Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism

We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic profiles for benchmarking purposes based on a well-established model for red blood cell metabolism. A variety of data sets is generated, accounting for different properties of real metabolic networks, such as experimental noise, metabolite correlations, and temporal dynamics. These data sets are made available online. We apply ARACNE, a mainstream transcriptional networks reverse engineering algorithm, to these data sets and observe performance comparable to that obtained in the transcriptional domain, for which the algorithm was originally designed.Comment: 14 pages, 3 figures. Presented at the DIMACS Workshop on Dialogue on Reverse Engineering Assessment and Methods (DREAM), Sep 200

Strategies for protecting intellectual property when using CUDA applications on graphics processing units

Recent advances in the massively parallel computational abilities of graphical processing units (GPUs) have increased their use for general purpose computation, as companies look to take advantage of big data processing techniques. This has given rise to the potential for malicious software targeting GPUs, which is of interest to forensic investigators examining the operation of software. The ability to carry out reverse-engineering of software is of great importance within the security and forensics elds, particularly when investigating malicious software or carrying out forensic analysis following a successful security breach. Due to the complexity of the Nvidia CUDA (Compute Uni ed Device Architecture) framework, it is not clear how best to approach the reverse engineering of a piece of CUDA software. We carry out a review of the di erent binary output formats which may be encountered from the CUDA compiler, and their implications on reverse engineering. We then demonstrate the process of carrying out disassembly of an example CUDA application, to establish the various techniques available to forensic investigators carrying out black-box disassembly and reverse engineering of CUDA binaries. We show that the Nvidia compiler, using default settings, leaks useful information. Finally, we demonstrate techniques to better protect intellectual property in CUDA algorithm implementations from reverse engineering

Multiple-sensor integration for efficient reverse engineering of geometry

This paper describes a multi-sensor measuring system for reverse engineering applications. A sphere-plate artefact is developed for data unification of the hybrid system. With the coordinate data acquired using the optical system, intelligent feature recognition and segmentation algorithms can be applied to extract the global surface information of the object. The coordinate measuring machine (CMM) is used to re-measure the geometric features with a small amount of sampling points and the obtained information can be subsequently used to compensate the point data patches which are measured by optical system. Then the optimized point data can be exploited for accurate reverse engineering of CAD model. The limitations of each measurement system are compensated by the other. Experimental results validate the accuracy and effectiveness of this data optimization approach

Instantaneous modelling and reverse engineering of data-consistent prime models in seconds!

A theoretical framework that supports automated construction of dynamic prime models purely from experimental time series data has been invented and developed, which can automatically generate (construct) data-driven models of any time series data in seconds. This has resulted in the formulation and formalisation of new reverse engineering and dynamic methods for automated systems modelling of complex systems, including complex biological, financial, control, and artificial neural network systems. The systems/model theory behind the invention has been formalised as a new, effective and robust system identification strategy complementary to process-based modelling. The proposed dynamic modelling and network inference solutions often involve tackling extremely difficult parameter estimation challenges, inferring unknown underlying network structures, and unsupervised formulation and construction of smart and intelligent ODE models of complex systems. In underdetermined conditions, i.e., cases of dealing with how best to instantaneously and rapidly construct data-consistent prime models of unknown (or well-studied) complex system from small-sized time series data, inference of unknown underlying network of interaction is more challenging. This article reports a robust step-by-step mathematical and computational analysis of the entire prime model construction process that determines a model from data in less than a minute

Development Of Reverse Engineering System For Generating 3d Cad Body From 2d Image_875008757

Reverse engineering has the potential to be integrated into remote manufacturing applications, based on the internet technology today. However, reverse engineering using common scan-based device requires the physical object and the data acquisition device such as 3D laser scanner to co-exist at the same location, unless the physical object is made transferable within the cyber space. Reverse engineering based on 2D image is one of the potential solution for implementing remote reverse engineering process because 2D image is transferable with cyber space. However, reverse engineering based on 2D image must produce high dimensional accuracy outputs as exact as possible similar to the actual physical object in order to be relevant to the manufacturing industry. This research focused on developing a system for implementing reverse engineering based on 2D image, together with some unique techniques such as data segmentation, computer image processing methods and data refinement that were included into the system. Then, verification on the system was performed based on the implementation on real case objects, and the dimensional accuracy of each produced result was numerically analysed for further discussions. The results showed that reverse engineering based on 2D image is possible to be similar to the actual objects at accuracy level of less than 0.4mm. The proposed system will be the starting point for remote reverse engineering application, and has the potential to be an alternative solution whenever there is no data acquisition device such as 3D scanner available on the spot. The originality of this research is on the system and methodology used for producing 3D results from 2D data. The proposed system is not just suitable for remote reverse engineering application, but also is valuable for low cost reverse engineering application as well

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks

Motivation: The generation of time series transcriptomic datasets collected under multiple experimental conditions has proven to be a powerful approach for disentangling complex biological processes, allowing for the reverse engineering of gene regulatory networks (GRNs). Most methods for reverse engineering GRNs from multiple datasets assume that each of the time series were generated from networks with identical topology. In this study, we outline a hierarchical, non-parametric Bayesian approach for reverse engineering GRNs using multiple time series that can be applied in a number of novel situations including: (i) where different, but overlapping sets of transcription factors are expected to bind in the different experimental conditions; that is, where switching events could potentially arise under the different treatments and (ii) for inference in evolutionary related species in which orthologous GRNs exist. More generally, the method can be used to identify context-specific regulation by leveraging time series gene expression data alongside methods that can identify putative lists of transcription factors or transcription factor targets. Results: The hierarchical inference outperforms related (but non-hierarchical) approaches when the networks used to generate the data were identical, and performs comparably even when the networks used to generate data were independent. The method was subsequently used alongside yeast one hybrid and microarray time series data to infer potential transcriptional switches in Arabidopsis thaliana response to stress. The results confirm previous biological studies and allow for additional insights into gene regulation under various abiotic stresses. Availability: The methods outlined in this article have been implemented in Matlab and are available on request