José Pereira

José M. S. Pereira is a Biochemistry PhD student at CICECO-University of Aveiro Institute of Materials since 2018. He finished his Master’s on Biotechnology in the University of Aveiro, where the focus of his thesis was on the subject of bioremediation of waste water sources by filtration with activated bio-carbons. As a product of his Master’s thesis, José Pereira developed, a peer-reviewed online tool for the design of atomic carbon models. Starting his PhD, José Pereira shifted his focus for the computational design of peptides, while continuing to pursue scientific software development. He participated in the Board of European Students of Technology 2017 Winter Course, in Paris, France, was awarded a Fulbright scholarship for a 4-month student exchange at Rutgers University, New Jersey, USA, and won the TOP3 award at European Innovation Academy 2021 for his work on ProtoSyn (, the developed software on the scope of his PhD thesis. He authored 2 peer-reviewed papers and participated in over 20 conferences.


13:00 UTC

ProtoSyn.jl: a package for molecular manipulation and simulation

07/27/2022, 1:00 PM — 1:10 PM UTC

ProtoSyn.jl is an open-source alternative to molecular manipulation and simulations software, built with a modular architecture and offering a clean canvas where new protocols and models can be tested and benchmarked. By delivering good documentation, ProtoSyn.jl aims to lower the entry barrier to inexperienced scientists and allow a “plug-and-play” experience when implementing modifications. Learn more on the project’s GitHub page:

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Julia ComputingRelational AIJulius Technology

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Invenia LabsBeacon BiosignalsMetalenzASMLG-ResearchConningPumas AIQuEra Computing Inc.Jeffrey Sarnoff

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