Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

Gattaca provides the first base-pair resolution artificial genomes for tracking somatic mutations within agent based modeling. Through the incorporation of human reference genomes, mutational context, sequence coverage/error information Gattaca is able to realistically provide comparable sequence data for in-silico comparative evolution studies with human somatic evolution studies. This user-friendly method, incorporated into each in-silico cell, allows us to fully capture somatic mutation spectra and evolution.

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Agent-based Modeling and Computational Experiments in Industrial Organization: Growing Firms and Industries in silico

Eastern Economic Journal ◽

10.1057/eej.2010.30 ◽

2010 ◽

Vol 37 (1) ◽

pp. 28-34 ◽

Cited By ~ 4

Author(s):

Myong-Hun Chang

Keyword(s):

Industrial Organization ◽

In Silico ◽

Agent Based Modeling ◽

Computational Experiments ◽

Agent Based

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Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation

Vaccines ◽

10.3390/vaccines9080818 ◽

2021 ◽

Vol 9 (8) ◽

pp. 818

Author(s):

Bowen Zheng ◽

Muhammad Suleman ◽

Zonara Zafar ◽

Syed Shujait Ali ◽

Syed Nouman Nasir ◽

...

Keyword(s):

T Lymphocytes ◽

In Silico ◽

Critical Role ◽

Computational Modelling ◽

Agent Based Modeling ◽

Effective Vaccine ◽

Hepatitis G Virus ◽

Agent Based ◽

Persistent Infections ◽

Immunogenic Peptides

Pegivirus, HPgV, which was earlier known as Gb virus and hepatitis G virus, is an enveloped, positive-stranded RNA and lymphotropic virus classified into the Flaviviridae family. The transmission routes primarily involve blood products, and infections are worldwide, leading up to 25% of persistent infections. To date, no effective therapeutic means are available to clear Pegivirus infections. Effective vaccine therapeutics is the best alternative to manage this disease and any associated potential pandemic. Thus, whole proteome-based mining of immunogenic peptides, i.e., CTL (cytotoxic T lymphocytes), HTL (helper T lymphocytes), and B cell epitopes, was mapped to design a vaccine ensemble. Our investigation revealed that 29 different epitopes impart a critical role in immune response induction, which was also validated by exploring its physiochemical properties and experimental feasibility. In silico expression and host immune simulation were examined using an agent-based modeling approach and confirmed the induction of both primary and secondary immune factors such as IL, cytokines, and antibodies. The current study warrants further lab experiments to demonstrate its efficacy and safety.

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