Department of Biomedical Informatics, Emory University

Biomedical research to advance healthcare

Technologies
python, javascript, java, bash, Colab
Topics
cloud, data integration, workflows, data security, ML/AL
Biomedical research to advance healthcare
Biomedical Informatics is a multidisciplinary field that is motivated by our desire to improve diagnosis, clinical care, and human health, through novel computational approaches to use (and learn from) biomedical and clinical data. We use our expertise in computer science and informatics by developing various enabling tools, technologies, and algorithms to solve specific biomedical and clinical applications. And in doing so help advance our understanding of disease and treatment, and also develop useful software and applications. Members of the department work in a variety of areas that range from machine learning, healthcare middleware that leverages cloud computing, clinical information systems, clinically oriented image analysis, and biomedical knowledge modeling. The driving applications for the various ongoing projects include cancer research, organ transplant, HIV, medical imaging, radiation therapy, and clinical data analytics. All development work that is undertaken is free and open-source. We have had a diverse set of successful GSoC projects in the past. In previous years, GSoC contributors have worked on diverse projects such as: geospatial systems for exploring microscopy environments that leveraged Hadoop; GPU accelerated pipelines for computational analysis of digitized biopsies; interactive visualization platforms for viewing massive images (>1GB); systems for data agnostic sharing of biomedical research datasets; Apache Drill based data integration and de-duplication platform for SQL and NoSQL databases; CNN based high throughput analysis of digitized biopsies; A GUI for Tensorflow; integrated architectures for biomedical data integration and federation; and information visualization of heterogeneous medical data. Many of these projects have been published in reputable journals and presented at major conferences. Some of the projects proved to be so successful that they were adopted in major national/international biomedical research initiatives.
2022 Program

Successful Projects

Contributor
amit_62
Mentor
Pradeeban, Shubham Awasthi, Mark Arnold
Organization
Department of Biomedical Informatics, Emory University
A server environment for the concore framework
This program incorporates server-based deployment workflow files to the server in a secure manner. It allows composing the workflows, aware of the...
Contributor
Nitesh Kumar Kushwaha
Mentor
Pradeeban, PUNEET SHARMA, Nishchal Singi
Organization
Department of Biomedical Informatics, Emory University
Better representations of scanner utilization from DICOM metadata
Niffler enables computing scanner utilization using real-time DICOM metadata extraction. Niffler acquires images from the PACS in real-time...
Contributor
Praroop Chanda
Mentor
PUNEET SHARMA, Marijn
Organization
Department of Biomedical Informatics, Emory University
MRIQC- Automated analysis of weekly MRI Quality Control Images for ACR Accreditation
The aim of this project is to automatically detect the key features of MRI phantom images and use those features to determine the state of the...
Contributor
Aviral Kumar Goel
Mentor
NAN LI, Shubham Awasthi, Mark Arnold
Organization
Department of Biomedical Informatics, Emory University
Adopt DHGWorkflow for concore with a seamless integration
Concore is a framework for closed-Loop peripheral neuromodulation control systems. The CONTROL-CORE protocol, known as concore, allows modular...
Contributor
Nada Ahmed Elmasry
Mentor
Mahmoud, Babak Mahmoudi
Organization
Department of Biomedical Informatics, Emory University
A Python based tool for viewing and basic analysis of files with NumPy format
The project is an open-source Python package for loading, analysis, and visualization of electrophysiological data. The package will enable users to...
Contributor
Yahia Zakaria
Mentor
Ryan Birmingham, NAN LI
Organization
Department of Biomedical Informatics, Emory University
Interactive Multidimensional Visualizations for Eaglescope
Eaglescaope is a framework for creating interactive visualizations and selection dashboards without coding. This project aims to expand upon the...
Contributor
Pavan_Bellam
Mentor
zzaiman, Ananth Reddy
Organization
Department of Biomedical Informatics, Emory University
Workflow module for Niffler framework
Niffler provides various modules to handle different DICOM related tasks. Some of the modules are to be executed sequentially by the user to get the...
Contributor
Mehul Sinha
Mentor
Özgür Kara, Parisa Sarikhani, Babak Mahmoudi
Organization
Department of Biomedical Informatics, Emory University
Extending the Graphical User Interface for OpenAI Gym
This proposal aims to extend VisualRLComposer, a GUI for OpenAI Gym. The project will be extended by adding: multi environment experimentation which...