WIDE - A Distributed Architecture for Workflow Management

This paper presents the distributed architecture of the WIDE workflow management system. We show how distribution and scalability are obtained by the use of a distributed object model, a client/server architecture, and a distributed workflow server architecture. Specific attention is paid to the extended transaction support and active rule support subarchitectures

Towards MKM in the Large: Modular Representation and Scalable Software Architecture

MKM has been defined as the quest for technologies to manage mathematical knowledge. MKM "in the small" is well-studied, so the real problem is to scale up to large, highly interconnected corpora: "MKM in the large". We contend that advances in two areas are needed to reach this goal. We need representation languages that support incremental processing of all primitive MKM operations, and we need software architectures and implementations that implement these operations scalably on large knowledge bases. We present instances of both in this paper: the MMT framework for modular theory-graphs that integrates meta-logical foundations, which forms the base of the next OMDoc version; and TNTBase, a versioned storage system for XML-based document formats. TNTBase becomes an MMT database by instantiating it with special MKM operations for MMT.Comment: To appear in The 9th International Conference on Mathematical Knowledge Management: MKM 201

Two Case Studies of Subsystem Design for General-Purpose CSCW Software Architectures

This paper discusses subsystem design guidelines for the software architecture of general-purpose computer supported cooperative work systems, i.e., systems that are designed to be applicable in various application areas requiring explicit collaboration support. In our opinion, guidelines for subsystem level design are rarely given most guidelines currently given apply to the programming language level. We extract guidelines from a case study of the redesign and extension of an advanced commercial workflow management system and place them into the context of existing software engineering research. The guidelines are then validated against the design decisions made in the construction of a widely used web-based groupware system. Our approach is based on the well-known distinction between essential (logical) and physical architectures. We show how essential architecture design can be based on a direct mapping of abstract functional concepts as found in general-purpose systems to modules in the essential architecture. The essential architecture is next mapped to a physical architecture by applying software clustering and replication to achieve the required distribution and performance characteristics

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Increasing the Efficiency of Rule-Based Expert Systems Applied on Heterogeneous Data Sources

Nowadays, the proliferation of heterogeneous data sources provided by different research and innovation projects and initiatives is proliferating more and more and presents huge opportunities. These developments create an increase in the number of different data sources, which could be involved in the process of decisionmaking for a specific purpose, but this huge heterogeneity makes this task difficult. Traditionally, the expert systems try to integrate all information into a main database, but, sometimes, this information is not easily available, or its integration with other databases is very problematic. In this case, it is essential to establish procedures that make a metadata distributed integration for them. This process provides a “mapping” of available information, but it is only at logic level. Thus, on a physical level, the data is still distributed into several resources. In this sense, this chapter proposes a distributed rule engine extension (DREE) based on edge computing that makes an integration of metadata provided by different heterogeneous data sources, applying then a mathematical decomposition over the antecedent of rules. The use of the proposed rule engine increases the efficiency and the capability of rule-based expert systems, providing the possibility of applying these rules over distributed and heterogeneous data sources, increasing the size of data sets that could be involved in the decision-making process