“…To improve the computational efficiency of cell simulations involving high particle number systems, the authors have implemented a hybrid stochastic–deterministic (CME–ODE) method into the publically available, GPU‐based lattice microbes (LM) software suite and its python interface pyLM. LM and pyLM provide a convenient way to simulate complex cellular systems and interface with high‐performance RDME/CME/ODE solvers. …”
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“…We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochastic simulation studies from Python software. We parameterize fitness and similarity landscapes for polymerases and study a replicating population of sequences (randomly) participating in template-directed polymerization. …”
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“…Because there has been a significant amount of study in this field, the presented model focuses on boosting accuracy while using a transfer learning strategy. Python and Google Colab were utilized to perform this investigation. …”
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“…This user-friendly calculation makes the CP-Tool and the actual erosion risk more accessible for authorities and GIS users. With Python and QGIS as open source resources, it is also possible to easily improve the tools. …”
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“…The proposed method has been implemented in Java, openjdk version “11.0.11”; and for the analysis of the tested RGB images, Python 3.6 was used. Comprehensive experiments on widely used metrics demonstrate the effectiveness of the proposed method against differential attacks, brute force attacks and statistical attacks, while achieving superb results compared to related schemes. …”
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“…Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. …”
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“…Bakta is implemented in Python 3 and runs on MacOS and Linux systems. It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta. …”
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“…Here we present Slinker, a bioinformatics pipeline written in Python and Bpipe that uses a data-driven approach to assemble sample-specific superTranscripts. …”
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“…Here we have developed two plugins (brainreg and brainreg-segment) for the Python-based image viewer napari, to accurately map any object in a common coordinate space. …”
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“…Inspired by previous studies that take an allocation of macromolecule resources into account, we developed a simplified Python-based workflow for constructing enzymatic constrained metabolic network model (ECMpy) and constructed an enzyme-constrained model for Escherichia coli (eciML1515) by directly adding a total enzyme amount constraint in the latest version of GEM for E. coli (iML1515), considering the protein subunit composition in the reaction, and automated calibration of enzyme kinetic parameters. …”
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“…Within this article, a self-developed ML-based Python framework is presented, which offers advantages, especially in the development of structural components in early development phases. …”
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“…The system has a field of view of 5.5 × 8 mm(2), a 3 μm resolution, a 10 frames per second acquisition rate, and is controlled with a Python-based graphical interface. We exemplify the capabilities of the Incubascope on biological applications such as the hatching of Artemia salina eggs, the growth of the slime mould Physarum polycephalum and of encapsulated spheroids of mammalian cells.…”
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“…Here, we present Squidpy, a Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins. …”
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“…The workflow consists of a set of Python codes of which the execution is managed within Nextflow to annotate coding variants based on 37 criteria. …”
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“…We found that the worsening of both frequency discrimination and F0 discrimination at high frequencies could be well accounted for (in relative terms) by optimal decoding of all available information at the level of the auditory nerve. A Python package is provided to reproduce these results, and to simulate responses to acoustic stimuli from the three previously published models of the human auditory nerve used in our analyses.…”
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“…MEDUSA includes several tools, as fastp, Bowtie2, DIAMOND, Kaiju, MEGAHIT, and a novel tool implemented in Python to transfer annotations to BLAST/DIAMOND alignment results. …”
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“…There were 23 acupoints extracted from 11 RCTs. We used Python to calculate the association between acupoints and disease. …”
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“…Structural Interaction Network Analysis Protocols (SINAPs) is a proprietary python tool developed to (i) quickly solve key interactions able to distinguish two protein states, either from two sets of molecular dynamics simulations or from two crystallographic structures, and (ii) render a user-friendly 3D view of these key interactions through a plugin of UCSF Chimera, one of the most popular open-source viewing software for biomolecular systems. …”
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“…SCRcalc was developed using the Python 3.8.7 programming language. It incorporates equations and parameters of mechanistic models for the calculation of the organ equivalent dose (OED), the excess absolute risk (EA R) and the lifetime attributable risk (LA R) of carcinogenesis for various organs due to radiotherapy. …”
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“…Experimental data were analyzed by Python programming language and least squares method to obtain a saturated dissolved oxygen concentration model. …”
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