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Research Projects

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

Active

The 4DN DCIC data portal page lists available datasets and their associated metadata. Screenshot of the 4DN data browser showing a bar chart of the available data. The x axis is experiment type, the y axis is experiment sets, and the bars are colored by groups of mouse or human data.

4D Nucleome Data Portal

Collect, store, curate, display, and analyze data generated in the 4DN Network.
Cistrome Explorer provides scalable, interactive, and modular visualizations for epigenomics data with associated metadata. Screenshot of the Cistrome Explorer tool showing a central genome browser heatmap flanked by aligned metadata bar plots.

Cistrome Explorer

Web-based Interactive Visual Analytics Tool for Exploring Epigenomics Data with Associated Metadata
An image of the Discovery dashboard showing a high level summary of the patient’s profile and their medical data, including personal demographics, health records and healthcare providers.

Discovery

A tool for accessing and visualizing patient information from multiple providers.
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.
Our review paper established an ontology of genomic visualization tools. Figure titled ‘Visualization Taxonomy’ with seven categories next to each other, each with a number of small images below. The categories are layout, partition, abstraction, arrangement, views, scales, and foci.

GenoCAT

GenoCAT provides a database of genomic visualization tools. Each tool has been sorted and grouped based on various attributes, and the website has been designed to help you find what you’re looking for.
Diverse Genomics Visualizations Using Gosling.js. Screenshot of a large number of genomics visualizations displayed using the Gosling genomics visualization grammar.

Gosling

A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization
A screenshot of the Halyos dashboard showing personal health risks, measurements, and suggested preventative treatments.

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. Screenshot of the interactive visualization tool HiGlass showing a grid of four heatmaps that display genome contact matrices.

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.
Screenshot of aligned matrices on the left and snippets of matrices scattered on the right.

HiPiler

HiPiler is an interactive visualization interface for the exploration and visualization of regions-of-interest such as loops in large genome interaction matrices.
HuBMAP data portal. Screenshot of the interactive visualization tool, Vitessce, embedded on the HuBMAP Data Portal website. The image of Vitessce features 2D tissue data and interactive controls.

HuBMAP Data Portal

Curate, display, and analyze data generated by the HuBMAP Consortium.
Longitudinal data visualization of samples taken in different timepoints.

OncoThreads

OncoThreads is a visualization tool for longitudinal cancer genomics data.

Precision VISSTA

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.
Screenshot

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.
Screenshot

Caleydo StratomeX

Integrative visualization of stratified heterogeneous data for disease subtype analysis.

tableschema-to-template

Given a YAML description of the data, generate an Excel template with input validation

Universal Discovery Interface (UDI)

Connect biomedical research data from thousands of sources and overcome barriers caused by incompatible data dialects.
Screenshot of an image showing intersection of gene mutations in a cohort. The image consists of a black and white bar graph with numbers listed above each bar. Below the bar graph, right-justified to be aligned with the y-axis, are five gene names. Running along the bottom of the x-axis is a grid of light gray dots, with one dot corresponding to the intersection of each gene name row and bar column. Some of the dots are filled in black with vertical lines connecting them. To the left of the gene names is a horizontal bar plot. The bars are light blue and right justified.

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. An image of a healthcare provider showing a patient a phone which is annotated with ‘AI’ and ‘Visualization.

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.
Visual Integration Tool for Exploration of Spatial Single-Cell Experiments. Screenshot of the interactive visualization tool, Vitessce, featuring multiple color-coordinated 2D views of cellular data and interactive controls.

Vitessce

Visual Integration Tool for Exploration of Spatial Single-Cell Experiments
High-Resolution Multiplexed Tissue Data on the Web. Schematic of current approach of server and client side rendering and viv approach.

Viv

Library for Multiscale Visualization of High-Resolution Multiplexed Tissue Data on the Web

Inactive

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.

Refinery Platform website
Refinery Platform repository