PIP-DB:the protein isoelectric point database

A protein's isoelectric point or pI corresponds to the solution pH at which its net surface charge is zero. Since the early days of solution biochemistry, the pI has been recorded and reported, and thus literature reports of pI abound. The Protein Isoelectric Point database (PIP-DB) has collected and collated these data to provide an increasingly comprehensive database for comparison and benchmarking purposes. A web application has been developed to warehouse this database and provide public access to this unique resource. PIP-DB is a web-enabled SQL database with an HTML GUI front-end. PIP-DB is fully searchable across a range of properties.

Performance management of event processing systems

This thesis is a study of performance management of Complex Event Processing (CEP) systems. Since CEP systems have distinct characteristics from other well-studied computer systems such as batch and online transaction processing systems and database-centric applications, these characteristics introduce new challenges and opportunities to the performance management for CEP systems. Methodologies used in benchmarking CEP systems in many performance studies focus on scaling the load injection, but not considering the impact of the functional capabilities of CEP systems. This thesis proposes the approach of evaluating the performance of CEP engines’ functional behaviours on events and develops a benchmark platform for CEP systems: CEPBen. The CEPBen benchmark platform is developed to explore the fundamental functional performance of event processing systems: filtering, transformation and event pattern detection. It is also designed to provide a flexible environment for exploring new metrics and influential factors for CEP systems and evaluating the performance of CEP systems. Studies on factors and new metrics are carried out using the CEPBen benchmark platform on Esper. Different measurement points of response time in performance management of CEP systems are discussed and response time of targeted event is proposed to be used as a metric for quality of service evaluation combining with the traditional response time in CEP systems. Maximum query load as a capacity indicator regarding to the complexity of queries and number of live objects in memory as a performance indicator regarding to the memory management are proposed in performance management of CEP systems. Query depth is studied as a performance factor that influences CEP system performance.

CEPBen:a benchmark for complex event processing systems

Complex Event processing (CEP) has emerged over the last ten years. CEP systems are outstanding in processing large amount of data and responding in a timely fashion. While CEP applications are fast growing, performance management in this area has not gain much attention. It is critical to meet the promised level of service for both system designers and users. In this paper, we present a benchmark for complex event processing systems: CEPBen. The CEPBen benchmark is designed to evaluate CEP functional behaviours, i.e., filtering, transformation and event pattern detection and provides a novel methodology of evaluating the performance of CEP systems. A performance study by running the CEPBen on Esper CEP engine is described and discussed. The results obtained from performance tests demonstrate the influences of CEP functional behaviours on the system performance. © 2014 Springer International Publishing Switzerland.

KM governance:the mechanisms for guiding and controlling KM program

Purpose: To establish and sustain their KM programs organizations need to establish mechanisms to ensure their governance. KM programs require business integration, senior management involvement and decision making authority. The present research investigates the KM governance mechanisms organizations use to guide and control their KM programs. The research seeks to contribute to a better understanding of the governance of KM and to support organizations in the development of their KM programs. Methodology: The study employs multiple case research methodology to analyze the KM governance arrangements of twelve international organizations and identify patterns in their governance configurations. Findings: The analysis identifies a range of structural, process and relational mechanisms that are critical for governing an organizational KM program. Different patterns among the KM governance mechanisms are identified which lead to the development of generic KM governance typologies. Research implications: The development of the KM governance framework allows future research to systematically investigate the KM governance phenomenon. As the present study is based on a configurational analysis future research should particularly target the performance implications of different KM governance configurations. Practical implications: The research provides insights into the diversity of KM governance mechanisms and their impact on a KM program. The KM governance framework can assist managers in reviewing their present and prospective KM programs and thereby support benchmarking or re-organization efforts. Originality: Building on prior research that has focused on individual KM governance aspects, the present study adopts a comprehensive perspective integrating structural, process and relational governance mechanisms.

Applications of data envelopment analysis in education

Non-parametric methods for efficiency evaluation were designed to analyse industries comprising multi-input multi-output producers and lacking data on market prices. Education is a typical example. In this chapter, we review applications of DEA in secondary and tertiary education, focusing on the opportunities that this offers for benchmarking at institutional level. At secondary level, we investigate also the disaggregation of efficiency measures into pupil-level and school-level effects. For higher education, while many analyses concern overall institutional efficiency, we examine also studies that take a more disaggregated approach, centred either around the performance of specific functional areas or that of individual employees.

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

Price-cap regulation in the English and Welsh water industry:a proposal for measuring productivity performance

Privately owned water utilities typically operate under a regulated monopoly regime. Price-cap regulation has been introduced as a means to enhance efficiency and innovation. The main objective of this paper is to propose a methodology for measuring productivity change across companies and over time when the sample size is limited. An empirical application is developed for the UK water and sewerage companies (WaSCs) for the period 1991-2008. A panel index approach is applied to decompose and derive unit-specific productivity growth as a function of the productivity growth achieved by benchmark firms, and the catch-up to the benchmark firm achieved by less productive firms. The results indicated that significant gains in productivity occurred after 2000, when the regulator set tighter reviews. However, the average WaSC still must improve towards the benchmarking firm by 2.69% over a period of five years to achieve comparable performance. This study is relevant to regulators who are interested in developing comparative performance measurement when the number of water companies that can be evaluated is limited. Moreover, setting an appropriate X factor is essential to improve the efficiency of water companies and this study helps to achieve this challenge.

Energy Efficiency Analysis of Water and Wastewater Utilities Based on the IBNET Database

A víz- és szennyvíz-szolgáltató vállalatok működési költségeinek jelentős hányadát teszi ki a villamosenergia-költség. Elemzésünk az IBNET (International Benchmarking Network for Water and Sanitation Utilities) adatbázisa alapján vizsgálja a közép-kelet-európai és a FÁK országokban működő víziközművek energiahatékonyságát. Többváltozós statisztikai elemzés segítségével tárjuk fel a különböző működési jellemzők energiahatékonyságot befolyásoló hatását. A Világbank által kezdeményezett IBNET programról bővebb információ a www.ib-net.org oldalon található, angol nyelven.

Education 2.0: Exploring the challenges of Corvinus University in the long tail economy of global higher education

Our basic storyline is how the business and economics higher education landscape has changed with the introduction of the Bologna programs. We borrowed the fashionable long tail concept from e-business, and used it for modeling the new landscape of internationalization of universities. Internationalization, mobility, and the appearance of the internet generation at the gates of our universities in our opinion has brought us to a new e-era which, appropriately to our web analogies we might as well call Education 2.0.In our paper first we show the characteristics of the long tail model of the Bologna-based European higher education and potential messages for strategy making in this environment. We illustrate that benchmarking university strategies situated in the head of the long tail model will not always provide strategic guidance for universities sitting in the tail. For underlining some key concerns in the Hungarian niche, we used Corvinus University as a case study to illustrate some untapped challenges of the Hungarian Bologna reform. We explored three areas which are crucial elements of the “tail” strategy in our opinion: a) the influence of state regulation, b) social situations and impacts and c) internal university capabilities.

E-learning Skill and Use in EU Countries – A Statistical Analysis

The article investigates the division between member states of the European Union considering the aspect of their level of information and communication technology (ICT) development focusing on e-learning. With the help of discriminant analysis the countries are categorized into groups based on their ICT maturity and e-learning literacy level of development. Making a comparison with a benchmarking tool, the ITU (International Telecommunication Union)’s ICT Development Index (IDI) the results are confirmed partly correct. The article tries to find economical explanations for the re-grouping of the countries ranking. Finally the author examines the reliability of Hungary’s ranking results and the factors which may affect this divergence from the real picture.

A semantic paradigm for intelligent data access

An implementation of Sem-ODB—a database management system based on the Semantic Binary Model is presented. A metaschema of Sem-ODB database as well as the top-level architecture of the database engine is defined. A new benchmarking technique is proposed which allows databases built on different database models to compete fairly. This technique is applied to show that Sem-ODB has excellent efficiency comparing to a relational database on a certain class of database applications. A new semantic benchmark is designed which allows evaluation of the performance of the features characteristic of semantic database applications. An application used in the benchmark represents a class of problems requiring databases with sparse data, complex inheritances and many-to-many relations. Such databases can be naturally accommodated by semantic model. A fixed predefined implementation is not enforced allowing the database designer to choose the most efficient structures available in the DBMS tested. The results of the benchmark are analyzed. ^ A new high-level querying model for semantic databases is defined. It is proven adequate to serve as an efficient native semantic database interface, and has several advantages over the existing interfaces. It is optimizable and parallelizable, supports the definition of semantic userviews and the interoperability of semantic databases with other data sources such as World Wide Web, relational, and object-oriented databases. The query is structured as a semantic database schema graph with interlinking conditionals. The query result is a mini-database, accessible in the same way as the original database. The paradigm supports and utilizes the rich semantics and inherent ergonomics of semantic databases. ^ The analysis and high-level design of a system that exploits the superiority of the Semantic Database Model to other data models in expressive power and ease of use to allow uniform access to heterogeneous data sources such as semantic databases, relational databases, web sites, ASCII files, and others via a common query interface is presented. The Sem-ODB engine is used to control all the data sources combined under a unified semantic schema. A particular application of the system to provide an ODBC interface to the WWW as a data source is discussed. ^

A study of learners' perceived value and satisfaction for implied effectiveness of online learning systems

Online learning systems (OLS) have become center stage for corporations and educational institutions as a competitive tool in the knowledge economy. The satisfaction construct has received extensive coverage in information systems literature as an indicator of effectiveness but has been criticized for lack of validity; yet, the value construct has been largely ignored, although it has a long history in psychology, sociology, and behavioral science. The purpose of this dissertation is to investigate the value and satisfaction constructs in the context of OLS, and their perceived by learners relationship for implied effectiveness of OLS. ^ First, a qualitative phase is employed to gather OLS values from learners' focus groups, followed by a pilot phase to refine a proposed instrument, and a main phase to validate the survey. Responses were received from 75 students in four focus groups, 141 in the pilot, and 207 the main survey. Extensive data cleaning and exploratory factor analysis were done to identify factors of learners' perceived value and satisfaction of OLS. Then, Value-Satisfaction grids and the Learners' Value Index of Satisfaction (LeVIS) were developed as benchmarking tools of OLS. Moreover, Multicriteria Decision Analysis (MCDA) techniques were employed to impute value from satisfaction scores in order to reduce survey response time. ^ The results provided four satisfaction and four value factors with high reliability (Cronbach's α). Moreover, value and satisfaction were found to have low linear and nonlinear correlations, indicating that they are two distinct uncorrelated constructs. This is consistent with the literature. Value-Satisfaction grids and the LeVIS index indicated relatively high effectiveness for technology and support characteristics, relatively low effectiveness for professor's characteristics, while course and learner characteristics indicated average effectiveness. ^ The main contributions of this study include identifying, defining, and articulating the relationship between value and satisfaction constructs as assessment of users' implied IS effectiveness, as well as assessing the accuracy of MCDA procedures to predict value scores, thus reducing by half the survey questionnaire size. ^

Statistical analysis and meta-analysis of microarray data

The microarray technology provides a high-throughput technique to study gene expression. Microarrays can help us diagnose different types of cancers, understand biological processes, assess host responses to drugs and pathogens, find markers for specific diseases, and much more. Microarray experiments generate large amounts of data. Thus, effective data processing and analysis are critical for making reliable inferences from the data. ^ The first part of dissertation addresses the problem of finding an optimal set of genes (biomarkers) to classify a set of samples as diseased or normal. Three statistical gene selection methods (GS, GS-NR, and GS-PCA) were developed to identify a set of genes that best differentiate between samples. A comparative study on different classification tools was performed and the best combinations of gene selection and classifiers for multi-class cancer classification were identified. For most of the benchmarking cancer data sets, the gene selection method proposed in this dissertation, GS, outperformed other gene selection methods. The classifiers based on Random Forests, neural network ensembles, and K-nearest neighbor (KNN) showed consistently god performance. A striking commonality among these classifiers is that they all use a committee-based approach, suggesting that ensemble classification methods are superior. ^ The same biological problem may be studied at different research labs and/or performed using different lab protocols or samples. In such situations, it is important to combine results from these efforts. The second part of the dissertation addresses the problem of pooling the results from different independent experiments to obtain improved results. Four statistical pooling techniques (Fisher inverse chi-square method, Logit method. Stouffer's Z transform method, and Liptak-Stouffer weighted Z-method) were investigated in this dissertation. These pooling techniques were applied to the problem of identifying cell cycle-regulated genes in two different yeast species. As a result, improved sets of cell cycle-regulated genes were identified. The last part of dissertation explores the effectiveness of wavelet data transforms for the task of clustering. Discrete wavelet transforms, with an appropriate choice of wavelet bases, were shown to be effective in producing clusters that were biologically more meaningful. ^

A comprehensive portfolio construction under stochastic environment

Prior research has established that idiosyncratic volatility of the securities prices exhibits a positive trend. This trend and other factors have made the merits of investment diversification and portfolio construction more compelling. ^ A new optimization technique, a greedy algorithm, is proposed to optimize the weights of assets in a portfolio. The main benefits of using this algorithm are to: (a) increase the efficiency of the portfolio optimization process, (b) implement large-scale optimizations, and (c) improve the resulting optimal weights. In addition, the technique utilizes a novel approach in the construction of a time-varying covariance matrix. This involves the application of a modified integrated dynamic conditional correlation GARCH (IDCC - GARCH) model to account for the dynamics of the conditional covariance matrices that are employed. ^ The stochastic aspects of the expected return of the securities are integrated into the technique through Monte Carlo simulations. Instead of representing the expected returns as deterministic values, they are assigned simulated values based on their historical measures. The time-series of the securities are fitted into a probability distribution that matches the time-series characteristics using the Anderson-Darling goodness-of-fit criterion. Simulated and actual data sets are used to further generalize the results. Employing the S&P500 securities as the base, 2000 simulated data sets are created using Monte Carlo simulation. In addition, the Russell 1000 securities are used to generate 50 sample data sets. ^ The results indicate an increase in risk-return performance. Choosing the Value-at-Risk (VaR) as the criterion and the Crystal Ball portfolio optimizer, a commercial product currently available on the market, as the comparison for benchmarking, the new greedy technique clearly outperforms others using a sample of the S&P500 and the Russell 1000 securities. The resulting improvements in performance are consistent among five securities selection methods (maximum, minimum, random, absolute minimum, and absolute maximum) and three covariance structures (unconditional, orthogonal GARCH, and integrated dynamic conditional GARCH). ^

A methodology to select an enterprise resource planning system for a small or medium sized enterprise

Enterprise Resource Planning (ERP) systems are software programs designed to integrate the functional requirements, and operational information needs of a business. Pressures of competition and entry standards for participation in major manufacturing supply chains are creating greater demand for small business ERP systems. The proliferation of new offerings of ERP systems introduces complexity to the selection process to identify the right ERP business software for a small and medium-sized enterprise (SME). The selection of an ERP system is a process in which a faulty conclusion poses a significant risk of failure to SME’s. The literature reveals that there are still very high failure rates in ERP implementation, and that faulty selection processes contribute to this failure rate. However, the literature is devoid of a systematic methodology for the selection process for an ERP system by SME’s. This study provides a methodological approach to selecting the right ERP system for a small or medium-sized enterprise. The study employs Thomann’s meta-methodology for methodology development; a survey of SME’s is conducted to inform the development of the methodology, and a case study is employed to test, and revise the new methodology. The study shows that a rigorously developed, effective methodology that includes benchmarking experiences has been developed and successfully employed. It is verified that the methodology may be applied to the domain of users it was developed to serve, and that the test results are validated by expert users and stakeholders. Future research should investigate in greater detail the application of meta-methodologies to supplier selection and evaluation processes for services and software; additional research into the purchasing practices of small firms is clearly needed.^