计算生物学

对生物数据和系统进行分析、可视化和建模

MathWorks^® 计算生物学产品为生物信息学和系统药理学应用提供执行各种分析工作流的工具。

使用 App 或在命令行构建端到端生物信息学管道，并在本地或集群环境中运行这些分析工作流。您可以使用 App 查看和探查集成的下一代测序 (NGS) 数据，识别差异表达的基因或特征，并从 NGS 数据中发现拷贝数变异。

使用集成的 App 或在命令行中，为定量系统药理学 (QSP)、基于生理学的药物代谢动力学特性 (PBPK) 和药物代谢动力学特性/药效学 (PK/PD) 应用创建和分析动态模型。例如，您可以运行并行仿真和参数扫描来评估目标可行性和表征生物变异性。您还可以使用局部和全局敏感度分析来识别关键参数，并通过非线性回归和混合效应方法来估计模型参数。然后，使用自动生成的报告和部署的应用程序共享您的工作和模型。

适用产品：计算生物学

Bioinformatics Toolbox

Read, analyze, and visualize genomic and proteomic data

SimBiology

Model, simulate, and analyze biological systems

主题

下一代测序

Count RNA-Seq Reads Using Biopipeline Designer (Bioinformatics Toolbox)
Create a bioinformatics pipeline to count RNA-Seq reads that are mapped to genomic features.
Visualize NGS Data Using Genomics Viewer App (Bioinformatics Toolbox)
View NGS alignment data for single nucleotide variation in cytochrome p450 gene.
Identifying Differentially Expressed Genes from RNA-Seq Data (Bioinformatics Toolbox)
Use a negative binomial model to test RNA-Seq data for differentially expressed genes.

定量系统药理学

Incorporate SGLT2 Inhibition into Physiologically Based Glucose-Insulin Model Using SimBiology Model Builder (SimBiology)
Update a glucose-insulin model to integrate sodium-glucose co-transporter 2 (SGLT2) receptor inhibition by a hypothetical compound.
Find Important Parameters for Receptor Occupancy with Global Sensitivity Analysis Using SimBiology Model Analyzer (SimBiology)
Perform GSA analyses, such as Sobol indices, elementary effects, and multiparametric GSA, to find important model parameters in a target-mediated drug disposition model.
Explore Biological Variability with Virtual Patients Using SimBiology Model Analyzer (SimBiology)
Generate sample values for model parameters to represent virtual patients, simulate to explore tumor growth variability, and investigate the effects of dosing regimens on tumor size.

PBPK 和 PK/PD 建模

Create Model of Receptor-Ligand Kinetics (SimBiology)
Create and simulate a simple receptor-ligand kinetics model using SimBiology apps.
Calculate NCA Parameters and Fit Model to PK/PD Data Using SimBiology Model Analyzer (SimBiology)
Calibrate model parameters by performing noncompartmental analysis and fitting to experimental PKPD data using nonlinear regression.
Model the Population Pharmacokinetics of Phenobarbital in Neonates (SimBiology)
Perform nonlinear mixed-effects modeling using clinical pharmacokinetic data.
Estimate the Bioavailability of a Drug (SimBiology)
Fit a model of absorption and excretion of the drug ondansetron to estimate its bioavailability.

精选示例

Perform PK/PD Modeling and Simulation to Guide Dosing Strategy for Antibiotics

Perform a Monte Carlo simulation of a pharmacokinetic/pharmacodynamic (PK/PD) model for an antibacterial agent. This example is adapted from Katsube et al. [1] This example also shows how to use the SimBiology® SimFunction object to perform parameter scans in parallel.