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
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
Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. It is performed for heterologous pathways generated by RetroPath2.0. The tool performs the following steps:
-Merges a user-defined GEM SBML model with each given heterologous pathway individually.
-Performs FBA using the CobraPy package. Three different analysis methods are proposed; two of which are native CobraPy methods - standard FBA and Parsimonious FBA, the other one proposed
Calculate the formation energy of chemical species either using an internal database or estimate it by decomposing them using the component contribution method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound.
Given the mono-component reactions generated by the tool "Pathways to SBML", this node adds the cofactors associated with each mono-component reaction generated by RetroPath2.0. The advanced parameters include the name of the heterologous pathway defined by "Pathways to SBML" node, the compartment ID of the SBML file (default is MNXC3, the MetaNetX ID for the cytoplasm). The tool also updates the reaction rule to include the SMILES cofactors to the reaction rule.
This tool takes for input the outputs of both RetroPath2.0 and RP2paths and generates a series of SBML files with mono-component reactions. Since more than one reaction rule may be associated with a single reaction, the best scoring reaction steps are considered before combining them to individual pathways. The number of combinations is controlled by the "Max reaction rules per reaction" parameter in the Advanced Options. The default value is 2, with a minimum of 1 with no maximum. A higher substep
RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. The advanced options include a time out parameter in minutes to limit the execution time of the tool. Similar to the RetroPath2.0 node, an internal limit is set on RAM usage for this server version of the tool.
This tool performs retrosynthesis search for possible metabolic routes between a source molecule and a collection of sink molecules. It takes as input, files from RetroRules, source and sink compounds (can be generated as explained in SynBioCAD Utilities), and the maximal pathway length (i.e; the number of steps). Only a single source molecule is processed at this time. Using Advanced Options, you can define the maximum number of compounds to keep for a next iteration (TopX), the minimal (dmin)
Given a collection or a single SBML file, this tool generates a CSV file output with all pathway information from the analysis tools (thermodynamics, FBA, etc). You can also specify the heterologous reactions and chemical species by providing the name of the heterologous pathway or SBML file ID.
This tool uses the MIRIAM cross-references as well as in-house annotations that contain chemical structure descriptions (InChI, InChIkey, and SMILES) to identify similar chemical species and reactions. Thereafter, the divergent chemical species and reactions are inserted into the target SBML model. The tool can take as input a single source SBML or a collection of source SBML in a TAR format, but must have have a single target SBML file. Typical use case of this tool would be to insert a heterologous
Sink refers to the collection of chemical species used by the restrosynthesis algorithm of RetroPath2.0 to finish metabolic route exploration. This tool uses an SBML file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytoplasm, Golgi apparatus, nucleus, etc) and uses its MIRIAM annotation to find their InChI structures. You can use "Remove dead-end metabolites using FVA evaluation? to conduct Flux Variability Analysis to remove metabolites that