Computational Systems Biology
Sauro Lab
University of Washington
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What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
Student Projects 
Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
5. Matlab Interface
6. Optimization
6. Bifurcation
maintained by Frank Bergmann

Student Projects


Alex Bratt Engineering Robust Gene Regulatory Networks for Synthetic Biology


Alec Nielsen Ribosomal Binding Site Measurements and Translation Rate Standardization

Charles Watts Ordering Rules in Stoichiometric Matrices to find Meaningful Conservation Laws

James Athappilly Evaluating Flash as a Platform on which to Build Web Based Pathway Modeling Tools


Si Yuan Shen SBML2TikZ: Generating Vector Graphics Script for the Systems Biology Markup Language

Jee Hoon Jang A Noninvasive, Real-time in vivo Tool for Monitoring Glycolysis

Bennett Ng Investigating the optimal distribution of feedback controls in biochemical networks.

Future Project Ideas

Wet-Lab Projects
  1. Predict the evolutionary half-life of a synthetic circuit knowing the initial expression level.
  2. Evolving a circuit to express high levels of a small molecule.
  3. Build a 1ml chemostat and use it to do controlled synthetic biology experiments.
  4. Synthetic circuits are prone to break down due to mutations, because mutant cells can grow faster. To prevent this, we propose introduce an auxiliary circuit that is activated when a mutation occurs in different parts of the original circuit. We can design the auxiliary circuit computationally and confirm by experiment.
  5. Mutational bistable switch. This project is to study the stochastic nature of mutations in genetic circuits. The first task is to design and engineer a bistable switch circuit consisting of two separate modules. Each module is an expression cassette that controls the expression of a repressor protein and reporter protein (GFP and RFP), where each repressor controls expression of the other module. Each module is flanked by repeated transcriptional terminators that in theory have relatively equal probability of causing deletions between these repeated sequences. Thus, if one repressor is deleted, it can no longer repress the other module and GFP is expressed. If the other repressor is deleted, it expresses RFP. This circuit can be characterized by monitoring the relative percentage of the population that is GFP vs. RFP over multiple generations and one question is whether there is a selection regime to push the switch into one stable state or the other.
  6. Optimization of expression levels in a metabolic pathway. Foreign metabolic pathways encoded on plasmids often are not expressed optimally, resulting in a metabolic burden for the host and low expression that can not be easily measured. This project is to introduce the metabolic pathways that produce lycopene (three enzymatic steps) and/or beta-carotene (four enzymatic steps) into E. coli and optimize its expression. This could be performed in a number of ways, including re-design of the genetic circuit, making mutations on the chromosome, changing the copy number of the plasmid, or codon optimizing the genetic circuit for expression in E. coli. The other component of this project is to determine a method for measuring the output (lycopene and/or beta-carotene) in a plate reader without acetone extraction.
  7. Optimization of evolutionary robustness in a metabolic pathway. There is a potential for a metabolic pathway encoded on a plasmid to mutate to a nonfunctional version when a mutant arises in the population with a significant fitness advantage. This project is to introduce the metabolic pathways that produce lycopene (three enzymatic steps) and/or beta-carotene (four enzymatic steps) into E. coli and optimize evolutionary robustness. This will involve evolutionary propagation of E. coli populations over multiple generations, identifying and sequencing plasmids from mutants, and then re-engineering plasmids to be more robust to mutation over evolutionary time.
Computational Projects
  1. Develop software for the UW synthetic biology part registry. To help synthetic biologists exchange the information needed to re-use components in new designs.
  2. Generate and simulate in silico random networks generated from the the pool of parts found in the Parts Registry.
  3. Generate a new database of parts from the Biomodels database
  4. Make a study of the types and construction of models stored on biomodels
  5. Develop new search algorithms and simulation approaches using the UW supercomputer
  6. Develop interesting synthetic biology, graphical and/or simulation software for the iPhone/iPad
  7. TinkerCell Lite will allow users to draw linear sequences of DNA parts such as promoters, RBS, and coding regions. Users can also specify regulations between genes. The image and the model can be exported as different formats, including SBML, PDF, TeX etc.
  8. Collect a set of published synthetic biology experiments that have supporting models. Use TinkerCell's model-substitution feature to automatically check how different models for the same systems agree with the experimental results. The selected papers should cover different types of systems, so that we can assess where some models work better than others.
studentprojects.txt · Last modified: 2010/09/24 12:53 by mgaldzicki

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