Penn TMC: Data Analysis Core

点击翻译按钮获取中文摘要

The proper curation of data and processes for a large-scale public resource generation project is critical to the success of projects like the HuBMAP TMCs. The goal of the Data Analysis Core is to support the resource generation operations of the Penn Center for Multiscale Molecular Map of the Female Reproductive System with data coordination. We will provide computational infrastructure to process all data, implement Quality Control (QC) procedures, and enable data provenance. We will develop metadata and provenance models of the clinical procedures, molecular procedures, and informatics procedures. We will also develop QC methods for all processes and implement automatic systems for QC checks. We will process all primary data, such as sequencing and image data, and prepare the data for deposition to HuBMAP HIVE groups and other public repositories. We will also provide analyses for the Center, including multi-modal integration and spatial integration. We will carry out data normalization, batch correction, alignments between datasets and across scales, as well as integration of multi-modal data types. We will develop a 3D digital model of the female reproductive system and use the model to guide spatial indexing of the samples as well as to align the molecular data to their spatial contexts. We will provide additional analytics specific to the project such as reconstructing periodic temporal dynamics. Finally, we will coordinate with HIVE to deposit and disseminate data, programs and analysis outputs, and material reagents. We will work with the HuBMAP HIVE groups to transform and QC the data to the standards of the consortium and deposit the data with the consortium. We will also work with the consortium to develop metadata standards, controlled vocabularies, ontologies, and other community standards. We will also document all protocols, reagents, tissue biobanks, programs, and analysis pipelines with data models and provide a public database for all associated information of the Penn Center.