or information resource | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NIGMS R01 GM098316; NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-02-15 09:21:33 | 127 | |||||||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | data or information resource, database, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-02-15 09:18:31 | 0 | ||||||
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Allopathfinder Resource Report Resource Website |
Allopathfinder (RRID:SCR_002702) | AlloPathFinder | software application, source code, software resource | Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure. | allosteric communication, allostery, allosteric, pathway, protein, residue, prediction, myosin, computational model, protein model, structure-based protein classification, protein classification, myosin allosteric communication |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; Jane Coffin Childs Memorial Fund ; NIGMS U54 GM072970; NIGMS GM33289 |
PMID:17900617 | Free, Available for download, Freely available | nif-0000-23327 | SCR_002702 | Predicting allosteric communication in myosin via a conserved residue pathway | 2026-02-15 09:18:22 | 0 | |||||
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PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | service resource, analysis service resource, data analysis service, production service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-02-15 09:18:54 | 1 | |||||
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lapdftext Resource Report Resource Website |
lapdftext (RRID:SCR_006167) | lapdftext, LA-PDFText, | text extraction software, software application, software resource | Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. | text mining, pdf, text extraction, natural language processing |
is listed by: FORCE11 has parent organization: University of Southern California; Los Angeles; USA |
NSF 0849977; NIGMS RO1-GM083871; NIMH 1R01MH079068-01A2; NCRR U24 RR025736-01 |
PMID:22640904 | Acknowledgement requested, GNU General Public License, v3 | nlx_151668 | SCR_006167 | Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles | 2026-02-15 09:19:11 | 0 | |||||
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ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | service resource, analysis service resource, data analysis service, production service resource | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/ https://bio.tools/esefinder |
http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-02-15 09:19:27 | 211 | ||||
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Brown University Transgenic and Gene Targeting Core Facility Resource Report Resource Website |
Brown University Transgenic and Gene Targeting Core Facility (RRID:SCR_017690) | MTGTF | access service resource, core facility, service resource | MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request. | Genetically, modified, mouse, model, support, molecular, design, transgenic, knock-out, ES, cell, targeting, system, CRISPR/Cas9, genotype, analysis, sperm, embryo, cryopreservation, storage, fertilization, vasectomy, service, core | NIGMS P30 GM103410 | Open | ABRF_79, SCR_017708 | SCR_017690 | Mouse Transgenic and Gene Targeting Facility | 2026-02-15 09:22:12 | 0 | |||||||
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West Virginia University Flow Cytometry and Single Cell Core Facility Resource Report Resource Website 10+ mentions |
West Virginia University Flow Cytometry and Single Cell Core Facility (RRID:SCR_017738) | access service resource, core facility, service resource | Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins. | Single, cell, analysis, sorting, flow, cytometry, West Virginia, service, core | NCRR RR020866; NIGMS P30 GM103488; NIGMS P20 GM103434; NIGMS U54 GM104942; NIGMS U51 GM104942; NIH Office of the Director S10 OD016165; NIGMS P20 GM109098 |
Open | ABRF_221 | SCR_017738 | FCSCCF, WVU Flow Cytometry and Single Cell Core Facility | 2026-02-15 09:22:13 | 14 | ||||||||
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Arkansas University College of Medicine Flow Cytometry Core Facility Resource Report Resource Website |
Arkansas University College of Medicine Flow Cytometry Core Facility (RRID:SCR_017741) | access service resource, core facility, service resource | Core provides flow cytometry instrumentation and analysis. Instruments include Fortessa, FacsAria and Image Stream. | Flow, cytometry, biopolymer, proteomics, data, analysis, service, core | NIGMS P20 GM103625 | ABRF_215 | SCR_017741 | Biopolymers and Proteomics Core Facility | 2026-02-15 09:21:25 | 0 | |||||||||
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South Dakota University SD BRIN Proteomics Core Facility Resource Report Resource Website |
South Dakota University SD BRIN Proteomics Core Facility (RRID:SCR_017743) | access service resource, core facility, service resource | Core provides proteomics services to researchers from South Dakota and the surrounding region to rapidly analyze and identify protein expression patterns in their experimental systems.Develops experimental design, protocols, data analysis and interpretation.Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to requirements.Offers training in use of common equipment such as scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation. | Proteomics, protein, expression, analysis, data, experimental, design, training, service, core | NIGMS ; Sanford School of Medicine and South Dakota Biomedical Research Infrastructure Network |
Open | ABRF_224 | SCR_017743 | Proteomics Core | 2026-02-15 09:22:06 | 0 | ||||||||
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Kansas University at Lawrence High Throughput Screening Laboratory Core Facility Resource Report Resource Website 1+ mentions |
Kansas University at Lawrence High Throughput Screening Laboratory Core Facility (RRID:SCR_017752) | KU-HTSL | access service resource, core facility, service resource | Core offers high throughput screening of large chemical libraries of compounds to identify novel chemical entities that target biological system of interest.Provides target identification and validation, assay development, high throughput screening, hit confirmation, data mining and medicinal chemistry to facilitate hit to lead development. | Screening, large, chemical, library, compound, novel, entity, target, identification, validation, assay, development, data, mining, medicinal, chemistry, service, core | NIGMS P30 GM103495; State of Kansas ; University of Kansas |
Open | ABRF_254 | SCR_017752 | High Throughput Screening Laboratory at KU | 2026-02-15 09:22:06 | 1 | |||||||
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Nemours/A.I.duPont Hospital for Children Cell Science Core Facility Resource Report Resource Website |
Nemours/A.I.duPont Hospital for Children Cell Science Core Facility (RRID:SCR_017854) | CSC | access service resource, core facility, service resource | Core specializes in cell, protein, and small molecules analysis as well as cell culture techniques. Services include:2-D gel electrophoresis, 2-D DIGE, LC-MS/MS, HPLC, flow cytometry, fluorescence-activated cell sorting (FACS), cell and tissue culture, and immortalization of cell lines. Our staff works closely with investigators to help design, perform, and analyze experiments.Offers training and assistance in flow cytometry, tissue culture, and operation many of our walk-up instruments.Instruments:Cell Sorter: FACS Aria III, BD Biosciences;Flow Cytometers, analyzers:C6, Accuri/BD Biosciences;Novocyte 3000, ACEA Biosciences;software for analysis: FSC Express, DeNovo software;LC-MS/MS: 6460 Triple Quadrupole, Agilent;Typhoon Trio Scanner, GE Lifesciences;Blood Analyzer: Hemavet 950, Drew Scientific.Plate Readers:;Victor Nivo 5F, Perkin Elmer;Luminometer: Centro XS, Berthold.Services:Cell Sorting (FACS);2-D gel electrophoresis/2D-DIGE;LC-MS/MS analysis of compounds; Cell immortilization. | Cell, protein, small, molecules, analysis, culture, electrophoresis, 2D DIGE, LC-MS/MS, HPLC, FACS, immortalization, flow, cytometry, sorting, training, service, core, | NIGMS P30 GM114736 | Open | ABRF_662 | SCR_017854 | Cell Science Core | 2026-02-15 09:22:07 | 0 | |||||||
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University of Nebraska Medical Center Animal Behavior Core Facility Resource Report Resource Website 1+ mentions |
University of Nebraska Medical Center Animal Behavior Core Facility (RRID:SCR_018830) | access service resource, core facility, service resource | Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare. | USEDit, acoustic, behavioral, cognitive, expertise, equipment, space service, ABRF, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NIGMS 1P20GM130447 | Restricted | ABRF_1021 | https://coremarketplace.org/?FacilityID=1021 | SCR_018830 | UNMC Animal Behavior Core, University of Nebraska Medical Center UNMC Animal Behavior Core, Animal Behavior Core | 2026-02-15 09:22:17 | 4 |
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