Workflow Nodes

The ligase chain reaction (LCR) is a method of DNA amplification that differs from PCR in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard PCR cycling.

This tool uses a multi-objective algorithm to predict the best synthesis and assembling strategy for the previously designed plasmid using either Golden gate assembly, or Gibson assembly, or a mix of both. Given a set of designs (one design is a construct name and list of its parts), it finds a valid and efficient assembly plan to build all the designs. The designs and sequences of parts are provided as an SBOL file (see test_input.xml for an example).

This tool allows for the design and optimization of novel, reusable synthetic biology parts. For each enzyme predicted, it recovers the DNA sequence from the UNIPROT ID, runs a codon optimization protocol, and adds various strength calculated RBS (ribosome binding site) to it.

This tool takes as input a TAR collection of rpSBML files, that contain for each heterologous reaction a ranked list of UniProt identifiers for the sequences, and the list of links to the DNA registry SynBioHub for the desired vector backbones, resistance cassette, and promoters (generated using the tool "OptDoE Parts Reference Generator"). An optimal design of experiments is performed by using OptBioDes based on logistic regression analysis with an assumed linear model for the response. The
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Scans for the reaction rules and makes a REST request to Selenzyme and finds the enzymatic sequences (through Uniprot ID's) of all the reactions in heterologous pathways of rpSBML files.

Convert a single or multiple SBML files to SBOL using the UNIPROT id's from Selenzyme. Here the Ribosome Binding Site (RBS) strengths are characterized to be later used by the PartsGenie node.

After performing FBA, thermodynamic analysis on the heterologous pathways generated by Retropath2.0 this tool normalizes the different values from each heterologous pathway, and performs a weighted sum function using the following attributes:
- Length of the heterologous pathways
- Flux to the target compound
- Thermodynamic feasibility of the heterologous pathway
- Sum of the reaction rule scores