Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Letter - Ian Green to Sean O'Sullivan, July 1977

A correspondence between Ian Green and Sean O'Sullivan from July 1977. The first letter is from 4 July 1977 from Sean O'Sullivan, titled "The Nation's Business". He requests a discussion about "Caucus morale". O'Sullivan requests that Joe Clark individually acknowledge members of the party and say "a few words about how proud he is of the men and women who form the P.C. Caucus, and how well they represent the country--moreover, how well they are prepared to help form the next Government." A response from Ian Green (Legislative Assistant) is positive and he forwards the memo to Jodi White, Director of Communications.

Place Card - Girl in Green Dress with Flower

A place card with an illustration of a girl in a green dress and red flowers.

Business Card from Green Acre Kennels

Business card from Green Acre Kennels, Aylmer East, Quebec, n.d.

Planification en contexte mégaévénementiel et reconversion urbaine : le cas du Green Point Urban Park à Cape Town en Afrique du Sud


Depuis les années 2000, nous observons de plus en plus de pays en développement (PED) hôtes de mégaévénements. En accueillant un mégaévénement en leur sol, les PED espèrent améliorer leur cadre urbain et attirer des investissements étrangers. Ceci étant dit, les retards en termes d’infrastructures et d’équipements que connaissent ces pays et les stricts cadres normatifs imposés par des organismes internationaux comme la FIFA, nous amènent à questionner la possibilité d’intégrer les aménagements mégaévénementiels, à leur contexte local. En ce sens, le processus de planification, dans lequel les cadres normatifs externes et locaux sont négociés, peut être vu comme un moment charnière ayant une incidence sur le potentiel de reconversion. Dans le cadre de ce mémoire, nous avons entamé une réflexion à ce sujet en examinant le processus de planification d’un aménagement mégaévénementiel, le Green Point Urban Park (GPUP) à Cape Town, et son incidence sur son potentiel de reconversion. Plus précisément, nous allons, en premier lieu, décrire le processus de planification du site, nous allons par la suite évaluer son potentiel de reconversion, puis nous allons faire ressortir des liens entre le processus de planification et le potentiel de reconversion des aménagements mégaévénementiels. En somme, notre travail met en évidence une relation entre, d’une part, la prépondérance du cadre normatif imposé par l’organisme international et la dynamique du système d’acteurs au moment de la planification du GPUP et, d’autre part, la difficile reconversion de ce dernier après la Coupe du monde de 2010.

The green economy challenge to IPE

Note d'analyse

Haematological responses of green mussel Perna viridis (Linnaeus) to heavy metals copper and mercury

Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology

Solid acid-catalyzed dehydration/Beckmann rearrangement of aldoximes: towards high atom efficiency green processes

Rare earth metal ion exchanged (La3+, Ce3+, RE3+) KFAU-Y zeolites were prepared by simple ion-exchange methods and have been characterized using different physico-chemical techniques. In this paper a novel application of solid acid catalysts in the dehydration/ Beckmann rearrangement of aldoximes; benzaldoxime and 4-methoxybenzaldoxime is reported. Dehydration/Beckmann rearrangement reactions of benzaldoxime and 4-methoxybenzaldoxime is carried out in a continuous down flow reactor at 473K. 4-Methoxybenzaldoxime gave both Beckmann rearrangement product (4-methoxyphenylformamide) and dehydration product (4-methoxybenzonitrile) in high overall yields. The difference in behavior of the aldoximes is explained in terms of electronic effects. The production of benzonitrile was near quantitative under heterogeneous reaction conditions. The optimal protocol allows nitriles to be synthesized in good yields through the dehydration of aldoximes. Time on stream studies show a fast decline in the activity of the catalyst due to neutralization of acid sites by the basic reactant and product molecules.

Beckmann rearrangement of E,E-cinnamaldoxime on rare earth exchanged (Ce3+, La3+, and RE3+) HFAU-Y zeolites: An efficient green process for the synthesis of isoquinoline

In this paper, a novel application of solid acid catalysts in the Beckmann rearrangement of E,E-cinnamaldoxime in the synthesis of an important heterocyclic compound; isoquinoline is reported. E,E-Cinnamaldoxime under ambient reaction conditions on zeolite catalysts underwent Beckmann rearrangement to produce isoquinoline in yields of ca. 86–95%. Cinnamonitrile and cinnamaldehyde were formed as by-products. LaH-Y zeolite produces maximum amount of the desired product (yield 95.6%). However, the catalysts are susceptible for deactivation due to the basic nature of the reactants and products, which neutralize the active sites. H-Y zeolite is more susceptible (22% deactivation in 10 h) for deactivation compared to the cerium-exchanged counterpart (18% deactivation in 10 h). Thus, the optimal protocol allows isoquinoline to be synthesised in excellent yields through the Beckmann rearrangement of cinnamaldoxime. The reaction is simple, effective, does not involve any other additives, and environmentally benign.