amirhossein207 Goto Github PK
Name: Amirhossein Masroor
Type: User
Bio: Masters student in Chemical Engineering at Shiraz University
Blog: AmirHossein207.github.io
Name: Amirhossein Masroor
Type: User
Bio: Masters student in Chemical Engineering at Shiraz University
Blog: AmirHossein207.github.io
My personal website.
Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
Collection of pipelines, workflows and scripts for processing SNP and gene expression arrays and NGS data
MATLAB scripts and utilities for the COMETS software for spatial DFBA
Fermentation simulator used in paper: "A study of a diauxic growth experiment using an expanded dynamic flux balance framework", Karlsen et al. 2022
GWAS Tutorial for Beginners
lightMM: a novel tool for calculating kinetic constants in the Michaelis-Menten equation from two substrate concentrations
Linear Algebra for Data Science. A Textbook for Students and Practitioners
A Matlab implementation of Thermodynamics-based Flux Analysis
A code for the paper "Estimating kinetic constants in the Michaelis-Menten model from one enzymatic assay using Approximate Bayesian Computation"
This is the code accompanying my master's thesis
PhenoMapping is a computational framework that provides some workflows and methodologies for the understanding of mechanisms underlying phenotypes using genome-scale models (GEMs). PhenoMapping classifies the information in a GEM as organism-specific information and context-specific information. Organism-specific information includes the (i) biochemistry/metabolic functions annotated to the genes, (ii) the localization of enzymes, (iii) the intracellular transportability of metabolites, and (iv) the enzymatic irreversibilities defined/ad hoc pre-assigned directionalities. Context-specific information involves (i) the medium composition, (ii) the reaction directionalities given a set of metabolomics data, (iii) the reaction flux levels given a set of gene expression data, and (iv) the possibility of regulation of gene expression between isoenzymes given a set of gene expression data. PhenoMapping is modular and allows the independent study of these mechanisms. The PhenoMapping workflow suggests a sequence that one can follow for the study of these mechanisms and analysis and interpretation of the results. PhenoMapping was developed for the analysis of high-throughput fitness phenotypic data throughout the life cycle of the malaria parasite P. berghei, and served to curate the genome-scale model of this organism (iPbe) and generate context-specific models for the blood (iPbe-blood) and liver (iPbe-liver) stages - both of which show approximately 80% accuracy and 0.5 Matthew Correlation Coefficient (MCC) with the phenotypic data.
Work with PLINK from R
A Python 3 implementation of Thermodynamics-based Flux Analysis
A sequential gene scanner for both gene deletions and upregulations, based on flux balance analysis
Codes from various Systems Biology course written in Matalb
Integration of gene expression data with TFA constraints
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.