a survey

Building ontologies in a collaborative and increasingly community-driven fashion has become a central paradigm of modern ontology engineering. This understanding of ontologies and ontology engineering processes is the result of intensive theoretical and empirical research within the Semantic Web community, supported by technology developments such as Web 2.0. Over 6 years after the publication of the first methodology for collaborative ontology engineering, it is generally acknowledged that, in order to be useful, but also economically feasible, ontologies should be developed and maintained in a community-driven manner, with the help of fully-fledged environments providing dedicated support for collaboration and user participation. Wikis, and similar communication and collaboration platforms enabling ontology stakeholders to exchange ideas and discuss modeling decisions are probably the most important technological components of such environments. In addition, process-driven methodologies assist the ontology engineering team throughout the ontology life cycle, and provide empirically grounded best practices and guidelines for optimizing ontology development results in real-world projects. The goal of this article is to analyze the state of the art in the field of collaborative ontology engineering. We will survey several of the most outstanding methodologies, methods and techniques that have emerged in the last years, and present the most popular development environments, which can be utilized to carry out, or facilitate specific activities within the methodologies. A discussion of the open issues identified concludes the survey and provides a roadmap for future research and development in this lively and promising field

Collaborative ontology engineering: a survey

Building ontologies in a collaborative and increasingly community-driven fashion has become a central paradigm of modern ontology engineering. This understanding of ontologies and ontology engineering processes is the result of intensive theoretical and empirical research within the Semantic Web community, supported by technology developments such as Web 2.0. Over 6 years after the publication of the first methodology for collaborative ontology engineering, it is generally acknowledged that, in order to be useful, but also economically feasible, ontologies should be developed and maintained in a community-driven manner, with the help of fully-fledged environments providing dedicated support for collaboration and user participation. Wikis, and similar communication and collaboration platforms enabling ontology stakeholders to exchange ideas and discuss modeling decisions are probably the most important technological components of such environments. In addition, process-driven methodologies assist the ontology engineering team throughout the ontology life cycle, and provide empirically grounded best practices and guidelines for optimizing ontology development results in real-world projects. The goal of this article is to analyze the state of the art in the field of collaborative ontology engineering. We will survey several of the most outstanding methodologies, methods and techniques that have emerged in the last years, and present the most popular development environments, which can be utilized to carry out, or facilitate specific activities within the methodologies. A discussion of the open issues identified concludes the survey and provides a roadmap for future research and development in this lively and promising fiel

Proceedings, MSVSCC 2018

Proceedings of the 12th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 19, 2018 at VMASC in Suffolk, Virginia. 155 pp

STRUCTURAL MODELING OF PROTEIN-PROTEIN INTERACTIONS USING MULTIPLE-CHAIN THREADING AND FRAGMENT ASSEMBLY

Since its birth, the study of protein structures has made progress with leaps and bounds. However, owing to the expenses and difficulties involved, the number of protein structures has not been able to catch up with the number of protein sequences and in fact has steadily lost ground. This necessitated the development of high-throughput but accurate computational algorithms capable of predicting the three dimensional structure of proteins from its amino acid sequence. While progress has been made in the realm of protein tertiary structure prediction, the advancement in protein quaternary structure prediction has been limited by the fact that the degree of freedom for protein complexes is even larger and even fewer number of protein complex structures are present in the PDB library. In fact, protein complex structure prediction till date has largely remained a docking problem where automated algorithms aim to predict the protein complex structure starting from the unbound crystal structure of its component subunits and thus has remained largely limited in terms of scope. Secondly, since docking essentially treats the unbound subunits as "rigid-bodies" it has limited accuracy when conformational change accompanies protein-protein interaction. In one of the first of its kind effort, this study aims for the development of protein complex structure algorithms which require only the amino acid sequence of the interacting subunits as input. The study aimed to adapt the best features of protein tertiary structure prediction including template detection and ab initio loop modeling and extend it for protein-protein complexes thus requiring simultaneous modeling of the three dimensional structure of the component subunits as well as ensuring the correct orientation of the chains at the protein-protein interface. Essentially, the algorithms are dependent on knowledge-based statistical potentials for both fold recognition and structure modeling. First, as a way to compare known structure of protein-protein complexes, a complex structure alignment program MM-align was developed. MM-align joins the chains of the complex structures to be aligned to form artificial monomers in every possible order. It then aligns them using a heuristic dynamic programming based approach using TM-score as the objective function. However, the traditional NW dynamic programming was redesigned to prevent the cross alignment of chains during the structure alignment process. Driven by the knowledge obtained from MM-align that protein complex structures share evolutionary relationships and the current protein complex structure library already contains homologous/structurally analogous protein quaternary structure families, a dimeric threading approach, COTH was designed. The new threading-recombination approach boosts the protein complex structure library by combining tertiary structure templates with complex alignments. The query sequences are first aligned to complex templates using the modified dynamic programming algorithm, guided by a number of predicted structural features including ab initio binding-site predictions. Finally, a template-based complex structure prediction approach, TACOS, was designed to build full-length protein complex structures starting from the initial templates identified by COTH. TACOS, fragments the templates aligned regions of templates and reassembles them while building the structure of the threading unaligned region ab inito using a replica-exchange monte-carlo simulation procedure. Simultaneously, TACOS also searches for the best orientation match of the component structures driven by a number of knowledge-based potential terms. Overall, TACOS presents the one of the first approach capable of predicting full length protein complex structures from sequence alone and introduces a new paradigm in the field of protein complex structure modeling

Agency is molecular: moved by being moved to moving or co-constitution in intra-active knowledge production

This practice-based PhD aims to intertwine theoretical research and artistic practice on the basis of knowledge production by conceptually thinking through motion, with movement informing the methodological counterpart in performative research settings. I argue that movement and the concept of motion, in their immanent potential for in/determinancy, transport possibilities of transversality that have been neglected in western Modernity. Both offer the means of moving beyond the bifurcated exceptionalism of Modernity's epistemology. The project interrogates its own positioning from within by affirming embodied ways of knowing, which are marginalised within the rationalised epistemes in European Universalisms (Wallerstein). In doing so it also takes a stand against appropriation. From a feminist position, new materialism's situatedness (Haraway) and relational objectivity (Barad) are particularly suitable tools for a shift from within. The apparatus definitions of Agential Realism gather insights through agential cuts that provide a transient exteriority-within, allowing modifying the bounds of knowing from within. The primary chapters examine the impact of practicing through theory and coalesce into a final experiment that reverses the process. Applied to the path of thoughts, movement's induction of changes to matter initiates an essential process of creating space for delinking (Mignolo/Walsh) and unlearning (Singh). The foundation of both practice- and theory-based approaches is Barad's notion of intra-active doing-being, which provides an understanding of agential intertwinement by approaching matter through and with interferences. In experiments, electronic devices were set to receive techno-sound-reverberations as diffractional concerns (noise), that transposed mattering (meaning) from co-constitutional forms. These 'voices', enacted in material-discursive experiments of various entangled engagements in different molecular matterings (body-mind, nature-culture, non-human-human, other-self) are typically ignored, denied, or misunderstood by the notorious bifurcation of the western metaphysical matrix (Jackson). Listening to matter’s iterative performativity (Barad) disclosed uneven levels of capacity (Wilderson) within such non-interrogated generalisations as the flattening to 'we' of the Anthropocene discourse. This awareness of interferential reverberations demands a multidirectional pluriverse of capabilities, which compromises any one-world (Law) exceptionality

COMPUTER-SUPPORTED COLLABORATIVE KNOWLEDGE BUILDING IN ENGINEERING DESIGN

Engineering design is defined as a process of devising a technical system, component, or process to satisfy desired needs. Collaborative engineering design (CED) is a knowledge- intensive process that involves multidisciplinary people working jointly, sharing resources and outcomes, and building new knowledge while solving problems. People need to collaborate synchronously or asynchronously, either in the same place or distributed geographically. This thesis proposes that engineering design can be modeled not only as a process of knowledge transformation, but as a process of collaborative knowledge building (CKB). CKB is a goal-driven collaborative process of generating and refining ideas and concepts of value to the community. Properly applied and supported, CKB has the potential to improve both learning and design outcomes resulting from collaborative design projects. Existing collaboration tools have evolved without a clear understanding of designers’ needs, even though a portion of the required functionalities has been achieved separately. This thesis proposes an integrated CKB-orientated model for collaborative engineering design, incorporating the key elements of Stahl’s CKB model, Lu’s ECN-based collaborative engineering model, Nonaka’s knowledge creation theory, and Sim and Duffy’s model of a design activity. Based on the model, a set of specific requirements for collaboration tools are presented and some functionalities not existing currently are identified

Emergent pedagogies in design research education

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Architecture, 1997.Includes bibliographical references (leaves 63-64).Recent demand for applied knowledge within architectural practice has resulted in the proliferation of university based research groups. Given the role advanced degree programs play in educating architectural researchers, an opportunity exists to educate architects towards bridging the traditional gap between practice and academia, as well as addressing the dichotomy of research and teaching within the university. Traditionally, research methods from other disciplines are taught in an attempt to redress the research deficiencies of a professional education. This investigation begins with a different premise: the operations of design, central to an architect's intellectual and operational repertoire, should be the catalyst for developing research methods specific to architecture. Further, these methods should be accompanied by a knowledge base which expresses the operations of design. A modified educational paradigm consisting of methods, knowledge, and the building of abilities through 'thoughtful performances', structures an experimental curriculum. Each attribute becomes a dimension for substantiation and assessment. Student engagement and entanglement within this locus reveals the potential directions of design research education. The subsequent analyses of the student work indicates four major trends: Intersubjectivity the need for common understanding; Transparency- the effortless application of methods, Emergence- acknowledgment of form's evolution; and Apprentissage- French for learning which occurs from within apprenticeship. Given these attributes, and the subsequent imperative to redefine architectural research, we formulate a paradigmatic architectural researcher, the "Architect Scholar' and speculate on an educational program designed to foster these characteristics within students.by Joseph Press.M.S