相关论文: Python Unleashed on Systems Biology

We introduce pyGSL, a Python library that provides efficient implementations of state-of-the-art graph structure learning models along with diverse datasets to evaluate them on. The implementations are written in GPU-friendly ways, allowing…

Multiplexed immunofluorescence microscopy captures detailed measurements of spatially resolved, multiple biomarkers simultaneously, revealing tissue composition and cellular interactions in situ among single cells. The growing scale and…

This paper presents a distributed platform for Natural Language Processing called PyPLN. PyPLN leverages a vast array of NLP and text processing open source tools, managing the distribution of the workload on a variety of configurations:…

When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition,…

We present Simphony, a free and open-source software toolbox for abstracting and simulating photonic integrated circuits, implemented in Python. The toolbox is both fast and easily extensible; plugins can be written to provide compatibility…

Generative models for molecules have shown considerable promise for use in computational chemistry, but remain difficult to use for non-experts. For this reason, we introduce open-source infrastructure for easily building generative…

In this paper, we introduce OWLAPY, a comprehensive Python framework for OWL ontology engineering. OWLAPY streamlines the creation, modification, and serialization of OWL 2 ontologies. It uniquely integrates native Python-based reasoners…

Pattern matching is a powerful tool for symbolic computations, based on the well-defined theory of term rewriting systems. Application domains include algebraic expressions, abstract syntax trees, and XML and JSON data. Unfortunately, no…

SpeechPy is an open source Python package that contains speech preprocessing techniques, speech features, and important post-processing operations. It provides most frequent used speech features including MFCCs and filterbank energies…

Models used for control design are, to some degree, uncertain. Model uncertainty must be accounted for to ensure the robustness of the closed-loop system. $\mu$-analysis and $\mu$-synthesis methods allow for the analysis and design of…

Hardware generation languages (HGLs) increase hardware design productivity by creating parameterized modules and test benches. Unfortunately, existing tools are not widely adopted due to several demerits, including limited support for…

Fanpy is a free and open-source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it…

Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching…

Across an aggregation of EuSpRIG presentation papers, two maxims hold true: spreadsheets models are akin to software, yet spreadsheet developers are not software engineers. As such, the lack of traditional software engineering tools and…

We introduce cellanneal, a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimization of Spearman's rank correlation coefficient between experimental and computational mixture gene expression…

Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…

We present the labscript suite, an open-source experiment control system for automating shot-based experiments and their analysis. Experiments are composed as Python code, which is used to produce low-level hardware instructions. They are…

Numpy and SciPy are program libraries for the Python scripting language, which apply to a large spectrum of numerical and scientific computing tasks. The Sage project provides a multiplatform software environment which enables one to use,…

This study introduces a novel software tool leveraging large language model (LLM) prompts, designed to automate the generation of academic articles from Python code a significant advancement in the fields of biomedical informatics and…

FluidDyn is a project to foster open-science and open-source in the fluid dynamics community. It is thought of as a research project to channel open-source dynamics, methods and tools to do science. We propose a set of Python packages…