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http://www.mc.vanderbilt.edu/root/vumc.php?site=chtn%20western%20division
The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator.
Proper citation: Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center (RRID:SCR_006661) Copy
Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.
Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy
https://github.com/walaj/svaba
Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.
Proper citation: SvABA (RRID:SCR_022998) Copy
https://github.com/hetio/hetmatpy
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Proper citation: HetMatPy (RRID:SCR_023409) Copy
Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.
Proper citation: X2K Web (RRID:SCR_023624) Copy
Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models.
Proper citation: CancerModels.Org (RRID:SCR_023931) Copy
http://rnainformatics.org.cn/RiboToolkit/
Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs.
Proper citation: RiboToolkit (RRID:SCR_024406) Copy
Center for patient care, education and research on cancer. The institute focuses its research on prevention methods, early detection, treatment and finding cures.
Proper citation: Karmanos Cancer Institute (RRID:SCR_000508) Copy
https://seer.cancer.gov/csr/1975_2016/
Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States.
Proper citation: NCI SEER Cancer Statistics Review (RRID:SCR_024685) Copy
https://seer.cancer.gov/lymphomarecode/lymphoma-2020.html
Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry.
Proper citation: NCI Lymphoid Neoplasm Recode 2020 Revision Definition (RRID:SCR_024686) Copy
Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.
Proper citation: OpenMM (RRID:SCR_000436) Copy
Division of NCI that takes prospective cancer detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging tests, and other therapeutic interventions (radiation, surgery, immunotherapy) in patients. DCTD, like all of NCI, supports many programs that could not be done without government funding - investigators supported by the division engage in scientifically sound, high-risk research that may yield great benefits for patients with cancer, but are too difficult or risky for industry or academia to pursue. This includes a particular emphasis on the development of distinct molecular signatures for cancer, refined molecular assays, and state-of-the-art imaging techniques that will guide oncologic therapy in the future. The division has eight major programs that work together to bring unique molecules, diagnostic tests, and therapeutic interventions from the laboratory bench to the patient bedside: * Cancer Diagnosis Program * Cancer Imaging Program * Cancer Therapy Evaluation Program * Developmental Therapeutics Program * Radiation Research Program * Translational Research Program * Biometrics Research Branch * Office of Cancer Complementary and Alternative Medicine
Proper citation: DCTD (RRID:SCR_004196) Copy
http://code.google.com/p/annotare/
A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.
Proper citation: Annotare (RRID:SCR_000319) Copy
http://bioconductor.org/packages/release/bioc/html/nondetects.html
Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.
Proper citation: nondetects (RRID:SCR_001702) Copy
https://github.com/QTIM-Lab/DeepNeuro
Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.
Proper citation: DeepNeuro (RRID:SCR_016911) Copy
https://github.com/plaisier-lab/sygnal
Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.
Proper citation: SYGNAL (RRID:SCR_023080) Copy
https://github.com/Shenhav-and-Korem-labs/SCRuB
Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program.
Proper citation: SCRuB (RRID:SCR_023518) Copy
https://github.com/qianli10000/mtradeR
Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.
Proper citation: mtradeR (RRID:SCR_022977) Copy
https://www.sbpdiscovery.org/biomedical-research/shared-resources/cancer-metabolism
Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility (RRID:SCR_014873) Copy
http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/
Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.
Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy
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