BrickIt iconBrickIt 0.1

BrickIt helps synthetic biologists to plan, track and organize their local biobrick samples.
BrickIt aims to create a portable web-based registry that helps synthetic biologists to plan, track and organize their local biobrick samples. The database-backed web server can be downloaded as virtual machine to quickly set up a local registry which coordinates the work within a lab, institute or community.

Although the data remain local, the web server itself is an open-source project and new functions or improvements can be easily exchanged between the different local registries. BrickIt thus also offers a platform for the shared development of tools and infrastructure that foster the collaboration within the Synthetic Biology community. BrickIt and everything it relies on are open source and free. BrickIt itself is licensed under the GPL.

Background

Synthetic biologists aim to design and implement complex devices from a set of standardized biological building blocks which are termed biobricks. Biobricks are fragments of DNA that are openly and freely shared across the community of synthetic biologists -- a public repository at the MIT (http://parts.mit.edu) collects the description of each submitted biobrick and also keeps samples of the physical DNA. What we are lacking are means to support the work in the individual labs before the submission of finished and tested biobricks. Typical projects rely on tens or more basic biobricks and easily produce hundreds of intermediate constructs that are floating around in countless test tubes.

Architecture

Brickit implements a database-backed Django web server. Django is a popular modular and object-oriented web framework written in the Python programming language. Both the data model and the web-interface are encapsulated in a quite simple Python package -- the database is created on the fly and does not need to be manipulated directly. This has the advantage that (1) it is easy to set up (so easy that even I managed :-) without prior knowledge of databases or SQL), (2) all parts of the project are formulated in a single elegant language which allows for easy modification, (3) actual data, data model, and data representation are clearly separated, (4) improvements to both the web interface and the data model can be coordinated with proven tools for shared software development (subversion, sourceforge).

A full BrickIt web server installation, complete with operating system, postgresql database and apache, is provided as Virtual Machine for fast deployment.

Status

Note, the project has barely started (pre-alpha-state?). The basic architecture is in place and seems to work (see screenshots) but improvements are needed everywhere: The data model needs to be discussed, the user interface needs to be better customized, the virtual server may not be perfectly configured, the exchange of Biobricks between brickit registries or with the MIT parts registry is not implemented, ...

How to contribute

Your help is greatly appreciated, in fact, needed if we want to move beyond the current prototype stage. Even if you don't know Python, there are tasks for many expertises: web design, javascript, databases, system administration ... or you could help by testing, documenting, improving this wiki (or creating a better one), discussing the data model, ...

last updated on:
February 21st, 2008, 14:16 GMT
price:
FREE!
developed by:
Raik Gruenberg
license type:
GPL v3 
category:
ROOT \ Information Management

FREE!

In a hurry? Add it to your Download Basket!

user rating 16

UNRATED
3.2/5
 

0/5

1 Screenshot
BrickIt

Add your review!

SUBMIT