Making standard for regulatory relationships

So far, we have made standard for logical gene module and genetic circuit (RFC 101 and RFC 97 version 2.0). In order to store and share the regulatory relationships between biological parts in circuit, we need a standard to standardize those relationships and give logic symbol to describe them.

To achieve this goal, we need

1 A complete standard of logical gene module.All of the logic genetic gates could be described in our standard,and all the inputs ,outputs and related variables could be quantified. As a result, any logic genetic gates in any genetic circuits could be simplified into a logical gene module.

2 All the stimulants and products could be quantified. Credible equantion could be applied to thess signals and the prediction can reflect biological phenomena.

Updating Database

The information stored in the database is not perfect now. We will update our database both from structure and content in the next version. The structure can be improved to coordinate the new version genetic circuit standard . More and better quality of circuits will be recorded from collecting and uploading.

Also, the database would collect all of the experiment data in the world for each circuit, and an actual measurement would be taken by our wet lab to ensure the working state of these circuit. In the anticipation, the database will be non-redundant, so that all of the high rank circuits we provided will be useful and well reproductive.

Further more, we will collect and call for more information for those incomplete circuits, such as useful parts or useful genes or measured data, to help build them successful.

Improving SBOL

We use extensions in SBOL exported by Circuit+ and this may result in some errors when other software reading this SBOL. We will fix this bug in the next version of Circuit+. We think we can also add our software to SBOL’s website as an example of how to use SBOL and join in the g+ group of SBOL to build a better SBOL.

Redesign LGD

In the first plan of our software, Logical Genetic Designer, which is also can be written as LGD, would be very powerful. Except the functions that Logical Genetic Diagram have, Logical Genetic Designer can also help users to redesign the circuits and show the relations in the new circuits. It can also show the relations between parts in circuit and gene that on the typical plasmids of E. coli. What’s more, it can even do modeling. Equipped with Logical Genetic Designer, you can designer your circuit very easily and wet lab time will be reduced. However, as freshmen when we came up with this idea, we found it too difficult. So we decided to do that step by step and this is why you can see LGD’s first version, Logical Genetic Designer. Believe us and we will make a true LGD in the future.

Cooperate with the Registry of Standard Biological Parts

We will contact the Registry of Standard Biological Parts. We have employed some data from the Registry through their API. The Registry and Circuit+ have many things in common and they are complementary to some degree. We think cooperation of the Registry of Standard Biological Parts and Circuit+ will open a new age of synthetic biology.

Promote the software

We will promote our software as well as synthetic biology in the future. The open database needs your participation and we are waiting for you!