Related papers: Python Unleashed on Systems Biology
We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software to design custom Coarse-Grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides and globular proteins in the Extensible…
Active inference is an account of cognition and behavior in complex systems which brings together action, perception, and learning under the theoretical mantle of Bayesian inference. Active inference has seen growing applications in…
Python has emerged as one of the most popular programming languages, extensively utilized in domains such as machine learning, data analysis, and web applications. Python's dynamic nature and extensive usage make it an attractive candidate…
Existing Python libraries and tools lack the ability to efficiently compute statistical test results for large datasets in the presence of missing values. This presents an issue as soon as constraints on runtime and memory availability…
Pattern matching is a powerful tool for symbolic computations. Applications include term rewriting systems, as well as the manipulation of symbolic expressions, abstract syntax trees, and XML and JSON data. It also allows for an intuitive…
The solutions of a system of polynomials in several variables are often needed, e.g.: in the design of mechanical systems, and in phase-space analyses of nonlinear biological dynamics. Reliable, accurate, and comprehensive numerical…
ABCpy is a highly modular scientific library for Approximate Bayesian Computation (ABC) written in Python. The main contribution of this paper is to document a software engineering effort that enables domain scientists to easily apply ABC…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…
This paper presents SunPy (version 0.5), a community-developed Python package for solar physics. Python, a free, cross-platform, general-purpose, high-level programming language, has seen widespread adoption among the scientific community,…
Synchrotron processes, the radiative processes associated with the interaction of energetic charged particles with magnetic field, are of interest in many areas in astronomy, from the interstellar medium to extreme environments near compact…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
This paper introduces and evaluates a freely available cellular nonlinear network simulator optimized for the effective use of GPUs, to achieve fast modelling and simulations. Its relevance is demonstrated for several applications in…
Python is rapidly becoming the lingua franca of machine learning and scientific computing. With the broad use of frameworks such as Numpy, SciPy, and TensorFlow, scientific computing and machine learning are seeing a productivity boost on…
In the modern semiconductor industry, automatic generation of parameterized and recurring layout structures plays an important role and should be present as a feature in Electronic Design Automation (EDA)-tools. Currently these layout…
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…
pPython seeks to provide a parallel capability that provides good speed-up without sacrificing the ease of programming in Python by implementing partitioned global array semantics (PGAS) on top of a simple file-based messaging library…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
We present a Python extension to the massively parallel HPC simulation toolkit waLBerla. waLBerla is a framework for stencil based algorithms operating on block-structured grids, with the main application field being fluid simulations in…