13 papers · ranked by Valyu relevance
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…
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…
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…
Moritz D. Lürig
Digital images are a ubiquitous way to represent phenotypes. More and more ecologists and evolutionary biologists are using images to capture and analyze high dimensional phenotypic data to understand complex developmental and evolutionary processes. Therefore, images are being collected at ever increasing rates…
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…
Yangyang Li, Rendong Yang
We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows.…
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…
Tina Hollandt, Markus Baur, Caroline Wöhr
Considering animal welfare, animals should be kept in animal-appropriate and stress-free housing conditions in all circumstances. To assure such conditions, not only basic needs must be met, but also possibilities must be provided that allow animals in captive care to express all species-typical behaviors. Rack housing…
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…
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…
Guillaume Viejo, Daniel Levenstein, Sofia Skromne Carrasco, Dhruv Mehrotra + 6 more
Datasets collected in neuroscientific studies are of ever-growing complexity, often combining high dimensional time series data from multiple data acquisition modalities. Handling and manipulating these various data streams in an adequate programming environment is crucial to ensure reliable analysis, and to facilitate…
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…
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…