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on page 1 showing 20 out of 129 results from 1 sources

Cite this (3D Slicer, RRID:SCR_005619)

URL: http://slicer.org/

Resource Type: Resource, data visualization software, software application, data processing software, image analysis software, software resource

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

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Cite this (Add Health (National Longitudinal Study of Adolescent Health), RRID:SCR_007434)

URL: http://www.cpc.unc.edu/projects/addhealth

Resource Type: Resource, data or information resource, database

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

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Cite this (Adenoma Polyp Tissue Bank, RRID:SCR_005366)

URL: http://www.pathology.med.ohio-state.edu/HTRN/apc/default.asp

Resource Type: Resource, biomaterial supply resource, material resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York.

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Cite this (Aged Rodent Tissue Arrays, RRID:SCR_007332)

URL: http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Resource Type: Resource, biomaterial analysis service, analysis service resource, service resource, production service resource, material analysis service

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

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Cite this (AIDS and Cancer Specimen Resource, RRID:SCR_004216)

URL: http://acsr.ucsf.edu/

Resource Type: Resource, biomaterial supply resource, material resource, tissue bank, cell repository

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.

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Cite this (AIDS Malignancy Bank, RRID:SCR_004417)

URL: http://www.uclaaidsinstitute.org/researchareas/clinical_malignancy.php

Resource Type: Resource, database, biomaterial supply resource, tissue bank, cell repository, material resource, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 27, 2012. The National Cancer Institute established centers in the United States and its territories for the collection and distribution of tissues, blood and secretions from patients with clinically-characterized AIDS related malignancies in 1994. The AIDS Malignancy Bank makes these tissues available to qualified investigators in the United States for research on AIDS malignancies. It is hoped that by providing access to these high-quality specimens, research in AIDS-related malignancies will be encouraged and expanded. The AMB contains formalin-fixed paraffin-embedded tissues, fresh-frozen tissues, malignant-cell suspensions, fine-needle aspirates, and cell lines from AIDS-related malignancies. The bank also contains serum, plasma, urine, bone marrow, cervical secretions, anal swabs, saliva semen and multi-site autopsy tissues from patients with AIDS-related malignancies who have participated in clinical trials. The bank has an associated database that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. Researchers pay for preparation and shipping of specimens.

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    Annotare

Cite this (Annotare, RRID:SCR_000319)

URL: http://code.google.com/p/annotare/

Resource Type: Resource, software resource, software application, standalone software

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.

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Cite this (ArrayQuest, RRID:SCR_010935)

URL: http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

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Cite this (Biospecimen Research Database, RRID:SCR_001944)

URL: https://brd.nci.nih.gov/brd/

Resource Type: Resource, data or information resource, database

Free and publicly accessible literature database for peer-reviewed primary and review articles in the field of human Biospecimen Science. Each entry has been created by a Ph.D. level scientist to capture relevant parameters, pre-analytical factors, and original summaries of relevant results.

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    caHUB

Cite this (caHUB, RRID:SCR_009657)

URL: http://cahub.cancer.gov/about/

Resource Type: Resource, narrative resource, standard specification, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures.

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Cite this (Cancer Biomedical Informatics Grid, RRID:SCR_003328)

URL: http://cabig.cancer.gov

Resource Type: Resource, organization portal, portal, knowledge environment, data or information resource

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.

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Cite this (Cancer Genome Anatomy Project, RRID:SCR_003072)

URL: http://cgap.nci.nih.gov/

Resource Type: Resource, topical portal, portal, data or information resource

Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools

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Cite this (Cancer Methylome System, RRID:SCR_012013)

URL: http://cbbiweb.uthscsa.edu/KMethylomes/

Resource Type: Resource, data or information resource, database

Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.

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Cite this (Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility, RRID:SCR_004382)

URL: http://cancer.case.edu/sharedresources/tissue/

Resource Type: Resource, database, biomaterial supply resource, tissue bank, service resource, storage service resource, material storage repository, material resource, data or information resource

The Case Comprehensive Cancer Center''s Biorepository and Tissue Processing Core Facility (BTPC) serves two primary functions: 1. To build an inventory of remnant human tissues, blood and other body fluids (collectively termed biospecimens) targeted towards cancer and other medical research, for later assignment to investigators; and 2. To provide long term, controlled storage of biospecimens for specific researchers. These samples are for research purposes only and may not be used for clinical diagnosis or implantation into humans. Clinical information relating to the samples and donors are collected and maintained in a secure database. Samples and data are de-identified or de-linked before release to the researcher unless he/she has specific IRB approval to gain access to this information. Remnant biospecimens are prospectively collected from surgical procedures, autopsies and clinical laboratories for the BTPC by the Human Tissue Procurement Facility (HTPF), which operates under UH-IRB Protocol 01-02-45. Blood and bone marrow specimens are collected for the BTPC by the Hematopoietic Stem Cell Core Facility (HSCC), which operates under UH-IRB Protocol 09-90-195. The Division of Surgical Pathology at University Hospitals Case Medical Center (UHCMC) has clinical archives of paraffin blocks that can be made available through the BTPC for retrospective research studies under the approval of the Vice Chair for Clinical Affairs at UHCMC. Surgical Pathologists associated with the BTPC are responsible for determining which blocks can be made available and how much material can be removed from the blocks. Types of Tissue Available * Malignant, benign, diseased, normal and normal human tissues * Normal adjacent tissues available paired with tumor specimens in many cases * Tissues are collected from over 50 anatomic sites * Frozen specimens, OCT-embedded and paraffin-embedded tissues * Large array of paraffin-embedded specimens from clinical archives of paraffin blocks and QC research blocks maintained by the HTPF * Peripheral blood and bone marrow samples from initial visits and follow-up procedures are processed to obtain serum and cell fractions for storage * No samples are collected from individuals with known infectious illnesses * Fetal biospecimens are not collected due to state and local statutes

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Cite this (Case Comprehensive Cancer Center, RRID:SCR_004387)

URL: http://cancer.case.edu/

Resource Type: Resource, topical portal, portal, data or information resource

The Case Comprehensive Cancer Center (Case CCC) based at Case Western Reserve University (CWRU) is a partnership organization supporting all cancer-related research efforts at CWRU, University Hospitals Case Medical Center, and the Cleveland Clinic. Located in Cleveland, Ohio, the Case CCC serves the cancer research and clinical needs of an urban manufacturing and rural agricultural region containing 3.8 million people in Northern Ohio. The Mission of the Case CCC is to: * Improve the prevention, diagnosis and therapy of cancer through discovery, evaluation and dissemination. * Stimulate and support innovative, coordinated interdisciplinary clinical research on cancer diagnosis, treatment, prevention and control. * Develop clinical applications of discovery and make these available to Northern Ohio residents as quickly as possible through the integrated efforts of the major health systems in the region. * Develop cancer prevention and control activities that build on the expertise of the Center and result in a reduction of cancer morbidity and mortality in Northern Ohio and the nation. The Case CCC is organized into 9 interdisciplinary scientific programs plus one program initiative. There is a unified clinical research effort consisting of 11 Clinical Trials Disease Teams that develop and prioritize clinical trials between the partner institutions, and a single Protocol Review and Monitoring System, Data Safety and Monitoring Plan, and Institutional Review Board. These components serve to integrate cancer research, cancer therapeutics, and prevention services at the partner institutions and throughout the region. Research programs of the Case CCC are extending into CWRU affiliated hospitals including MetroHealth Medical Center (the region''s county hospital), Louis Stokes Veterans Affairs Hospital, and 13 community medical centers operated by University Hospitals and Cleveland Clinic. The Center operates an NCI-supported Cancer Information Service (CIS) serving the northern half of Ohio as part of the Midwest consortium and has an active outreach program for clinical practice-based prevention and screening initiatives, educational programs, minority recruitment, and facilitation of patient referrals. Case CCC is a member of NCI''s CaBIG initiative and is actively pursuing electronic databases for clinical trials, tissue repositories, and related bioinformatics.

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Cite this (caTIES - Cancer Text Information Extraction System, RRID:SCR_003444)

URL: http://caties.cabig.upmc.edu/

Resource Type: Resource, software resource, software application, data processing software, data access protocol, web service

The Cancer Text Information Extraction System (caTIES) provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations. caTIES focuses on two important challenges of bioinformatics * Information extraction (IE) from free text * Access to tissue. Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed. Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers. caTIES has three goals designed to solve these problems: * Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies to populate caBIG-compliant data structures. * Provide researchers with the ability to query, browse and create orders for annotated tissue data and physical material across a network of federated sources. With caTIES the SPR acts as a locator to tissue resources. * Pioneer research for distributed text information extraction within the context of caBIG. caTIES focuses on IE from SPRs because they represent a high-dividend target for automated analysis. There are millions of SPRs in each major hospital system, and SPRs contain important information for researchers. SPRs act as tissue locators by indicating the presence of tissue blocks, frozen tissue and other resources, and by identifying the relationship of the tissue block to significant landmarks such as tumor margins. At present, nearly all important data within SPRs are embedded within loosely-structured free-text. For these reasons, SPRs were chosen to be coded through caTIES because facilitating access to information contained in SPRs will have a powerful impact on cancer research. Once SPR information has been run through the caTIES Pipeline, the data may be queried and inspected by the researcher. The goal of this search may be to extract and analyze data or to acquire slides of tissue for further study. caTIES provides two query interfaces, a simple query dashboard and an advanced diagram query builder. Both of these interfaces are capable of NCI Metathesaurus, concept-based searching as well as string searching. Additionally, the diagram interface is capable of advanced searching functionalities. An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time. caTIES provides the following web services by default: MMTx Service, TIES Coder Service

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    caTRIP

Cite this (caTRIP, RRID:SCR_003409)

URL: https://cabig.nci.nih.gov/tools/caTRIP

Resource Type: Resource, software resource, software application, data analysis software, data processing software

THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity.

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Cite this (cBioPortal, RRID:SCR_014555)

URL: http://www.cbioportal.org/

Resource Type: Resource, data or information resource, portal, database

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

  • From Current Category

    CDP

Cite this (CDP, RRID:SCR_004236)

URL: http://www.cancerdiagnosis.nci.nih.gov/

Resource Type: Resource, topical portal, portal, funding resource, data or information resource

National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB).

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Cite this ( Center for Inherited Disease Research , RRID:SCR_007339)

URL: http://www.cidr.jhmi.edu/

Resource Type: Resource, resource, production service resource, analysis service resource, training service resource, material analysis service, service resource, biomaterial analysis service, data computation service

Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies.

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