Uncurated Protocols Library

This is a Protocol for transforming plasmid DNA into P. putida cells by electroporation. This is a fast and easy-to-use method of introducing plasmid DNA in P. putida cells with high transformation efficiency. This Protocol is adapted from [1] and encompasses the steps for the preparation of competent cells and transformation of plasmid DNA by electroporation.

All Inputs of the Protocol, listed in the section 4.1., can be acquired either from other IBISBA Protocols or purchased from commercial
...

This document constitutes deliverable 4.4 of the IBISBA 1.0 project. IBISBA 1.0 receives funding from the EU H2020 research and innovation programme under grant agreement No 730976.

A vision paper describing the founding principles behind IBISBA

This DMP relates to the IBISBA 1.0 project

Given a collection of SBML files with the heterologous pathways, calculate the FBA and the Gibbs free energy of the pathways.

Given one or a collection of heterolgous pathways in SBML files, generate the SBOL for the constructs and the assembly protocols to build them

Perform retrosynthesis using RetroPath2.0 and convert the heterologous pathways to SBML files

Galaxy workflow that predicts heterologous pathways for the production of a compound of interest in an organism of interest

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
...

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.