Alumni

Software testing

Nicholas Vecchietti

From 2012 to 2016, Nicholas worked in Caterina’s group at UMMS as a research trainee. While in the lab, Nicholas was involved in a project aimed at the development of methods to label and track infectious HIV-1 in living human cells. The aim of the project was to identify viral particles that successfully integrate their proviral DNA into the host chromosomes, map their intracellular path, and identify their intracellular interaction partners, in the hope of laying the foundations for the rational design of anti-HIV-1 therapy. As part of this project, Nicholas provided invaluable feedback on the usability of the OMEGA software.

Currently, Nicholas is a Scientist with the Chemical Micro-Biology Team at the Merck Research Labs Exploratory Science Center in Cambridge MA.

Jasmine Michelle Rainey – Clark

Jasmine did her Ph.D. thesis in the laboratory of Eric Hunter at the Emory Vaccine Center. Her work centered on examining the molecular basis for retroviral assembly and trafficking in the infected cells by employing life imaging and biochemical approaches. She was involved in strategic scientific planning for the development of OMEGA, and she provided key feedback on the usability and functionality of the OMEGA software. In addition, the data she and Lara provided was essential for benchmarking purposes throughout the development process.

Currently, Jasmine is an Instructor at the Nell Hodgson Woodruff School of Nursing of Emory University in Atlanta GA. In 2018 she was elected to the Georgia House of Representatives for District 108. Congratulations Jasmine!

Lara Pereira

Lara was a post-doctoral scientist in Eric’s laboratory at the Emory Vaccine Center. Her work at the Emory Vaccine Center focused on examining host cell factors involved in retroviral assembly, trafficking, and release by employing live cell imaging and biochemical approaches. She was involved in strategic scientific planning and in providing key feedback on the usability and functionality of the OMEGA software. In addition, the data she and Jasmine provided was essential for benchmarking purposes throughout the development process.

Currently, Lara is a Senior Service Fellow at the Centers for Disease Control and Prevention in Atlanta GA. Her work centers on the prevention of HIV/AIDS, Viral Hepatitis, STD, and TB.

Software engineering

Vanni Galli

Vanni is a Senior Software Engineer at the Institute for Information Systems and Networking laboratory of the Department of Innovative Technology (DTI) at the University of Applied Sciences of Southern Switzerland (SUPSI). He specializes in software development tailored at offering ad-hoc solutions for enterprise-level information management tasks. He single-handedly developed the first public alpha-release of OMEGA and laid the foundation for all subsequent work.

Recently, Vanni has been involved in big-data software development projects such as B-DATARISK, a project aimed at assessing and reporting risk associated with the development of SME and start-ups in Switzerland.

Tiziano Leidi

Tiziano is the Director of the Institute for Information Systems and Networking laboratory of the Department of Innovative Technology (DTI) at the University of Applied Sciences of Southern Switzerland (SUPSI). He specializes in signal processing and solutions for parallel (multi-cores, GPUs) and distributed processing. Furthermore, he is interested in simulation, rapid prototyping and mass customization of software through techniques like component-based, model-driven, aspect-oriented and generative programming. Tiziano and his team developed a coarse- and fine-grained parallel version of the single particle tracking algorithm, which is currently integrated into the OMEGA infrastructure.

Software design

Raffaello Giulietti

Raffaello is a software engineer at the Institute for Information Systems and Networking laboratory of the Department of Innovative Technology (DTI) at the University of Applied Sciences of Southern Switzerland (SUPSI). He specializes in the definition, design, and development of object-oriented software projects. He favors using tools offering multithreading capabilities and open, community-driven standardization. He had a key role in the design and development of the OMEGA application.

Bernd Rinn

Bernd lives and works in Switzerland where he is the Head of ITS Scientific IT Services at ETH-Zurich and he is a Swiss Bioinformatics Institute Group Leader. Bernd and his group were involved in key design decisions for the OMEGA application and were instrumental in getting development off the ground. Specifically, they developed prototype data hubs based on the OpenBis information system, for managing, annotating and querying virus trajectories. They also helped in the development of data formats for single-particle tracking, trajectory segmentation, motion analysis, and error evaluation, which laid the foundations for the development and publication of the MIAPTE proposal.

Funding

Peter Kunszt

Peter is an entrepreneur and a Big Data expert of the very first hour before the term was even coined. His passion is to build distributed computing systems with the specific aim of bringing people together to tackle large multidisciplinary computational tasks. From 2009 to 2013 he led the Systemsx.ch Biology IT (SyBIT) project of the Swiss Initiative for Systems Biology SystemsX.ch from the ETH Zurich. In this, he passionately employed his vast experience to help biological scientists and physicians gaining insight from large and complex omics and imaging datasets. Peter provided essential seed funding for the development of the OMEGA alpha prototype tool, and for this, we owe him a big debt of gratitude.
Currently, Peter leads the Development Lab at Dynatrace – Barcelona.

Support

Federico Santoni

Federico is a Bioinformatician and Computational Biologist who specializes in the use of distributed computing paradigms for the analysis of biological data-sets. Federico gave a major contribution at the onset of this project in defining its strategic goals, in planning its architectural design and in enlisting initial support. For this, the entire OMEGA team owes him a great debt of gratitude.

Currently, Federico is a Principal Investigator at the Laboratory of Genetic Diagnostics of the Lausanne University Hospital, in Lausanne, Switzerland.

Andrea Danani

Andrea leads the Computational Biophysics group at the IDSIA– Dalle Molle Institute for Artificial Intelligence of the University of Applied Sciences of Southern Switzerland (SUPSI). He specializes in developing multiscale computational tools for the understanding of complex molecular systems. He was involved in porting (translation, ex-novo writing, etc.), optimization and integration and of single particle tracking, trajectory segmentation and statistical analysis algorithms in the OMEGA infrastructure. His role was essential to allow the development of the OMEGA alpha prototype.

Massimo Maiolo

Massimo is a Ph.D. student in the Applied Computational Genomics laboratory of the Zurich University of Applied Sciences (ZHAW). While doing his Master Thesis work in the Laboratory of Andrea Danani, Massimo was involved in porting (translation, ex-novo writing, etc.), optimization and integration and of single particle tracking, trajectory segmentation and statistical analysis algorithms in the OMEGA infrastructure.