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Mauro Silberberg

dblp:358/3608 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2024
0000-0002-2402-1100ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › systems biology
chemical reaction network simulation
0.812024
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems · Bioinform. 2024
Bioinformatics and computational biology › systems biology
dynamical system modeling
0.812024
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems · Bioinform. 2024
Bioinformatics and computational biology
systems biology
0.812024
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems · Bioinform. 2024

Methods — techniques the papers use, named apart from their topics

stochastic simulation · 0.8just-in-time compilation · 0.8deterministic simulation · 0.8
YearPublicationVenuePosition
2024 Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems
abstract
MOTIVATION: Chemical reaction networks (CRNs) play a pivotal role in diverse fields such as systems biology, biochemistry, chemical engineering, and epidemiology. High-level definitions of CRNs enables to use various simulation approaches, including deterministic and stochastic methods, from the same model. However, existing Python tools for simulation of CRN typically wrap external C/C++ libraries for model definition, translation into equations and/or numerically solving them, limiting their extensibility and integration with the broader Python ecosystem. RESULTS: In response, we developed Poincaré and SimBio, two novel Python packages for simulation of dynamical systems and CRNs. Poincaré serves as a foundation for dynamical systems modeling, while SimBio extends this functionality to CRNs, including support for the Systems Biology Markup Language (SBML). Poincaré and SimBio are developed as pure Python packages enabling users to easily extend their simulation capabilities by writing new or leveraging other Python packages. Moreover, this does not compromise the performance, as code can be just-in-time compiled with Numba. Our benchmark tests using curated models from the BioModels repository demonstrate that these tools may provide a potentially superior performance advantage compared to other existing tools. In addition, to ensure a user-friendly experience, our packages use standard typed modern Python syntax that provides a seamless integration with integrated development environments. Our Python-centric approach significantly enhances code analysis, error detection, and refactoring capabilities, positioning Poincaré and SimBio as valuable tools for the modeling community. AVAILABILITY AND IMPLEMENTATION: Poincaré and SimBio are released under the MIT license. Their source code is available on GitHub (https://github.com/maurosilber/poincare and https://github.com/hgrecco/simbio) and can be installed from PyPI or conda-forge.
Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik-Sheriff, Hernán E. Grecco
Bioinform.1