SIEGE: Smoking Induced Epithelial Gene Expression Database

The SIEGE (Smoking Induced Epithelial Gene Expression) database is a clinical resource for compiling and analyzing gene expression data from epithelial cells of the human intra-thoracic airway. This database supports a translational research study whose goal is to profile the changes in airway gene expression that are induced by cigarette smoke. RNA is isolated from airway epithelium obtained at bronchoscopy from current-, former- and never-smoker subjects, and hybridized to Affymetrix HG-U133A Genechips, which measure the level of expression of ~22 500 human transcripts. The microarray data generated along with relevant patient information is uploaded to SIEGE by study administrators using the database's web interface, found at http://pulm.bumc.bu.edu/siegeDB. PERL-coded scripts integrated with SIEGE perform various quality control functions including the processing, filtering and formatting of stored data. The R statistical package is used to import database expression values and execute a number of statistical analyses including t-tests, correlation coefficients and hierarchical clustering. Values from all statistical analyses can be queried through CGI-based tools and web forms found on the �Search� section of the database website. Query results are embedded with graphical capabilities as well as with links to other databases containing valuable gene resources, including Entrez Gene, GO, Biocarta, GeneCards, dbSNP and the NCBI Map Viewer.

Multiplexing VBR Traffic Flows with Guaranteed Application-level QoS Using Statistical Rate Monotonic Scheduling

Quality of Service (QoS) guarantees are required by an increasing number of applications to ensure a minimal level of fidelity in the delivery of application data units through the network. Application-level QoS does not necessarily follow from any transport-level QoS guarantees regarding the delivery of the individual cells (e.g. ATM cells) which comprise the application's data units. The distinction between application-level and transport-level QoS guarantees is due primarily to the fragmentation that occurs when transmitting large application data units (e.g. IP packets, or video frames) using much smaller network cells, whereby the partial delivery of a data unit is useless; and, bandwidth spent to partially transmit the data unit is wasted. The data units transmitted by an application may vary in size while being constant in rate, which results in a variable bit rate (VBR) data flow. That data flow requires QoS guarantees. Statistical multiplexing is inadequate, because no guarantees can be made and no firewall property exists between different data flows. In this paper, we present a novel resource management paradigm for the maintenance of application-level QoS for VBR flows. Our paradigm is based on Statistical Rate Monotonic Scheduling (SRMS), in which (1) each application generates its variable-size data units at a fixed rate, (2) the partial delivery of data units is of no value to the application, and (3) the QoS guarantee extended to the application is the probability that an arbitrary data unit will be successfully transmitted through the network to/from the application.

Design and Implementation of Statistical Rate Monotonic Scheduling in KURT Linux

Statistical Rate Monotonic Scheduling (SRMS) is a generalization of the classical RMS results of Liu and Layland [LL73] for periodic tasks with highly variable execution times and statistical QoS requirements. The main tenet of SRMS is that the variability in task resource requirements could be smoothed through aggregation to yield guaranteed QoS. This aggregation is done over time for a given task and across multiple tasks for a given period of time. Similar to RMS, SRMS has two components: a feasibility test and a scheduling algorithm. SRMS feasibility test ensures that it is possible for a given periodic task set to share a given resource without violating any of the statistical QoS constraints imposed on each task in the set. The SRMS scheduling algorithm consists of two parts: a job admission controller and a scheduler. The SRMS scheduler is a simple, preemptive, fixed-priority scheduler. The SRMS job admission controller manages the QoS delivered to the various tasks through admit/reject and priority assignment decisions. In particular, it ensures the important property of task isolation, whereby tasks do not infringe on each other. In this paper we present the design and implementation of SRMS within the KURT Linux Operating System [HSPN98, SPH 98, Sri98]. KURT Linux supports conventional tasks as well as real-time tasks. It provides a mechanism for transitioning from normal Linux scheduling to a mixed scheduling of conventional and real-time tasks, and to a focused mode where only real-time tasks are scheduled. We overview the technical issues that we had to overcome in order to integrate SRMS into KURT Linux and present the API we have developed for scheduling periodic real-time tasks using SRMS.