11 papers · ranked by Valyu relevance
Noel M O'Boyle, Chris Morley, Geoffrey R Hutchison
Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We…
Nir Goren, Efi Fogel, Dan Halperin
We introduce Python bindings that enable the convenient, efficient, and reliable use of software modules of Cgal (The Computational Geometry Algorithms Library), which are written in C++, from within code written in Python. There are different tools that facilitate the creation of such bindings. We present a short…
Isabella Basso Amaral, Renato Cordeiro Ferreira, Alfredo Goldman
—The Python programming language is best known for its syntax and scientific libraries, but it is also notorious for its slow interpreter. Optimizing critical sections in Python entails special knowledge of the binary interactions between program ming languages, and can be cumbersome to interface manually, with…
Yury V. Zaytsev, Abigail Morrison
NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, [11]). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., [1]). The introduction of…
Yangyang Li, Rendong Yang
Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern…
Andreas Dedner, Martin Nolte
In this paper we present the new Dune-Python module which provides Python bindings for the Dune core, which is a C++ environment for solving partial differential equations. The aim of this new module is to firstly provide the general infrastructure for exporting realizations of statically polymorphic interfaces based…
Pierre Fernique, Christophe Pradal, Nick Higham
Most of Python and R scientific packages incorporate compiled scientific libraries to speed up the code and reuse legacy libraries. While several semi-automatic solutions exist to wrap these compiled libraries, the process of wrapping a large library is cumbersome and time consuming. In this paper, we introduce…
Hao Li, Gopi Krishnan Rajbahadur, Cor‐Paul Bezemer
Learning Software Quality Authors: ['Hao Li' 'Gopi Krishnan Rajbahadur' 'Cor‐Paul Bezemer'] Bindings for machine learning frameworks (such as TensorFlow and PyTorch) allow developers to integrate a framework's functionality using a programming language different from the framework's default language (usually Python).…
Tianyang Wang, Ziqian Bi, Keyu Chen, Jiawei Xu + 11 more
Management: Object-Oriented Programming Authors: ['Tianyang Wang' 'Ziqian Bi' 'Keyu Chen' 'Jiawei Xu' 'Qian Niu' 'Junyu Liu' 'Benji Peng' 'Ming Li' 'Sen Zhang' 'Xiaoyong Pan' 'Jinlang Wang' 'Pohsun Feng' 'Caitlyn Heqi Yin' 'Yizhu Wen' 'Ming Liu'] | III | Advancing Your Skills | | 9 | | --- | --- | --- | --- | | 1 |…
Berk Ekmekci, Charles E. McAnany, Cameron Mura
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware…
Sebastian Bassi, Fran Lewitter
This article introduces the world of the Python computer language. It is assumed that readers have some previous programming experience in at least one computer language and are familiar with basic concepts such as data types, flow control, and functions. Python can be used to solve several problems that research…