Wet Work

Undergraduates from the team performed all wet lab work, from plasmid mini-preps to PCRs to gel extractions.

We filled our own pipette tip boxes, prepared our own TBE buffer and poured our own agarose gels. We even rode our bikes to the laboratory supply center to buy our own 96-well plates for liquid culture analysis.

We based our protocols on existing Facciotti lab procedures and information on OpenWetWare.org.

We revised and improved the mutagenic PCR protocol from this paper to function well with standard BioBrick primers and to produce mutations at a suitable rate for our project.

Data Analysis

The information and graphics on our data and project pages comes from analysis performed by undergraduate team members.

Keegan wrote scripts in Octave which were used by all team members to parse raw data from our plate reader for mutant screening, promoter activity assays and fluorescence emission scans. Similar scripts were also used to output our 2D and 3D graphs.

Wiki and Graphic Design

We designed and built this website from the ground up.

The layout was a group effort, with templates designed by Tim. Much of the wiki formatting was removed using CSS code from the 2009 TU Delft iGEM team.

Tim was the primary designing powerhouse behind the wiki and contributed largely to the Notebook section, particularly the gallery. He also implemented the Lightbox 2 code from this site to allow photo viewing from our Flickr account.

Keegan implemented the JQuery javascript library, CSS and HTML code to format our pages, animate the custom menu bar, and enable automatic in-line linking of all instances of BioBrick parts on our site to their corresponding partsregistry.org pages.

Photographs and Animations

All of the photographs on this site were taken by members of our team.

Tim borrowed a DSLR to take nearly all of the photographs of plates, lab equipment, and lab personnel. Aaron also took some shots with the DSLR, and all team members used the cameras on their phones to document progress and take snapshots. The 3D animations in the projects page were created by Tim and Keegan by exporting 3D data from protein models from PyMol into Blender and exporting animation frames which were then compiled into .avi files.

GIMP: An Alternative to Photoshop

We used Gimp (GNU Image Manipulation Program) for all of our image editing. This program has a majority of the same features as Adobe Photoshop while being free and lightweight. GIMP even has some functions which haven't appeared in its more expensive counterparts!

You can visit the GIMP webiste here.

Blender

Blender is an extremely powerful 3D modeling and animation program. We did all of our 3D modelling and animation using blender. All of the protein structures on our wiki were exported from PyMOL into Blender where we animated and rendered them.

You can visit the Blender website here.

Octave

Octave is a language designed for numerical computations similar to MATLAB. We did all of our data analysis using Octave. This open-source program made sorting through thousands of lines of fluorescence data quick and easy using some simple scripts.

You can visit the Octave website here.