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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

https://www.borch.dev/uploads/screpertoire/

Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis.

Proper citation: scRepertoire (RRID:SCR_025691) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) Copy   

•   Source: SciCrunch Registry

https://cellrank.readthedocs.io/en/stable/

Software package for directed single cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease. Automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes.

Proper citation: CellRank (RRID:SCR_022827) Copy   

•   Source: SciCrunch Registry

https://mcmicro.org

Software tool as scalable, modular image processing pipeline for multiplexed tissue imaging. Transforms multi channel whole slide images into single cell data.

Proper citation: MCMICRO (RRID:SCR_022832) Copy   

•   Source: SciCrunch Registry

https://github.com/mhammell-laboratory/TEtranscripts

Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool.

Proper citation: TEtranscripts (RRID:SCR_023208) 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://cabig.cancer.gov

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes.

Proper citation: Cancer Biomedical Informatics Grid (RRID:SCR_003328) Copy   

•   Source: SciCrunch Registry

http://www.cbioportal.org/

A portal that provides visualization, analysis and download of large-scale cancer genomics data sets.

Proper citation: cBioPortal (RRID:SCR_014555) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/cgi-bin/hgLiftOver

Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments.

Proper citation: liftOver (RRID:SCR_018160) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/mosdepth

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

Proper citation: mosdepth (RRID:SCR_018929) Copy   

•   Source: SciCrunch Registry

https://cran.rstudio.com/web/packages/accucor/index.html

Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data.

Proper citation: AccuCor (RRID:SCR_023046) Copy   

•   Source: SciCrunch Registry

http://neurosurgery.ucsf.edu/index.php/research_tissue_bank.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Brain Tumor Research Center Tissue Bank began collecting tissue in 1978 and has established an organized repository of characterized tissues--frozen, paraffin-embedded, blood and cultures--that are maintained in a manner useful for a wide range of studies. Samples are collected only from patients who have agreed to have their tissues banked and used for future research. Consent documents are maintained in a secure area and associated clinical data are held in a double-password protected computer database. Each sample received into the Tissue Bank is non-identifying number. No protected health information (PHI) is released. To obtain samples, investigators submit a request form to the Manager. The request form requires an explanation of the tissue requested (type, number of samples, justification), description of the study, CHR approval (see new policy regarding human vs. non-human research) and Project Leader authorization. The Manager reviews each request for feasibility before presentation to the Scientific Core Committee. The UCSF Neurosurgery Tissue Bank makes its inventory of stock cell lines available to all investigators. Requested cells are grown in T-25 flasks and shipped FedEx Priority Overnight at the receipient's expense. However, if you prefer, we can ship the frozen cells, packed in dry ice. (Note: some countries restrict dry ice shipments.)

Proper citation: UCSF Brain Tumor Tissue Bank (RRID:SCR_000647) Copy   

•   Source: SciCrunch Registry

https://brd.cancer.gov/

Database to find literature, established protocols, and best practices for collecting, storing, and handling biological samples. Its main purpose is to help researchers improve the quality and reproducibility of biospecimen-based medical and genetic research. Provides a library of validated protocols that laboratories use to properly process human biospecimens (like blood or tissue) without degrading their molecular integrity. Offers procedural guidelines (BEBPs) backed by scientific literature to protect samples from pre-analytical variables (e.g., storage temperature, time-to-freezing). Catalogs thousands of peer-reviewed articles focused on biospecimen science.

Proper citation: Biospecimen Research Database (RRID:SCR_001944) Copy   

•   Source: SciCrunch Registry

http://cancer.gov/cancertopics/pdq/cancerdatabase

NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish.

Proper citation: Physician Data Query (RRID:SCR_006833) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry