Related papers: BSTModelKit.jl: A Julia Package for Constructing, …
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
We present Groebner.jl, a Julia package for computing Groebner bases with the F4 algorithm. Groebner.jl is an efficient, portable, and open-source software. Groebner.jl works over integers modulo a prime and over the rationals, supports…
Approximating partial differential equations for extensive industrial and scientific applications requires leveraging the power of modern high-performance computing. In large-scale parallel computations, the geometrical discretisation…
Bioelectrochemistry is crucial for understanding biological functions and driving applications in synthetic biology, healthcare, and catalysis. However, current simulation methods fail to capture both the stochastic nature of molecular…
Chemellia is an open-source framework for atomistic machine learning in the Julia programming language. The framework takes advantage of Julia's high speed as well as the ability to share and reuse code and interfaces through the paradigm…
DiffEqFlux.jl is a library for fusing neural networks and differential equations. In this work we describe differential equations from the viewpoint of data science and discuss the complementary nature between machine learning models and…
Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…
We introduce $\texttt{RandomMeas$.$jl}$, a modular and high-performance open-source software package written in Julia for implementing and analyzing randomized measurement protocols in quantum computing. Randomized measurements provide a…
LongMemory.jl is a package for time series long memory modelling in Julia. The package provides functions to generate long memory, estimate model parameters, and forecast. Generating methods include fractional differencing, stochastic error…
Since the first observations of interstellar molecules, astrochemical simulations have been employed to model and understand its formation and destruction path- ways. With the advent of high-resolution telescopes such as JWST and ALMA, the…
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely…
This paper presents a method for modeling biological systems which combines formal techniques on intervals, numerical simulations and satisfaction of Signal Temporal Logic (STL) formulas. The main modeling challenge addressed by this…
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks.…
The julia package integrates the Julia programming language into Stata. Users can transfer data between Stata and Julia, issue Julia commands to analyze and plot, and pass results back to Stata. Julia's econometric ecosystem is not as…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
We introduce Dionysos.jl, a modular package for solving optimal control problems for complex dynamical systems using state-of-the-art and experimental techniques from symbolic control, optimization, and learning. More often than not with…
There are plenty of excellent plotting libraries. Each excels at a different use case: one is good for printed 2D publication figures, the other at interactive 3D graphics, a third has excellent L A TEX integration or is good for creating…
The consideration of stochastic uncertainty in optimal and predictive control is a well-explored topic. Recently Polynomial Chaos Expansions (PCE) have received considerable attention for problems involving stochastically uncertain system…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…