Automatic verification of any number of concurrent, communicating processes

The automatic verification of concurrent systems by model-checking is limited due to the inability to generalise results to systems consisting of any number of processes. We use abstraction to prove general results, by model-checking, about feature interaction analysis of a telecommunications service involving any number of processes. The key idea is to model-check a system of constant number (m) of concurrent processes, in parallel with an "abstract" process which represents the product of any number of other processes. The system, for any specified set of selected features, is generated automatically using Perl scripts

Generalising feature interactions in email

We report on a property-based approach to feature interaction analysis for a client-server email system. The model is based upon Hall's email model presented at FIW'00, but the implementation is at a lower level of abstraction, employing non-determinism and asynchronous communication; it is a challenge to avoid deadlock and race conditions. The analysis is more extensive in two ways: interaction analysis is fully automated, based on model-checking the entire state-space, and results are scalable, that is they generalise to email systems consisting of any number of email clients. Abstraction techniques are used to prove general results. The key idea is to model-check a system consisting of a constant number (m) of client processes, in parallel with a mailer process and an ``abstract'' process which represents the product of any number of other (unfeatured, isomorphic) client processes. We give a lower bound for the value of m. All of the models -- for any specified set of client processes and selected features -- are generated automatically using Perl scripts

PeRL : a circum-Arctic Permafrost Region Pond and Lake database

Ponds and lakes are abundant in Arctic permafrost lowlands. They play an important role in Arctic wetland ecosystems by regulating carbon, water, and energy fluxes and providing freshwater habitats. However, ponds, i. e., waterbodies with surface areas smaller than 1.0 x 10(4) m(2), have not been inventoried on global and regional scales. The Permafrost Region Pond and Lake (PeRL) database presents the results of a circum-Arctic effort to map ponds and lakes from modern (2002-2013) high-resolution aerial and satellite imagery with a resolution of 5m or better. The database also includes historical imagery from 1948 to 1965 with a resolution of 6m or better. PeRL includes 69 maps covering a wide range of environmental conditions from tundra to boreal regions and from continuous to discontinuous permafrost zones. Waterbody maps are linked to regional permafrost landscape maps which provide information on permafrost extent, ground ice volume, geology, and lithology. This paper describes waterbody classification and accuracy, and presents statistics of waterbody distribution for each site. Maps of permafrost landscapes in Alaska, Canada, and Russia are used to extrapolate waterbody statistics from the site level to regional landscape units. PeRL presents pond and lake estimates for a total area of 1.4 x 10(6) km(2) across the Arctic, about 17% of the Arctic lowland (Peer reviewe

The Higher Derivative Expansion of the Effective Action by the String Inspired Method. Part II

We apply the string inspired worldline formalism to the calculation of the higher derivative expansion of one-loop effective actions in non-Abelian gauge theory. For this purpose, we have completely computerized the method, using the symbolic manipulation programs FORM, PERL and M. Explicit results are given to sixth order in the inverse mass expansion, reduced to a minimal basis of invariants specifically adapted to the method. Detailed comparisons are made with other gauge-invariant algorithms for calculating the same expansion. This includes an explicit check of all coefficients up to fifth order.Comment: 37 pages, LaTeX, 3 figures, typos corrected, to appear in Ann. Phys. (N.Y.

Study of Upsilon(3S,2S) -> eta Upsilon(1S) and Upsilon(3S,2S) -> pi+pi- Upsilon(1S) hadronic trasitions

We study the Upsilon(3S,2S)->eta Upsilon(1S) and Upsilon(3S,2S)->pi+pi- Upsilon(1S) transitions with 122 million Upsilon(3S) and 100 million Upsilon(2S) mesons collected by the BaBar detector at the PEP-II asymmetric energy e+e- collider. We measure B[Upsilon(2S)->eta Upsilon(1S)]=(2.39+/-0.31(stat.)+/-0.14(syst.))10^-4 and Gamma[Upsilon(2S)->eta Upsilon(1S)]/Gamma[Upsilon(2S)-> pi+pi- Upsilon(1S)]=(1.35+/-0.17(stat.)+/-0.08(syst.))10^-3. We find no evidence for Upsilon(3S)->eta Upsilon(1S) and obtain B[Upsilon(3S)->eta Upsilon(1S)]<1.0 10^-4 and Gamma[Upsilon(3S)->eta Upsilon(1S)]/Gamma[Upsilon(3S)->pi+pi- Upsilon(1S)]<2.3 10^-3 as upper limits at the 90% confidence level. We also provide improved measurements of the Upsilon(2S) - Upsilon(1S) and Upsilon(3S) - Upsilon(1S) mass differences, 562.170+/-0.007(stat.)+/-0.088(syst.) MeV/c^2 and 893.813+/-0.015(stat.)+/-0.107(syst.) MeV/c^2 respectively.Comment: 8 pages, 16 encapsulated postscript figures, submitted to Phys.Rev.

Creation of a Computational Pipeline to Extract Genes from Quantitative Trait Loci for Diabetes and Obesity

Type 2 Diabetes is a disease of relative insulin deficiency resulting from a combination of insulin resistance and decreased beta-cell function. Over the past several years, over 60 genes have been identified for Type 2 Diabetes in human genome-wide association studies (GWAS). It is important to understand the genetics involved with Type 2 diabetes in order to improve treatment and understand underlying molecular mechanisms. Heterogeneous stock (HS) rats are derived from 8 inbred founder strains and are powerful tools for genetic studies because they provide a basis for high resolution mapping of quantitative trait loci (QTL) in a relatively short time period. By measuring diabetic traits in 1090 HS male rats and genotyping 10K single nucleotide polymorphisms (SNPs) within these rats, Dr. Solberg Woods\u27 lab conducted genetic analysis to identify 85 QTL for diabetes and adiposity traits. To identify candidate genes within these QTL, we propose creation of a bioinformatics pipeline that combines general gene information, information from the rat genome database including disease portals and Variant Visualizer as well as the Attie Diabetes Expression Database. My project has involved writing code to pull data from these databases to determine which genes within each QTL are potential candidate genes. I have scripted the code to analyze genes within a single QTL or multiple QTL simultaneously. The resulting output is a single excel file for each QTL, listing all genes that are found in the disease portals, all genes that have a highly conserved non-synonymous variant change and all genes that are differentially expressed in the Attie database. The program also highlights genes that are found in all three categories. After creating the pipeline, I ran the program for 85 QTL identified in my laboratory. The program identified 63 high priority candidate genes for future follow-up. This work has helped my laboratory rapidly identify candidate genes for type 2 diabetes and obesity. In the future, the code can be modified to identify candidate genes within QTL for any complex trait