Pattern Reconstruction from Images for DNA-based Computing

Background

Post-silicon means of computation have become one promising approach to tackle today’s challenges of computing systems such as high energy consumption. In an explorative project, we investigate the possibility of building a DNA-based computing system. It promises higher memory density, improved in-memory calculation, and on-chip DNA-sequencing.

Description

In this task, you will invent a reconstruction algorithm to identify DNA-inputs using 2D and 3D videos of a micro-fluidic system. The microfluidic system will combine different DNA-snippets and a video is taken of the system. You will develop a reconstruction method (by linear programming, combinatorics of machine learning); the problem can be modeled as a string-matching algorithm.

Tasks

  • Derivation of a model
  • Formulation of an optimization method
  • Solution of the optimization problem
  • Integration into experimental setup 

Requirements

  • Interest in modelling and optimization
  • Experience with programming, preferably Python
  • Nice to have: Knowledge of linear programming