20 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…
Steven Shave, Yan-Kai Chen, Nhan T. Pham, Manfred Auer
Understanding multicomponent binding interactions in protein-ligand, protein-protein and competition systems is essential for fundamental biology and drug discovery. Hand deriving equations quickly becomes unfeasible when the number of components is increased, and direct analytical solutions only exist to a certain…
Yangyang Li, Rendong Yang
We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows.…
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…
Dilawar Singh, Steven S. Andrews
Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ applicaton programming interface (API), which were convenient, but limited extensibility. We added a Python API to Smoldyn…
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…
David Miguel Susano Pinto, Mick A Phillips, Nicholas Hall, Julio Mateos–Langerak + 5 more
Custom built microscopes often require control of multiple hardware devices and precise hardware coordination. It is also desirable to have a solution that is scalable to complex systems and translatable between components from different manufacturers. Here we report Python-Microscope, a free and open source Python…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Dimitar Georgiev, Simon Vilms Pedersen, Ruoxiao Xie, Álvaro Fernández-Galiana + 2 more
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Andrew McNutt, David Koes
Determination of the bound pose of a ligand is a critical first step in many in silico drug discovery tasks. Molecular docking is the main tool for the prediction of non-covalent binding of a protein and ligand system. Molecular docking pipelines often only utilize the information of one ligand binding to the protein…
Endre Bakken Stovner, Pål Sætrom
Complex genomic analyses often use sequences of simple set operations like intersection, overlap, and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and…
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…