Parallel replication for distributed video-on-demand systems.

Lie, Wai-Kwok Peter.Thesis (M.Phil.)--Chinese University of Hong Kong, 1997.Includes bibliographical references (leaves 79-83).Abstract --- p.iAcknowledgments --- p.iiChapter 1 --- Introduction --- p.1Chapter 2 --- Background & Related Work --- p.5Chapter 2.1 --- Early Work on Multimedia Servers --- p.6Chapter 2.2 --- Compression of Multimedia Data --- p.6Chapter 2.3 --- Multimedia File Systems --- p.7Chapter 2.4 --- Scheduling Support for Multimedia Systems --- p.8Chapter 2.5 --- Inter-media Synchronization --- p.9Chapter 2.6 --- Related Work on Replication in VOD Systems --- p.9Chapter 3 --- System Model --- p.12Chapter 4 --- Replication Methodology --- p.15Chapter 4.1 --- Replication Triggering Policy --- p.16Chapter 4.2 --- Source & Target Nodes Selection Policies --- p.17Chapter 4.3 --- Replication Policies --- p.18Chapter 4.3.1 --- Policy 1: Injected Sequential Replication --- p.20Chapter 4.3.2 --- Policy 2: Piggybacked Sequential Replication --- p.22Chapter 4.3.3 --- Policy 3: Injected Parallel Replication --- p.25Chapter 4.3.4 --- Policy 4: Piggybacked Parallel Replication --- p.28Chapter 4.3.5 --- Policy 5: Injected & Piggybacked Parallel Replication --- p.34Chapter 4.3.6 --- Policy 6: Multi-Source Injected & Piggybacked Parallel Replication --- p.36Chapter 4.4 --- Dereplication Policy --- p.37Chapter 5 --- Distributed Architecture for VOD Server --- p.39Chapter 5.1 --- Server Node --- p.40Chapter 5.2 --- Movie Manager --- p.42Chapter 5.3 --- Metadata Manager --- p.42Chapter 5.4 --- Protocols for Distributed VOD Architecture --- p.43Chapter 5.4.1 --- Protocol for Servicing New Customers --- p.43Chapter 5.4.2 --- Protocol for Servicing Existing Customers --- p.45Chapter 5.4.3 --- Protocol for Single/Multi-Source Injected & Parallel Replication --- p.46Chapter 5.4.4 --- Protocol for Dereplication --- p.48Chapter 5.5 --- Failure Handling --- p.49Chapter 5.5.1 --- Handling of Server Node Failures --- p.50Chapter 5.5.2 --- Handling of Movie Manager Failures --- p.52Chapter 6 --- Results --- p.55Chapter 6.1 --- Performance Metric --- p.56Chapter 6.2 --- Simulation Environment --- p.58Chapter 6.3 --- Results of Experiments without Dereplication --- p.59Chapter 6.3.1 --- Comparison of Different Replication Policies --- p.60Chapter 6.3.2 --- Effect of Early Acceptance/Migration --- p.61Chapter 6.3.3 --- Answer to the Resources Consumption Tradeoff issue --- p.62Chapter 6.3.4 --- Effect of Varying Movie Popularity Skewness --- p.64Chapter 6.3.5 --- Effect of Varying Replication Threshold --- p.64Chapter 6.3.6 --- Comparison of Different Target Node Selection Policies --- p.65Chapter 6.4 --- Overall Impact of Dynamic Replication --- p.66Chapter 7 --- Comparison with BSR-based Policy --- p.71Chapter 8 --- Conclusions --- p.75Chapter 8.1 --- Summary --- p.75Chapter 8.2 --- Future Research Directions --- p.76Bibliography --- p.7

A bioinformatics approach for conceptual genome mining

Recent advances in sequencing technology have set the stage for a steadily growing number of microbial whole-genome sequences. At the same time, bioinformatic analysis increasingly sheds light on the genome-encoded capacity of certain microorganisms for the production of secondary metabolites. This work describes the development of a bioinformatic toolkit to underpin discovery and dereplication efforts in a genomics-based workflow aimed at the characterization of multimodular biosynthetic gene clusters from bacterial genomes. Key to the “conceptual genome mining” approach implemented here is the comparison of pathways architectures represented by arrangement and properties of domains in complex PKS-, NRPS- and hybrid pathways rather than resorting to DNA- or protein-level sequence similarity. The new analysis framework named BiosynML toolkit was interfaced to antiSMASH, the de-facto standard for automatic annotation of biosynthetic pathways, and integrated with an existing in-house research database system (Mxbase). BiosynML methods were tested using 42 characterized pathways from 71 myxobacterial genomes and also applied to publicly accessible genomes from relevant microbial taxa. BiosynML tools were ultimately used to create an overview of 1347 pathways of which 783 distinct models were identified. This analysis revealed minimal overlap between suborders and enabled the tentative estimation of myxobacterial secondary metabolite gene cluster richness.Die fortschreitende Verbesserung von Sequenziertechnologien ermöglicht den Zugang zu einer stetig wachsenden Zahl von mikrobiellen Genomsequenzen. Gleichzeitig liefern bioinformatische Methoden ein immer besseres Bild des genetischen Potentials der Mikroorganismen für die Produktion von Sekundärmetaboliten. Die vorliegende Arbeit befasst sich mit der Entwicklung von bioinformatischen Werkzeugen um die Entdeckung, die Dereplikation und letztendlich die Charakterisierung von multimodularen Biosynthesewegen in mikrobiellen Genomen zu unterstützen. Kernstück des Ansatzes ist der „konzept-basierte“ Vergleich der Architekturen von komplexen PKS-, NRPS- und hybriden Genclustern, der sich auf Anordnung und Eigenschaften biosynthetischer Domänen stützt anstelle von Sequenzähnlichkeit. Das neu entwickelte Softwarewerkzeug, genannt BiosynML, wurde mit antiSMASH (dem de-facto Standard für die automatische Annotation von Biosynthesewegen) verknüpft und in eine bestehende Forschungsdatenbank (Mxbase) integriert. BiosynML Methoden wurden anhand der Biosynthesewege für 42 bekannte Naturstoffe in 71 myxobakteriellen Genomsequenzen getestet und auf öffentlich zugängliche Genome relevanter Mikroorganismen angewendet. Die Analyse von 1347 Biosyntheswegen aus den Genomen der Myxobakterien, darunter ein derepliziertes Set von 783 Typen, ergab eine nur minimale Überlappung zwischen Unterordnungen und ermöglichte die Abschätzung der Diversität an myxobakteriellen Sekundärmetaboliten-Genclustern

A bioinformatics approach for conceptual genome mining

Recent advances in sequencing technology have set the stage for a steadily growing number of microbial whole-genome sequences. At the same time, bioinformatic analysis increasingly sheds light on the genome-encoded capacity of certain microorganisms for the production of secondary metabolites. This work describes the development of a bioinformatic toolkit to underpin discovery and dereplication efforts in a genomics-based workflow aimed at the characterization of multimodular biosynthetic gene clusters from bacterial genomes. Key to the “conceptual genome mining” approach implemented here is the comparison of pathways architectures represented by arrangement and properties of domains in complex PKS-, NRPS- and hybrid pathways rather than resorting to DNA- or protein-level sequence similarity. The new analysis framework named BiosynML toolkit was interfaced to antiSMASH, the de-facto standard for automatic annotation of biosynthetic pathways, and integrated with an existing in-house research database system (Mxbase). BiosynML methods were tested using 42 characterized pathways from 71 myxobacterial genomes and also applied to publicly accessible genomes from relevant microbial taxa. BiosynML tools were ultimately used to create an overview of 1347 pathways of which 783 distinct models were identified. This analysis revealed minimal overlap between suborders and enabled the tentative estimation of myxobacterial secondary metabolite gene cluster richness.Die fortschreitende Verbesserung von Sequenziertechnologien ermöglicht den Zugang zu einer stetig wachsenden Zahl von mikrobiellen Genomsequenzen. Gleichzeitig liefern bioinformatische Methoden ein immer besseres Bild des genetischen Potentials der Mikroorganismen für die Produktion von Sekundärmetaboliten. Die vorliegende Arbeit befasst sich mit der Entwicklung von bioinformatischen Werkzeugen um die Entdeckung, die Dereplikation und letztendlich die Charakterisierung von multimodularen Biosynthesewegen in mikrobiellen Genomen zu unterstützen. Kernstück des Ansatzes ist der „konzept-basierte“ Vergleich der Architekturen von komplexen PKS-, NRPS- und hybriden Genclustern, der sich auf Anordnung und Eigenschaften biosynthetischer Domänen stützt anstelle von Sequenzähnlichkeit. Das neu entwickelte Softwarewerkzeug, genannt BiosynML, wurde mit antiSMASH (dem de-facto Standard für die automatische Annotation von Biosynthesewegen) verknüpft und in eine bestehende Forschungsdatenbank (Mxbase) integriert. BiosynML Methoden wurden anhand der Biosynthesewege für 42 bekannte Naturstoffe in 71 myxobakteriellen Genomsequenzen getestet und auf öffentlich zugängliche Genome relevanter Mikroorganismen angewendet. Die Analyse von 1347 Biosyntheswegen aus den Genomen der Myxobakterien, darunter ein derepliziertes Set von 783 Typen, ergab eine nur minimale Überlappung zwischen Unterordnungen und ermöglichte die Abschätzung der Diversität an myxobakteriellen Sekundärmetaboliten-Genclustern

Computational applications in secondary metabolite discovery (caismd): An online workshop

We report the major conclusions of the online open-access workshop “Computational Applications in Secondary Metabolite Discovery (CAiSMD)” that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from fve continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational meth‑ odologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the “omics” age. The invited experts gave keynote lectures, trained participants in handson sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were ofered the opportunity to give oral presentations (15 min) and present posters in the form of fash presentations (5 min) upon submission of an abstract. The fnal program available on the workshop website (https://caismd.indiayouth.info/) comprised of 4 keynote lec‑ tures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions

Advancement of Natural Products: Optimization of Instrumentation and Examples of their Application to the Isolation of New Compounds

The world of natural products has a long rich history dating back thousands of years and was the origin of medicine as we know it. Advancements in the field of natural products can be seen not only in the isolation of new molecules, but also in the advancement of new tools that are used to elucidate the structure of new compounds, identify lead compounds, as well as monitor the pharmokinetics of bioactive substances. The third chapter in this dissertation introduces a new tool that could be used in the later steps of drug development by being able to rapidly quantify a fluorinated compound in complex mixtures, the fourth chapter includes a comparison of an advanced spheroid bioassay with the traditional 2D assay that can be used to identify appropriate lead compounds, and the fifth chapter reveals techniques for applying natural products to a less discussed target: agricultural fungicides