Project Plan for BIOMOD-2011

I am a part of the team DA-NanoTrons, representing my college DA-IICT in BIOMOD-2011.

Our team is -

• Faculty mentors
  • Manish K. Gupta [DA-IICT, Gandhinagar]
  • Taslimarif Saiyed [NCBS, Bangalore]
  
  
• Team members 
• Avinash Parida
• Denny George
• Mayank Kandpal 

Project plan :

Part 1 : (BIOMOD-2011)

Providing an interface for the users to input equations corresponding to 2-D shapes, which will generate a caDNAno friendly .json file output. This can directly be opened with cadnano and the structure can be further edited there. (So its like a basic cadnano template creator which can then be used and made into more complex structures on caDNAno)

The application will be a standalone for now and might be integrated into caDNAno later on.

We can even provide some default templates for some very basic equations.

Plan of Action :

1.1 Understand the format of cadnano gerenated json files and try to create simple files which are correctly displayed in cadnano. this would be done by creating some simple files in caDNAno and understanding the structure of files after saving them.  Initially dont worry about 3d, just create 2d .json file structures and run them on caDNAno.

1.2 Hack through the cadnano ActionScript code-base to understand their auto-stapling algorithm.

1.3 What would the program do :

    1.3.1 Take equation as input

    1.3.2 Generate the outline of the corresponding 2D shape

    1.3.3 Generate a single loop which fills the entire structure  

    1.3.3 Divide the loop into 7000 parts (there is a reason behind 7000)

    1.3.4 Select a point to break the loop and thus create a single long scaffold.

    1.3.5 Assign each division a base-pair (ACGT) ordered in the sequence of the standard M13mp18 virus DNA sequence. I have a rough visualization of the expected output after this stage, which I would share soon.

    1.3.6 Use the auto stapling algo to generate staples in the structure. (optional)

    1.3.7 Automatic StapleError correction feature (optional, will skip this most probably in Phase-1)

    1.3.8 Create the cadnano friendly json file corresponding to the structure and staples we generated.

How we could divide the work :

For parallely working on different things, we all need to be clear on how we would be storing the structure in each stage in the backend. In other words, what the output format/structure of each stage would look like.

For example, if we are clear initially how the backend would look like in step 1.3.6, then one person can start working directly on a manualy created output of step 1.3.6 and work on how to create a cadnano friendly json from the structure that we finally come up with.

Thus, before we begin with any coding, we need to be clear with what output we expect in each stage. For this, we need to first of all decide a platform which we would be working on. Considering the requirements. I am assuming java (or python) would be the best choice.

In case we find other platforms with better library support we would use that.  So first step is to hunt down the available libraries for each task.

Parallel task 1 : 1.3.1 - 1.3.5

Parallel task 2 : 1.3.6

Parallel task 3 : 1.3.7

FallBack Plan for part 1:

If we are too technically handicapped to understand the auto-stapling algorithm, we can simply skip step 1.3.6 and jump to 1.3.7, i,e, just generate the single long scaffold corresponding to the 2D structure represented by the equation and convert it to .json format which would can be opened in cadnano. The user can then use the autostapling feature within cadnano.

Part 2 : (to be done in the next year’s Biomod, OR if time permits(unlikely), within the current Biomod timeline)

2.1 Provide support for equations of 3D structures.

2.2 Either create Views Interface so that the user doesnt need to switch to cadnano just for checking out the output. OR port the entire application as a cadnano plugin itself.