13 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…
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…
Dominique Sydow, Jaime Rodríguez-Guerra, Talia B. Kimber, David Schaller + 7 more
Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming --- especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide…
Stephen Coshatt, He Yang, Shushan Wu, Jin Ye + 5 more
As machine learning and artificial intelligence are being integrated into cyber-physical systems, it is becoming important for engineers to know and understand these topics. In particular, sensor data is on the rise in these systems and therefore engineers need to understand which models are appropriate to time-series…
Laura Mickes, Travis M. Seale-Carlisle, Xueqing Chen, Stewart Boogert
'Stewart Boogert'] pyWitness is a python toolkit for recognition memory experiments, with a focus on eyewitness identification (ID) data analysis and model fitting. The current practice is for researchers to use different statistical packages to analyze a single dataset. pyWitness streamlines the process. In addition…
Odd Petter Sand, Elise Lockwood, Marcos D. Caballero, Knut Mørken
We present here the lessons learned by iteratively designing a tutorial for first-year university students using computer programming to work with mathematical models. Alternating between design and implementation, we used video-taped task interviews and classroom observations to ensure that the design promoted student…
Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao + 1 more
SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) is a powerful and versatile software tool designed to computationally estimate the kinetics and thermodynamics of complex molecular processes, particularly emphasizing the process of receptor-ligand binding and unbinding. We present a suite of tutorials for…
Rebecca Brunk, Kriti Shukla, Bryant Hutson, Yue Wang + 7 more
Genomic sequencing and other big biological data is unquestionably of paramount value, however the success in recruiting highly skilled individuals with diverse backgrounds has been limited. A main reason for this deficiency could be due to the lack of educational resources and early exposure to the field. With the…
Martin Seifrid, Felix Strieth-Kalthoff, Mohammad Haddadnia, Tony Wu + 7 more
We introduce Chemspyd, a lightweight, open-source Python package for operating the popular laboratory robotic platforms from Chemspeed Technologies. As an add-on to the existing proprietary software suite, Chemspyd enables dynamic communication with the automated platform, laying the foundation for its modular…
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…
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…
Hsuan-Ta Lin, Po-Ming Lee, Tzu-Chien Hsiao
Tutorial tactics are policies for an Intelligent Tutoring System (ITS) to decide the next action when there are multiple actions available. Recent research has demonstrated that when the learning contents were controlled so as to be the same, different tutorial tactics would make difference in students' learning gains.…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…