The GATO gene annotation tool for research laboratories

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

Supervisor-Student Relations: Examining the Spectrum of Conflicts of Interest in Bioscience Laboratories

Much attention has been given to financial conflicts of interest (COI) in bioscience research. Yet to date, surprisingly little attention has focused on other COIs that arise in supervisor-student relations. We examine a spectrum of related situations, ranging from standard graduate supervision through to dual relationships sometimes found in research with commercial potential. We illustrate some of the less-obvious factors that can bias supervisory judgment, and situate financial COI along a spectrum of forces that are deserving of recognition. We conclude by providing two sets of recommendations: one for individual supervisors, and the other for institutions and policy-makers.

Dynamic Facility Location with Modular Capacities : Models, Algorithms and Applications in Forestry

Les décisions de localisation sont souvent soumises à des aspects dynamiques comme des changements dans la demande des clients. Pour y répondre, la solution consiste à considérer une flexibilité accrue concernant l’emplacement et la capacité des installations. Même lorsque la demande est prévisible, trouver le planning optimal pour le déploiement et l'ajustement dynamique des capacités reste un défi. Dans cette thèse, nous nous concentrons sur des problèmes de localisation avec périodes multiples, et permettant l'ajustement dynamique des capacités, en particulier ceux avec des structures de coûts complexes. Nous étudions ces problèmes sous différents points de vue de recherche opérationnelle, en présentant et en comparant plusieurs modèles de programmation linéaire en nombres entiers (PLNE), l'évaluation de leur utilisation dans la pratique et en développant des algorithmes de résolution efficaces. Cette thèse est divisée en quatre parties. Tout d’abord, nous présentons le contexte industriel à l’origine de nos travaux: une compagnie forestière qui a besoin de localiser des campements pour accueillir les travailleurs forestiers. Nous présentons un modèle PLNE permettant la construction de nouveaux campements, l’extension, le déplacement et la fermeture temporaire partielle des campements existants. Ce modèle utilise des contraintes de capacité particulières, ainsi qu’une structure de coût à économie d’échelle sur plusieurs niveaux. L'utilité du modèle est évaluée par deux études de cas. La deuxième partie introduit le problème dynamique de localisation avec des capacités modulaires généralisées. Le modèle généralise plusieurs problèmes dynamiques de localisation et fournit de meilleures bornes de la relaxation linéaire que leurs formulations spécialisées. Le modèle peut résoudre des problèmes de localisation où les coûts pour les changements de capacité sont définis pour toutes les paires de niveaux de capacité, comme c'est le cas dans le problème industriel mentionnée ci-dessus. Il est appliqué à trois cas particuliers: l'expansion et la réduction des capacités, la fermeture temporaire des installations, et la combinaison des deux. Nous démontrons des relations de dominance entre notre formulation et les modèles existants pour les cas particuliers. Des expériences de calcul sur un grand nombre d’instances générées aléatoirement jusqu’à 100 installations et 1000 clients, montrent que notre modèle peut obtenir des solutions optimales plus rapidement que les formulations spécialisées existantes. Compte tenu de la complexité des modèles précédents pour les grandes instances, la troisième partie de la thèse propose des heuristiques lagrangiennes. Basées sur les méthodes du sous-gradient et des faisceaux, elles trouvent des solutions de bonne qualité même pour les instances de grande taille comportant jusqu’à 250 installations et 1000 clients. Nous améliorons ensuite la qualité de la solution obtenue en résolvent un modèle PLNE restreint qui tire parti des informations recueillies lors de la résolution du dual lagrangien. Les résultats des calculs montrent que les heuristiques donnent rapidement des solutions de bonne qualité, même pour les instances où les solveurs génériques ne trouvent pas de solutions réalisables. Finalement, nous adaptons les heuristiques précédentes pour résoudre le problème industriel. Deux relaxations différentes sont proposées et comparées. Des extensions des concepts précédents sont présentées afin d'assurer une résolution fiable en un temps raisonnable.

Short-term Response of Breeding Barred Owls to Forestry in a Boreal Mixedwood Forest Landscape

Forestry and other activities are increasing in the boreal mixedwood of Alberta, with a concomitant decrease in older forest. The Barred Owl (Strix varia) is an old-growth indicator species in some jurisdictions in North America. Hence, we radio-tagged Barred Owls in boreal mixedwood in Alberta to determine whether harvesting influenced habitat selection. We used three spatial scales: nest sites, i.e., nest tree and adjacent area of 11.7 m radius around nests, nesting territory of 1000 m radius around nests, and home range locations within 2000 m radius of the home range center. Barred Owls nested primarily in balsam poplar (Populus balsamifera) snags > 34 cm dbh and nest trees were surrounded by large, > 34 cm dbh, balsam poplar trees and snags. Nesting territories contained a variety of habitats including young < 80-yr-old, deciduous-dominated stands, old deciduous and coniferous-dominated stands, treed bogs, and recent clear-cuts. However, when compared to available habitat in the study area, they were more likely to contain old conifer-dominated stands and recent cutblocks. We assumed this is because all of the recent harvest occurred in old stands, habitat preferred by the owls. When compared with random sites, locations used for foraging and roosting at the home range scale were more likely to be in young deciduous-dominated stands, old conifer-dominated stands and cutblocks > 30 yr old, and less likely to occur in old deciduous-dominated stands and recent cutblocks. Hence, although recent clearcuts occurred in territories, birds avoided these microhabitats during foraging. To meet the breeding requirements of Barred Owls in managed forests, 10–20 ha patches of old deciduous and mixedwood forest containing large Populus snags or trees should be maintained. In our study area, nest trees had a minimum dbh of 34 cm. Although cut areas were incorporated into home ranges, the amount logged was low, i.e., 7%, in our area. Hence more research is required to determine harvest levels tolerated by owls over the long term.

An Estimate of Nest Loss in Canada Due to Industrial Forestry Operations

Annual loss of nests by industrial (nonwoodlot) forest harvesting in Canada was estimated using two avian point-count data sources: (1) the Boreal Avian Monitoring Project (BAM) dataset for provinces operating in this biome and (2) available data summarized for the major (nonboreal) forest regions of British Columbia. Accounting for uncertainty in the proportion of harvest occurring during the breeding season and in avian nesting densities, our estimate ranges from 616 thousand to 2.09 million nests. Estimates of the impact on numbers of individuals recruited into the adult breeding population were made based on the application of survivorship estimates at various stages of the life cycle. Future improvements to this estimate are expected as better and more extensive avian breeding pair density estimates become available and as provincial forestry statistics become more refined, spatially and temporally. The effect of incidental take due to forestry is not uniform and is disproportionately centered in the southern boreal. Those species whose ranges occur primarily in these regions are most at risk for industrial forestry in general and for incidental take in particular. Refinements to the nest loss estimate for industrial forestry in Canada will be achieved primarily through the provision of more accurate estimates of the area of forest harvested annually during the breeding season stratified by forest type and Bird Conservation Region (BCR). A better understanding of survivorship among life-history stages for forest birds would also allow for better modeling of the effect of nest loss on adult recruitment. Finally, models are needed to project legacy effects of forest harvesting on avian populations that take into account forest succession and accompanying cumulative effects of landscape change.