Adding Robustness in Dynamic Preemptive Scheduling

In this paper we introduce a robust earliest deadline scheduling algorithm for deal ing with hard aperiodic tasks under overloads in a dynamic realtime environment The algorithm synergistically combines many features including dynamic guarantees graceful degradation in overloads deadline tolerance resource reclaiming and dy namic reguarantees A necessary and sucient schedulability test is presented and an ecient On guarantee algorithm is proposed The new algorithm is evaluated via simulation and compared to several baseline algorithms The experimental results show excellent performance of the new algorithm in normal and overload conditions Static realtime systems are designed for worst case situations Assuming that all the assumptions made in the design and analysis are correct we can say that the level of guarantee for these systems is absolute and all tasks will make their deadlines Unfortunately static systems are not always possible becaus

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

<p>Abstract</p> <p>Background</p> <p>Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts.</p> <p>Results</p> <p>To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (<it>e.g</it>., for biomolecular sequences, alignments, structures) and functionality (<it>e.g</it>., to parse/write standard file formats).</p> <p>Conclusions</p> <p>PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at <url>http://muralab.org/PaPy</url>, and includes extensive documentation and annotated usage examples.</p

Evaluation of 309 Environmental Chemicals Using a Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity Assay

The vast landscape of environmental chemicals has motivated the need for alternative methods to traditional whole-animal bioassays in toxicity testing. Embryonic stem (ES) cells provide an in vitro model of embryonic development and an alternative method for assessing developmental toxicity. Here, we evaluated 309 environmental chemicals, mostly food-use pesticides, from the ToxCast™ chemical library using a mouse ES cell platform. ES cells were cultured in the absence of pluripotency factors to promote spontaneous differentiation and in the presence of DMSO-solubilized chemicals at different concentrations to test the effects of exposure on differentiation and cytotoxicity. Cardiomyocyte differentiation (α,β myosin heavy chain; MYH6/MYH7) and cytotoxicity (DRAQ5™/Sapphire700™) were measured by In-Cell Western™ analysis. Half-maximal activity concentration (AC50) values for differentiation and cytotoxicity endpoints were determined, with 18% of the chemical library showing significant activity on either endpoint. Mining these effects against the ToxCast Phase I assays (∼500) revealed significant associations for a subset of chemicals (26) that perturbed transcription-based activities and impaired ES cell differentiation. Increased transcriptional activity of several critical developmental genes including BMPR2, PAX6 and OCT1 were strongly associated with decreased ES cell differentiation. Multiple genes involved in reactive oxygen species signaling pathways (NRF2, ABCG2, GSTA2, HIF1A) were strongly associated with decreased ES cell differentiation as well. A multivariate model built from these data revealed alterations in ABCG2 transporter was a strong predictor of impaired ES cell differentiation. Taken together, these results provide an initial characterization of metabolic and regulatory pathways by which some environmental chemicals may act to disrupt ES cell growth and differentiation

Studies on the xanthine oxidase activity of mammalian cells

Xanthine oxidase in man is confined to but a few tissues and is absent from cultured cell strains. In rodents, however, the enzyme is more widely distributed among the tissues and can be demonstrated in most cell lines. Rodents possess the enzyme uricase and are therefore able to carry purine catabolism one step further than man. Preliminary results suggest that uricase is restricted to but a few rodent tissues and is absent from cultured rodent cells. Hence it may be that in each species only the final enzyme of purine catabolism is tissue restricted. In other experiments, mammalian cells were grown in the presence of compounds known to induce xanthine oxidase in a eukaryotic fungus (Aspergillus nidulans) . These compounds did not induce the enzyme in mammalian cells.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44184/1/10528_2004_Article_BF00487339.pd

Transport and Display Mechanisms For Multimedia Conferencing Across Packet-Switched Networks

: A transport protocol that supports real-time communication of audio/video frames across campus-area packet switched networks is presented. It is a &quot;best effort&quot; protocol that attempts to ameliorate the effect of jitter, load variation, and packet loss, to provide low latency, synchronized audio and video communications. This goal is realized through four transport and display mechanisms, and a real-time implementation of these mechanisms that integrates operating system services (e.g., scheduling and resource allocation, and device management) with network communication services (e.g., transport protocols), and with application code (e.g., display routines). The four mechanisms are: a facility for varying the synchronization between audio and video to achieve continuous audio in the face of jitter, a network congestion monitoring mechanism that is used to control audio/video latency, a queueing mechanism at the sender that is used to maximize frame throughput without unnecessarily in..

Bringing real-time scheduling theory and practice closer for multimedia computing

guru @ ora.wustl.edu This paper seeks to bridge the gap between theory and practice of real-time scheduling in the domain of multimedia computer systems. We show that scheduling algorithms that are good in theory, often have practical limitations. However when these algorithms are modi ed based on practical considerations, existing theoretical results cannot be used as they are. In this paper we motivate the need for new scheduling schemes for multimedia protocol processing, and demonstrate their real-time performance in our prototype implementation. We then explain the observed results by analysis and measurement. More speci cally, weshow that using strict preemption can introduce overheads in protocol processing such asmorecontext switching and extra system calls. We present our scheduling scheme called rate-monotonic with delayed preemption (rmdp) and showhow it reduces both these overheads. We then develop the analytical framework to analyze rmdp and other scheduling schemes that lie in the region between strict (immediate) preemption and no preemption. Byproducts of our analysis include simpler schedulability tests for non-preemptive scheduling, and a variant of rate-monotonic scheduling that has fewer preemptions. Finally, we measure the overhead due to context switching on Pentium and Sparc-1 machines and its impact on real-time performance. We show that when scheduling clock interrupts occur every 1 millisecond, rmdp can lessen the overhead of context switching leading to an increase in utilization of as much as8%.