Team:Hannover/Software
Software-Tools
Description
This year, our team consisted not only of biology or biotechnology students, but also computer science students. Therefore, we had the opportunity to design and program software and a platform.
First, we aimed to simplify the organization of an iGEM team by modifying a platform to share ideas, files, and knowledge.
Secondly, we also designed a spotter program to specifically place oligonucleotides that will visualize a picture upon specific binding of a GFP-tagged TALE.
Moreover, we programmed software to automatically design and synthesize TALEs for their desired application. Combined with a pipetting robot, this software can be used to design new TALE sequences without much effort. Like this, the usage of TALEs is easy and quicker than CRISPR/Cas9.
Originated out of our project, we do think that our software can improve lab work in general and help not only teams in the competition, but also researchers in the lab. Find out more about our software on the following pages.
Phabricator
Phabricator is an open source software for anything related to Project Management, suitable for easily running an iGEM Team. Our Team contributed to Phabricator, extending it with a Twitter plug-in that displays a news feed in a side panel. This keeps the participants up to date on what's happening in iGEM throughout the world!
Download Phabricator Widget Source Code:
- The open source program, patched with our widget
- Only the patch that contains our contribution and adds the Twitter widget to Phabricator
To use the widget, you simply have to create a normal Text Widget with the title "iGEM News" and it will automatically be turned into a twitter widget by the inlined javascript.
CyberPrinter
Ever wanted to print images with a spotter without the hassle of programming it? CyberPrinter can convert any image into a spotting program for the spotter "GeSim Nanoplotter 2.1". Just download the image or draw one with you favorite drawing software. Then make the image monochrome and run CyberPrinter to obtain the spotting program!
CyberPrinter optimizes the number of instructions for quick printing with limited spotting material. Possible applications are the hassle-free drawing of fluorescent images or laying out DNA oligos in a precise pattern.
We wanted to spot “iGEM” on a chip. This is why we programmed this software. It was very easy to use and helped us a lot. Spotting the chip wasn’t a problem anymore.
Download CyberPrinter Source Code
Modeling: TALsetter
Welcome to the age of affordable and freely customizable restriction enzymes!
If you only want to use the TALsetter, you don't need any further libraries. Just download the jar at https://static.igem.org/mediawiki/2016/e/ed/T--Hannover--talsetter.zip
TALsetter, our main software, finally gives the world an easy way to design TALE proteins specific to their needs! One obstacle for the use of TALEN in production is the time of designing the protein. TALsetter takes care of that. And to top it off, it can even control a pipetting robot to construct the DNA sequence from basic building blocks for you.
The product is a perfectly tailored vector for expressing the TALE with the most effective binding domains for your specified application. These parameters are freely configurable:
- Target DNA sequence
- Task of the TALE protein
- Nuclease, which produces 2 TALEN to bind on opposing sides of the DNA
- Single TALE with an arbitrary functional domain ("Guess Scan")
- Or just a translation from DNA sequence to TALE RVD (Repeat-variable diresidue) sequence ("Exact Scan")
This program is inspired by the tool TALgetter by Jan Grau et al., which detects DNA binding sites of a particular TAL effector. Since our task is the inverse - to search for TAL effectors that bind to a particular DNA, we decided to name it TALsetter.
TALsetter designs TALEs by modeling binding strength according to heuristics derived from recent papers about TAL effectors. (Grau et al., 2013 and Boch et al., 2009) By trying out every meaningful binding site and rating them according to their predicted binding strength, we obtain the best possible TAL effectors. This eliminates the need to design them yourself.
Once a candidate TAL effector is chosen, it can be exported to a CSV file readable by a PIRO pipetting robot. The pipetting instructions will look like this in PIRO's interface:
The process mixes the DNA fragments of TALEs together with an enzyme solution, which binds them together in the correct order into hexarepeats with 6 nucleotide binding sites. A following step of combining those hexarepeats using another enzyme solution creates the final DNA vector for expressing the desired TAL effector. All in vitro and hassle-free!
