GS-Box

A simple & efficient tool for Gene-Socket

Every excellent technique should be simple and efficient to use! As an excellent technique, gene-socket also does well in this respect------ it has its' own optimization tool: GS-BOX. GS-BOX is a bioinformatics tool which is designed for customs to build their own gen-sockets easily and efficiently. What need the customs do with the tool? Just input the gene circuit sequences and then GS-BOX will design the experimental process automatically and every detail that customs will need to use!

Solutions

As you see, we built 2 parts to help biologists to insert their gene of interest( GOI ) into the chromosome. When we built this tool, we thought about a question: can Gene-Socket only insert simple genes like GFP into chromosome? Now, we can announce that the answer is "No". With the help of Gene-Socket, we can build kinds of gene circuits no matter how complex they are.

If we just want to insert one part into the chromosome, what should we do? We can add two homeoregions next to the part, then link them to the part BBa_k1433009. In this way, we can use Gene-Socket to insert the new gene-combination into chromosome. (See how we solve the problem in the picture). We call this occasion "Mode 1".

Now we want to build a more complex circuit. We want to insert a promoter, an RBS and a CDS. If we still use the old method, our promoter will not work. It seems that we need to find a new way. What if we change the homeoregions? We can replace the old promoter with a new one by designing the homeoregions. (See how we solve the problem in the picture). We call this occasion "Mode 2".

Well, what if our circuit contains a terminator? It will stop the gene expression and break our hearts. But if we link the circuit with a new part, BBa_k1433010, the problem seems to be solved. (See how we solve the problem in the picture). We call this occasion "Mode 3".

As you see, If you want to use GS-Box to insert your part into the chromosome,there are 3 classical mode for you.

• Mode 1: You choose to use the our official promoter & terminator
• Mode 2: Your don't want to use our promoter
• Mode 3: Your part contains a terminator

With the methods that we have used above, we can solve most problems when we want to insert a gene-circuit into chromosome, but sometimes the situation may be more complex. We cannot list all of the situations for you, but we have given you the tool and the idea to solve a new problem. Join the designers’ team and enjoy it!

Example

Example 1:
I just want to insert a simple gene---GFP(see the picture below). This situation is very simple. According to "Solutions", this is the mode 1, and I need to modify it as the picture below.


Example 2:
I want to insert a circuit, which contains a promoter, a RBS and GFP(see the picture below). According to "Solutions", this is the mode 2, and I need to modify it as the picture below.


Example 3:
I want to insert a circuit which contains a RBS, a GFP and a terminator(see the picture below). According to "Solutions", this is the mode 3, and I need to modify it as the picture below.

Download

GS-Box is an useful web tool, it contains some fuctions that people often use. So we share all the codes of GS-Box(except images) to help other IGEMers to use GS-Box in their own computers or share with more people. As you see, we submit a ZIP named "all codes" below and you can download it for free. In the ZIP, there is a "Read me" txt, please read it before you use it. You can also download our database which is strictly chosen and the data is OK to use. Before you use the codes and the database, you need to install a local-BLAST, which is developed by NCBI.

ALL codes / Database