Computer Aided Simulation of DNA Fingerprint Amplified Fragment Length Polymophism (AFLP) Using Suffix Tree Indexing and Data Mining

AFLP is one of the DNA Fingerprinting techniques which have broad application as genetic marker in various fields. Begin with the DNA sequence digestion using one or more particular restriction enzyme, ligation of the adapters to the overhanging sticky ends followed by DNA fragments amplification using PCR. The PCR reaction uses primers that match the adapter sequence and have some (1 to 3) dditional “selective” bases which could be any bases, this reduces the number of bands that will be amplified. Such technique intended to increase the amplified fragments peculiarity so the polymorphism of the organism being studied could be well visualized by gel electrophoresis. The computer aided of AFLP simulation developed in this research was aimed to predict this electrophoresis result by simulate the digestion, ligation and PCR process using some pattern recognition algorithm applied to the DNA sequence from online databases. Through this simulation the researcher could determine the best combination of restriction enzyme and selective bases for their laboratory experiment. Suffix tree indexing was conducted during the exploration process of the genome sequence (in FASTA format) to find the restriction sites rapidly and create fragments of it. Data modeling enable the system draws the fragments into virtual DNA’s electrophoresis pattern. Data mining accomplish the simulation by exploring overall possible virtual DNA’s electrophoresis pattern and determine the best restriction enzyme and selective bases combination by calculating certain quantitative criteria

Hardware-based Security for Virtual Trusted Platform Modules

Virtual Trusted Platform modules (TPMs) were proposed as a software-based alternative to the hardware-based TPMs to allow the use of their cryptographic functionalities in scenarios where multiple TPMs are required in a single platform, such as in virtualized environments. However, virtualizing TPMs, especially virutalizing the Platform Configuration Registers (PCRs), strikes against one of the core principles of Trusted Computing, namely the need for a hardware-based root of trust. In this paper we show how strength of hardware-based security can be gained in virtual PCRs by binding them to their corresponding hardware PCRs. We propose two approaches for such a binding. For this purpose, the first variant uses binary hash trees, whereas the other variant uses incremental hashing. In addition, we present an FPGA-based implementation of both variants and evaluate their performance

TCG based approach for secure management of virtualized platforms: state-of-the-art

There is a strong trend shift in the favor of adopting virtualization to get business benefits. The provisioning of virtualized enterprise resources is one kind of many possible scenarios. Where virtualization promises clear advantages it also poses new security challenges which need to be addressed to gain stakeholders confidence in the dynamics of new environment. One important facet of these challenges is establishing 'Trust' which is a basic primitive for any viable business model. The Trusted computing group (TCG) offers technologies and mechanisms required to establish this trust in the target platforms. Moreover, TCG technologies enable protecting of sensitive data in rest and transit. This report explores the applicability of relevant TCG concepts to virtualize enterprise resources securely for provisioning, establish trust in the target platforms and securely manage these virtualized Trusted Platforms

Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.

BackgroundRestriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning."ResultsWe report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation.ConclusionThe new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.

BackgroundGenetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species.ResultsHere we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations.ConclusionCSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding

Collaborating in virtual teams

Abstract. This paper describes some early results from observin

myTrustedCloud: Trusted cloud infrastructure for security-critical computation and data managment

Copyright @ 2012 IEEECloud Computing provides an optimal infrastructure to utilise and share both computational and data resources whilst allowing a pay-per-use model, useful to cost-effectively manage hardware investment or to maximise its utilisation. Cloud Computing also offers transitory access to scalable amounts of computational resources, something that is particularly important due to the time and financial constraints of many user communities. The growing number of communities that are adopting large public cloud resources such as Amazon Web Services [1] or Microsoft Azure [2] proves the success and hence usefulness of the Cloud Computing paradigm. Nonetheless, the typical use cases for public clouds involve non-business critical applications, particularly where issues around security of utilization of applications or deposited data within shared public services are binding requisites. In this paper, a use case is presented illustrating how the integration of Trusted Computing technologies into an available cloud infrastructure - Eucalyptus - allows the security-critical energy industry to exploit the flexibility and potential economical benefits of the Cloud Computing paradigm for their business-critical applications

Source Behavior for ATM ABR Traffic Management: An Explanation

The Available Bit Rate (ABR) service has been developed to support data applications over Asynchronous Transfer Mode (ATM) networks. The network continuously monitors its traffic and provides feedback to the source end systems. This paper explains the rules that the sources have to follow to achieve a fair and efficient allocation of network resources.Comment: IEEE Communications Magazine, November 1, 1996, vol 34, no11, pp50-5