Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Monday, December 30, 2019

Getting started with TPOT for automated machine learning

A great post from Dr. Trang Le on how to get started with automated machine learning (AutoML) with our Tree-Based Pipeline Optimization Tool (TPOT) in Python.

Thursday, December 26, 2019

The Human Pancreas Analysis Program (HPAP)

We are assisting with the bioinformatics support for The Human Pancreas Analysis Program (HPAP) which consists of two interlocking, collaborative projects at three institutions that seek to provide comprehensive molecular profiling in unprecedented detail of the pancreatic islet at various stages of type 1 diabetes (T1D) pathogenesis- pre-diabetic (positive islet autoantibodies), recent onset, and T1D of durations less than 10 years.
In the past decade, there have been dramatic advances in our ability to phenotype and molecularly profile human cells and tissues. HIRN-HPPAP will develop and apply these new technologies to study cells and tissues relevant to the beta cell loss in T1D with unprecedented resolution, including at the genomic, epigenomic, protein, and functional levels. Here we will employ state-of-the-art technologies to determine all aspects of pancreatic islet cell and immune cell biology as it pertains to the pathogenesis of type 1 diabetes. We will profile both the endocrine and immune systems with multiple modalities, and make the vast data accumulated available through the highly accessible PANC-DB, which will be developed through the project. These extensive and high quality datasets will be made available to the HIRN and the diabetes research community at-large for further discovery.