Computer Science Publications

Seeds for Effective Oligonucleotide Design

Lucian Ilie et al. — Mon, 29 Aug 2011 17:12:56 PDT

BACKGROUND: DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms.

RESULTS: We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F - score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones.

CONCLUSIONS: Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide design.

Better Score Function for Peptide Identification with ETD MS/MS Spectra

Xiaowen Liu et al. — Wed, 03 Feb 2010 20:31:28 PST

Background: Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. Traditionally the to-be-measured peptides are fragmented with the collision induced dissociation (CID) method. More recently, the electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. However, the existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID.

Results: To take full advantage of ETD data, in this paper we develop a new score function to evaluate the match between a peptide and an ETD MS/MS spectrum. Experiments on real data demonstrated that this newly developed score function significantly improved the de novo sequencing accuracy of the PEAKS software on ETD data.

Conclusion: A new and better score function for ETD MS/MS peptide identification was developed. The method used to develop our ETD score function can be easily reused to train new score functions for other types of MS/MS data.

Geometrical Tile Design for Complex Neighborhoods

Eugen Czeizler et al. — Sun, 10 Jan 2010 18:24:43 PST

Recent research has showed that tile systems are one of the most suitable theoretical frameworks for the spatial study and modeling of self-assembly processes, such as the formation of DNA and protein oligomeric structures. A Wang tile is a unit square, with glues on its edges, attaching to other tiles and forming larger and larger structures. Although quite intuitive, the idea of glues placed on the edges of a tile is not always natural for simulating the interactions occurring in some real systems. For example, when considering protein self-assembly, the shape of a protein is the main determinant of its functions and its interactions with other proteins. Our goal is to use geometric tiles, i.e. square tiles with geometrical protrusions on their edges, for simulating tiled paths (zippers) with complex neighborhoods, by ribbons of geometric tiles with simple, local neighborhoods. This paper is a step toward solving the general case of an arbitrary neighborhood, by proposing geometric tile designs that solve the case of a "tall" von Neumann neighborhood, the case of the f-shaped neighborhood, and the case of a 3 x 5 "filled" rectangular neighborhood. The techniques can be combined and generalized to solve the problem in the case of any neighborhood, centered at the tile of reference, and included in a 3 x (2k+1) rectangle.

Verifiable Electronic Voting System: An Open Source Solution

Halina Kaminski et al. — Wed, 04 Mar 2009 17:04:21 PST

Elections, referenda and polls are vital processes for the operation of a modern democracy. They form the mechanism for transferring power from citizens to their representatives. Although some commentators claim that the pencil-and-paper systems used in countries such as Canada and UK are still the best method of avoiding voterigging, recent election problems, and the need for faster, better, cheaper vote counting, have stimulated great interest in managing the election process through the use of electronic voting systems. While computer scientists, for the most part, have been warning of the possible perils of such action, vendors have forged ahead with their products, claiming increased security and reliability. Many democracies have adopted electronic systems, and the number of deployed systems is rising. Although the electronic voting process has gained popularity and users, it is a great challenge to provide a reliable system. The existing systems available to perform the election tasks are far from trustworthy. In this paper we describe VEV (Verifiable E-Voting), an electronic voting system which is opne, but also provides for secret and secure voting, and can be used and verified over existing network system.

Open Source Software Licensing Patterns

Halina Kaminski et al. — Wed, 25 Feb 2009 17:07:09 PST

A Framework for Automatic SLA Creation

Halina Kaminski et al. — Wed, 25 Feb 2009 16:57:15 PST

Negotiation is fundamental to business. Increased automation of business to business or business to customer interaction is demanding efficient but flexible systems that can manage the negotiation process with minimal direct human intervention. Industries that provide online services rely on Service Level Agreements as the basis for their contractual relationship. Here we look at a means for generating these with a negotiating tool (SLA Negotiation Manager) that complies with e-negotiation rules and creates the agreements from existing business objectives.

An Ontology for Autonomic License Management

Qian Zhao et al. — Wed, 25 Feb 2009 16:42:07 PST

The license agreement can be seen as the knowledge source for a license management system. As such, it may be referenced by the system each time a new process is initiated. To facilitate access, a machine readable representation of the license agreement is highly desirable, but at the same time we do not want to sacrifice too much readability of such agreements by human beings. Creating an ontology as a formal knowledge representation of licensing not only meets the representation requirements, but also offers improvements to knowledge reusability owing to the inherent sharing nature of such representations. Furthermore, the XML-based ontology languages such as OWL (Web Ontology Language) can be user friendly for the non-developers who are often those responsible for implementing and managing such license agreements. This paper shows our use of ontology to represent the license agreement in a development prototype. The ultimate goal is to build ontology for the license management domain that will facilitate autonomic knowledge management. Knowledge based on such ontology can then be shared and utilized by many types of license management system.

Policy Driven Licensing Model for Component Software

Zhao Qian et al. — Thu, 19 Feb 2009 16:34:56 PST

Today, it is almost inevitable that software is licensed, rather than sold outright. As a part of the licensing policy, some protection mechanisms, whether hardware, legal or code-based, are invariably built into the license. The application of such mechanisms has primarily been in the realm of off-the-shelf, packaged, consumer software. However, as component-based software gradually becomes mainstream in software development, new component-oriented licensing systems are required. This paper proposes an enterprise component licensing model for the management of software component licenses. The model provides a comprehensive license management framework allowing for extensibility and flexibility. Furthermore, we identify differences between stand-alone software and component software, describe a high level model for policy driven component licensing, and discuss both the benefits and drawbacks of the enterprise component licensing model for the management of software component licenses.

Who Counts Your Votes?

Halina Kaminski et al. — Wed, 21 Jan 2009 16:18:10 PST

Open and fair elections are paramount to modern democracy. Although some people claim that the penciland- paper systems used in countries such as Canada and UK are still the best method of avoiding vote rigging, recent election problems have sparked great interest in managing the election process through the use of electronic voting systems. It is a goal of this paper to describe a voting system that is secret and secure as well as verifiable and useable over an existing computer network. We have designed and implemented an electronic voting system – Verifiable E-Voting (VEV) – with an underlying protocol that secures the election process from malicious practices at the same time as allowing voters and candidates to verify the correctness of their votes.

Policies, Rules and Their Engines: What do They Mean for SLAs?

Mark Perry et al. — Wed, 21 Jan 2009 16:17:04 PST

In our model for autonomic management of service level agreements (SLA), the roles played by policy and rules must be clearly differentiated. Although policy is typically an ideal we wish to achieve through the implementation of rules, the use of the terms policy and rule are often treated similarly and that consequently policy-engine and rule-engine are often used synonymously. It is our position that in the management of SLAs these terms have specific meanings. The definitions and models embodied are illustrated.

Differentiating Web Service Offerings

Halina Kaminski et al. — Tue, 06 Jan 2009 13:43:57 PST

The advent of Service Oriented Architecture (SOA) paradigm and increasing use of Web Services (WS) implies that the future will see a large number of services transferred between providers and consumers, using many applications or agents working on behalf of humans. Discovering and using the services is the easy part. Negotiating and selecting the best services from amongst the plethora of similar ones, depending on their cost and quality, is the challenging issue. However, existing WS-I standards neither cater to provision of Service Level Agreements (SLAs), nor their exchange between parties. These standards are confined merely to WS description (WSDL). Once WS are discovered and selected, SLAs are merely used to monitor service compliance. We propose a novel method that allows service-providers to dynamically generate the SLAs, and then transfer them to clients for selection amongst competitive service providers. The clients use Application to Application (A2A) communication to choose the best service provider at run time, and then bind to it to available services. Our method complies with all WS-I standards, and hence does not require any modifications to the UDDI or WSDL. Instead of using the SLA as just a contractual document for compliance monitoring of the service, we also use it as a means of service selection. We demonstrate and validate our method using a prototype developed in laboratory settings, which uses multiple ‘Weather Service Providers’ to obtain various indicators for weather forecasting.

Employing Intelligent Agents to Automate SLA Creation

Halina Kaminski et al. — Tue, 06 Jan 2009 13:23:43 PST

Service Level Agreements (SLAs) are commonly prepared and signed agreements that form the contracts between a service provider and its customers, defining the obligations and liabilities of the parties. Naturally, SLAs should reflect the business needs of both customer and supplier. SLAs are usually formed through either the adoption of a boilerplate agreement from the provider, or through a mediation/negotiation process between the parties. With the increasing adoption of software supply being implemented as a network service, such schemes are rigid or slow and costly, This paper proposes a system that the parties can use to facilitate both fast and flexible agreements. It proposes automation of SLA creation from a set of Service Level Objectives (SLOs), making use of software agents and adopting a social order function by incorporating it into the decision process.

SLA Automated Negotiation Manager for Computing Services

Halina Kaminski et al. — Tue, 06 Jan 2009 13:14:37 PST

Success in today’s marketing arena can often depend on companies embracing effective new technologies and integrating them into their business model. In the computing service supply industry, Service Level Agreements (SLAs) are commonly prepared and signed agreements between the service provider and its customers. SLAs should match business needs of both sides of the agreement as closely as possible. This paper focuses on at the steps and activities that the service provider can take to facilitate agreement. It proposes an automated way for creating SLA’s from a set of Service Level Objectives (SLOs). The SLA should achieve business goals, including the maximization of customer satisfaction. To automate the preparation of effective SLAs each company should set SLOs that support business needs.

Agent Design of SmArt License Management System Using Gaia Methodology

Qian Zhao et al. — Tue, 06 Jan 2009 12:56:55 PST

Modern software services and data centers require a license management system to regulate the agreements that have been reached between subscriber and provider. License management helps to track usage and protect service from abuse. License agreements provide the basis for enforcement and regulation. The automation of license agreements is desired by providers and subscribers to improve transaction efficiency, give flexibility, and minimize unwanted cost.

We have proposed a framework, called SmArt (Semantic Agreement) system, that enables agreement automation in the autonomic computing context using ontology and agent technologies. This paper applies the SmArt system to the domain of license management and presents its agent design with Gaia methodology.