JBEI / ART
A machine learning tool to improve the effectiveness of strain engineering in synthetic biology
☆56Updated this week
Alternatives and similar repositories for ART:
Users that are interested in ART are comparing it to the libraries listed below
- teemi: A Python package for reproducible and FAIR microbial strain construction. Simulate the entire dbtl-cycle, generate genetic parts, …☆40Updated this week
- Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies☆54Updated last year
- Release of the whole cell E. coli model.☆63Updated 2 months ago
- Computational tools for extremely low-cost, massively parallel amplicon-based sequencing of every variant in protein mutant libraries.☆32Updated 2 years ago
- Evolutionary velocity with protein language models☆84Updated last year
- Mutation effects predicted from sequence co-variation☆63Updated 7 years ago
- Models, design algorithms, and other software related to Salis lab publications☆28Updated 3 months ago
- Fast protein structure searching or your money back☆95Updated last week
- METIS: A versatile active learning workflow for optimization of genetic and metabolic networks☆27Updated 2 years ago
- Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".☆57Updated 3 years ago
- Species-aware DNA language modeling☆18Updated 2 years ago
- A Python framework for structural systems biology☆107Updated 4 years ago
- Inference of couplings in proteins and RNAs from sequence variation☆106Updated 2 years ago
- PSIPRED Protein Secondary Structure Predictor☆54Updated 3 months ago
- Visualise RNA secondary structure in consistent, reproducible and recognisable layouts☆68Updated last week
- Toolbox for including enzyme constraints on a genome-scale model.☆68Updated 4 months ago
- A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence☆52Updated 2 months ago
- Multi-class signal peptide prediction and structure decoding model.☆83Updated 2 weeks ago
- Improving RNA structure prediction through multitask learning on diverse crowdsourced data.☆53Updated 7 months ago
- A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.☆37Updated last year
- StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy☆41Updated this week
- MMseqs2 app to run on your workstation or servers☆70Updated this week
- Transmembrane proteins predicted through Language Model embeddings☆33Updated 3 weeks ago
- Learning Kinetic Models from Time Series Proteomics and Metabolomics Data☆28Updated 2 years ago
- Degenerate Codon Design☆13Updated 5 years ago
- BRENDA parser in python☆21Updated 2 years ago
- ☆62Updated last year
- nucleic acid folding☆88Updated 6 months ago
- PyMOL extension to color AlphaFold structures by confidence (pLDDT).☆85Updated 6 months ago
- PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.☆23Updated last year