BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data by Jean-Christophe Lachance (6619307)

“…Despite its importance, no standardized computational platform is currently available to generate species-specific biomass objective functions in a data-driven, unbiased fashion. To fill this gap in the metabolic modeling software ecosystem, we implemented BOFdat, a Python package for the definition of a <b>B</b>iomass <b>O</b>bjective <b>F</b>unction from experimental <b>dat</b>a. …”

Comparison of the user-friendly graphical interfaces and functions of the single nucleotide polymorphism (SNP) analysis pipelines. by Dong-Jun Lee (14068673)

Subjects:

Python code for a rule-based NLP model for mapping circular economy indicators to SDGs by Zahir Barahmand (18008947)

“…The package includes:</p><ul><li>The complete Python codebase implementing the classification algorithm</li><li>A detailed manual outlining model features, requirements, and usage instructions</li><li>Sample input CSV files and corresponding processed output files to demonstrate functionality</li><li>Keyword dictionaries for all 17 SDGs, distinguishing strong and weak matches</li></ul><p dir="ltr">These materials enable full reproducibility of the study, facilitate adaptation for related research, and offer transparency in the methodological framework.…”

Frequency-dependent pre- and post- synaptic plasticity in rate-based models. by Toviah Moldwin (10866708)

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics by Paolo Cifani (1575613)

“…Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. …”

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics by Paolo Cifani (1575613)

“…Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. …”

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)

Modeling with uniform <i>σ</i> values. by Giacomo Janson (8138517)

Effect of <i>|Δd</i>_<i>n</i><i>|</i> perturbation on 3D modeling. by Giacomo Janson (8138517)

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling by Giacomo Janson (8138517)

“…This program implements the “modeling by satisfaction of spatial restraints” strategy and its core algorithm has not been altered significantly since the early 1990s. …”

Hist-8000 sequence similarity scores are closer to the ground truth than the corresponding Sum-of-learnt-Trigrams scores. (NW, Hist-8000) and (NW, Hist-SDM12) are both higher than... by Frixos Papadopoulos (22001664)

Genetic algorithms can be applied to higher-dimensional design problems. by Lu Hong (399882)

Example of use of the slightly off-axis strategies. by Raul Castañeda (13932971)

Example of the fully-compensated phase reconstruction package for off-axis DHM holograms recorded in telecentric configuration. by Raul Castañeda (13932971)

The algorithm underlying neoVM. by Tanmoy Sarkar (627505)

Comparison of edge detector and CHT in detecting droplets. by Manibarathi Vaithiyanathan (6655274)

Glioblastoma multiforme (GBM) pathway modules identified by the netboxr package from cancer genomics alteration data without the use of pre-defined gene sets. by Eric Minwei Liu (9592176)

Supporting data for "Personalized Electromyography Based Control Algorithm Development and Training System for Hand Prosthesis" for HKU Libraries by Xiaojun Wang (9067289)

<b>Algorithm Pseudocode</b> by Yibin Zhao (22425801)

DataSheet2_Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.PDF by Miguel Castresana-Aguirre (12521683)

“…<p>Functional analysis of gene sets derived from experiments is typically done by pathway annotation. …”