28 papers · ranked by Valyu relevance
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…
Daniel Alabi, Joseph Ekpenyong, Alida Monaco
The NaijaCoder in-person summer camps are intensive programs for high school and pre-college students in Nigeria. The programs are meant to provide free instruction on the basics of algorithms and computer programming. In 2024, the camps were held in two locations within the country: (i) the Federal Capital Territory…
Berk Ekmekci, Charles E. McAnany, Cameron Mura, Francis Ouellette
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…
Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers + 22 more
'Ralf Gommers' 'Pauli Virtanen' 'David Cournapeau' 'Eric Wieser' 'Julian Taylor' 'Sebastian Berg' 'Nathaniel J. Smith' 'Robert Kern' 'Matti Picus' 'Stephan Hoyer' 'Marten H. van Kerkwijk' 'Matthew Brett' 'Allan Haldane' 'Jaime Fernández del Río' 'Mark Wiebe' 'Pearu Peterson' 'Pierre Gérard-Marchant' 'Kevin Sheppard'…
Silin Chen, Ziqian Bi, Junyu Liu, Benji Peng + 13 more
Mathematics Fundamental: From Theory to Practice Authors: ['Silin Chen' 'Ziqian Bi' 'Junyu Liu' 'Benji Peng' 'Sen Zhang' 'Xiaoyong Pan' 'Jiawei Xu' 'Jinlang Wang' 'Keyu Chen' 'Caitlyn Heqi Yin' 'Pohsun Feng' 'Yizhu Wen' 'Tianyang Wang' 'Ming Li' 'Jin‐Tao Ren' 'Qian Niu' 'Ming Liu'] | I | | Python Data Structures and…
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…
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…
Theodoros Giannakopoulos, Gianni Pavan
Audio information plays a rather important role in the increasing digital content that is available today, resulting in a need for methodologies that automatically analyze such content: audio event recognition for home automations and surveillance systems, speech recognition, music information retrieval, multimodal…
Leonid Bystrykh
Genome biology shows substantial progress in its analytical and computational part in the last decades. Differential gene expression is one of many computationally intense areas; it is largely developed under R programming language. Here we explain possible reasons for such dominance of R in gene expression data. Next…
Kyla H. Levin, Kyle Gwilt, Emery D. Berger, Stephen N. Freund
—The advent of large language models (LLMs) has paved the way for a new era of programming tools with both significant capabilities and risks, as the generated code lacks guarantees of correctness and reliability. Developers using LLMs currently face the difficult task of optimizing, integrating, and maintaining code…
Pattara Leelaprute, Bodin Chinthanet, Supatsara Wattanakriengkrai, Raula Gaikovina Kula + 2 more
'Raula Gaikovina Kula' 'Pongchai Jaisri' 'Takashi Ishio'] In the field of data science, and for academics in general, the Python programming language is a popular choice, mainly because of its libraries for storing, manipulating, and gaining insight from data. Evidence includes the versatile set of machine learning…
T. Jenness
The LSST software systems make extensive use of Python, with almost all of it initially being developed solely in Python 2. Since LSST will be commissioned when Python 2 is end-of-lifed it is critical that we have all our code support Python 3 before commissioning begins. Over the past year we have made significant…
Vasudha Jha, Robert H. Cudmore
Brightest path tracing is a widely used image processing technique in several fields including biology, geography, and geology. However, despite the availability of many image processing libraries in Python, few offer an out-of-the-box implementation of a bright-est path tracing algorithm. This paper presents a Python…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Authors not listed
Electrochemiluminescence (ECL) is a vital analytical technique widely used in immunosensing and emerging applica-tions in biological imaging. Traditional ECL simulations rely on finite element methods, which provide valuable insights into reaction dynamics and spatial distribution of species. However, such methods are…
Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik-Sheriff, Hernán E. Grecco
Chemical Reaction Networks (CRNs) play a pivotal role in diverse fields such as systems biology, biochemistry, chemical engineering, and epidemiology. High-level modelling of CRNs enables various simulation approaches, including deterministic and stochastic methods. However, existing Python tools for CRN modelling…
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…
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…
Ruksit Rojpaisarnkit, Gregório Robles, Raula Gaikovina Kula, Dong Wang + 3 more
Textbooks Authors: ['Ruksit Rojpaisarnkit' 'Gregório Robles' 'Raula Gaikovina Kula' 'Dong Wang' 'Chaiyong Ragkhitwetsagul' 'Jesús M. González-Barahona' 'Kenichi Matsumoto'] Abstract—Python, one of the most prevalent programming languages today, is widely utilized in various domains, including web development, data…
Alex M. Ascension, Marcos J. Araúzo-Bravo
Big Data analysis is a discipline with a growing number of areas where huge amounts of data is extracted and analyzed. Parallelization in Python integrates Message Passing Interface via mpi4py module. Since mpi4py does not support parallelization of objects greater than 2^31^ bytes, we developed BigMPI4py, a Python…
Rıza Özçelik, Laura van Weesep, Sarah de Ruiter, Francesca Grisoni
In this work, we introduce peptidy -- a lightweight Python library that facilitates converting peptides (expressed as aminoacid sequences) to numerical representations suited to machine learning. peptidy is free from external dependencies, integrates seamlessly into modern Python environments, and supports a range of…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Tyler Kolisnik, Faeze Keshavarz-Rahaghi, Rachel Purcell, Adam Smith + 1 more
Random Forest models are widely used in genomic data analysis and can offer insights into complex biological mechanisms, particularly where features influence the target in interactive, non-linear, or non-additive ways. Currently, some of the most efficient random forest methods, in terms of computational speed, are…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
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…
Esben Bjerrum, Tobias Rastemo, Ross Irwin, Christos Kannas + 1 more
Recent years have seen a large interest in using the Simplified Molecular Input Line Entry System (SMILES) chemical language as input for deep learning architectures solving chemical tasks. Many successful applications have been demonstrated within de novo molecular design, quantitative structure-activity relationship…
Shirin Faraji, Johannes Ehrmaier, Maximilian Menger
Here, PySurf is introduced as an innovative code framework, which is specifically designed for rapid prototyping and development tasks for data-science applications in computational chemistry. To illustrate the potential of the framework, a code for nonadiabatic surface-hopping simulations based on the Landau-Zener…
Authors not listed
Solving optimization problems, especially for nonlinear and constrained systems, is a challenge. Decades of specialized algorithms have been developed for general and special cases of root finding, minimization (including constraints), for parameter estimation, and mapping connected spaces. These approaches typically…