Factors shaping the evolution of electronic documentation systems

The main goal is to prepare the space station technical and managerial structure for likely changes in the creation, capture, transfer, and utilization of knowledge. By anticipating advances, the design of Space Station Project (SSP) information systems can be tailored to facilitate a progression of increasingly sophisticated strategies as the space station evolves. Future generations of advanced information systems will use increases in power to deliver environmentally meaningful, contextually targeted, interconnected data (knowledge). The concept of a Knowledge Base Management System is emerging when the problem is focused on how information systems can perform such a conversion of raw data. Such a system would include traditional management functions for large space databases. Added artificial intelligence features might encompass co-existing knowledge representation schemes; effective control structures for deductive, plausible, and inductive reasoning; means for knowledge acquisition, refinement, and validation; explanation facilities; and dynamic human intervention. The major areas covered include: alternative knowledge representation approaches; advanced user interface capabilities; computer-supported cooperative work; the evolution of information system hardware; standardization, compatibility, and connectivity; and organizational impacts of information intensive environments

Machine Learning for Fluid Mechanics

The field of fluid mechanics is rapidly advancing, driven by unprecedented volumes of data from field measurements, experiments and large-scale simulations at multiple spatiotemporal scales. Machine learning offers a wealth of techniques to extract information from data that could be translated into knowledge about the underlying fluid mechanics. Moreover, machine learning algorithms can augment domain knowledge and automate tasks related to flow control and optimization. This article presents an overview of past history, current developments, and emerging opportunities of machine learning for fluid mechanics. It outlines fundamental machine learning methodologies and discusses their uses for understanding, modeling, optimizing, and controlling fluid flows. The strengths and limitations of these methods are addressed from the perspective of scientific inquiry that considers data as an inherent part of modeling, experimentation, and simulation. Machine learning provides a powerful information processing framework that can enrich, and possibly even transform, current lines of fluid mechanics research and industrial applications.Comment: To appear in the Annual Reviews of Fluid Mechanics, 202

A Framework for Globally Optimizing Mixed-Integer Signomial Programs

Mixed-integer signomial optimization problems have broad applicability in engineering. Extending the Global Mixed-Integer Quadratic Optimizer, GloMIQO (Misener, Floudas in J. Glob. Optim., 2012. doi:10.1007/s10898-012-9874-7), this manuscript documents a computational framework for deterministically addressing mixed-integer signomial optimization problems to ε-global optimality. This framework generalizes the GloMIQO strategies of (1) reformulating user input, (2) detecting special mathematical structure, and (3) globally optimizing the mixed-integer nonconvex program. Novel contributions of this paper include: flattening an expression tree towards term-based data structures; introducing additional nonconvex terms to interlink expressions; integrating a dynamic implementation of the reformulation-linearization technique into the branch-and-cut tree; designing term-based underestimators that specialize relaxation strategies according to variable bounds in the current tree node. Computational results are presented along with comparison of the computational framework to several state-of-the-art solvers. © 2013 Springer Science+Business Media New York

Analysis of large scale linear programming problems with embedded network structures: Detection and solution algorithms

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Linear programming (LP) models that contain a (substantial) network structure frequently arise in many real life applications. In this thesis, we investigate two main questions; i) how an embedded network structure can be detected, ii) how the network structure can be exploited to create improved sparse simplex solution algorithms. In order to extract an embedded pure network structure from a general LP problem we develop two new heuristics. The first heuristic is an alternative multi-stage generalised upper bounds (GUB) based approach which finds as many GUB subsets as possible. In order to identify a GUB subset two different approaches are introduced; the first is based on the notion of Markowitz merit count and the second exploits an independent set in the corresponding graph. The second heuristic is based on the generalised signed graph of the coefficient matrix. This heuristic determines whether the given LP problem is an entirely pure network; this is in contrast to all previously known heuristics. Using generalised signed graphs, we prove that the problem of detecting the maximum size embedded network structure within an LP problem is NP-hard. The two detection algorithms perform very well computationally and make positive contributions to the known body of results for the embedded network detection. For computational solution a decomposition based approach is presented which solves a network problem with side constraints. In this approach, the original coefficient matrix is partitioned into the network and the non-network parts. For the partitioned problem, we investigate two alternative decomposition techniques namely, Lagrangean relaxation and Benders decomposition. Active variables identified by these procedures are then used to create an advanced basis for the original problem. The computational results of applying these techniques to a selection of Netlib models are encouraging. The development and computational investigation of this solution algorithm constitute further contribution made by the research reported in this thesis.This study is funded by the Turkish Educational Council and Mugla University

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

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