Tools
CAVE is a cloud-based platform that calculates and visualizes optimal metabolic pathways using flux balance analysis, and serves as a GEM quality control tool with network modification capabilities, all supported by a scalable serverless architecture.
Reaction Enzyme Mining & Evaluation (REME) Platform, the first integrated web platform for reaction enzyme mining and evaluation, is explicitly designed to solve two fundamental bioengineering problems: 1. Mining potential enzymes for natural and non-natural bio-related reactions; 2. Evaluating the catalysis possibility of provided (or mined) enzymes and reactions.
WPHP enables users to design optimal synthetic pathways for products in different host organisms. The results provide the yield of product, the flux distribution of pathway and the enzyme or genes encoding every reaction and the visual representation of any pathway.
QHEPath is a cloud-based, serverless web tool for quantitative heterologous pathway design. It relies on a quality-controlled universal model from the BiGG database and employs an algorithm to compute multiple suboptimal and optimal pathways for product synthesis.
ECRECer is a deep learning based bioinformatic toolkit to recommend EC numbers with high accuracy and high recall.
Model Quality Control (MQC) is an online tool designed for the quality assessment and automatic correction of genome-scale metabolic network models (GEMs). It focuses on identifying errors such as incorrect exchange reaction boundaries, faulty net generation of reducing equivalents, energy, and metabolites. Furthermore, MQC verifies whether the yield of each carbon-containing metabolite exceeds the theoretical optimal yield and evaluates if the organism can be simulated to grow while ensuring that the biomass composition equation is mass balanced. MQC then automatically corrects these errors, with a specific emphasis on ensuring accurate quantitative pathway calculations from the model.
OptME is a user-friendly web platform designed to assist researchers in metabolic engineering design. OptME simplifies computational target design—a key step in the DBTL (Design-Build-Test-Learn) cycle—by narrowing experimental scope and prioritizing metabolic engineering targets.OptME integrates classic algorithms like FSEOF (PMID:20348305) and OptForce (PMID:20419153) with newer approaches such as iBridge (PMID:37935194). It supports both stoichiometric-based and enzyme-constrained models (PMID:35858410), offering a comprehensive toolset that connects computational models with experimental workflows.
GEDpm-cg enables users to perform the efficient, automated and high-throughput design of single nucleotide editing in C. glutamicum chromosome. The counter-selection HR system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for genetic modification, vector DNA assembly and sequencing verification were provided as design results
AutoESD is a web tool for Automatic Editing Sequence Design for genetic manipulation of microorganisms, and it enables users to perform the precise, automated and high-throughput design of sequence manipulation tasks across species and technical variations, at any genomic locus for all manipulation types with adequate sequence length. The screening-marker-based homologous-recombination system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for sequence manipulation, vector DNA assembly and sequencing verification were provided as design results.
AutoESDCas is a A web tool for Automatic Editing Sequence Design for genetic manipulation of microorganisms based on CRISPR/Cas system, and it enables users to perform the precise, automated and high-throughput design of genome editing tasks. It facilitates all types of genetic manipulation as well as different CRISPR/Cas system-mediated homologous recombination genome editing technology variants and experimental requirements. The editing sequences such as sgRNAs, homology arms and primers for the whole-workflow of genome editing can be designed. Based on these editing sequences, genome editing experiments could be implemented.
FSsgRNA-Analyzer is A cloud platform for NGS data processing in CRISPR based functional screening, and it enables experimental biologist to perform the sgRNA data analysis easily during CRISPR based functional screening. The cloud platform is based on a novel serverless architecture, which enables high reliability, robustness and scalability. After users uploading raw sequence data and target sgRNA data, FSsgRNA-Analyzer can execute the primary analysis for NGS data (read cleaning, mapping and sgRNA counting), then perform the secondary analysis (correlation or differential analysis) among samples under different culture/selection conditions.
GSCAS-MTM is a web tool designed to generate optimized schedule trees for the parallel construction of a large number of objective strains. Our tool utilizes two complementary algorithms, GSCAS (Greedy Search of Common Ancestor Strains) and MTM (Minimizing Total Manipulations), to efficiently design strain construction schedules.
DNA synthesis is widely used in synthetic biology to construct and assemble de novo nucleotides, such as synthetic engineered protein, artificial synthetic genome. Many sequence features (e.g., GC content, repeats) are known to affect the process of DNA synthesis. SCP4SSD, a serverless cloud platform, was developed for nucleotide sequence synthesis difficulty prediction.
AutoVTC is a web tool specifically designed to streamline comprehensive, automated, and high-throughput mutation scanning for targeted genetic manipulation. This efficient tool excels in calling high-quality single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and double peaks from Sanger sequencing chromatograms.