Andrzej M. Goscinski

Cloud Computing Principles and Paradigms

The primary purpose of this book is to capture the state-of-the-art in Cloud Computing technologies and applications. The book will also aim to identify potential research directions and technologies that will facilitate creation a global market-place of cloud computing services supporting scientific, industrial, business, and consumer applications. We expect the book to serve as a reference for larger audience such as systems architects, practitioners, developers, new researchers and graduate level students. This area of research is relatively recent, and as such has no existing reference book that addresses it.This book will be a timely contribution to a field that is gaining considerable research interest, momentum, and is expected to be of increasing interest to commercial developers. The book is targeted for professional computer science developers and graduate students especially at Masters level. As Cloud Computing is recognized as one of the top five emerging technologies that will have a major impact on the quality of science and society over the next 20 years, its knowledge will help position our readers at the forefront of the field.

Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins

Cysteine is susceptible to a variety of modifications by reactive oxygen and nitrogen oxide species, including glutathionylation; and when two cysteines are involved, disulfide formation. Glutathione-cysteine adducts may be removed from proteins by glutaredoxin, whereas disulfides may be reduced by thioredoxin. Glutaredoxin is homologous to the disulfide-reducing thioredoxin and shares similar binding modes of the protein substrate. The evolution of these systems is not well characterized. When a single Cys is present in a protein, conjugation of the redox buffer glutathione may induce conformational changes, resulting in a simple redox switch that effects a signaling cascade. If a second cysteine is introduced into the sequence, the potential for disulfide formation exists. In favorable protein contexts, a bistable redox switch may be formed. Because of glutaredoxins similarities to thioredoxin, the mutated protein may be immediately exapted into the thioredoxin-dependent redox cycle upon addition of the second cysteine. Here we searched for examples of protein substrates where the number of redox-active cysteine residues has changed throughout evolution. We focused on cross-strand disulfides (CSDs), the most common type of forbidden disulfide. We searched for proteins where the CSD is present, absent and also found as a single cysteine in protein orthologs. Three different proteins were selected for detailed study—CD4, ERO1, and AKT. We created phylogenetic trees, examining when the CSD residues were mutated during protein evolution. We posit that the primordial cysteine is likely to be the cysteine of the CSD which undergoes nucleophilic attack by thioredoxin. Thus, a redox-active disulfide may be introduced into a protein structure by stepwise mutation of two residues in the native sequence to Cys. By extension, evolutionary acquisition of structural disulfides in proteins can potentially occur via transition through a redox-active disulfide state.

GENESIS: an efficient, transparent and easy to use cluster operating system

Present operating systems are not built to support parallel computing--they do not provide services to manage parallelism, i.e., to globally manage parallel processes and computational resources. The cluster operating environments that are used to assist the execution of parallel applications do not provide support for both programming paradigms, message passing (MP) or distributed shared memory (DSM)--they are mainly offered as separate components implemented at the user level as library and independent server processes. Due to poor operating systems users must deal with clusters as a set of independent computers rather than to see this cluster as a single powerful computer. A single system image (SSI) of the cluster is not offered to users. There is a need for an operating system for clusters. We claim and demonstrate in this paper that it is possible to develop a cluster operating system that is able to efficiently manage parallelism; use cluster resources efficiently; support MP in the form of standard MP and PVM, and DSM; offer SSI; and make it easy to use. We show that to achieve these aims this operating system should inherit many features of a distributed operating system and provide new services which address the needs of parallel processes, clusters resources, and application developers. In order to substantiate the claim the first version of a cluster operating system managing parallelism and offering SSI, called GENESIS:, has been developed.

The RHODOS migration facility

Abstract With the growing move of parallel processing towards networks of workstations (NOWs), caused by a low cost to performance ratio, process migration has once again become an important area of research. This paper reports on research into the design, implementation and performance of RHODOSs process migration facility which reflects RHODOSs aspiration to support both parallel execution and load balancing on a distributed system. This design is original in that it applies strictly to the microkernel and client/server paradigms. Furthermore, following RHODOSs adherence to the object based approach, the RHODOS process Migration Manager only coordinates process migration. The actual transfer of the processs resources: process state, address space and communication state, are performed by the Process, Space and IPC Managers, respectively. Following the presentation of the design issues, research into the implementation and testing of RHODOSs process migration facility is presented. Performance measurements of this implementation have also been taken to determine the cost of using the supposedly slower microkernel based approach and the results are reported in this paper. A summary of process migration for modern distributed operation systems is presented.

Trader cooperation to enable object sharing among users of homogeneous distributed systems

This paper demonstrates that it is possible to build a trading service which allows users to access objects of remote distributed systems. This service is an extension to an original RHODOS trader, which provides the maximum possible autonomy and flexibility to users yet at the same time allows them to share allaccessible objects (resource, service) within a local distributed computer system. We demonstrate that concepts such as attribute names, name domains, the operations of object export, import and withdrawal are necessary to achieve object sharing among a number of users of independent homogeneous distributed computer systems which together form a large homogeneous distributed system. We also show how location transparency can be achieved by cooperation between traders based on attribute names, and that the use of attributes has the potential to make resource sharing effective and efficient.

Toward a framework for cloud security

While the emergence of cloud computing has made it possible to rent information technology infrastructures on demand, it has also created new security challenges. The primary security concern is trusting data (or resources in general) on another organizations system. This document seeks to examine the current state of security in cloud computing and presents a set of challenges to address the security needs of clouds. The end result is a framework to help the design and implementation of effective cloud security infrastructures.

Towards an operating system managing parallelism of computing on clusters

Abstract Parallelism management is a difficult task, in particular in parallel systems based on clusters (of PCs or workstations). We claim in this paper that parallelism management should be provided by an operating system that inherits many features of a distributed operating system and provides new services that address the needs of parallel processes, cluster’s resources, and application programmers. This system, in order to allow parallel programs to achieve high performance, transparency and ease of use, should provide services such as establishment of a virtual machine; mapping processes to computers; concurrent process creation and process duplication supported by process migration; computation co-ordination; group communication; and distributed shared memory. In order to substantiate the claim the first version of a cluster operating system managing parallelism, called GENESIS, has been developed and presented in this paper. The results of the execution of some parallel applications, that further substantiate our claim, are shown.

Managing Replicated Remote Procedure Call Transactions

This paper addresses the problem of building reliable computing programs over remote procedure call (RPC) systems by using replication and transaction techniques. We first establish the computational model: the RPC transactions. Based on this RPC transaction model, we present the design of our system for managing RPC transactions in the replicated-server environment. Finally, we present some results of a correctness study on the system and two examples of the system.

PPFSCADA: Privacy preserving framework for SCADA data publishing

Supervisory Control and Data Acquisition (SCADA) systems control and monitor industrial and critical infrastructure functions, such as electricity, gas, water, waste, railway, and traffic. Recent attacks on SCADA systems highlight the need for stronger SCADA security. Thus, sharing SCADA traffic data has become a vital requirement in SCADA systems to analyze security risks and develop appropriate security solutions. However, inappropriate sharing and usage of SCADA data could threaten the privacy of companies and prevent sharing of data. In this paper, we present a privacy preserving strategy-based permutation technique called PPFSCADA framework, in which data privacy, statistical properties and data mining utilities can be controlled at the same time. In particular, our proposed approach involves: (i) vertically partitioning the original data set to improve the performance of perturbation; (ii) developing a framework to deal with various types of network traffic data including numerical, categorical and hierarchical attributes; (iii) grouping the portioned sets into a number of clusters based on the proposed framework; and (iv) the perturbation process is accomplished by the alteration of the original attribute value by a new value (clusters centroid). The effectiveness of the proposed PPFSCADA framework is shown through several experiments on simulated SCADA, intrusion detection and network traffic data sets. Through experimental analysis, we show that PPFSCADA effectively deals with multivariate traffic attributes, producing compatible results as the original data, and also substantially improving the performance of the five supervised approaches and provides high level of privacy protection.

A unified framework for the deployment, exposure and access of HPC applications as services in clouds

Clouds have provided on-demand, scalable and affordable High Performance Computing (HPC) resources to discipline (e.g., Biology, Medicine, Chemistry) scientists. However, the steep learning curve of preparing a HPC cloud and deploying HPC applications has hindered many scientists to achieve innovative discoveries for which HPC resources must be relied on. With the world moving to web-based tools, scientists are also seeking more web-based technologies to support their research. Unfortunately, the discipline problems of high-performance computational research are both unique and complex, which make the development of web-based tools for this research difficult. This paper presents our work on developing a unified cloud framework that allows discipline users to easily deploy and expose HPC applications in public clouds as services. To provide a proof of concept, we have implemented the cloud framework prototype by integrating three components: (i) Amazon EC2 public cloud for providing HPC infrastructure, (ii) a HPC service software library for accessing HPC resources, and (iii) the Galaxy web-based platform for exposing and accessing HPC application services. This new approach can reduce the time and money needed to deploy, expose and access discipline HPC applications in clouds.