21095960
The TRIPLES database: a community resource for yeast molecular biology
TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae-a relational database housing nearly half a million data points generated from an ongoing study using large-scale transposon mutagenesis to characterize gene function in yeast. At present, TRIPLES contains three principal data sets (i.e. phenotypic data, protein localization data and expression data) for over 3500 annotated yeast genes as well as several hundred non-annotated open reading frames. In addition, the TRIPLES web site provides online order forms linked to each data set so that users may request any strain or reagent generated from this project free of charge. In response to user requests, the TRIPLES web site has undergone several recent modifications. Our localization data have been supplemented with approximately 500 fluorescent micrographs depicting actual staining patterns observed upon indirect immunofluorescence analysis of indicated epitope-tagged proteins. These localization data, as well as all other data sets within TRIPLES, are now available in full as tab-delimited text. To accommodate increased reagent requests, all orders are now cataloged in a separate database, and users are notified immediately of order receipt and shipment. Also, TRIPLES is one of five sites incorporated into the new functional analysis tool Function Junction provided by the Saccharomyces Genome Database. TRIPLES may be accessed from the Yale Genome Analysis Center (YGAC) homepage at http://ygac.med.yale.edu.
23929618
Organelle DB: an updated resource of eukaryotic protein localization and function
Organelle DB () is a web-accessible relational database presenting a supplemented catalog of organelle-localized proteins and major protein complexes. Since its release in 2004, Organelle DB has grown by 20% to encompass over 30 000 proteins from 138 eukaryotic organisms. Each protein in Organelle DB is presented with its subcellular localization, primary sequence and a detailed description of its function, as available. All records in Organelle DB have been annotated using controlled vocabulary from the Gene Ontology consortium. Protein localization data are inherently visual, and Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we report here the development of Organelle View, an extension of Organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image. Among other applications, Organelle View may serve as an educational aid engaging introductory biology students through a visually ‘fun’ interface. Organelle View can be accessed from the Organelle DB home page or directly at .
2987975
Data streaming algorithms for efficient and accurate estimation of flow size distribution
Knowing the distribution of the sizes of traffic flows passing through a network link helps a network operator to characterize network resource usage, infer traffic demands, detect traffic anomalies, and accommodate new traffic demands through better traffic engineering. Previous work on estimating the flow size distribution has been focused on making inferences from sampled network traffic. Its accuracy is limited by the (typically) low sampling rate required to make the sampling operation affordable. In this paper we present a novel data streaming algorithm to provide much more accurate estimates of flow distribution, using a "lossy data structure" which consists of an array of counters fitted well into SRAM. For each incoming packet, our algorithm only needs to increment one underlying counter, making the algorithm fast enough even for 40 Gbps (OC-768) links. The data structure is lossy in the sense that sizes of multiple flows may collide into the same counter. Our algorithm uses Bayesian statistical methods such as Expectation Maximization to infer the most likely flow size distribution that results in the observed counter values after collision. Evaluations of this algorithm on large Internet traces obtained from several sources (including a tier-1 ISP) demonstrate that it has very high measurement accuracy (within 2%). Our algorithm not only dramatically improves the accuracy of flow distribution measurement, but also contributes to the field of data streaming by formalizing an existing methodology and applying it to the context of estimating the flow-distribution.
7291217
Merging workflows: A new perspective on connecting business processes
This paper describes the concept of workflow merge and methods for merging business processes. We grouped merges in four categories according to the type of merge: sequential, parallel, conditional, and iterative, and describe the corresponding algorithms for performing these operations. We give results that allow us to determine whether a merge operation is sound. It is shown that to avoid invalid merges, one should choose merge points between which a sub-workflow, called a merge region, is well structured. These findings can provide useful guidance for future workflow merge research. We also raise issues of more complex merge problems, such as merge conflicts, semantic ambiguities and workflow splits.
6247338
Fairness measures for resource allocation
In many optimization problems, one seeks to allocate a limited set of resources to a set of individuals with demands. Thus, such allocations can naturally be viewed as vectors, with one coordinate representing each individual. Motivated by work in network routing and bandwidth assignment, we consider the problem of producing solutions that simultaneously approximate all feasible allocations in a coordinate-wise sense. This is a very strong type of "global" approximation guarantee, and we explore its consequences in a range of discrete optimization problems, including facility location, scheduling, and bandwidth assignment in networks. A fundamental issue-one not encountered in the traditional design of approximation algorithms-is that good approximations in this global sense need not exist for every problem instance; there is no a priori reason why there should be an allocation that simultaneously approximates all others. As a result, the existential questions concerning such good allocations lead to a new perspective on a number of basic problems in resource allocation, and on the structure of their feasible solutions.
7207895
Space-code bloom filter for efficient traffic flow measurement
Per-flow traffic measurement is critical for usage accounting, traffic engineering, and anomaly detection. Previous methodologies are either based on random sampling (e.g., Cisco's NetFlow), which is inaccurate, or only account for the "elephants". Our paper introduces a novel technique for measuring per-flow traffic approximately, for all flows regardless of their sizes, at very high-speed (say, OC192+). The core of this technique is a novel data structure called Space Code Bloom Filter (SCBF). A SCBF is an approximate representation of a multiset; each element in this multiset is a traffic flow and its multiplicity is the number of packets in the flow. SCBF employs a Maximum Likelihood Estimation (MLE) method to measure the multiplicity of an element in the multiset. Through parameter tuning, SCBF allows for graceful tradeoff between measurement accuracy and computational and storage complexity. SCBF also contributes to the foundation of data streaming by introducing a new paradigm called blind streaming. We evaluated the performance of SCBF on packet traces gathered from a tier-1 ISP backbone and through mathematical analysis. Our preliminary results demonstrate that SCBF achieves reasonable mea-surement accuracy with very low storage and computational complexity.
5840162
The Case for Non-Cooperative Multihoming of Users to Access Points in IEEE 802.11 WLANs
In many cases, a mobile user has the option of connecting to one of several IEEE 802.11 access points (APs),each using an independent channel. User throughput in each 
AP is determined by the number of other users as well as the 
frame size and physical rate being used. We consider the scenario where users could multihome, i.e., split their traffic amongst all the available APs, based on the throughput they obtain and the price charged. Thus, they are involved in a non-cooperative game with each other. We convert the problem into a fluid model and show that under a pricing scheme, which we call the cost price mechanism, the total system throughput is maximized,i.e., the system suffers no loss of efficiency due to selfish dynamics. We also study the case where the Internet Service 
Provider (ISP) could charge prices greater than that of the cost price mechanism. We show that even in this case multihoming outperforms unihoming, both in terms of throughput as well as profit to the ISP.