The cost required for the process of sequencing genomes has decreased drastically in the last few years. The knowledge of full genomes has increased the pace of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. The multitude of sequencing technologies has resulted in various formats for storing the sequences. This has resulted in the creation of many tools for DNA analysis. There are various tools for sorting, indexing, analyzing read groups and other tasks. The analysis of genomics often requires the creation of pipelines, which processes the DNA sequences by chaining together many tools. This results in the creation of complex scripts that glue together these tools and pass the output from one stage to the other. Also, there are tools which allow creation of these pipelines with a graphical user interface. But these are complex to use and it is difficult to quickly add the new tools being developed to existing workflows. To solve these issues, we developed BioFlow; a web based genomic workflow management system. The use of BioFlow does not require any programming skills. The integrated workflow designer allows creation and saving workflows. The pipeline is created by connecting the tools with a visual connector. BioFlow provides an easy and simple interface that allows users to quickly add tools for use in any workflow. Audit logs are maintained at each stage, which helps users to easily identify errors and fix them. / Master of Science

Partial Post Quantum Cryptography migration of GitLab Community Edition source code with 3 main contributions 1. Devloped RubyCrypt - a simple scanner to assist the Cryptographic Inventory Compilation of Ruby apps 2. Configured git to use PQC signature (CRYSTALS-Dilithium) for commit signing 3. Included CRYSTALS-Dilithium to ssh_data, a common cryptographic Ruby gem used by GitLab (& GitHub):1. Introduction 2. Theoretical Background - Post Quantum Cryptography 2.1. Code-based Cryptography 2.1.1. McEliece Cryptosystem 2.2. Lattice-based Cryptography 2.2.1. CRYSTALS-Dilithium 3. Post Quantum Cryptography Migration of GitLab - a Case Study 3.1. Problem Statement 3.2. Related Work 3.2.1. Software Tools for Static Program Analysis 3.3. Chosen Approach 4. Implementation 4.1. Cryptographic Inventory Compilation 4.1.1. Results 4.2. Migration Planning 4.3. Migration Execution 4.3.1. PQC Commit Signatures in git 4.3.2. Including Dilithium to ssh_data 5. Conclusion and Outlook 6. References List of Tables List of Figures List of Source Code Acronyms Notation / Partielle Migration des GitLab Community Edition Source Codes auf Verfahren der Post-Quanten-Kryptographie mit 3 Hauptergebnissen 1. Entwicklung von RubyCrypt - einem simplen Scanner zur Unterstützung der Inventarisierung verwendeter Kryptographie in Ruby-Anwendungen 2. Konfiguration von git zur Verwendung des quantensicheren Signaturalgorithmus CRYSTALS-Dilithium zur Signatur von Commits 3. Integration von CRYSTALS-Dilithium in ssh_data, ein populäres kryptographisches Ruby gem welches in GitLab (und GitHub) verwendet wird:1. Introduction 2. Theoretical Background - Post Quantum Cryptography 2.1. Code-based Cryptography 2.1.1. McEliece Cryptosystem 2.2. Lattice-based Cryptography 2.2.1. CRYSTALS-Dilithium 3. Post Quantum Cryptography Migration of GitLab - a Case Study 3.1. Problem Statement 3.2. Related Work 3.2.1. Software Tools for Static Program Analysis 3.3. Chosen Approach 4. Implementation 4.1. Cryptographic Inventory Compilation 4.1.1. Results 4.2. Migration Planning 4.3. Migration Execution 4.3.1. PQC Commit Signatures in git 4.3.2. Including Dilithium to ssh_data 5. Conclusion and Outlook 6. References List of Tables List of Figures List of Source Code Acronyms Notation

With mobile web browsers holding around eight percent of the global browser market share in terms of usage, web development for these platforms is becoming critically important as usage moves from the desktop towards mobile devices. Recent advances in client side browser technology like HTML5 and WebSockets have allowed web browser applications to approach feature parity with thick client desktop applications. This paper explores the possibility of a real-time online multiplayer game playable from just a mobile device's web browser. It does not focus on gameplay or graphics, rather it focuses on the backend infrastructure needed to support such a game. The framework devised to support this sort of interaction, Marionette, is well suited towards addressing sharing of location-specific, short-lived information between people using their smartphones without the use of any external software or proprietary software packages on the client side. / text

Phenotypes and diseases may be related by seemingly dissimilar phenotypes in other species by means of the orthology of underlying genes. Such "orthologous phenotypes," or "phenologs," are examples of deep homology, and one member of the orthology relationship may be used to predict candidate genes for its counterpart. (There exists evidence of "paralogous phenotypes" as well, but validation is non-trivial.) In Chapter 2, I demonstrate the utility of including plant phenotypes in our database, and provide as an example the prediction of mammalian neural crest defects from an Arabidopsis thaliana phenotype, negative gravitropism defective. In the third chapter, I describe the incorporation of additional phenotypes into our database (including chicken, zebrafish, E. coli, and new C. elegans datasets). I present a method, developed in coordination with Martin Singh-Blom, for ranking predicted candidate genes by way of a k nearest neighbors naïve Bayes classifier drawing phenolog information from a variety of species. The fourth chapter relates to a computational method and application for identifying shared and overlapping pathways which contribute to phenotypes. I describe a method for rapidly querying a database of phenotype--gene associations for Boolean combinations of phenotypes which yields improved predictions. This method offers insight into the divergence of orthologous pathways in evolution. I demonstrate connections between breast cancer and zebrafish methylmercury response (through oxidative stress and apoptosis); human myopathy and plant red light response genes, minus those involved in water deprivation response (via autophagy); and holoprosencephaly and an array of zebrafish phenotypes. In the first appendix, I present the SciRuby Project, which I co-founded in order to bring scientific libraries to the Ruby programming language. I describe the motivation behind SciRuby and my role in its creation. Finally in Appendix B, I discuss the first beta release of NMatrix, a dense and sparse matrix library for the Ruby language, which I developed in part to facilitate and validate rapid phenolog searches. In this work, I describe the concept of phenologs as well as the development of the necessary computational tools for discovering phenotype orthology relationships, for predicting associated genes, and for statistically validating the discovered relationships and predicted associations. / text

Thesis (D.A.)--Illinois State University, 2003. / Title from title page screen, viewed November 10, 2005. Dissertation Committee: Walker D. Wyman, Jr. (chair), M. Paul Holsinger, Lawrence W. McBride. Includes bibliographical references and abstract Also available in print.

Phenomenon called Web 2.0 was described in this work, including its origins and following criticism. Changes that it brought were described using its applications and used technologies. Library 2.0 concept was introduced and either its advantages and disadvantages were evaluated. Contemporary situation concerning Web 2.0 technologies usage in libraries and their catalogues was described. Oportunity to use libraries data was accented and possible ways of getting them were explored. Simple uniform interface was created and demonstrated.

Rephotography has been a popular research topic in the photography field for a long time. The purpose of rephotography itself is to repeatedly take photographs of the same scene at a different time. As a result, the sequence of rephotographs with the reference, often historical, the picture provides a compelling visualization of the evolution of the subject or capture its changes in time. However, the act of rephotography is difficult for the rephotographers as they have to cope with the ambiguous motions in six degrees of freedom and with the changes of the subject itself or its surrounding environment.        This thesis aims to create a mobile application that would help its users to capture a rephotograph more accurately and allow them to share the scenes amongst other users. The designed application uses available on-device sensors to navigate the user to the location and guide the user during the rephotography process to capture a precise rephotograph. Furthermore, the application contains user interface elements designed explicitly for rephotography. Moreover, the work describes topics about user interface design, iOS application development, and designing and deploying backend API for the mobile application.

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Abstract :The main goal of this stud y was to quantify the effect s of landscape structure on the abundance of Ruby-throate d Hummingbird s (Archilochus colubris) in forest patches and this, while accounting for its indirect effects on open flower community an d the occurrence of Yellow-bellied Sapsucker s (Sphympicus varius), a potential commensal of hummingbirds. We sampled 40 forest patches (0. 5 to >10 0 ha ) where we had installed 2 nectar feeders (forest edge and 40 m within forest ) during 2 breeding season s (2006 and 2007) . We visited forest patches weekly and recorded the number of hummingbirds detected within 10 m of feeders during 10 min. Mean daily artificial nectar consumption by hummingbirds, as well as their relative total abundance an d the respective relative abundance of adult males and females, were all affected by forest cover. Except for the relative total abundance, this effect of forest cover depended upon the size of forest patches. Nectar consumption and abundance generally peaked in forest patches of intermediate size found in landscapes characterized by intermediate forest cover. Mea n daily artificial nectar consumption and the relative total abundance, a s well as that of males, were higher at feeders located on the forest edge compared to 40 m inside forest patches. Regarding indirect landscape effects, landscape structure influenced the structure of open flower communities surrounding feeders, which in turn, affected the relative total abundance of hummingbirds, a s well as that of adult males. On the other hand, we failed to find strong evidence that landscape structure affected the occurrence of Yellow-bellied Sapsuckers or that the latter influenced Ruby-throated Hummingbird abundance patterns. These results support the idea that landscape structure may affect the abundance pattern of a species directly as well as through mechanisms which are themselves dependent upon the composition and configuration of landscapes //Résumé : La structure des paysages peut influencer l'écologie d'une espèce directement, en contraignant ses mouvements, par exemple, de même qu'indirectement en affectant, entre autres, l'abondance de ses proies ou prédateurs. Quoique plusieurs études aient tenté de quantifier l'influence de la structure du paysage sur les patrons d'abondance, rares sont celles qui ont mesuré simultanément les effets directs et indirects du paysage. L'objectif de ce mémoire consiste à modéliser simultanément les effets directs de la structure du paysage sur l'abondance relative du Colibri à gorge rubis ( Archilochus colubris ) et sa consommation de nectar artificiel ainsi que les effets indirects par lesquels le paysage peut aussi agir tels la disponibilité en ressources alimentaires (communautés floristiques) et la relation interspécifique de commensalisme avec le Pic maculé ( Sphyrapicus varius ). Pour ce faire, j'ai échantillonné 40 îlots forestiers (0,5 à >100 ha) dans la région de l'Estrie (Québec, Canada). À chacun d'eux, j'ai installé deux abreuvoirs (en bordure et 40 m à l'intérieur) durant les étés 2006 et 2007 et ont été visités de façon hebdomadaire. J'ai détecté une relation quadratique du couvert forestier dans le paysage avec l'abondance totale relative, celle des mâles et des femelles ainsi que pour la consommation quotidienne moyenne. Ces effets varient en fonction de la taille d'îlot sauf pour l'abondance relative totale. Les valeurs maximales se situent à des niveaux intermédiaires de couvert forestier et de taille d'îlots. Certaines caractéristiques mesurées étaient à l'échelle locale comme la position de l'abreuvoir dans l'îlot forestier ou la structure de la végétation. J'ai détecté un effet de bordure pour toutes les variables sauf l'abondance des femelles. L'indice de structure de végétation n'avait d'influence que sur l'abondance des mâles. Concernant les effets indirects, l'ensemble des variables du paysage explique 69,61% de l'indice de communauté floristique et ce dernier a un effet significatif sur l'abondance totale et l'abondance des colibris mâles. Pour la relation avec le pic, les variables du paysage mesurées n'ont pas permis de détecter un effet. De plus, bien qu'étant une variable non significative, les modèles incluant la présence du Pic maculé étaient généralement parmi les plus performants. L'ensemble de ces résultats soutient l'importance de combiner l'écologie du paysage et l'écologie comportementale dans les mêmes modèles afin de tenir compte non seulement des effets directs mais aussi des effets indirects du paysage //