A Bidirectional Collaboration Framework for Bio-Model Development

High-level graph data structures have gained favour in representing biologicalknowledge in a computationally executable form, but the information containedtherein must remain accessible to all users no matter their background. Bidirectionalgraph transformations may be used to synchronise and maintain the consistencyof these graph data structures as they evolve through the process of creatingand refining a bio-model knowledge base. We outline a bidirectional collaborationframework by which users with vastly differing backgrounds may contribute to thedevelopment and evolution of such a knowledge base, and examine a simple example to illustrate its merits. We also identify avenues for further research necessary to refine the framework. No prior biological knowledge is assumed

Multi-aspect, robust, and memory exclusive guest os fingerprinting

Precise fingerprinting of an operating system (OS) is critical to many security and forensics applications in the cloud, such as virtual machine (VM) introspection, penetration testing, guest OS administration, kernel dump analysis, and memory forensics. The existing OS fingerprinting techniques primarily inspect network packets or CPU states, and they all fall short in precision and usability. As the physical memory of a VM always exists in all these applications, in this article, we present OS-Sommelier+, a multi-aspect, memory exclusive approach for precise and robust guest OS fingerprinting in the cloud. It works as follows: given a physical memory dump of a guest OS, OS-Sommelier+ first uses a code hash based approach from kernel code aspect to determine the guest OS version. If code hash approach fails, OS-Sommelier+ then uses a kernel data signature based approach from kernel data aspect to determine the version. We have implemented a prototype system, and tested it with a number of Linux kernels. Our evaluation results show that the code hash approach is faster but can only fingerprint the known kernels, and data signature approach complements the code signature approach and can fingerprint even unknown kernels

SKYWare: The Unavoidable Convergence of Software towards Runnable Knowledge

There Has Been A Growing Awareness Of Deep Relations Between Software And Knowledge. Software, From An Efficiency Oriented Way To Program Computing Machines, Gradually Converged To Human Oriented Runnable Knowledge. Apparently This Has Happened Unintentionally, But Knowledge Is Not Incidental To Software. The Basic Thesis: Runnable Knowledge Is The Essence Of Abstract Software. A Knowledge Distillation Procedure Is Offered As A Constructive Feasibility Proof Of The Thesis. A Formal Basis Is Given For These Notions. Runnable Knowledge Is Substantiated In The Association Of Semantic Structural Models (Like Ontologies) With Formal Behavioral Models (Like Uml Statecharts). Meaning Functions Are Defined For Ontologies In Terms Of Concept Densities. Examples Are Provided To Concretely Clarify The Meaning And Implications Of Knowledge Runnability. The Paper Concludes With The Runnable Knowledge Convergence Point: Skyware, A New Term Designating The Domain In Which Content Meaning Is Completely Independent Of Any Underlying Machine

Co-Evolution of Source Code and the Build System: Impact on the Introduction of AOSD in Legacy Systems

Software is omnipresent in our daily lives. As users demand ever more advanced features, software systems have to keep on evolving. In practice, this means that software developers need to adapt the description of a software application. Such a description not only consists of source code written down in a programming language, as a lot of knowledge is hidden in lesser known software development artifacts, like the build system. As its name suggests, the build system is responsible for building an executable program, ready for use, from the source code. There are various indications that the evolution of source code is strongly related to that of the build system. When the source code changes, the build system has to co-evolve to safeguard the ability to build an executable program. A rigid build system on the other hand limits software developers. This phenomenon especially surfaces when drastic changes in the source code are coupled with an inflexible build system, as is the case for the introduction of AOSD technology in legacy systems. AOSD is a young software development approach which enables developers to structure and compose source code in a better way. Legacy systems are old software systems which are still mission-critical, but of which the source code and the build system are no longer fully understood, and which typically make use of old(-fashioned) technology. This PhD dissertation focuses on finding an explanation for this co-evolution of source code and the build system, and on finding developer support to grasp and manage this phenomenon. We postulate four "roots of co-evolution" which represent four different ways in which source code and the build system interact with each other. Based on these roots, we have developed tool and aspect language support to understand and manage co-evolution. The roots and the tool support have been validated in case studies, both in the context of co-evolution in general and of the introduction of AOSD technology in legacy systems. The dissertation experimentally shows that co-evolution indeed is a real problem, but that specific software development and aspect language support enables developers to deal with it

An Integrative and Uniform Model for Metadata Management in Data Warehousing Environment

Due to the increasing complexity of data warehouses, a centralized and declarative management of metadata is essential for data warehouse administration, maintenance and usage. Metadata are usually divided into technical and semantic metadata. Typically, current approaches only support subsets of these metadata types, such as data movement metadata or multidimensional metadata for OLAP. In particular, the interdependencies between technical and semantic metadata have not yet been investigated sufficiently. The representation of these interdependencies form an important prerequisite for the translation of queries formulated at the business concept level to executable queries on physical data. Therefore, we suggest a uniform and integrative model for data warehouse metadata. This model uses a uniform representation approach based on the Uniform Modeling Language (UML) to integrate technical and semantic metadata and their interdependencies

Joining and aggregating datasets using CouchDB

Data mining typically requires implementing operations that involve cross-cutting entity boundaries and are awkward to implement in document-oriented databases. CouchDB, for example, models entities as documents, with highly isolated entity boundaries, and on which joins cannot be directly performed. This project shows how join and aggregation can be achieved across entity boundaries in such systems, as encountered for example in the pre-processing and exploration stages of educational data mining. A software stack is presented as a means by which this can be achieved; first, datasets are processed via ETL operations, then MapReduce is used to create indices of ordered and aggregated data. Finally, a Couchdb list function is used to iterate through these indices and perform joins, and to compute aggregated values on joined datasets such as variance and correlations. In terms of the case study, it is shown that the proposed approach to implementing cross-document joins and aggregation is effective and scalable. In addition, it was discovered that for the 2014 - 2016 UCT cohorts, NBT scores correlate better with final grades for the CSC1015F course than do Grade 12 results for English, Science and Mathematics

A Lightweight Framework for Universal Fragment Composition

Domain-specific languages (DSLs) are useful tools for coping with complexity in software development. DSLs provide developers with appropriate constructs for specifying and solving the problems they are faced with. While the exact definition of DSLs can vary, they can roughly be divided into two categories: embedded and non-embedded. Embedded DSLs (E-DSLs) are integrated into general-purpose host languages (e.g. Java), while non-embedded DSLs (NE-DSLs) are standalone languages with their own tooling (e.g. compilers or interpreters). NE-DSLs can for example be found on the Semantic Web where they are used for querying or describing shared domain models (ontologies). A common theme with DSLs is naturally their support of focused expressive power. However, in many cases they do not support non–domain-specific component-oriented constructs that can be useful for developers. Such constructs are standard in general-purpose languages (procedures, methods, packages, libraries etc.). While E-DSLs have access to such constructs via their host languages, NE-DSLs do not have this opportunity. Instead, to support such notions, each of these languages have to be extended and their tooling updated accordingly. Such modifications can be costly and must be done individually for each language. A solution method for one language cannot easily be reused for another. There currently exist no appropriate technology for tackling this problem in a general manner. Apart from identifying the need for a general approach to address this issue, we extend existing composition technology to provide a language-inclusive solution. We build upon fragment-based composition techniques and make them applicable to arbitrary (context-free) languages. We call this process for the composition techniques’ universalization. The techniques are called fragment-based since their view of components— reusable software units with interfaces—are pieces of source code that conform to an underlying (context-free) language grammar. The universalization process is grammar-driven: given a base language grammar and a description of the compositional needs wrt. the composition techniques, an adapted grammar is created that corresponds to the specified needs. The result is thus an adapted grammar that forms the foundation for allowing to define and compose the desired fragments. We further build upon this grammar-driven universalization approach to allow developers to define the non–domain-specific component-oriented constructs that are needed for NE-DSLs. Developers are able to define both what those constructs should be, and how they are to be interpreted (via composition). Thus, developers can effectively define language extensions and their semantics. This solution is presented in a framework that can be reused for different languages, even if their notion of ‘components’ differ. To demonstrate the approach and show its applicability, we apply it to two Semantic Web related NE-DSLs that are in need of component-oriented constructs. We introduce modules to the rule-based Web query language Xcerpt and role models to the Web Ontology Language OWL

A Pattern-based Foundation for Language-Driven Software Engineering

This work brings together two fundamental ideas for modelling, programming and analysing software systems. The first idea is of a methodological nature: engineering software by systematically creating and relating languages. The second idea is of a technical nature: using patterns as a practical foundation for computing. The goal is to show that the systematic creation and layering of languages can be reduced to the elementary operations of pattern matching and instantiation and that this pattern-based approach provides a formal and practical foundation for language-driven modelling, programming and analysis. The underpinning of the work is a novel formalism for recognising, deconstructing, creating, searching, transforming and generally manipulating data structures. The formalism is based on typed sequences, a generic structure for representing trees. It defines basic pattern expressions for matching and instantiating atomic values and variables. Horizontal, vertical, diagonal and hierarchical operators are different ways of combining patterns. Transformations combine matching and instantiating patterns and they are patterns themselves. A quasiquotation mechanism allows arbitrary levels of meta-pattern functionality and forms the basis of pattern abstraction. Path polymorphic operators are used to specify fine-grained search of structures. A range of core concepts such as layering, parsing and pattern-based computing can naturally be defined through pattern expressions. Three language-driven tools that utilise the pattern formalism showcase the applicability of the pattern-approach. Concat is a self-sustaining (meta-)programming system in which all computations are expressed by matching and instantiation. This includes parsing, executing and optimising programs. By applying its language engineering tools to its own meta-language, Concat can extend itself from within. XMF (XML Modeling Framework) is a browser-based modelling- and meta-modelling framework that provides flexible means to create and relate modelling languages and to query and validate models. The pattern functionality that makes this possible is partly exposed as a schema language and partly as a JavaScript library. CFR (Channel Filter Rule Language) implements a language-driven approach for layered analysis of communication in complex networked systems. The communication on each layer is visible in the language of an “abstract protocol” that is defined by communication patterns