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81

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.
Husar, Adam ; Ordyan, Mariam ; Garcia, Guadalupe C. ; et al.
PLoS Computational Biology. 4/24/2024, Vol. 20 Issue 4, p1-30. 30p.

PYTHON programming langu... SIMULATION software CHEMICAL models CHEMICAL reactions CELLULAR signal transduc... MODEL validation
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82

Constructing and analysing dynamic models with modelbase v1.2.3: a software update
van Aalst, Marvin ; Ebenhöh, Oliver ; MatuszyÅska, Anna
BMC Bioinformatics. April 20, 2021, Vol. 22 Issue 1

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83

From Tension to Triumph: Design and Implementation of an Innovative Algorithmic Metric for Quantifying Individual Performance in Women Volleyball’s Critical Moments
Carlos López-Serrano ; María Zakynthinaki ; Daniel Mon-López ; et al.
Applied Sciences, Vol 14, Iss 24, p 11906 (2024)

player effectiveness data analysis chocking set victory prediction Python programming interactive dashboards …
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84

FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries.
Montepietra, Daniele ; Tesei, Giulio ; Martins, João M. ; et al.
Communications Biology. 3/9/2024, Vol. 7 Issue 1, p1-10. 10p.

PYTHON programming langu... FLUORESCENCE resonance e... PROTEIN conformation MOLECULAR dynamics PEPTIDES
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85

Python interfaces for the Smoldyn simulator.
Singh, Dilawar ; Andrews, Steven S
Bioinformatics. 1/1/2022, Vol. 38 Issue 1, p291-293. 3p.

PYTHON programming langu... SOFTWARE development too... SYSTEMS biology BIOPHYSICS
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86

Mesa-Geo : A GIS Extension for the Mesa Agent-Based Modeling Framework in Python
Wang, Boyu ; Hess, Vincent ; Crooks, Andrew
Proceedings of the 5th ACM SIGSPATIAL International Workshop on GeoSpatial Simulation. :1-10

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87

Creation of Time Series Models based on Deep Learning for Generation of Probabilistic Forecasts Using GluonTS and Python
Cancino-Villatoro, Karina ; Castillo-Estrada, Christian ; Juarez-Ramirez, Reyes ; et al.
2023 11th International Conference in Software Engineering Research and Innovation (CONISOFT) CONISOFT Software Engineering Research and Innovation (CONISOFT), 2023 11th International Conference in. :265-274 Nov, 2023

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88

Comparative Analysis of AI Models for Python Code Generation: A HumanEval Benchmark Study
Ali Bayram ; Gonca Gokce Menekse Dalveren ; Mohammad Derawi
Applied Sciences, Vol 15, Iss 18, p 9907 (2025)

AI models code generation HumanEval Python machine learning Technology …
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89

GeneLens: A Python Package Implementing Monte Carlo Machine Learning and Network Analysis Methods for Biomarker Discovery and Gene Functional Annotation.
Osmak, G. J. ; Pisklova, M. V.
Molecular Biology. Oct2025, Vol. 59 Issue 5, p827-835. 9p.

MONTE Carlo method BIOMARKERS MACHINE learning PYTHON programming langu... GENE mapping GENETIC regulation …
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90

FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing
Chen, Hua-Chang ; Wang, Jing ; Shyr, Yu ; et al.
PLoS Computational Biology. January 22, 2024, Vol. 20 Issue 1, pe1011786.

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91

Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping.
Ren, Xiaoliang ; Shao, Yanwen ; Zhang, Yiwen ; et al.
Bioinformatics. Apr2023, Vol. 39 Issue 4, p1-2. 2p.

PYTHON programming langu... MOLECULAR biology CAENORHABDITIS HAPLOTYPES
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92

Fast and scalable querying of eukaryotic linear motifs with gget elm.
Luebbert, Laura ; Hoang, Chi ; Kumar, Manjeet ; et al.
Bioinformatics. Mar2024, Vol. 40 Issue 3, p1-4. 4p.

AMINO acid sequence PYTHON programming langu... SCIENTIFIC knowledge DATABASES PROTEIN analysis CELL communication
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93

Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA.
Huang, Zhuoli ; Zheng, Yuhui ; Wang, Weikai ; et al.
Communications Biology. 11/16/2024, Vol. 7 Issue 1, p1-15. 15p.

PYTHON programming langu... LIBRARY design & constru... FACTOR analysis RNA sequencing COLORECTAL cancer
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94

Identification of Drugs and Association of Genes with Diseases among Anxiety, Bipolar Disorder, Heart Disease and Stress: A Computational Biology Approach
Rooman, Mahadi Hasan ; Bose, Urmi ; Hasan, Md Rakibul ; et al.
2023 26th International Conference on Computer and Information Technology (ICCIT) Computer and Information Technology (ICCIT), 2023 26th International Conference on. :1-6 Dec, 2023

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95

CFVisual: an interactive desktop platform for drawing gene structure and protein architecture
Chen, Huilong ; Song, Xiaoming ; Shang, Qian ; et al.
BMC Bioinformatics. May 13, 2022, Vol. 23 Issue 1

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96

ClearFinder: a Python GUI for annotating cells in cleared mouse brain
Stefan Pastore ; Philipp Hillenbrand ; Nils Molnar ; et al.
BMC Bioinformatics, Vol 26, Iss 1, Pp 1-13 (2025)

Tissue clearing Atlas alignment Cell count 3D volumetric imaging Computer applications to... R858-859.7 …
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97

MxlPy—Python package for mechanistic learning and hybrid modelling in life science.
Aalst, Marvin van ; Nies, Tim ; Pfennig, Tobias ; et al.
Bioinformatics Advances. 2025, Vol. 5 Issue 1, p1-8. 8p.

MACHINE learning LIFE sciences SCIENTIFIC models PYTHON programming langu... SYSTEMS biology PREDICTION models …
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98

DNA Features Viewer: a sequence annotation formatting and plotting library for Python.
Zulkower, Valentin ; Rosser, Susan
Bioinformatics. 8/1/2020, Vol. 36 Issue 15, p4350-4352. 3p.

PYTHON programming langu... DNA COMPUTATIONAL biology ANNOTATIONS
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99

ssbio: a Python framework for structural systems biology.
Mih, Nathan ; Brunk, Elizabeth ; Chen, Ke ; et al.
Bioinformatics. 6/15/2018, Vol. 34 Issue 12, p2155-2157. 3p.

PYTHON programming langu... PROTEIN structure GENOMIC information retr... HOMOLOGY (Biology) POLYPEPTIDES
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100

An Implementation of the Python Code for Computing the Independent Number of Genus Graphs.
Anjum, Sana ; Alali, Amal S.
Mathematics (2227-7390). Sep2025, Vol. 13 Issue 18, p2951. 13p.

GRAPH theory INDEPENDENT sets CANCER treatment TOPOLOGICAL graph theory COMPUTATIONAL biology PYTHON programming langu... …
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