Bitstream generation has traditionally been the single part of the FPGA design flow that has not been openly reproduced. This work enables bitstream generation for "limited" resources without reverse-engineering or violating End-User License Agreement terms. Two use cases in particular have motivated this work--embedded bitstream generation and fast bitstream generation for small changes in design--both of which are not feasible with the Xilinx's bitstream generation tool. The approach is to first define a set of primitives which can implement an arbitrary digital design and create a library of micro-bitstreams of the primitives. An input design is then mapped to the set of primitives and a bitstream for the design is generated by merging the corresponding micro-bitstreams. This work uses architectural primitives. Initial support is limited to the Virtex-5 and Virtex-7 family of FPGAs from Xilinx, but it can be extended to other Xilinx architectures. Nearly all routing resources in the device, as well as the most common logic resources are supported by this work. / Master of Science

Microalgae are photosynthetic organisms considered to be one of the most promising high-value chemicals and biofuel-producing organisms. However, there are several challenges for the widespread implementation of industrial processes using microalgae. The work presented in this dissertation proposes solutions to the different challenges involving the use of microalgae as microbial cell factories. To investigate the application of anaerobic digestion as a way to generate nutrients for microbial growth, salmon offal was used as substrate for anaerobic digestion, and soil from a flooded run-off pond on the Virginia Tech campus in Blacksburg, VA. A fast reduction in volatile solids and the short-chain fatty acid production profile is favorable for the growth of microalgae. A novel algae strain Scenedesmus sp. A6 was isolated from a decorative waterfountain in a hotel in Madison, IN. Mixotrophic growth trials were conducted using wastewater from the salmon offal digestion, that demostrated the A6 isolate grows six times faster in the wastewater then autotrophically. Bioassays of ethanolic cell extracts of A6 cultures demonstrated antimicrobial activity against E. coli cells at concentrations above 50 µg/ml. Genome sequencing and assembly revealed multiple copies of genes involved with acetate and ammonia metabolism, and several genes involved with secondary metabolite synthesis. An alternative to the high capital investment of photobioreactors for the cultivation of microalgae is the use of open-source and open-hardware bioreactor controller. Here, the concept of an open-hardwate bioreactor control called ``BioBrain'' is introduced. The BioBrain device is based on the Arduino Mega micro-controller board, and is capable of monitoring and controlling culture conditions during simple strain characterization studies, with an estimated construction cost of less than $800 USD. Finally, a new primer design tool for the ligation-independant cloning technique 𝜆-PCR was developed called lambdaPrimeR. The contributions of this work are the discovery and development of different tools that can overcome the challenges of the use of microalgae as microbial cell factories in industrial processes. / Ph. D. / Microalgae are single-celled organisms capable of photosynthesis and have the potential to revolutionize fuel and high-value chemical production. However, the high process costs involving the cultivation and biomass harvesting of these organisms limits the number of industrial applications of microalgae. Therefore, reduction of the overall costs of any process involving microalgae is vital for the widespread use of these organisms in industry. On this dissertation, I explore different approaches to tackle the challenges of using microalgae as a high-value chemicals cell factories. First, the use of anaerobic digestion of salmon offal to generate low-cost nutrients for algae growth is successfully demonstrated, with the discovery of a novel algae isolate Scenedesmus sp. A6, capable of very robust growth on the anaerobic digestion wastewater. Further characterization of this novel isolate showed that it has antimicrobial activity against E. coli cells. Therefore, the Scenedesmus sp. A6 isolate has the potential to be used as a high-value chemical cell factory. Reduction in equipment and instrumentation costs was also achieved by the design and construction of an open-hardware and open-source bioreactor controller device called the “BioBrain”, and a low-cost modular bubble column photobioreactor called “The Big Large Tube”. Together, these two devices represent a significant reduction in equipment costs for the cultivation of microalgae. Finally, an open-source Bioinformatics tool called “lambdaPrimeR” was developed to facilitate the use of a novel Genetic Engineering technique called λ-PCR, that has the potential to make genetic engineering of microalgae much easier.

SQL injection attacks have been a problem since the early 2000s. Even though the issue is well known today, SQL injection vulnerabilities remain to be one of the most common security flaws. Our study looks at open source-projects written in Java and Python to examine the current state of SQL injection vulnerabilities. We take a deeper look into the vulnerabilities' code patterns and discuss suitable prevention methods.The open-source projects were mined from Github. The projects that contained a connection to a relational database were further analyzed with static analysis to find vulnerabilities. A subset of projects was picked out for deeper analysis of the source code. Among 167,644 Java projects that met the selection criteria, 24,416 were identified to have a connection to a relational database. The corresponding figures for Python were 294,637 and 20,994. Notably, concatenation is more prevalent in Java, whereas prepared statements are favored in Python. Additionally, the analysis revealed that the Python projects tended to have more recent updates and a higher number of contributors compared to the Java projects. Moreover, projects employing both prepared statements and concatenation were observed to be larger in size compared to those using only one of these methods or relying on hardcoded queries. With legacy projects and concatenation being more common in Java, it is suggested that Python projects better follow best practices when it comes to SQL injection. Although indications were found that the overall knowledge of SQL injection has increased since 2019, the use of identifier concatenation still is prevalent.

An Open-Source, extensible spacecraft simulation and modeling (Open-SESSAME) framework was developed with the aim of providing to researchers the ability to quickly test satellite algorithms while allowing them the ability to view and extend the underlying code. The software is distributed under the GPL (General Public License) and the package's extensibility allows users to implement their own components into the libraries, investigate new algorithms, or tie in existing software or hardware components for algorithm and flight component testing. This thesis presents the purpose behind the development of the framework, the software design architecture and implementation, and a roadmap of the future for the software package. / Master of Science

Weitgehend unbeobachtet von der Disziplin Wissensmanagement haben sich seit vielen Jahren Open Source Softwareentwickler erfolgreich im Wissensaustausch geübt. Ohne direkten Auftrag- oder Geldgeber arbeiten sie über lange Zeiträume und häufig sehr erfolgreich als virtuelles Team zusammen. Die dabei wirksamen Mechanismen sind von Unternehmen bislang wenig untersucht oder beachtet worden. Können sie davon profitieren, indem sie die Motivationsgrundlage von Open Source Projekten auf sich „übertragen“?

El presente trabajo gira alrededor del mundo de los <i>Serious Games</i> (Juegos Serios) abarcando aspectos tales como campos de aplicación, herramientas disponibles para el desarrollo y un paneo acerca de las plataformas utilizadas para el desarrollo y para su utilización. En el capítulo 1 se explicará la organización del presente trabajo, en el capítulo 2 se analizarán algunos de los campos de aplicación donde se ve un importante desarrollo de los juegos serios, en el capítulo 3 se describirán algunas herramientas privativas y otras FLOSS (Free/Libre Open Source Software), en el capítulo 4 se hablará acerca de la ludificación/gamificación y en el capítulo 5 se describirán las conclusiones y posibles trabajos futuros.

La mise en place de systèmes d’information hospitaliers centrés sur les processus de soins est porteuse de qualité des soins, de gestion éclairée des ressources et de productivité. C’est une nécessité qui s’impose à tous les pays quelque soit leur niveau de développement. Une question se pose toutefois : Étant données les différences de contextes financiers, technologiques et humains, faut-il, en Afrique, conduire une stratégie différenciée pour atteindre cet objectif partagé? Le but de notre travail était de mettre en place un modèle adapté au contexte culturel et économique des pays en développement. Notre méthodologie a été basée sur l’adaptation et l’implémentation d’un Open Source. Ces travaux ont permis la réalisation et la validation d’un modèle au Mali que nous avons baptisé Cinz@n. Il a été implémenté et testé à l’hôpital mère enfant de Bamako. Au delà de l’implémentation logicielle, l’accompagnement du changement et la formation, des personnes a été l’objet d’une attention particulière. Les résultats de l’évaluation de la couverture fonctionnelle, de l’ergonomique du système et de satisfaction des utilisateurs sont satisfaisants. 84% des utilisateurs pensent que le système a permis d’améliorer la qualité du travail, 100% des utilisateurs se sont dit prêts à continuer l’expérience. Cette même proportion a recommandé l’extension du système à tous les services de l’hôpital. L’analyse qualitative de la base des données a démontré un suivi rigoureux des consignes d’identification. Nous pouvons conclure que Cinz@n, ayant coûté que près de dix milles euros d’investissement et largement accepté par les utilisateurs peut servir de modèle pour l’Afrique Francophone. / The implementation of hospital information systems focused on care processes has been shown to improve the quality of care, the management of resources, and the productivity. These benefits are necessary in all countries, regardless of their level of development. However, a question does arise: “Given the differences in financial, technological and human contexts, should we, in Africa, undertake a differentiated strategy to achieve these shared goals?”. The aim of our study was to develop a model adapted to the cultural and economical contexts of developing countries. Our methodology was based on the adaptation and implementation of an Open Source software. This work led to the development and validation of a model in Mali named Cinz@n. It has been implemented and tested at the Mother-Child hospital in Bamako. Beyond the software implementation, change management and the training of stakeholders have been the subject of special attention. The results of the evaluation of the functional coverage, the ergonomics of the system and user satisfaction are satisfactory. 84% of users consider that the system has improved the quality of their work, and 100% of users are willing to continue the experiment, also recommending the extension of the system to all hospital departments. The qualitative analysis of the database showed strict usage of the patient identification procedures. We conclude that Cinz@n, with an investment cost of about ten thousand euros, and a wide acceptance by users can be a model for other implementations in French Speaking Africa.

The need of smart devices that uses sensors have never been higher and by the year 2020 it will be over 50 billion devices connected to the internet. All these devices that uses a sensor and are connected to the internet are a part of something called Internet of Things. The purpose of this study has therefore been to implement a stripped IoT platform that doesn’t use any external libraries to lower the cost for minor companies that doesn’t need the more advanced and expensive platforms. After the implementation various stress test will be performed to see the performance of the platform. The study has been done through web- based sources and as a programming language Java has been used in the development environment NetBeans, the database has been made with MySQL workbench. The result of the study has been a platform that uses REST to post and get data from the database. The external library mysql- connector-java-5.1.45 was essential for a connection to the database and therefore had to be used. The result of the stress test was that the platform performed well and could handle at least 500 REST calls per second with a small increase in response time, but the standard deviation was considerably higher. The conclusion was that the platform performed stable at 50 – 250 calls per second and because of it being stripped several platforms could be used in a company to divide the work load between them resulting in a both stable and scalable solution. / Behovet för smarta enheter som använder sensorer har aldrig varit högre och det är trott att vid år 2020 kommer mer än 50 miljarder enheter vara uppkopplad mot internet. Alla dessa enheter med sensorer som är anslutna mot internet går under namnet Internet of Things. Syftet med denna studie har därför varit att skapa en avskalad IoT plattform som inte använder externa bibliotek för att hålla ned kostnaderna för de mindre företagen som inte behöver de mer avancerade och dyrare plattformarna. Efter att plattformen blivit implementerad skulle stresstester utförs för att avgöra hur bra den presterar. Studien har genomförts med hjälp av webbaserade källor och programmeringen av plattformen har utförts i programmeringsmiljön NetBeans i språket Java och databasen är skapad i MySQL workbench. Resultatet av studien har gett en plattform som använder REST för att skicka till och hämta data från databasen. Att göra implementeringen utan att använda externa bibliotek gick inte då biblioteket mysql-connector-java-5.1.45 var essentiellt för uppkoppling mot databasen. Stresstesterna gav att plattformen presterade stabilt och kunde hantera åtminstone 500 REST förfrågningar per sekund med endast en liten ökning i svarstiden, dock blev standardavvikelsen för svarstiden betydligt högre. Slutsatsen av studien blev att eftersom plattformen fungerar stabilt för 50 – 250 förfrågningar per sekund och då den tar upp lite processorkraft kan flera plattformar användas i ett företag för att då fördela arbetskraften emellan dem vilket resulterar i en lösning som både är skalbar samt stabil.

Analytical ultracentrifugation (AUC) has made an important contribution to polymer and particle characterization since its invention by Svedberg (Svedberg and Nichols 1923; Svedberg and Pederson 1940) in 1923. In 1926, Svedberg won the Nobel price for his scientific work on disperse systems including work with AUC. The first important discovery performed with AUC was to show the existence of macromolecules. Since that time AUC has become an important tool to study polymers in biophysics and biochemistry. AUC is an absolute technique that does not need any standard. Molar masses between 200 and 1014 g/mol and particle size between 1 and 5000 nm can be detected by AUC. Sample can be fractionated into its components due to its molar mass, particle size, structure or density without any stationary phase requirement as it is the case in chromatographic techniques. This very property of AUC earns it an important status in the analysis of polymers and particles. The distribution of molar mass, particle sizes and densities can be measured with the fractionation. Different types of experiments can give complementary physicochemical parameters. For example, sedimentation equilibrium experiments can lead to the study of pure thermodynamics. For complex mixtures, AUC is the main method that can analyze the system. Interactions between molecules can be studied at different concentrations without destroying the chemical equilibrium (Kim et al. 1977). Biologically relevant weak interactions can also be monitored (K ≈ 10-100 M-1). An analytical ultracentrifuge experiment can yield the following information: • Molecular weight of the sample • Number of the components in the sample if the sample is not a single component • Homogeneity of the sample • Molecular weight distribution if the sample is not a single component • Size and shape of macromolecules & particles • Aggregation & interaction of macromolecules • Conformational changes of macromolecules • Sedimentation coefficient and density distribution Such an extremely wide application area of AUC allows the investigation of all samples consisting of a solvent and a dispersed or dissolved substance including gels, micro gels, dispersions, emulsions and solutions. Another fact is that solvent or pH limitation does not exist for this method. A lot of new application areas are still flourishing, although the technique is 80 years old. In 1970s, 1500 AUC were operational throughout the world. At those times, due to the limitation in detection technologies, experimental results were obtained with photographic records. As time passed, faster techniques such as size exclusion chromatography (SEC), light scattering (LS) or SDS-gel electrophoresis occupied the same research fields with AUC. Due to these relatively new techniques, AUC began to loose its importance. In the 1980s, only a few AUC were in use throughout the world. In the beginning of the 1990s a modern AUC -the Optima XL-A - was released by Beckman Instruments (Giebeler 1992). The Optima XL-A was equipped with a modern computerized scanning absorption detector. The addition of Rayleigh Interference Optics is introduced which is called XL-I AUC. Furthermore, major development in computers made the analysis easier with the help of new analysis software. Today, about 400 XL-I AUC exist worldwide. It is usually applied in the industry of pharmacy, biopharmacy and polymer companies as well as in academic research fields such as biochemistry, biophysics, molecular biology and material science. About 350 core scientific publications which use analytical ultracentrifugation are published every year (source: SciFinder 2008 ) with an increasing number of references (436 reference in 2008). A tremendous progress has been made in method and analysis software after digitalization of experimental data with the release of XL-I. In comparison to the previous decade, data analysis became more efficient and reliable. Today, AUC labs can routinely use sophisticated data analysis methods for determination of sedimentation coefficient distributions (Demeler and van Holde 2004; Schuck 2000; Stafford 1992), molar mass distributions (Brookes and Demeler 2008; Brookes et al. 2006; Brown and Schuck 2006), interaction constants (Cao and Demeler 2008; Schuck 1998; Stafford and Sherwood 2004), particle size distributions with Angstrom resolution (Cölfen and Pauck 1997) and the simulations determination of size and shape distributions from sedimentation velocity experiments (Brookes and Demeler 2005; Brookes et al. 2006). These methods are also available in powerful software packages that combines various methods, such as, Ultrascan (Demeler 2005), Sedift/Sedphat (Schuck 1998; Vistica et al. 2004) and Sedanal (Stafford and Sherwood 2004). All these powerful packages are free of charge. Furthermore, Ultrascans source code is licensed under the GNU Public License (http://www.gnu.org/copyleft/gpl.html). Thus, Ultrascan can be further improved by any research group. Workshops are organized to support these software packages. Despite of the tremendous developments in data analysis, hardware for the system has not developed much. Although there are various user developed detectors in research laboratories, they are not commercially available. Since 1992, only one new optical system called “the fluorescence optics” (Schmidt and Reisner, 1992, MacGregor et al. 2004, MacGregor, 2006, Laue and Kroe, in press) has been commercialized. However, except that, there has been no commercially available improvement in the optical system. The interesting fact about the current hardware of the XL-I is that it is 20 years old, although there has been an enormous development in microelectronics, software and in optical systems in the last 20 years, which could be utilized for improved detectors. As examples of user developed detector, Bhattacharyya (Bhattacharyya 2006) described a Multiwavelength-Analytical Ultracentrifuge (MWL-AUC), a Raman detector and a small angle laser light scattering detector in his PhD thesis. MWL-AUC became operational, but a very high noise level prevented to work with real samples. Tests with the Raman detector were not successful due to the low light intensity and thus high integration time is required. The small angle laser light scattering detector could only detect latex particles but failed to detect smaller particles and molecules due to low sensitivity of the detector (a photodiode was used as detector). The primary motivation of this work is to construct a detector which can measure new physico-chemical properties with AUC with a nicely fractionated sample in the cell. The final goal is to obtain a multiwavelength detector for the AUC that measures complementary quantities. Instrument development is an option for a scientist only when there is a huge potential benefit but there is no available commercial enterprise developing appropriate equipment, or if there is not enough financial support to buy it. The first case was our motivation for developing detectors for AUC. Our aim is to use today’s technological advances in microelectronics, programming, mechanics in order to develop new detectors for AUC and improve the existing MWL detector to routine operation mode. The project has multiple aspects which can be listed as mechanical, electronical, optical, software, hardware, chemical, industrial and biological. Hence, by its nature it is a multidisciplinary project. Again by its nature it contains the structural problem of its kind; the problem of determining the exact discipline to follow at each new step. It comprises the risk of becoming lost in some direction. Having that fact in mind, we have chosen the simplest possible solution to any optical, mechanical, electronic, software or hardware problem we have encountered and we have always tried to see the overall picture. In this research, we have designed CCD-C-AUC (CCD Camera UV/Vis absorption detector for AUC) and SLS-AUC (Static Light Scattering detector for AUC) and tested them. One of the SLS-AUC designs produced successful test results, but the design could not be brought to the operational stage. However, the operational state Multiwavelength Analytical Ultracentrifuge (MWL-AUC) AUC has been developed which is an important detector in the fields of chemistry, biology and industry. In this thesis, the operational state Multiwavelength Analytical Ultracentrifuge (MWL-AUC) AUC is to be introduced. Consequently, three different applications of MWL-AUC to the aforementioned disciplines shall be presented. First of all, application of MWL-AUC to a biological system which is a mixture of proteins lgG, aldolase and BSA is presented. An application of MWL-AUC to a mass-produced industrial sample (β-carotene gelatin composite particles) which is manufactured by BASF AG, is presented. Finally, it is shown how MWL-AUC will impact on nano-particle science by investigating the quantum size effect of CdTe and its growth mechanism. In this thesis, mainly the relation between new technological developments and detector development for AUC is investigated. Pioneering results are obtained that indicate the possible direction to be followed for the future of AUC. As an example, each MWL-AUC data contains thousands of wavelengths. MWL-AUC data also contains spectral information at each radial point. Data can be separated to its single wavelength files and can be analyzed classically with existing software packages. All the existing software packages including Ultrascan, Sedfit, Sedanal can analyze only single wavelength data, so new extraordinary software developments are needed. As a first attempt, Emre Brookes and Borries Demeler have developed mutliwavelength module in order to analyze the MWL-AUC data. This module analyzes each wavelength separately and independently. We appreciate Emre Brookes and Borries Demeler for their important contribution to the development of the software. Unfortunately, this module requires huge amount of computer power and does not take into account the spectral information during the analysis. New software algorithms are needed which take into account the spectral information and analyze all wavelengths accordingly. We would like also invite the programmers of Ultrascan, Sedfit, Sedanal and the other programs, to develop new algorithms in this direction. / Die analytische Chemie versucht die chemische Zusammensetzung, chemische und physikalische Eigenschaften von biologischen oder künstlichen Materialien zu bestimmen. Mit der Entwicklung deren Methoden können genauere Informationen über die Umweltverschmutzung, das Ozonloch, Proteinfunktionen und Wechselwirkungen im menschlichen Körper erlangt werden. Es sind eine Vielzahl von analytischen Techniken vorhanden, die durch Verbesserungen in der Mikroelektronik, Mechanik, Informatik und Nanotechnologie einer markanten Entwicklung unterworfen wurden. In dieser Arbeit wurde versucht die Detektionskapazität der analytischen Ultrazentrifuge zu erhöhen. Die analytische Ultrazentrifuge (AUZ) ist eine gut bekannte, sehr leistungsstarke Trennungsmethode. AUZ benutzt die Zentrifugalkraft zum Trennen von Stoffen. Die Probe kann für die Messung gelöst oder in einer Flüssigkeit dispergiert werden. Makromoleküle, Proteine und kolloidale Systeme in Lösung können in einer AUZ Zelle zwischen 1000-60000 Rotationen pro Minute zentrifugiert werden, wie beispielsweise in der kommerziellen Beckmann AUZ. Die Rotationsbeschleunigung entspricht 73-262mal der Erdschwerebeschleunigung (= 9.81 m s-2) für eine radiale Position von 6.5 Zentimeter. Diese Kraft ist der Schlüsselfaktor für die Fähigkeit der AUZ sogar kleine Moleküle und Ionen zu trennen. Die Experimente wurden bei kontrollierter Rotationsgeschwindigkeit und Temperatur ausgeführt. Drei verschiedene, neue Detektoren wurden im Rahmen dieser Arbeit konstruiert und getestet. Diese Detektoren haben die analytischen Informationen sehr verbessert. Dies wurde für Proteine, halbleitende Nanopartikel sowie auch für industrielle Produkte gezeigt.

Many companies are fighting a continuous battle to remain competitive, and find ways to improve innovativeness. Consequently they tend to imitate successful modes of organizing, translating ideas to fit their particular contexts. This study focuses on the translation process of Open Source Software Development into a practical set of behavior patterns and work structures within Hewlett-Packard and its partners. Through this process of translation, a hybrid mode of Open Source Software Development work organization emerged, The Progressive Open Source. This instance of translation conveys a process of adopting and subsequently reconstructing a non-traditional form of work organization within the boundaries of the traditional organization. Some of the central characteristics of Open Source Software Development were adopted, reshaped, or compromised. The study argues that the Internet continues to change the way work is conducted, and it is protecting and promoting a new era of collaborative, participatory and global approach towards innovation. Openness is the hallmark of these new processes. Moreover, openness has emerged as a viable strategy for organizations. Catharina Melian is a researcher at the Stockholm School of Economics and the Centre for Media and Economic Psychology. / Diss. Stockholm : Handelshögskolan i Stockholm, 2007