Cost Function Networks to Solve Large Computational Protein Design Problems

International audienc

Ontology based knowledge formulation and an interpretation engine for intelligent devices in pervasive environments

Ongoing device miniaturization makes it possible to manufacture very small devices; therefore more of them can be embedded in one space. Pervasive computing con- cepts, envisioning computers distributed in a space and hidden from users' sight, presented by Weiser in 1991 are becoming more realistic and feasible to implement. A technology supporting pervasive computing and Ambient Intelligence also needs to follow miniaturization. The Ambient Intelligence domain was mainly focused on supercomputers with large computation power and it is now moving towards smaller devices, with limited computation power, and takes inspiration from dis- tributed systems, ad-hoc networks and emergent computing. The ability to process knowledge, understand network protocols, adapt and learn is becoming a required capability from fairly small and energy-frugal devices. This research project con- sists of two main parts. The first part of the project has created a context aware generic knowledgebase interpretation engine that enables autonomous devices to pervasively manage smart spaces using Communicating Sequential Processes as the underlying design methodology. In the second part a knowledgebase containing all the information that is needed for a device to cooperate, make decisions and react was designed and constructed. The interpretation engine is designed to be suitable for devices from different vendors, as it enables semantic interoperability based on the use of ontologies. The knowledge, that the engine interprets, is drawn from an ontology and the model of the chosen ontology is fixed in the engine. This project has investigated, designed and built a prototype of the knowledge base interpretation engine. Functional testing was performed using a simulation implemented in JCSP. The implementation simulates many autonomous devices running in parallel, communicating using a broadcast-based protocol, self-organizing into sub-networks and reacting to users' requests. The main goal of the project was to design and investigate the knowledge interpretation engine, determine the number of functions that the engine performs, to enable hardware realisation, and investigate the knowledgebase represented with use of RDF triples and chosen ontology model. This project was undertaken in collaboration with NXP Semiconductor Research Eindhoven, The Netherlands.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Cost Function Networks to Solve Large Computational Protein Design Problems

International audienc

Ontology based knowledge formulation and an interpretation engine for intelligent devices in pervasive environments

Ongoing device miniaturization makes it possible to manufacture very small devices; therefore more of them can be embedded in one space. Pervasive computing concepts, envisioning computers distributed in a space and hidden from users' sight, presented by Weiser in 1991 are becoming more realistic and feasible to implement.A technology supporting pervasive computing and Ambient Intelligence also needs to follow miniaturization. The Ambient Intelligence domain was mainly focused on supercomputers with large computation power and it is now moving towards smaller devices, with limited computation power, and takes inspiration from distributed systems, ad-hoc networks and emergent computing. The ability to process knowledge, understand network protocols, adapt and learn is becoming a required capability from fairly small and energy-frugal devices. This research project consists of two main parts. The first part of the project has created a context aware generic knowledgebase interpretation engine that enables autonomous devices to pervasively manage smart spaces using Communicating Sequential Processes as the underlying design methodology. In the second part a knowledgebase containing all the information that is needed for a device to cooperate, make decisions and react was designed and constructed. The interpretation engine is designed to be suitable for devices from different vendors, as it enables semantic interoperability based on the use of ontologies. The knowledge, that the engine interprets, is drawn from an ontology and the model of the chosen ontology is fixed in the engine. This project has investigated, designed and built a prototype of the knowledge base interpretation engine. Functional testing was performed using a simulation implemented in JCSP. The implementation simulates many autonomous devices running in parallel, communicating using a broadcast-based protocol, self-organizing into sub-networks and reacting to users' requests. The main goal of the project was to design and investigate the knowledge interpretation engine, determine the number of functions that the engine performs, to enable hardware realisation, and investigate the knowledgebase represented with use of RDF triples and chosen ontology model. This project was undertaken in collaboration with NXP Semiconductor Research Eindhoven, The Netherlands

Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise “glycocodes” that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics

'A Poet Early, and Always in his Soul': the eighteenth-century reception of Milton's Poems (1645)

This thesis explores the reception of Milton’s first volume of poetry, now known as the Poems (1645), during their first 150 or so years of life. It is a broadly chronological study of the Poems’ publication, citation, and critical appreciation both as a discrete volume and, more often, as broken up into its constituent parts in anthologies, miscellanies, adaptations, and translations. Running throughout this history is a thematic analysis of the eighteenth century’s changing critical approach to these early Miltonic works, including notable editions of the poems, especially those from 1673, 1695, 1752, and 1785. My project is occasioned by the absence to date of a sustained, book-length study of the reception of Milton’s Poems. Such reception studies of Milton as do exist either chronicle receptions of his entire oeuvre, or focus exclusively on Paradise Lost. My critical field encompasses these existing reception histories, as well as studies primarily devoted to analysis of the Poems (1645). It also pays attention to scholarship on eighteenth-century poetics and its main proponents, to books about miscellany and anthology culture, and to histories of the emerging concept of an English literary canon around the middle of the eighteenth century. The aim of my study is, first, to illuminate an area of Milton criticism that has not, proportionally at least, been much studied; secondly, to continue a relatively recent critical tendency towards privileging the Poems as a separate body of work, meriting scholarly attention not just as the prelude to Paradise Lost but as a collection in its own right, with its own themes, its own dilemmas, and its own preoccupations

An Enhanced Hardware Description Language Implementation for Improved Design-Space Exploration in High-Energy Physics Hardware Design

Detectors in High-Energy Physics (HEP) have increased tremendously in accuracy, speed and integration. Consequently HEP experiments are confronted with an immense amount of data to be read out, processed and stored. Originally low-level processing has been accomplished in hardware, while more elaborate algorithms have been executed on large computing farms. Field-Programmable Gate Arrays (FPGAs) meet HEP's need for ever higher real-time processing performance by providing programmable yet fast digital logic resources. With the fast move from HEP Digital Signal Processing (DSPing) applications into the domain of FPGAs, related design tools are crucial to realise the potential performance gains. This work reviews Hardware Description Languages (HDLs) in respect to the special needs present in the HEP digital hardware design process. It is especially concerned with the question, how features outside the scope of mainstream digital hardware design can be implemented efficiently into HDLs. It will argue that functional languages are especially suitable for implementation of domain-specific languages, including HDLs. Casestudies examining the implementation complexity of HEP-specific language extensions to the functional HDCaml HDL will prove the viability of the suggested approach