Related papers: Julia for Biologists
This paper demonstrates how certified computational tools can be used to address various problems in control theory. In particular, we introduce PACE.jl, a Julia package that implements symbolic elimination techniques, including (among…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
In the last few decades or so, we witness a paradigm shift in our nature studies - from a data-processing based computational approach to an information-processing based cognitive approach. The process is restricted and often misguided by…
We discuss computability and computational complexity of conformal mappings and their boundary extensions. As applications, we review the state of the art regarding computability and complexity of Julia sets, their invariant measures and…
Large language models (LLMs) have ushered in a new era for processing complex information in various fields, including science. The increasing amount of scientific literature allows these models to acquire and understand scientific…
Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small datasets, and provide adaptive suggestions for sequential…
We present NEP-PACK a novel open-source library for the solution of nonlinear eigenvalue problems (NEPs). The package provides a framework to represent NEPs, as well as efficient implementations of many state-of-the-art algorithms. The…
In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance.…
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
We present the Julia interface Polymake.jl to polymake, a software for research in polyhedral geometry. We describe the technical design and how the integration into Julia makes it possible to combine polymake with state-of-the-art…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Biological science produces large amounts of data in a variety of formats, which necessitates the use of computational tools to process, integrate, analyse, and glean insights from the data. Researchers who use computational biology tools…
We introduce two new packages, Nemo and Hecke, written in the Julia programming language for computer algebra and number theory. We demonstrate that high performance generic algorithms can be implemented in Julia, without the need to resort…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…