13 papers · ranked by Valyu relevance
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…
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.…
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…
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…
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…
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…