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biochemistry

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MolecularNodes

BradyAJohnston /MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

blender proteins structural-biology pdb protein-data-bank protein-structure visualisation molecule molecular-dynamics molecular-graphics protein biochemistry molecular blender-addon molecular-modeling sciart protein-visualization geometry-nodes

UpdatedMar 20, 2025
Python

opencobra /cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

python flux bioinformatics modeling systems-biology computational-biology biochemistry metabolism cobra metabolic-models sbml metabolic-network cell-design strain-engineering sbml-model sbml-simulation

UpdatedMar 15, 2025
Python

weisscharlesj /SciCompforChemists

Scientific Computing for Chemists is a free text for teaching basic computing skills to chemists using Python, Jupyter notebooks, and the other Python packages. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, nmrglue, SymPy, scikit-image, and scikit-learn.

python science chemistry book numpy chemical biochemistry scientific-computing scipy jupyterlab simulations textbook jupyter-notebooks computing computer-programming jupyter-lab nmrglue chemists

UpdatedMar 16, 2025
Jupyter Notebook

fogleman /ribbon

Ribbon diagrams of proteins in #golang.

go chemistry protein-data-bank protein biochemistry 3d

UpdatedFeb 19, 2022
Go

copasi /COPASI

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

chemistry simulation dynamics modeling systems-biology biochemistry chemical-kinetics kinetics copasi

UpdatedMar 20, 2025
C++

micom-dev /micom

Python package to study microbial communities using metabolic modeling.

python flux community modeling systems-biology biochemistry microbiome hacktoberfest cobra microbiota cobrapy metabolic-models

UpdatedMar 3, 2025
Python

20n /act

Computational synthetic biology: Predicting DNA edits for bioengineering

data-mining deep-learning synthetic-biology biochemistry fermentation metabolic-network bioengineering computational-synthetic-biology acetaminophen reaction-operators metabolic-engineering enzyme-function

UpdatedMar 27, 2017
Java

maxscheurer /pycontact

Analysis of non-covalent interactions in MD trajectories

python bioinformatics chemistry analysis simulation toolkit dynamics molecular-structures molecular-dynamics computational-biology qt5 biochemistry interactions biophysics

UpdatedJan 3, 2025
Python

dwhswenson /contact_map

Contact map analysis for biomolecules; based on MDTraj

bioinformatics molecular-dynamics computational-biology biochemistry protein-protein-interaction protein-ligand-interactions

UpdatedDec 20, 2024
Python

katrinleinweber /PhD-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

markdown latex makefile biology pandoc latexmk latex-document biochemistry make zotero phd-thesis electron-microscopy microscopy citer eds diatom biofilm markdown-template

UpdatedOct 20, 2021
Shell

jaleezyy /covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

bioinformatics sequencing metagenomics biochemistry virology

UpdatedJan 16, 2025
Python

jiaqingxie /Theories-of-Graph-Neural-Networks

A List of Papers on Theoretical Foundations of Graph Neural Networks

topology optimization ode biochemistry np-hard pde combinatorial-optimization invariance gnn equivariance expressive-power

UpdatedOct 13, 2023

BRENDApyrser

Robaina /BRENDApyrser

A Python parser for the BRENDA database

python bioinformatics enzyme computational-biology biochemistry metabolism brenda enzyme-kinetics

UpdatedSep 15, 2023
Python

resendislab /corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

flux bioinformatics genome modeling systems-biology biochemistry metabolism reconstruction cobra cobrapy metabolic-models metabolic-network metabolic-reconstruction

UpdatedJul 15, 2024
Python

NoahHenrikKleinschmidt /qpcr

A python package to analyse qPCR data for single-use or high-throughput application

python pipeline biology biochemistry data-analysis qpcr qpcr-analysis

UpdatedDec 11, 2024
Python

IBM /AutoPeptideML

AutoML system for building trustworthy peptide bioactivity predictors

biochemistry automl interpretable-machine-learning peptide-prediction trustworthy-ai protein-language-model

UpdatedMar 13, 2025
Python

m2d2-labs /awesome-ml-for-biochemistry

Community-curated resources for research at the intersection of AI and molecular sciences

machine-learning awesome bioinformatics deep-learning cheminformatics ml biochemistry drug-discovery awesome-list

UpdatedAug 12, 2024

ddoak /peppy

A VR app which allows creation and manipulation of dynamic models of polypeptides. Focus is fun and learning.

unity structural-biology protein-structure virtual-reality biochemistry

UpdatedJan 1, 2020
C#

shyambhakta /wetlabcalc

Wetlab Calculator

laboratory genetics biology dna biochemistry biology-lab-protocols pcr wetlab-protocol restriction-enzyme polymerase-chain-reaction biotechnology goldengate wetlab-calculator

UpdatedDec 3, 2024

HussainAther /biology

genomics, biochemistry, biotechnology, cell biology, biophysics, ecology

genomics biology biochemistry biophysics biotechnology cell-biology

UpdatedMay 18, 2023
Python

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