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Research Projects

The following list is a sample of research projects that the lab is involved in.

The 4DN DCIC data portal page lists available datasets and their associated metadata

4D Nucleome Data Portal

Collect, store, curate, display, and analyze data generated in the 4DN Network.

Components of django_docker_engine

django-docker-engine

django-docker-engine is a Django app that manages the creation of, and proxies requests to, Docker containers.

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Halyos

Halyos is a tool for patients to explore their EHR data. It is designed to present patient data in a way that allows patients to better understand their health data.

HiGlass provides synchronized navigation of multiple views showing matrices from different experimental conditions, types or cell lines.

HiGlass

HiGlass is a tool for exploring genomic contact matrices and tracks. It can be configured to explore and compare contact matrices across multiple scales.

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HiPiler

HiPiler is an interactive visualization interface for the exploration and visualization of regions-of-interest such as loops in large genome interaction matrices.

Longitudinal data visualization of samples taken in different timepoints.

OncoThreads

OncoThreads is a visualization tool for longitudinal cancer genomics data.

Precision Vista

An interactive visualization interface to explore time-varied mobile health and survey data, enabling precise recommendations for lifestyle modifications to improve inflammatory bowel disease (IBD) outcomes.

Refinery incorporates the Satori tool for ontology-guided visual exploration of data sets within the system. The example shown is from the Harvard Stem Cell Institute Stem Cell Commons site, which is an instance of Refinery.

Refinery Platform

A cloud-based data management, analysis, and visualization platform for reproducible biomedical research.

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SATORI

An ontology-guided visual exploration system that combines a powerful metadata search with a tree map and a node-link diagram that visualize the repository structure, provide context to retrieved data sets, and serve as an interface to drive semantic querying and browsing of the repository.

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Caleydo StratomeX

Integrative visualization of stratified heterogeneous data for disease subtype analysis.

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UpSetR

An R package to generate static UpSet plots.

Data-Driven Visual Consent will aid in shared decision making by allowing patients to take an active role in treatment planning.

Data-Driven Visual consent is a tool for patients to understand the risk of pursuing a surgical intervention. The application calculates personalized risk scores using patient data and preferences and renders an intuitive visualization.