27 papers · ranked by Valyu relevance
Venus N. Sherathiya, Michael D. Schaid, Jillian L. Seiler, Gabriela C. Lopez + 1 more
Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be challenging for…
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…
Alex Sheng
We develop a simple and straightforward methodology to create AI computer agents that can carry out diverse computer tasks and self-improve by developing tools and augmentations to enable themselves to solve increasingly complex tasks. As large language models (LLMs) have been shown to benefit from nonparametric…
Hanxing Ding, Shuchang Tao, Liang Pang, Zihao Wei + 4 more
Language Models Authors: ['Hanxing Ding' 'Shuchang Tao' 'Liang Pang' 'Zihao Wei' 'Jinyang Gao' 'Bolin Ding' 'Huawei Shen' 'Xueqi Chen'] Tool learning has emerged as a crucial capability for large language models (LLMs) to solve complex real-world tasks through interaction with external tools. Existing approaches face…
Muhammad Aziz
Computational chemistry software designed to compute the chemical properties of compounds falls under the category of dry research. The computational calculation of chemicals is a broad term. In this current study, chemical properties are estimated through computational methods, which is valuable for newly synthesis…
Thomas Donoghue, Sandra Maesta-Pereira, Claire Zhixian Han, Salman Ehtesham Qasim + 1 more
A common method of collecting and analyzing neural activity is to implant electrodes that record the electrical activity of the brain, from which action potentials of individual neurons can be recorded (). After pre-processing to detect spike waveforms and cluster them into groups representing putative single neurons…
Stephan Lukasczyk, Gordon Fraser
Automated unit test generation is a well-known methodology aiming to reduce the developers' effort of writing tests manually. Prior research focused mainly on statically typed programming languages like Java. In practice, however, dynamically typed languages have received a huge gain in popularity over the last decade.…
Laura Wiggins, Stuart Lacy, Graeme Park, Joanne Marrison + 5 more
We previously developed the CellPhe toolkit^1^, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image analysis tools and to enhance interoperability with widely used software for cell segmentation and tracking, we developed…
Yuting Miao, Shimon Weiss, Xiyu Yi
Super-resolution optical fluctuation imaging (SOFI) is a highly democratizable technique that provides optical super-resolution (SR) without requirement of sophisticated imaging instruments. An open source package for SOFI algorithm is needed to support not only the utilization of SOFI, but also the community adoption…
Oscar Castro, Pierrick Bruneau, Jean-Sébastien Sottet, Dario Torregrossa
'Dario Torregrossa'] Python has become the prime language for application development in the Data Science and Machine Learning domains. However, data scientists are not necessarily experienced programmers. While Python lets them quickly implement their algorithms, when moving at scale, computation efficiency becomes…
Benjamin M. Gyori, Charles Tapley Hoyt
Understanding the complex molecular processes governing how cells respond to external stimuli crucially relies on prior knowledge about signaling, regulatory, and metabolic pathways. Standardized representations are necessary to exchange such pathway knowledge and allow interoperability between tools. BioPAX () is a…
Anselm W. Hahn, Joseph Zsombor-Pindera, Pierre Kennepohl, Serena DeBeer
In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows…
Robert Neil McArthur, Thomas King-Fung Wong, Yapeng Lang, Richard Andrew Morris + 4 more
piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREE’s phylogenetic inference engine. piqtree builds IQ-TREE as a Python package, presenting a library of Python functions for performing many of IQ-TREE’s capabilities including phylogenetic…
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…
Daewon Lee, Pier Luigi Martelli
A variety of real-world phenomena such as biological pathways, communication networks and social relationships can be represented as networks (). An insightful visualization of networks facilitates understanding of the analyzed networks and leads to important discoveries. Therefore, open-source software for analyzing…
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…
Christopher Pyles, Francois van Schalkwyk, Gerard Gorman, Marijan Beg + 3 more
'Marijan Beg' 'Lee Stott' 'Nir Levy' 'Ran Gilad-Bachrach'] We continuously interact with computerized systems to achieve goals and perform tasks in our personal and professional lives. Therefore, the ability to program such systems is a skill needed by everyone. Consequently, computational thinking skills are essential…
Zejun Zhang, Zhenchang Xing, Xin Xia, Xiwei Xu + 1 more
Compared to other programming languages (e.g., Java), Python has more idioms to make Python code concise and efficient. Although pythonic idioms are well accepted in the Python community, Python programmers are often faced with many challenges in using them, for example, being unaware of certain pythonic idioms or do…
Mohammed Zniber, Youssef Fatihi, Tan-Phat Huynh, Sofia Forslund
Metabolomics is an emerging field within systems biology and represents the final step in the ‘omics’ cascade (, ). As a technology-driven discipline, metabolomics utilizes advancements in analytical chemistry and computational techniques to improve data collection, analysis, and interpretation (). Key platforms in…
Authors not listed
nDTomo is a Python-based software suite for the simulation, reconstruction and analysis of X-ray chemical imaging and computed tomography data. It provides a collection of Python function-based tools designed for accessibility and education as well as a graphical user interface (GUI). Prioritising transparency and ease…
Li Li, Jiawei Wang, Haowei Quan
Despite being the most popular programming language, Python has not yet received enough attention from the community. To the best of our knowledge, there is no general static analysis framework proposed to facilitate the implementation of dedicated Python static analyzers. To fill this gap, we design and implement such…
Wei Cheng, Xiangrong Zhu, Wei Hu
Code sharing and reuse is a widespread use practice in software engineering. Although a vast amount of open-source Python code is accessible on many online platforms, programmers often find it difficult to restore a successful runtime environment. Previous studies validated automatic inference of Python dependencies…
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…
Florian Rupprecht, Jason Kai, Biraj Shrestha, Steven Giavasis + 4 more
In numerous scientific domains, established tools have often been developed with complex command-line interfaces. Such is the case for brain imaging and bioinformatics, making the use of powerful legacy tools in modern workflow paradigms challenging. We present (i) Styx, a compiler for generating language-native…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Wubin Ding, David Goldberg, Wanding Zhou
PyComplexHeatmap was designed to visualize matrix data and associated metadata through sophisticated, richly annotated heatmap layouts. We have integrated the R grammar-of-graphics semantics with the Python-native matplotlib/Pandas-based data science ecosystem, allowing users to utilize built-in matplotlib colormaps…
J. Harry Moore, Matthias R. Bauer, Jeff Guo, Atanas Patronov + 2 more
We present Icolos, a workflow manager written in Python as a tool for automating complex structure-based workflows. Icolos can be used as a standalone tool, for example in virtual screening campaigns, or can be used in conjunction with deep learning-based molecular generation facilitated for example by REINVENT, a…