Newsletter
0.1 myCMIE
0.1.1 My Cancer Molecular Information Exchange
myCMIE, a web application that simplifies Molecular Profiling Reports (MPRs) for cancer treatment decisions. It integrates genomic data, drug options, and clinical trials into a user-friendly platform for efficient treatment insights. myCMIE connects patient data with public datasets, for context-informed treatment and conjecture with therapeutic implication through interactive visualizations and collaborative tools for healthcare stakeholders. The app is deployed on Amazon Web Service (AWS) and is available at: https://kowalski-labapps.dellmed.utexas.edu/CO3inW3/
Introducing myCMIE 2.0 (New!)
0.1.2 Update Overview
This doucment provides a detailed summary of the enhancements applied to the myCMIE 2.0 development version, aimed at expanding the platform’s capabilities for molecular profile inquiry.
0.1.3 Hybrid Clustering Function Enhancement
The hybrid clustering function’s capability has been improved to ensure more accurate data integration and analysis. These improvements are essential for identifying complex data patterns within molecular datasets.
0.1.4 Expansion of Multi-Model Match Support
The Multi-Model Match feature now includes support for the following databases:
- Patient-derived xenograft (PDX)
- Samstein et al. 2018, TMB-MSKCC (MSKCC)
- Molecular Taxonomy of Breast Cancer International Consortium (METABRIC)
These additions complement the previously available The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) databases, extending the breadth of comparative molecular analysis.
0.1.5 Molecular Filter Update
The Molecular Filter has been upgraded to enable sample selection based on specific genetic alterations (e.g., ‘ERBB2: AMP’). The new ‘Filter Mode’ allows users to employ AND/OR logic for more refined filtering options.
0.1.6 Enhancements in Community Exploration Tools
The “Explore Your Community” feature has been updated to include oncoplots for several data types:
- Drug sensitivity oncoplots for CCLE and PDX
- Pathway oncoplots with CCLE driver genes
- Immune abundance oncoplots from TCGA and CCLE
- Expression oncoplots for TCGA and CCLE
- Survival oncoplots using TCGA, CCLE, MSKCC, and METABRIC
These tools are designed to aid researchers in the visualization and interpretation of complex molecular data.
0.1.7 Implementation Notes
myCMIE platform interface has been update to reflect the newly supported databases within the Multi-Model Match feature.
All visual functions have been be re-designed/enhanced for their ability to represent data accurately and comprehensively. Feedback regarding these updates is welcome to assistant us for a continuous platform development.