For a few years, a revolution has been underway:
it is becoming possible to create DNA faster, more reliably and, as an alternative of petrochemistry, to precisely drive living organisms to synthetize convenient molecules.
In the field of synthetic biology, and in addition to a multitude of experimental biology equipment, there are plenty of software tools to reach this aim. However, these tools are scattered and can be difficult to know and find them, difficult to install and make them interoperable, and sometimes results can change depending on which computer is used. To address these challenges, a community toolshed for synthetic biology, metabolic engineering, and industrial biotechnology has been developed: Galaxy-SynBioCAD.
Galaxy So today researchers and industrials use several tools by hand and have to reformate data from one analysis to the next to obtain the expected outcomes. This laborious work can be easily simplified by the Galaxy system. With its integrated solution, accessible from a single web portal, Galaxy platform helps scientists to handle these softwares (algorithms and tools) and hardwares (robots) resources, and promote a Findable, Accessible, Interoperable and Reusable research. Algorithms, tools and robots are effectively combined to simplify your design research.
To produce a compound of interest from a living organism, the team of Professor Faulon and his partners have developed dedicated tools and put them together into Galaxy workflows that enables to use them through a one-click interface. Workflows The first workflow, named Retrosynthesis, ask users the molecular structure of the molecule they wish to produce, and a formalized description of the living organism to be used for the synthesis.
Retrosynthesis technics are used to find metabolic
Retrosynthesis technics are used to find metabolic pathways starting from the native metabolites of the host organism and enabling the bioproduction of the desired molecule. The second workflow, names Pathway Analysis, takes the list of pathways built by the Retrosynthesis workflow and investigate which ones are the more appropriate for producing the molecule. Several criteria are taken into account such as speed of reactions, thermodynamics and other parameter such as length of the pathway or the taxonomic IDs.
The third workflow, named Genetic Design, asks the user one pathway, that would be typically the best one identified with the Pathway Analysis workflow, and delivers Python programmatic scripts to drive a robot that automate build of plasmids to produce enzymes necessary for the given bioproduction pathway. CONCLUSION We are clearly at a point where the pathway engineering process is not that far from being fully driven by computer software products. By chaining software tools and operate robots through Galaxy-SynBioCAD, it is as if we were in the days of MS-DOS and shifted to Windows. Revolution of synthetic biology can now run its course. It has many applications, from petro-chemistry to medicine and nanotechnologies.
Diode Production 