26 papers · ranked by Valyu relevance
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…
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…
Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele
The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. There is a pressing requirement for a framework that allows for fast, efficient, manageable, and reproducible RNA-Seq analysis. We have developed a Python package, (pyrpipe), that…
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…
Kiri Choi, J. Kyle Medley, Caroline Cannistra, Matthias König + 3 more
In this article, we present Tellurium, a powerful Python-based integrated environment designed for model building, analysis, simulation and reproducibility in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source integrated development environment (IDE) composed of multiple libraries…
Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele
Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of…
Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche + 4 more
'Michael Crusoe' 'Hedi Peterson' 'Jon Ison' 'Hervé Ménager'] Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such…
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.…
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…
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…
Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer, David R Stirling + 6 more
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or…
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…
Hamed Tahmooresi, Abbas Heydarnoori, Alireza Aghamohammadi
—Python is a popular, widely used, and general-purpose programming language. In spite of its ever-growing community, researchers have not performed much analysis on Python's topics, trends, and technologies which provides insights for developers about Python community trends and main issues. In this article, we examine…
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 G. D. Rowley, Christian Brenninkmeijer, Simon Davidson, Donal Fellows + 6 more
SpiNNaker is a massively parallel distributed architecture primarily focused on real time simulation of spiking neural networks. The largest realization of the architecture consists of one million general purpose processors, making it the largest neuromorphic computing platform in the world at the present time.…
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…
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…
Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
The Keras deep learning library is used for producing the neural network architectures . The trained model is saved as an H5 file to simplify its distribution to different Galaxy instances (Galaxy, [RRID:SCR_006281]()). The file is an HDF5 store containing the weights of different layers of the neural network and their…
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…
Mehdi Bahrami, N. C. Shrikanth, Shade Ruangwan, Lei Liu + 5 more
'Yuji Mizobuchi' 'Masahiro Fukuyori' 'Weipeng Chen' 'Kazuki Munakata' 'Tim Menzies'] A large scale collection of both semantic and natural language resources is essential to leverage active Software Engineering research areas such as code reuse and code comprehensibility. Existing machine learning models ingest data…
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…
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…
Marcel Friedrichs, Alban Shoshi, Piotr Jaroslaw Chmura, Jon Ison + 4 more
JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool…