Listed python codes of our algorithm with explanations (Python 3.9 recommended). by Takayuki Niizato (162226)

Example of landmark registration to align ‘peaks’ of high density in the probability density function (PDF) of CD4 expression on blood T cells for a target distribution and chosen... by Ross J. Burton (10941910)

Results of the application of different clustering algorithms to average functional connectivity from healthy subjects. by Francisco Páscoa dos Santos (16510676)

“…<p>A) Resulting cluster inertia from applying the k-means algorithm described in the methods to empirical averaged functional connectivity from healthy subjects, with different numbers of clusters. …”

Choice of extraction method is mainly responsible for the variability in the reaction content across models. by Anne Richelle (6589178)

Subjects:

Adaptive H-REMD simulation algorithm. by Danial Pourjafar-Dehkordi (7165523)

Histogram showing the distribution of different model parameters over selected individuals in the Genetic Algorithm. by Claudio D. T. Barros (10885464)

In this example the MPC algorithm perfectly tracks the noisy signal , which results in many false spikes. by Nicholas A. Rondoni (21573261)

Subjects:

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions by Anne Richelle (6589178)

Subjects:

Python-based Monte Carlo Simulation Tool by Yangfan Jiang (9372782)

New constraints added to the mutated reactions induced by modified gene expression. by Fangzhou Shen (5140994)

Subjects:

Flux through arginine and ornithine reactions is sensitive to intracellular metabolite concentrations. by Deborah A. Powers (15361394)

Code snippets to add user-specific custom functionality in PyNoetic. by Gursimran Singh (575288)

Subjects:

Python-Based Algorithm for Estimating NRTL Model Parameters with UNIFAC Model Simulation Results by Se-Hee Jo (20554623)

“…This algorithm conducts a series of procedures: (1) fragmentation of the molecules into functional groups from SMILES, (2) calculation of activity coefficients under predetermined temperature and mole fraction conditions by employing universal quasi-chemical functional group activity coefficient (UNIFAC) model, and (3) regression of NRTL model parameters by employing UNIFAC model simulation results in the differential evolution algorithm (DEA) and Nelder–Mead method (NMM). …”

<b>Opti2Phase</b>: Python scripts for two-stage focal reducer by Morgan Najera (21540776)

“…</li></ul><p dir="ltr">The scripts rely on the following Python packages. Where available, repository links are provided:</p><ol><li><b>NumPy</b>, version 1.22.1</li><li><b>SciPy</b>, version 1.7.3</li><li><b>PyGAD</b>, version 3.0.1 — https://pygad.readthedocs.io/en/latest/#</li><li><b>bees-algorithm</b>, version 1.0.2 — https://pypi.org/project/bees-algorithm</li><li><b>KrakenOS</b>, version 1.0.0.19 — https://github.com/Garchupiter/Kraken-Optical-Simulator</li><li><b>matplotlib</b>, version 3.5.2</li></ol><p dir="ltr">All scripts are modular and organized to reflect the design stages described in the manuscript.…”

Shadow prices of metabolites that decrease flux through reactions from Random Forest. by Deborah A. Powers (15361394)

Modular architecture design of PyNoetic showing all its constituent functions. by Gursimran Singh (575288)

Subjects:

Design and implementation of DelaySSA. The input data for DelaySSA are reaction information, initial states, parameters and delays. Combining these into the simulation function, th... by Ziyan Jin (21021976)

Subjects:

Model reactions. by Roukayatou R. Ouedraogo (20460980)

“…<p>A: There are 11 reactions considered in the model: 5 involving unbinding, degradation, or exposure (non-crawling reactions), and 6 crawling reactions (4 within the same protofibril and 2 to a neighboring protofibril). …”

Comparison of PyNoetic’s functionality for BCI design with other existing state-of-the-art frameworks. by Gursimran Singh (575288)

Subjects:

Gillespie algorithm for the autocatalytic chemical reaction network from Asymmetric autocatalytic reactions and their stationary distribution by Lea Popovic (19511274)

“…Mathematica code for the GIllespie algorithm used to simulate the continuous Markov chain model of the autocatalytic reaction network…”