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Project Title Work Group(s) Status Project Overview
OpenGWAS Phenotype Mapping
  • Knowledge Representation
Ongoing

Mapping of phenotype descriptions in the OpenGWAS database to ontologies

See project details
23andMe Phenotype Mapping
  • Knowledge Representation
Ongoing

Mapping of phenotype descriptions in 23andMe’s GWAS metadata to ontologies

See project details
Multiplexed Error Robust Fluorescence in Situ Hybridization(MERFISH)
  • Genetics / Genomics,
  • Image Analysis & Processing
Ongoing

Make MERFISH datasets accessible to the wider R/Bioconductor community.

See project details
Benchmark of Ontology Mapping Tools
  • Knowledge Representation
Ongoing

Survey of tools for ontology mapping and benchmark test of mapping accuracy

See project details
Programmatic Interface to HuBMAP Ontology
  • Knowledge Representation
Ongoing

Development of tool to programmatically interact with the HuBMAP ontology and to facilitate HuBMAP-based annotation tasks

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Drugging the undruggable – machine-learning-based cancer immunotherapy design
  • Genetics / Genomics,
  • Data & Analytics Platforms
Ongoing

Integrating candidate cis-regulatory elements from ENCODE, open chromatin regions from ATACdb, and super enhancers from SEdb into a machine learning framework for cancer immunotherapy

See project details
Designmatch Container
  • Data & Analytics Platforms
Ongoing

Create a Docker Image

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Leveraging geographic information systems for spatial transcriptomics
  • Data & Analytics Platforms,
  • Genetics / Genomics
Ongoing

Leverage a GIS database-backend to address big data problems in spatial transcriptomics

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Whole-genome sequencing analysis of fluoroquinolone resistance acquisition in Mycobacterium tuberculosis
  • Genetics / Genomics
Ongoing

CCB works with the Farhat lab on a large-scale whole-genome sequencing (WGS) analysis of fluoroquinolone resistance (FQ-R) acquisition in Mycobacterium tuberculosis. This will involve (1) processing of WGS data of 32k genetically diverse M. tuberculosis genomes, (2) reconstructing phylogenetic models that relate diverse strains based on their genome sequences, and (3) identifying key mutations that have contributed to FQ-R emergence and spread.

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Single-cell characterization of acute inflammation in patients with COVID-19
  • Genetics / Genomics
Ongoing

CCB works with the Kagan lab on a single-cell study of COVID as part of a collaboration between HMS and AbbVie. The Kagan lab will also provide information on a panel of cytokines that were quantified on the protein level, sequencing data for T-cell receptors, as well as a variety of phenotypic and clinical characteristics of the participants. CCB will develop additional visualization components for interactive exploration of the analytic components of the project.

See project details
C elegans Database
  • Data & Analytics Platforms
Complete

Build a relational database to catalog and track ~5000 transgenic or mutant C. elegans strains.

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Proteome-scale protein-protein interaction networks from the BioPlex project
  • Genetics / Genomics
Complete

Implement programmatic access to BioPlex from within R/Bioconductor and from within Python, along with a series of downstream applications of BioPlex,

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RNA sequencing atlas of vascular endothelial cells
  • Genetics / Genomics
Complete

Developed an O2-based RNA-seq pipeline that enabled efficient processing of raw sequencing output for 500 samples.

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Harvey Mudd College CS Clinic 21/22
  • Knowledge Representation
Complete

Development of ontology mapping tool components—UIs for interactive mapping; integration of embedding models; and test harness for continuous QA

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AlphaFold & ColabFold
  • Genetics / Genomics
Complete

Developing a pair of modules on the O2 HPC cluster to facilitate protein structure prediction

See project details