Multicriteria global optimization for biocircuit design

One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of regulatory regions, and have been designed to meet a single design criterion. In this contribution we introduce a multiobjective formulation for the design of biocircuits. We set up the basis for an advanced optimization tool for the modular and systematic design of biocircuits capable of handling high levels of complexity and multiple design criteria. Our methodology combines the efficiency of global Mixed Integer Nonlinear Programming solvers with multiobjective optimization techniques. Through a number of examples we show the capability of the method to generate non intuitive designs with a desired functionality setting up a priori the desired level of complexity. The presence of more than one competing objective provides a realistic design setting where every design solution represents a trade-off between different criteria. The tool can be useful to explore and identify different design principles for synthetic gene circuits

Differential Evolution Approach to Detect Recent Admixture

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals. reAdmix is an online tool available at http://chcb.saban-chla.usc.edu/reAdmix/.Comment: presented at ISMB 2014, VariSI

A GPU-Computing Approach to Solar Stokes Profile Inversion

We present a new computational approach to the inversion of solar photospheric Stokes polarization profiles, under the Milne-Eddington model, for vector magnetography. Our code, named GENESIS (GENEtic Stokes Inversion Strategy), employs multi-threaded parallel-processing techniques to harness the computing power of graphics processing units GPUs, along with algorithms designed to exploit the inherent parallelism of the Stokes inversion problem. Using a genetic algorithm (GA) engineered specifically for use with a GPU, we produce full-disc maps of the photospheric vector magnetic field from polarized spectral line observations recorded by the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectromagnetograph (VSM) instrument. We show the advantages of pairing a population-parallel genetic algorithm with data-parallel GPU-computing techniques, and present an overview of the Stokes inversion problem, including a description of our adaptation to the GPU-computing paradigm. Full-disc vector magnetograms derived by this method are shown, using SOLIS/VSM data observed on 2008 March 28 at 15:45 UT

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions