Related papers: Julia for Biologists
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…
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Like many groups considering the new programming language Julia, we faced the challenge of accessing the algorithms that we develop in Julia from R. Therefore, we developed the R package JuliaConnectoR, available from the CRAN repository…
Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
Since time immemorial an old adage has always seemed to ring true: you cannot use a high-level productive programming language like Python or R for real-time control and embedded-systems programming, you must rewrite your program in C. We…
We discuss what is special about the reproducibility of workflows in computer algebra. It is emphasized how the programming language Julia and the new computer algebra system OSCAR support such a reproducibility, and how users can benefit…
Program synthesis -- the automatic generation of code given a specification -- is one of the most fundamental tasks in artificial intelligence (AI) and the dream of many programmers. Numerous synthesizers have been developed for program…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
The rapid evolution of artificial intelligence, especially through multi-modal large language models, has redefined user interactions, enabling responses that are contextually rich and human-like. As AI becomes an integral part of daily…
JuMP is an open-source modeling language that allows users to express a wide range of optimization problems (linear, mixed-integer, quadratic, conic-quadratic, semidefinite, and nonlinear) in a high-level, algebraic syntax. JuMP takes…
Random variables and their distributions are a central part in many areas of statistical methods. The Distributions.jl package provides Julia users and developers tools for working with probability distributions, leveraging Julia features…
This paper proposes integrating Aspect-oriented Programming (AOP) into Julia, a language widely used in scientific and High-Performance Computing (HPC). AOP enhances software modularity by encapsulating cross-cutting concerns, such as…
Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
We introduce Lyceum, a high-performance computational ecosystem for robot learning. Lyceum is built on top of the Julia programming language and the MuJoCo physics simulator, combining the ease-of-use of a high-level programming language…
Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development,…
The Julia programming language has gained acceptance within the High-Performance Computing (HPC) community due to its ability to tackle two-language problem: Julia code feels as high-level as Python but allows developers to tune it to…
We provide an overview of the emergence of large language models for scientific computing applications. We highlight use cases that involve natural language processing of scientific documents and specialized languages designed to describe…
We present StochasticPrograms.jl, a user-friendly and powerful open-source framework for stochastic programming written in the Julia language. The framework includes both modeling tools and structure-exploiting optimization algorithms.…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…