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https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/

Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.

Proper citation: IBEX Knowledge Base (RRID:SCR_025296) Copy   

•   Source: SciCrunch Registry

http://www.phosphosite.org

A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.

Proper citation: PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) Copy   

•   Source: SciCrunch Registry

http://biospecimens.cancer.gov/

The NCI Office of Biorepositories and Biospecimen Research (OBBR) was established in 2005 in recognition of the critical role that biospecimens play in cancer research. The OBBR is responsible for developing a common biorepository infrastructure that promotes resource sharing and team science, in order to facilitate multi-institutional, high throughput genomic and proteomic studies. OBBR is focused on the following objectives: * Establish biobanking as a new area of research, in order to determine the impact of various collection and processing protocols on the usefulness of biospecimens in genomic and proteomic studies * Disseminate first-generation Best Practices in order to harmonize policies and procedures of NCI-supported biorepositories * Develop future generations of biorepository best practices, based on the data generated in the biobanking research programs above * Promote professional oversight of biospecimen standards development by standards organizations * Develop new technologies for biorepository operations * Develop a biorepository accreditation program * Coordinate with the international biobanking community to harmonize policies and procedures to facilitate multi-national research

Proper citation: NCI Office of Biospecimens (RRID:SCR_007076) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry

http://www.mouseatlas.org/

A portal to the Mouse Atlas of Gene Expression Project and Dissecting Gene Expression Networks in Mammalian Organogenesis Project. This Atlas will define the normal state for many tissues by determining, in a comprehensive and quantitative fashion, the number and identity of genes expressed throughout development. The resource will be comprehensive, quantitative, and publicly accessible, containing data on essentially all genes expressed throughout select stages of mouse development. Serial Analysis of Gene Expression (SAGE) is the gene expression methodology of choice for this work. Unlike expressed sequence tags (ESTs) and gene chip data, SAGE data are independent of prior gene discovery and are quantitative. Furthermore, SAGE data are digital, easily exchanged between laboratories for comparison and can be added to by scientists for years to come. Thus, this Atlas will include a data structure and data curation strategy that will facilitate the ongoing collection of gene expression data, even after the completion of this project. The Mouse Atlas project compromises 202 SAGE Libraries from 198 tissues. The list of libraries is available in a number of different groupings, including groups of libraries taken from specific tissue locations and libraries taken from specific developmental stages. Furthermore, this atlas will assemble gene expression profiles for a few focused experiments that will test hypotheses related to the techniques employed, tumor models and models of abnormal development. This will test the resource and provide quality control, validation and demonstrate applicability. Additionally, The Mammalian Organogenesis - Regulation by Gene Expression Networks (MORGEN) project will provide a complete, permanent, and accurate picture of mouse gene expression in the heart (atrioventricular canal and outflow tract), pancreas, and liver; new techniques to understand the interplay of proteins governing the expression of genes key to the development of these organ systems; and the identification of the master regulatory switches that control development of the tissues.

Proper citation: Mouse Gene Expression at the BC Cancer Agency (RRID:SCR_008091) Copy   

•   Source: SciCrunch Registry

http://pslid.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017.

Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. The annotations in PSLID provide a description of sample preparation and fluorescence microscope imaging.

Proper citation: Protein Subcellular Location Image Database (RRID:SCR_008663) Copy   

•   Source: SciCrunch Registry

http://www.pathwaycommons.org/

Data management software that runs the Pathway Commons web service. It makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Main features: * Import pipeline capable of aggregating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome. * Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats. * Data visualization and analysis via Cytoscape. * Simple HTTP URL based XML web service. * Complete software is freely available for local install. Easy to install and administer. * Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG) and aims to meet silver-level requirements for software interoperability and data exchange.

Proper citation: cPath (RRID:SCR_001749) Copy   

•   Source: SciCrunch Registry

https://david.ncifcrf.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

Proper citation: DAVID (RRID:SCR_001881) Copy   

•   Source: SciCrunch Registry

http://oligogenome.stanford.edu/

The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.

Proper citation: OligoGenome (RRID:SCR_006025) Copy   

•   Source: SciCrunch Registry

https://www.phenxtoolkit.org/

Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.

Proper citation: Phenotypes and eXposures Toolkit (RRID:SCR_006532) Copy   

•   Source: SciCrunch Registry

http://wiki.chasmsoftware.org/index.php/Main_Page

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.

Proper citation: CHASM/SNV-Box (RRID:SCR_006445) Copy   

•   Source: SciCrunch Registry

http://cancercontrol.cancer.gov/tcrb/tturc/

A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment.

Proper citation: Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) Copy   

•   Source: SciCrunch Registry

http://www.webgestalt.org/

Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.

Proper citation: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) Copy   

•   Source: SciCrunch Registry

http://drugtargetontology.org/

Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families.

Proper citation: Drug Target Ontology (RRID:SCR_015581) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/gen3va/

Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.

Proper citation: GEN3VA (RRID:SCR_015682) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/CREEDS/

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.

Proper citation: CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) Copy   

•   Source: SciCrunch Registry

https://www.rosettacommons.org/home

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.

Proper citation: Rosetta (RRID:SCR_015701) Copy   

•   Source: SciCrunch Registry

http://gigadb.org/dataset/100360

Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets.

Proper citation: VaDiR (RRID:SCR_015797) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/

Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy   

•   Source: SciCrunch Registry