The Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB)
iBioFAB is a fully integrated computational & physical infrastructure that supports rapid design, fabrication, validation/quality control, & analysis of genetic constructs & organisms. As the first "living foundry" in the world, the iBioFAB provides a new manufacturing paradigm for chemicals, materials, & biologics. It features a central robotic arm that transfers labware between instruments that perform distinct unit operations such as pipetting, incubation, or thermocycling.
ibiofoundry.illinois.edu/
CRISPR-COPIES
COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites (CRISPR-COPIES) is a user-friendly web application & a command line tool for rapid discovery of neutral integration sites. Designed to work for any organism w/ a genome in NCBI & for any CRISPR system, CRISPR-COPIES can identify neutral sites in a genome-wide manner. The identified sites can be used for characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, & human gene & cell therapy (editing).
github.com/Zhao-Group/COPIES
This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast & accurate off-target search and can identify genome-wide intergenic sites for most bacterial & fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in 3 diverse species: Saccharomyces cerevisiae, Cupriavidus necator, & a human cell line.
biorxiv.org/content/10.1101/…
PCR Primer Design & Variant Management
Mutagenesis provides streamlined primer design & worklist generation for site-directed mutagenesis workflows. The tool supports automated generation of mutation libraries, offering researchers a reproducible & scalable approach to engineering genetic variants.
github.com/Zhao-Group/Primer…
A generally applicable platform for autonomous enzyme engineering that integrates machine learning (ML) & large language models (LLMs) w/ biofoundry automation to eliminate the need for human intervention, judgement, & domain expertise.
Requiring only an input protein sequence & a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins.
nature.com/articles/s41467-0…
CLEAN
clean.platform.ibiofoundry.i…
CLEAN predicts Enzyme Commission (EC) numbers for enzyme sequences. This machine learning algorithm, Contrastive Learning enabled Enzyme ANnotation (CLEAN), was trained on high-quality data from UniProt, taking amino acid sequence as input & outputting a list of EC numbers ranked by the likelihood.
github.com/tttianhao/CLEAN
The contrastive learning framework empowers CLEAN to confidently (i) annotate understudied enzymes, (ii) correct mislabeled enzymes, & (iii) identify promiscuous enzymes w/ two or more EC numbers—functions that we demonstrate by systematic in silico & in vitro experiments.
science.org/doi/10.1126/scie…
Open Enzyme Database
openenzymedb.platform.molecu…
Open Enzyme Database: a community-wide repository for sharing enzyme data
academic.oup.com/nar/article…
The plasmid database (PLSDB)
Plasmids can be explored & filtered using the browsing tables. Nucleotide sequences can be searched in the database by either using Mash
mash.readthedocs.io/en/lates… for longer sequences (e.g. contigs or long reads), or by using BLASTn
blast.ncbi.nlm.nih.gov/Blast… for shorter sequences, e.g. genes.
ccb-microbe.cs.uni-saarland.…
PlasmidMaker_GuideDNA
Given any number of annotated '.DNA' file as an input, the code generates guides, primers & possible combinations of restriction enzymes for performing & verifying high-fidelity, scarless PfAgo-guided plasmid assembly. A standalone code to verify plasmids using restriction digestion enzymes is also provided.
github.com/Zhao-Group/Plasmi…
PlasmidMaker
A versatile, automated, & high throughput end-to-end platform for plasmid construction
nature.com/articles/s41467-0…