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Welcome to BrickIt!
- 1. setup Ubuntu server
- 2. setup Postgresql
- 3. setup Django
- 4. setup Brickit
- 5. setup Backup
- 6. setup Apache
- old instructions
- Quick local installation (Ubuntu/Debian)
- Quick local installation (OS X)
- Database migration
Quick overview
BrickIt aims to create a portable web-based registry that helps synthetic biologists to plan, organize and track 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.
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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.
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, ...
See also
BrickIt Presentation: [file:2007_brickit_biobrick_workshop.ppt] (Biobrick foundation workshop, Boston, 11/2007)
Introduction to Biobricks: [file:2007_12_bbseminar.ppt] (Seminar at the CRG, 12/2007)
Recommended Links
the MIT parts repository OpenWetware
Django home the Django tutorialPython
Update 03/01/2009
The new release is now also available for download as VMBrickit virtual machine.
Update 26/01/2009
BrickIt 0.2 released -- This new version of BrickIt constitutes a major overhaul. Both data model and user interface have seen a lot of changes and the layout of the python module has been adapted to better accommodate future development. There are several new features: At last, it is possible to compose Biobricks from other Biobricks, Sequencing data can be added to samples, and some more...
Check out the release notes!
Brickit 0.2 on sourceforge
Update 06/02/2008
The VMBrickit virtual machine has been updated to release 0.1 (svn revision 120 actually, which adds some example data). Note, there is no need to replace a running system, follow the update instructions instead.
Update 03/02/2008
BrickIt 0.1 released -- I've bundled the current version of the project into a first release for easy download and evaluation. See: BrickIt 0.1 on sourceforge
BrickIt 0.1 corresponds to the version in use at the CRG. The data model has been updated to account for different biobrick formats, to allow for the construction of composite biobricks (Unfortunately, the latter is not yet well supported by the web interface), and to fix some smaller inconsistencies we came across during our daily use. The release is tagged 'release-0.1' in the subversion repository. I will continue to add bugfixes and further improvements to the main ('trunk') development line -- as long as they don't break the existing CRG installation. Anything beyond that (i.e. changes to the data model) will first go into the 'devel' branch and will only be merged back for the next official release. Should there be any changes to the data model, I will include a script with 0.2 to migrate an existing installation without data loss. That means, it should be reasonably save to base your first small production registry on this BrickIt version -- as long as you don't expect anything too fancy...
See also: release notes.
Update 01/11/2007
The Brickit virtual machine (vmbrickit) is ready for download! See: Virtual Server
Update 05/09/2007
We have now refined our data model, the administration interface has received some filters and search fields, and some rules are enforced on the input of sample and container labels. All this is still easily done by adding tags and parameters to the model definition. The result looks already pretty useful and professional. But I guess we are now getting to the point where one should start to adapt looks and functionality with custom page templates and own python code...
