Related papers: Python Unleashed on Systems Biology
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
SfePy (Simple finite elements in Python) is a software for solving various kinds of problems described by partial differential equations in one, two or three spatial dimensions by the finite element method. Its source code is mostly (85\%)…
This article presents an open-source Python package for simulating micro-thermoelectric generators, based on the work by D. Beretta et al. (Sustainable Energy Fuels, 2017). Featuring a user-friendly graphical user interface and robust…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…
We present ongoing work on Guppy, a domain-specific language embedded in Python that allows users to write high-level hybrid quantum programs with complex control flow in Pythonic syntax, aiming to run them on actual quantum hardware.
Misconceptions about program execution hinder many novice programmers. We introduce SimpliPy, a notional machine designed around a carefully chosen Python subset to clarify core control flow and scoping concepts. Its foundation is a precise…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based…
Computational analysis has become ubiquitous within the heliophysics community. However, community standards for peer-review of codes and analysis have lagged behind these developments. This absence has contributed to the reproducibility…
Large Language Models (LLMs) have shown great potential in automating code generation; however, their ability to generate accurate circuit-level SPICE code remains limited due to a lack of hardware-specific knowledge. In this paper, we…
Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
ergodicity is an open-source Python library for computational work on stochastic dynamics, with particular emphasis on non-ergodicity, time-average behavior, heavy-tailed processes, and decision making under uncertainty. The package brings…
We have designed a Python-based Domain Specific Language (DSL) for modeling synchronous digital circuits. In this DSL, hardware is modeled as a collection of transactions -- running in series, parallel, and loops. When the model is executed…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
As supercomputers continue to grow in scale and capabilities, it is becoming increasingly difficult to isolate processor and system level causes of performance degradation. Over the last several years, a significant number of performance…