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2021-07-16-cell-factory-design

abc-sysbio

al3c

al3c

alphafold

Open source code for AlphaFold.

amici

Advanced Multilanguage Interface to CVODES and IDAS

antimony

arfba

Allosteric Regulation FBA (simulation method)

asar

Advanced metagenomic Sequence Analysis in R

auto-sklearn

Automated Machine Learning with scikit-learn

autoblast

Automatically performs rosetta homology modeling

autocd

Automated synthetic microbial Community Design

autohomology

Automatically performs rosetta based Homology modeling. For now, semi-automatic.

autokeggrec

AutoKEGGRec is an automated tool that creates first draft metabolic network reconstructions of single organisms, community reconstructions based on a list of organisms, and finally a consolidated reconstruction for a list of organisms. All reconstructions are based on data from KEGG.

avida

azimuth

A Shiny web app for mapping datasets using Seurat v4

baranwal_et_al_2022

PyTorch Implementation of LSTM-based dynamical model for predicting species abundance and metabolite concentrations in a heterogeneous community

basset

Convolutional neural network analysis for predicting DNA sequence activity.

bayes_reactive_sindy

bingo

biobox

a toolbox for the manipulation, modelling and analysis of molecular structures

biochempantry

Load bioinformatics datasets into a local database

biocode

Bioinformatics code libraries and scripts

biological-oscillators

Study the Oscillations in Biology

biomassmw

Determining the chemical formulae and molecular weights of macromolecules in genome-scale metabolic models

bionetfit

A fitting tool for rule-based models

bionetfit-1

An application for fitting BioNetGen models using a genetic algorithm

bioscrape

BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)

black_queen_critique

A simple model to test if horizontal gene transfer explains the evolution of metabolic dependencies

blast-tutorial

boundaryconditionsforancientmetabolism

Associated github repository for code and data from the article "Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism"