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http://www.biogrid.org.au

A federated data sharing platform and infrastructure that provides access to real-time clinical, imaging and biospecimen data across jurisdictions, institutions and diseases. The web-based platform provides a secure infrastructure that advances health research by linking privacy-protected and ethically approved data among a wide network of health collaborators. Access to de-identified health records data is granted to authorized researchers after an application process so patient privacy and intellectual property are protected. BioGrid Australia''s approved researchers are provided access to multiple institutional databases, via the BioGrid interface, preventing gaps in patient records and research analysis. This legal and ethical arrangement with participating collaborators allows BioGrid to connect data through a common platform where data governance and access is managed by a highly skilled team. Data governance, security and ethics are at the core of BioGrid''s federated data sharing platform that securely links patient level clinical, biospecimen, genetic and imaging data sets across multiple sites and diseases for the purpose of medical research. BioGrid''s infrastructure and data management strategies address the increasing need by authorized researchers to dynamically extract and analyze data from multiple sources whilst protecting patient privacy. BioGrid has the capability to link data with other datasets, produce tailored reports for auditing and reporting and provide statistical analysis tools to conduct more advanced research analysis. In the health sector, BioGrid is a trusted independent virtual real-time data repository. Government investment in BioGrid has facilitated a combination of technology, collaboration and ethics approval processes for data sharing that exist nowhere else in the world.

Proper citation: BioGrid Australia (RRID:SCR_006334) Copy   

•   Source: SciCrunch Registry

http://www.civm.duhs.duke.edu/

Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies.

Proper citation: Center for In Vivo Microscopy (RRID:SCR_001426) Copy   

•   Source: SciCrunch Registry

http://ranchobiosciences.com/gse4922/

Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.

Proper citation: GSE4922 (RRID:SCR_003557) Copy   

•   Source: SciCrunch Registry

https://omictools.com/l2l-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019.

Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: L2L Microarray Analysis Tool (RRID:SCR_013440) Copy   

•   Source: SciCrunch Registry

http://www.genesigdb.org

Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.

Proper citation: GeneSigDB (RRID:SCR_013275) Copy   

•   Source: SciCrunch Registry

https://humantumoratlas.org

HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.

Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy   

•   Source: SciCrunch Registry

https://www.cancermodels.org/

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   

•   Source: SciCrunch Registry

https://hints.cancer.gov/

Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information.

Proper citation: Health Information National Trends Survey (RRID:SCR_023943) Copy   

•   Source: SciCrunch Registry

https://ganjoho.jp/public/index.html

Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information.

Proper citation: Cancer Information Service (RRID:SCR_024445) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://pub.ist.ac.at/ttp/

Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above.

Proper citation: Tool for Tumor Progression (RRID:SCR_014700) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/cbica/captk/

Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.

Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy   

•   Source: SciCrunch Registry

https://ccsp.hms.harvard.edu/

Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium.

Proper citation: Harvard Medical School Center for Cancer Systems Pharmacology (RRID:SCR_022831) Copy   

•   Source: SciCrunch Registry

https://www.mitochondriasci.com/cancer.html

Creative Biogene provides comprehensive range of services and products to assist researchers in cancer related mitochondria studies. Offers tests and services with advantage of cell based and animal based models.

Proper citation: Creative Biogene Mitochondrial Gene Mutations (RRID:SCR_022082) Copy   

•   Source: SciCrunch Registry

http://cancer.osu.edu/research/cancerresearch/sharedresources/ltb/Pages/index.aspx

The OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource (LTBSR) facilitates the successful translation of basic leukemia research to the clinical setting via an extensive repository of tissue samples and accompanying pathologic, cytogenetic and clinical data for ready correlation of clinical and biological results. The LTBSR, which is an NCI-sponsored biorepository, has more than 40,000 vials of cryopreserved viable cells and 13,000 vials of matched frozen plasma and/or serum samples from more than 4,000 patients treated for leukemia and other malignancies. Committed to furthering translational research efforts for OSUCCC - James members and the cancer research community, the LTBSR provides investigators with training and technical support as well as procurement, processing, storage, retrieval and distribution of clinical research materials. In many cases, the LTBSR serves as the central processing lab for multi-site trials in which the principal investigator is an OSUCCC - James member. The LTBSR's goals are to: * Provide a central collection, processing and a state-of-the-art repository for samples collected from leukemia patients treated on OSUCCC - James protocols, and * Provide materials to investigators involved in collaborative studies with OSU, who examine relevant cellular and molecular properties of leukemia and correlate these properties with clinical or population-based outcomes.

Proper citation: Ohio State Leukemia Tissue Bank (RRID:SCR_000529) Copy   

•   Source: SciCrunch Registry

http://www.bionet.umn.edu/tpf/home.html

Procure and distribute human tissue and other biological samples in support of basic, translational, and clinical cancer research at the University of Minnesota. The TPF is a centralized resource with standardized patient consent, sample collection, processing, storage, quality control, distribution, and electronic record maintenance. Since the 1996 inception of the TPF, over 61,000 tissue samples including well-preserved samples of malignant and benign tumors, organ-matched normal tissue, and other types of diseased tissues, have been collected from surgical specimens obtained at the University of Minnesota Medical Center-Fairview (UMMC-F) University Campus. Surgical pathologists are intellectually engaged in TPF functions, providing researchers with specimen-oriented medical consultation to facilitate research productivity. Prior to surgery, TPF personnel identify and consent patients for procurement of tissue, blood, urine, saliva, and ascites fluid. Within the integrated working environment of the surgical pathology laboratory, freshly obtained tissues not needed for diagnosis are selected and provided by pathologists to TPF personnel. Tissue samples are then assigned an independent code and processed. TPF staff can also work with researchers to individualize the procurement of tissues to fit specific research needs.

Proper citation: University of Minnesota Tissue Procurement Facility (RRID:SCR_004270) Copy   

•   Source: SciCrunch Registry

http://magi.cs.brown.edu/

A tool for annotating, exploring, and analyzing gene sets that may be associated with cancer.

Proper citation: Mutation Annotation and Genomic Interpretation (RRID:SCR_002800) Copy   

•   Source: SciCrunch Registry

http://www.uab.edu/medicine/tcbf/tpsf-sidebar

The Tissue Procurement Shared Facility (TPSF) of the Comprehensive Cancer Center operates as a prospective service to collect, from UAB associated hospitals, normal, malignant, benign, and diseased fresh human tissues and fluids which are then preserved appropriate to protocol. The TPSF can provide normal, malignant, benign, or diseased remnant human tissues and/or fluids from surgical resections, autopsies, or clinical procedures for IRB-approved researchers. The preservation can include fresh storage in media or saline, snap-frozen storage in liquid nitrogen, freezing in OCT for frozen section preparation, or preservation in a fixative of choice. The TPSF can also provide procurement of control tissues including uninvolved tissues or matched tissues from patients with benign disease processes. The histology laboratory can provide paraffin blocks and/or stained or unstained slides. In addition, investigators can obtain access to rare tissues through the national Cooperative Human Tissue Network (CHTN). Although the facility operates as a prospective service specializing in the preparation of samples to protocol, limited banked frozen and paraffin-embedded samples may be available. Investigators are required to complete an application and provide a copy of their IRB approval as well as a brief description of the project for which the requested samples will be utilized. Samples are provided for research purposes only. Processing fees are to offset processing costs and should be included in all grant applications.

Proper citation: UAB Comprehensive Cancer Center Tissue Procurement Shared Facility (RRID:SCR_004222) Copy   

•   Source: SciCrunch Registry

http://www.georgiacancer.org/res-tissue.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013.
The Georgia Cancer Specimen and Tissue Bank is committed to a safe and reliable supply of tissue and cell products for research purposes. Work has begun already to build the state tumor bank initiative with operating sites in several locations through the state. We are confident that our results will yield a strong program that will benefit all Georgians and contribute to significant advances in cancer research and knowledge.

Proper citation: Biorepository Alliance of Georgia for Oncology (RRID:SCR_004184) Copy   

•   Source: SciCrunch Registry

http://acsr.ucsf.edu/

A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.

Proper citation: AIDS and Cancer Specimen Resource (RRID:SCR_004216) Copy   

•   Source: SciCrunch Registry