Several software packages relevant for reaction networks analyses

Abstract: This week's seminar will take a different format. Four different groups will be introducing their software packages that are relevant for reaction networks. This will be followed by breakout rooms to learn more about these packages.

Speakers:

$\color{blue}\underline{\textbf{1. Herbert Sauro (University of Washington) -- Tellurium}}$

$\textbf{Keywords:}$ Simulation, SBML, High Performance, reusable library

$\textbf{Website:}$ tellurium.analogmachine.org/, tellurium.readthedocs.io/en/latest/index.html

$\textbf{Recording:}$ youtu.be/yzVOZlQwM74

$\color{blue}\underline{\textbf{2. Torkel Loman (University of Oxford); Vincent Du (UNC Chapel Hill) -- Catalyst}}$

$\textbf{Keywords:}$ Chemical reaction networks, ODE Simulations, Stochastic simulations, Network analysis

$\textbf{Website:}$ github.com/SciML/Catalyst.jl

$\textbf{Recording:}$ youtu.be/h9zUQWoyWo0

$\color{blue}\underline{\textbf{3. Marcus Aichmayr (University of Kassel) -- Sign Vector Conditions}}$

$\textbf{Keywords:}$ chemical-reaction-networks, generalized mass-action systems, deficiency zero theorem, robustness, sign vectors, SageMath

$\textbf{Website:}$ github.com/MarcusAichmayr/sign_vector_conditions

$\textbf{Recording:}$ youtu.be/H_bYwr1KEi0

$\color{blue}\underline{\textbf{4. Janos Toth (Budapest University of Technology and Economics) -- ReactionKinetics.wl}}$

$\textbf{Keywords:}$ From Exact Stochastic Simulation to Qualitative and Structural Analysis of Reactions, a Wolfram Language (Mathematica) package, TÓTH, J.; NAGY, A. L.; PAPP, D., Springer, 2018.

$\textbf{Recording:}$ youtu.be/8j_7G_tJsb0

mathematical softwaresymbolic computationalgebraic geometrydynamical systemsprobability

Audience: researchers in the topic

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Seminar on the Mathematics of Reaction Networks

Series comments: Subscription link: list.ku.dk/postorius/lists/morn.list.ku.dk/

This seminar series focuses on progress in mathematical theory for the study of reaction networks, mainly in biology and chemistry. The scope is broad and accommodates works arising from dynamical systems, stochastics, algebra, topology and beyond.

We aim at providing a common forum for sharing knowledge and encouraging discussion across subfields. In particular we aim at facilitating interactions between junior and established researchers. These considerations will be represented in the choice of invited speakers and we will strive to create an excellent, exciting and diverse schedule.

The seminar runs twice a month, typically on the 2nd and 4th Thursday of the month, at 17:00 Brussels time (observe that this webpage shows the schedule in your current time zone). Each session consists of two 25-minute talks followed by 5-minute questions. After the two talks, longer discussions will take place for those interested. To this end, we will use breakout rooms. For this to work well, you need to have the latest version of Zoom installed (version 5.3.0 or higher), and use the desktop client or mobile app (not supported on ChromeOS).

We look forward hearing about new work and meeting many of you over zoom! Many of the talks are recorded; to see the recording, from Past Talks, open details of the listed talk for a video link.

The organizers.

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