Projects

Proteinarium Aug. 2021 - May 2022

proteinarium

Overview

Computational Biologists analyze the interaction information between proteins as it can be a model to show the general networking of varius cellular pathways. On top of this, it is inferred that (kind of like how road blocks on major highways ) - to find out which of the paths through the protein-protein interaction (PPI) network are most "critical," a heavy suite of graph analysis algorithms are utilized to measure network similarity, clustering, centrality, knockdown analysis, etc. Already built as a command line tool, Proteinarium now sees active use from numerous scientists in the PPI field.

My largest goal currently, on top of adding more analysis algorithms to the suite, is to build an entire visual webapp for the project, in which users will have a much more intuitive and efficient time handling their analysis requrests, and will be able to utilize the a computing cluster at Brown to run the heavier calculations.
  • A collaboration project with the Dr. Uzun and Dr. Schuster labs - completely overhauling a CLI tool for a wider focus; adding many more analysis programs and designing a web interface around it
  • Generates graph networks from protein-protein interaction data based on Dijkstra or DIAMoND
  • Clusters graphs by network similarity (Options of Jaccard Distance, Simson indices, Laplacian Spatial Distance)
  • Clusters graphs by network similarity (Jaccard Distance, Simson indices, Laplacian Spatial Distance) and arranges into a dendrogram in which control-target-knockdown effects are visible.
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