相关论文: Python Unleashed on Systems Biology
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
The purpose of this paper is to show how existing scientific software can be parallelized using a separate thin layer of Python code where all parallel communication is implemented. We provide specific examples on such layers of code, and…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
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…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
This work introduces SwarmRL, a Python package designed to study intelligent active particles. SwarmRL provides an easy-to-use interface for developing models to control microscopic colloids using classical control and deep reinforcement…
In this paper, we present resolvent4py, a parallel Python package for the analysis, model reduction and control of large-scale linear systems with millions or billions of degrees of freedom. This package provides the user with a friendly…
The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory…
mlpy is a Python Open Source Machine Learning library built on top of NumPy/SciPy and the GNU Scientific Libraries. mlpy provides a wide range of state-of-the-art machine learning methods for supervised and unsupervised problems and it is…
There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…
We present the Python package CELL, which provides a modular approach to the cluster expansion (CE) method. CELL can treat a wide variety of substitutional systems, including one-, two-, and three-dimensional alloys, in a general…
Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully…
We describe a novel, interdisciplinary, computational methods course that uses Python and associated numerical and visualization libraries to enable students to implement simulations for a number of different course modules. Problems in…
Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism. In particular, systems biology methods are applied to understand functional…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
OpenML is an online platform for open science collaboration in machine learning, used to share datasets and results of machine learning experiments. In this paper we introduce OpenML-Python, a client API for Python, opening up the OpenML…
We describe how Python can be leveraged to streamline the curation, modelling and dissemination of drug discovery data as well as the development of innovative, freely available tools for the related scientific community. We look at various…
In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…