TODOs

Todos for the BioBrick to PoBoL conversion
1) Get the DNA and Sequence Info (straightforward from or partsregistry DAS)
2) Set up the webpage
3) Have a OWL validator set up

After that we need to figure out how are we going to figure out what part is a promoter, and what repressor or activation sites it has (if any). [This is for main goal for converting a schematic to biobrick.]

Webpage for converting BB into PoBoL

I was thinking about a user friendly way to have BioBrick information converted into PoBoL. One of the ideas was to provide a GUI front end to the python scripts. In the GUI I was thinking it will be wonderful to have a web page preview of the actual BioBrick being saved, just to make sure right information is being parsed and entered.

However, after searching for how to embed a browser in Python (without using COM/CORBA, in which case firefox could be embedded in GUI), I think it will be lot easier if there was a web page, where on the left side there was an editable table of entries for info going into the PoBoL format and right side was a preview of the current BioBrick. Probably, I am going to password protect the page to avoid spammer.

Example run for current revision

Here is what the revision 6 in the repository parses. The part is BBaJ01120. The sequence information for parts is available from the DAS site's xml markup (which is why this script does not parse that yet).

$ python bb_parser.py
Date Entered:  2006-01-05
Sacrafical OnRFP Kan vector i12351 in pSB2K3 
a sacraficial kan vector used for swapping 
resistances by removing the onRFP indicator...
loss of color as success. Sequence and Features

# The '=' denote end of line(s)
# All the info is in dictionary
$ python bb_parser.py 
Key:             Data:
Designed by          Golden Bear=
Members of these groups may edit the part -   
Endy Lab, iGEM_Berkeley, Knight Lab, Part Editors, Registry=
Owner -              Golden Bear=
DNA Status           Planning=
Part Type            Intermediate=
Categories           //classic/intermediate/uncategorized=
Short Description    Sacrafical OnRFP Kan vector=

TwinParts          Info
BBa_J14463           Planning.
BBa_J14462           Planning.
BBa_I763033          Available.
BBa_J01121           Planning.
BBa_I13521           Available.

First Import Into the Repository

Alright, some code is in the repository. Although it's not very functional (which is different from working), I wanted some revision control over it.

Check it out and run "svn update" often!

Feel free to google svn how to or checkout (pun intended) my take on it at: HowTo:SVN.

Getting the registry data

I am working on writing a basic python script that will scrape off data from the registry pages and convert them into OWL format suitable for PoBoL. This is what I decided to do after I did not get any response from Randy asking him about the database for the parts registry.

I am learning python and the OWL format on the fly which should be fun. (I used Perl before as a scripting language).

SeToB?

This blog is for any features or news related to SeToB. It is a schematic to BioBrick conversion tool, which will be a web based application. The parts registry (http://partsregistry.org/Main_Page) holds all the BioBricks, which will be used by this tool. Rather than querying the partsregistry page, the BioBricks will be stored in PoBoL format, which should make the querying data easier. The schematic that the user will input will be of the form, Promoter, RBS, Gene, and Terminator to start with (and it will be in a UI form).

The specifications and/or tasks for this project can be looked at http://code.google.com/p/setob/wiki/Requirements