Fabricio Alves Barbosa da Silva
Fabricio Alves Barbosa da Silva is a FIOCRUZ’s (Oswaldo Cruz Foundation) senior public health researcher, head of the Computational Modeling of Multidrug-Resistant Bacteria research group. He has a Ph.D. from Université Pierre et Marie Curie (Paris VI) and was a visiting professor at the University of California - Irvine and the University of Lisbon; He published over 100 scientific works and has edited two books on Systems Biology in Springer’s Computational Biology series. PI of an INOVA-FIOCRUZ project on Systems Biology of COVID-19.
CellHeap: a Workflow for Processing COVID-19 Single-Cell RNA-seq Datasets in Supercomputers
Our group had identified several hundreds of Terabytes of COVID-19 single-cell RNA-seq (scRNA-seq) data available in public repositories up to this date. This data relates to multiple tissues, comorbidities, and conditions. We can expect this trend to continue, and it is not unrealistic to project amounts of COVID-19 scRNA-seq increasing to several Petabytes in the coming years. However, thoughtful analysis of this data requires large-scale computing infrastructures and software systems optimized for such platforms to generate biological knowledge. This talk will present CellHeap, a configurable, portable, and robust workflow for scRNA-seq customizable analyses, with quality control throughout the execution steps, ensuring reliable results and deployable on supercomputers. As an example, I will present the deployment of CellHeap in the Santos Dumont supercomputer (https://sdumont.lncc.br/) for analyzing COVID-19 scRNA-seq datasets and a case study that processed dozens of Terabytes of COVID-19 scRNA-seq raw data.