NCI Biomedical Informatics Blog
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- The Promise and the Challenge of Deep Learning in Pathology
- Predictive Modeling for Pre-clinical Drug Screening: Improving Models Derived From Observational Studies Using Machine Learning and Simulation
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The National Cancer Informatics Program (NCIP) will continue to make software assets developed as part of the NCI cancer Biomedical Informatics Grid® (caBIG®) program available to the biomedical-informatics and cancer-research community. The NCIP will also facilitate open community development of those assets to meet evolving research needs.
As part of the CBIIT Open-Development Initiative (ODI), the NCIP is migrating application source code, and in some instances associated data or documentation, into the GitHub open-development environment. NCI's goal in taking this step is to lower the barriers to community participation, stimulate innovation, and accelerate the ongoing development of these assets.
The applications listed on this page are those which, in addition to their development via the ODI mechanism, are supported within the NCIP. Other applications are available on the NCI wiki via this Index Page; the source code for these applications is also being migrated into GitHub.
Using AIM, researchers can annotate images according to the Digital Imaging and Communications in Medicine (DICOM) standard. The AIM Template Builder assists users in creating templates that facilitate annotation and image markup. Annotated image data can be submitted and stored in the AIM data service. Via caIntegrator, investigators can query and analyze stored AIM data.
- AIM wiki home page
- AIM downloads
- AIM documentation (technical and end user)
- AIM forum and support
- AIM GitHub Repository
- AIM docs GitHub Repository
Using caArray, researchers can find and retrieve microarray data as well as manage, annotate, and exchange data sets. The application integrates with caIntegrator, geWorkbench, and GenePattern. caArray also supports uploading large microarray data sets and secure sharing of these data sets with collaborators. An NCI-hosted caArray application is available.
- caArray wiki home page
- caArray downloads
- caArray documentation (technical and end user)
- caArray FAQs
- caArray forum and support
- caArray Github Repository
- caArray docs GitHub Repository
Using caIntegrator, researchers can build custom web-based portals that bring together clinical, imaging, and genomic data to support multidisciplinary investigations. Investigators can query and analyze integrated study data using a range of analytical and visualization tools. Additionally, the program provides strong, role-based security features, allowing investigators to control access to their data collections.
- caIntegrator wiki home page
- caIntegrator downloads
- caIntegrator documentation (technical and end user)
- caIntegrator FAQs
- caIntegrator forum and support
- caIntegrator GitHub Repository
- caIntegrator docs GitHub Repository
- caIntegrator data GitHub Repository
Using caAERS, research organizations can collect and report data on adverse events experienced by participants during clinical trials. A built-in, configurable rules engine supports classifying adverse events as serious or routine. Additionally, data from other clinical trial systems can be integrated with caAERS. The application supports compliance with regulations and protocols for adverse-event reporting.
- caAERS wiki home page
- caAERS downloads
- caAERS documentation (technical and end user)
- caAERS articles
- caAERS forum and support
Using CGWB, researchers can visualize and analyze in an integrated manner, somatic-mutation, gene-expression, copy-number variation, next-generation sequencing, and methylation data generated by multi-platform genome-wide assays. CGWB provides access to data drawn from a number of projects including The Cancer Genome Atlas (TCGA), the Therapeutically Applicable Research to Generate Effective Treatments (TARGET), the Tumor Sequencing Project (TSP), and the Catalogue of Somatic Mutations in Cancer (COSMIC), as well as data relating to the NCI60 cell lines. The application offers investigators three main analytical views: an integrated view using the University of California at Santa Cruz Genome Browser; a heat-map view that associates gene-expression and copy-number data with clinical data; and Bambino, an alignment viewer for next-generation sequencing data.
Researchers and biorepository administrators can use caTissue Suite for biospecimen inventory management, tracking, and annotation. The application permits users to monitor the collection, storage, quality assurance, and distribution of biospecimens as well as data related to the participant and study protocol from which biospecimens are collected. caTissue Suite also allows users to find and request specimens that may be used for translational research studies.
caTissue Suite can be used by biospecimen resource facilities of varying size and function, regardless of the nature of biospecimen transactions that occur or the type of biospecimens involved. The application also supports integration with associated free-text surgical pathology reports and discrete clinical and pathology annotations. caTissue Suite provides search functionality for both biorepository staff and research scientists, who may be interested in searching for and requesting biospecimens for correlative science studies.
- caTissue Suite wiki home page
- caTissue Suite downloads
- caTissue Suite documentation (technical and end user)
- caTissue Suite Knowledge Articles
- caTissue Suite forum and support
Using the geWorkbench desktop platform, researchers can analyze, visualize, and annotate microarray-based gene expression, sequence, and protein-structure data. geWorkbench integrates visualization tools, external databases, and computational services, offering researchers a comprehensive and extensible collection of tools for integrated analysis of genomic data.
- geWorkbench wiki home page
- geWorkbench downloads
- geWorkbench documentation (technical and end user)
- geWorkbench FAQs
- geWorkbench forum and support
Using Integration Hub, researchers can automatically capture clinical data from clinical systems and import the data into compatible databases. The application also integrates services and messaging the clinical trial applications.
- iHub wiki home page
- iHub downloads
- iHub documentation (technical and end user)
- iHub forum and support
Using NBIA, researchers can collect, manage, annotate, and share DICOM medical images with associated clinical and genomic data. In conjunction with the Clinical Trial Processor software from the Radiological Society of North America, the application supports customized de-identification of images. With NBIA, users can develop imaging resources, including databases that clinicians can use to improve clinical-decision support, accelerate decision-making, and provide quantitative imaging assessment of treatment response.
- NBIA wiki home page
- NBIA downloads
- NBIA documentation (technical and end user)
- NBIA forum and support
- NBIA GitHub Repository
- NBIA docs GitHub Repository
Using NCI OCR, investigators can easily meet the investigator-registration regulatory requirements for NCI- and non-NCI-sponsored clinical trials. The application automates the FDA 1572 investigator-registration process currently requiring submission of a series of paper forms including a Curriculum Vitae, the Financial Disclosure Form, and supporting documentation. Through a single web-based interface connecting to a secure central repository, investigators can maintain their profiles containing the accreditation information required for their clinical trials.
Using PSC, clinical-research organizations can create and manage patient calendars as these change during a study, through the screening process, registration, active monitoring, and long-term follow-up. Users can create and edit study calendar templates, generate and view calendars, and track the activities of clinical trial participants in all types of studies including those taking place in multi-site environments. PSC users can share templates between instances of PSC and use an adaptation to manage diverse patient-treatment options outside of clinical trials.
- PSC wiki home page
- PSC downloads
- PSC documentation (technical and end user)
- PSC Articles
- PSC forum and support
- PSC GitHub Repository
- PSC docs GitHub Repository