Certificates for Incremental Type Checking

The central topic of this thesis is the study of algorithms for type checking, both from the programming language and from the proof-theoretic point of view. A type checking algorithm takes a program or a proof, represented as a syntactical object, and checks its validity with respect to a specification or a statement. It is a central piece of compilers and proof assistants. We postulate that since type checkers are at the interface between proof theory and program theory, their study can let these two fields mutually enrich each other. We argue by two main instances: first, starting from the problem of proof reuse, we develop an incremental type checker; secondly, starting from a type checking program, we evidence a novel correspondence between natural deduction and the sequent calculus.

A Web GIS Decision Support System For Coastal Risk Assessment and Mitigation Planning

Coastal flooding poses serious threats to coastal areas around the world, billions of dollars in damage to property and infrastructure, and threatens the lives of millions of people. Therefore, disaster management and risk assessment aims at detecting vulnerability and capacities in order to reduce coastal flood disaster risk. In particular, non-specialized researchers, emergency management personnel, and land use planners require an accurate, inexpensive method to determine and map risk associated with storm surge events and long-term sea level rise associated with climate change. This study contributes to the spatially evaluation and mapping of social-economic-environmental vulnerability and risk at sub-national scale through the development of appropriate tools and methods successfully embedded in a Web-GIS Decision Support System. A new set of raster-based models were studied and developed in order to be easily implemented in the Web-GIS framework with the purpose to quickly assess and map flood hazards characteristics, damage and vulnerability in a Multi-criteria approach. The Web-GIS DSS is developed recurring to open source software and programming language and its main peculiarity is to be available and usable by coastal managers and land use planners without requiring high scientific background in hydraulic engineering. The effectiveness of the system in the coastal risk assessment is evaluated trough its application to a real case study.

Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

Modifiche al protocollo di trasporto LTP per migliorarne le prestazioni in presenza di perdite elevate

La presente tesi si pone come obiettivo quello di analizzare il protocollo LTP (in particolare in ION) e proporre dei miglioramenti utili al caso in cui siano presenti perdite elevate. Piu in dettaglio, una prima parte introduttiva motiva l'inefficacia del TCP/IP in ambito interplanetario e introduce l'architettura DTN Bundle Protocol (Cap.1). La tesi prosegue con la descrizione delle specifiche del protocollo LTP (Cap.2), in particolar modo evidenziando come un bundle venga incapsulato in un blocco LTP, come questo sia successivamente diviso in tanti segmenti LTP e come questi vengano successivamente inviati con il protocollo UDP o con un protocollo analogo. Viene quindi presentata un'approfondita analisi delle penalizzazioni dovute alle perdite dei segmenti LTP, sia di tipo dati che di segnalazione (Cap. 3). Quest'analisi permette di dimostrare la criticita degli effetti delle perdite, in particolare per quello che riguarda i segmenti LTP di segnalazione. Mentre in presenza di perdite basse tali effetti hanno in media un impatto minimo sul tempo di consegna di un blocco LTP (quindi del bundle in esso contenuto), in quanto avvengono raramente, in presenza di perdite elevate rappresentano un collo di bottiglia per il tempo di consegna di un blocco LTP. A tal proposito sono state proposte alcune modifiche che permettono di migliorare le prestazioni di LTP (Cap. 4) compatibilmente con le specifiche RFC in modo da garantire l'interoperabilita con le diverse implementazioni del protocollo. Successivamente nel Cap. 5 viene mostrato come sono state implementate le modifiche proposte in ION 3.4.1. Nel capitolo finale (Cap. 6) sono presenti i risultati numerici relativi ad alcuni test preliminari eseguiti confrontando la versione originale del protocollo con le versioni modificate contenenti i miglioramenti proposti. I test sono risultati molto positivi per elevate perdite, confermando cosi la validita dell'analisi e dei miglioramenti introdotti.

Domain-Specific Program Checking

Lint-like program checkers are popular tools that ensure code quality by verifying compliance with best practices for a particular programming language. The proliferation of internal domain-specific languages and models, however, poses new challenges for such tools. Traditional program checkers produce many false positives and fail to accurately check constraints, best practices, common errors, possible optimizations and portability issues particular to domain-specific languages. We advocate the use of dedicated rules to check domain-specific practices. We demonstrate the implementation of domain-specific rules, the automatic fixing of violations, and their application to two case-studies: (1) Seaside defines several internal DSLs through a creative use of the syntax of the host language; and (2) Magritte adds meta-descriptions to existing code by means of special methods. Our empirical validation demonstrates that domain-specific program checking significantly improves code quality when compared with general purpose program checking.

Spy: A Flexible Code Profiling Framework

Code profiling is an essential activity to increase software quality. It is commonly employed in a wide variety of tasks, such as supporting program comprehension, determining execution bottlenecks, and assessing code coverage by unit tests. Spy is an innovative framework to easily build profilers and visualize profiling information. The profiling information is obtained by inserting dedicated code before or after method execution. The gathered profiling information is structured in line with the application structure in terms of packages, classes, and methods. Spy has been instantiated on four occasions so far. We created profilers dedicated to test coverage, time execution, type feedback, and profiling evolution across version. We also integrated Spy in the Pharo IDE. Spy has been implemented in the Pharo Smalltalk programming language and is available under the MIT license.

Compensability index for compensation radiotherapy after treatment interruptions

Background The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. Methods We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. Results The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. Conclusions The compensability index calculation may serve as a decision support system based on existing and established recommendations.

Simulation of titration experiments

Nowadays computer simulation is used in various fields, particularly in laboratories where it is used for the exploration data which are sometimes experimentally inaccessible. In less developed countries where there is a need for up to date laboratories for the realization of practical lessons in chemistry, especially in secondary schools and some higher institutions of learning, it may permit learners to carryout experiments such as titrations without the use of laboratory materials and equipments. Computer simulations may also permit teachers to better explain the realities of practical lessons, given that computers have now become very accessible and less expensive compared to the acquisition of laboratory materials and equipments. This work is aimed at coming out with a virtual laboratory that shall permit the simulation of an acid-base titration and an oxidation-reduction titration with the use of synthetic images. To this effect, an appropriate numerical method was used to obtain appropriate organigram, which were further transcribed into source codes with the help of a programming language so as to come out with the software.

DEVELOPMENT OF AN OPTIMIZATION MODEL FOR BIOFUEL FACILITY SIZE AND LOCATION AND A SIMULATION MODEL FOR DESIGN OF A BIOFUEL SUPPLY CHAIN

A range of societal issues have been caused by fossil fuel consumption in the transportation sector in the United States (U.S.), including health related air pollution, climate change, the dependence on imported oil, and other oil related national security concerns. Biofuels production from various lignocellulosic biomass types such as wood, forest residues, and agriculture residues have the potential to replace a substantial portion of the total fossil fuel consumption. This research focuses on locating biofuel facilities and designing the biofuel supply chain to minimize the overall cost. For this purpose an integrated methodology was proposed by combining the GIS technology with simulation and optimization modeling methods. The GIS based methodology was used as a precursor for selecting biofuel facility locations by employing a series of decision factors. The resulted candidate sites for biofuel production served as inputs for simulation and optimization modeling. As a precursor to simulation or optimization modeling, the GIS-based methodology was used to preselect potential biofuel facility locations for biofuel production from forest biomass. Candidate locations were selected based on a set of evaluation criteria, including: county boundaries, a railroad transportation network, a state/federal road transportation network, water body (rivers, lakes, etc.) dispersion, city and village dispersion, a population census, biomass production, and no co-location with co-fired power plants. The simulation and optimization models were built around key supply activities including biomass harvesting/forwarding, transportation and storage. The built onsite storage served for spring breakup period where road restrictions were in place and truck transportation on certain roads was limited. Both models were evaluated using multiple performance indicators, including cost (consisting of the delivered feedstock cost, and inventory holding cost), energy consumption, and GHG emissions. The impact of energy consumption and GHG emissions were expressed in monetary terms to keep consistent with cost. Compared with the optimization model, the simulation model represents a more dynamic look at a 20-year operation by considering the impacts associated with building inventory at the biorefinery to address the limited availability of biomass feedstock during the spring breakup period. The number of trucks required per day was estimated and the inventory level all year around was tracked. Through the exchange of information across different procedures (harvesting, transportation, and biomass feedstock processing procedures), a smooth flow of biomass from harvesting areas to a biofuel facility was implemented. The optimization model was developed to address issues related to locating multiple biofuel facilities simultaneously. The size of the potential biofuel facility is set up with an upper bound of 50 MGY and a lower bound of 30 MGY. The optimization model is a static, Mathematical Programming Language (MPL)-based application which allows for sensitivity analysis by changing inputs to evaluate different scenarios. It was found that annual biofuel demand and biomass availability impacts the optimal results of biofuel facility locations and sizes.

Playing with the Real World

In this paper we provide a framework that enables the rapid development of applications using non-standard input devices. Flash is chosen as programming language since it can be used for quickly assembling applications. We overcome the difficulties of Flash to access external devices by introducing a very generic concept: The state information generated by input devices is transferred to a PC where a program collects them, interprets them and makes them available on a web server. Application developers can now integrate a Flash component that accesses the data stored in XML format and directly use it in their application.

Student2Student als Organisationsmodell für die Entwicklung von E-Learning-Ressourcen

Die E-Learning-Plattform VBA@HfTL unterstützt das Erlernen von grundlegenden Programmierkonzepten mithilfe der Programmiersprache Visual Basic for Applications (VBA). Diese Plattform wurde von Studierenden für Studierende der Fachrichtung Wirtschaftsinformatik entwickelt, so dass ein Student2Student (S2S)-Ansatz umgesetzt wurde. Der Beitrag führt die konzeptionellen Grundlagen dieses Ansatzes ein und erläutert die organisatorischen sowie technischen Rahmenbedingungen des Entwicklungsprojekts als Forschungsfallstudie. Das Projektergebnis zeigt, dass Studierende selbstorganisiert E-Learning-Ressourcen entwickeln und sich dabei interdisziplinäre Fachinhalte der Wirtschaftsinformatik aneignen können. Die resultierende E-Learning-Plattform liefert aufgrund der hohen Resonanz nicht nur einen wertvollen Beitrag zur Unterstützung von Lernprozessen in der Aus- und Weiterbildung, sondern bietet der Hochschule auch eine Möglichkeit zur Profilierung des Bildungsangebots im Rahmen der Öffentlichkeitsarbeit.

Top-Down Parsing with Parsing Contexts

The domain of context-free languages has been extensively explored and there exist numerous techniques for parsing (all or a subset of) context-free languages. Unfortunately, some programming languages are not context-free. Using standard context-free parsing techniques to parse a context-sensitive programming language poses a considerable challenge. Im- plementors of programming language parsers have adopted various techniques, such as hand-written parsers, special lex- ers, or post-processing of an ambiguous parser output to deal with that challenge. In this paper we suggest a simple extension of a top-down parser with contextual information. Contrary to the tradi- tional approach that uses only the input stream as an input to a parsing function, we use a parsing context that provides ac- cess to a stream and possibly to other context-sensitive infor- mation. At a same time we keep the context-free formalism so a grammar definition stays simple without mind-blowing context-sensitive rules. We show that our approach can be used for various purposes such as indent-sensitive parsing, a high-precision island parsing or XML (with arbitrary el- ement names) parsing. We demonstrate our solution with PetitParser, a parsing-expression grammar based, top-down, parser combinator framework written in Smalltalk.

Zooplankton abundance and size structure in the North Atlantic from MSM26_133-14

Data on zooplankton abundance and biovolume were collected in concert with data on the biophysical environment at 9 stations in the North Atlantic, from the Iceland Basin in the East to the Labrador Sea in the West. The data were sampled along vertical profiles by a Laser Optical Plankton Counter (LOPC, Rolls Royce Canada Ltd.) that was mounted on a carousel water sampler together with a Conductivity-Temperature-Depth sensor (CTD, SBE19plusV2, Seabird Electronics, Inc., USA) and a fluorescence sensor (F, ECO Puck chlorophyll a fluorometer, WET Labs Inc., USA). Based on the LOPC data, abundance (individuals/m**3) and biovolume (mm3/m**3) were calculated as described in the LOPC Software Operation Manual [(Anonymous, 2006), http://www.brooke-ocean.com/index.html]. LOPC data were regrouped into 49 size groups of equal log10(body volume) increments, see Edvardsen et al. (2002, doi:10.3354/meps227205). LOPC data quality was checked as described in Basedow et al. (2013, doi:10.1016/j.pocean.2012.10.005). Fluorescence was roughly converted into chlorophyll based on filtered chlorophyll values obtained from station 10 in the Labrador Sea. Due to the low number of filtered samples that was used for the conversion the resulting chlorophyll values should be considered with care. CTD data were screened for erroneous (out of range) values and then averaged to the same frequency as the LOPC data (2 Hz). All data were processed using especially developed scripts in the python programming language. The LOPC is an optical instrument designed to count and measure particles (0.1 to 30 mm equivalent spherical diameter) in the water column, see Herman et al., (2004, doi:10.1093/plankt/fbh095). The size of particles as equivalent spherical diameter (ESD) was computed as described in the manual (Anonymous, 2006), and in more detail in Checkley et al. (2008, doi:10.4319/lo.2008.53.5_part_2.2123) and Gaardsted et al. (2010, doi:10.1111/j.1365-2419.2010.00558.x).

Zooplankton abundance and size structure in the North Atlantic from MSM26_135-21

Data on zooplankton abundance and biovolume were collected in concert with data on the biophysical environment at 9 stations in the North Atlantic, from the Iceland Basin in the East to the Labrador Sea in the West. The data were sampled along vertical profiles by a Laser Optical Plankton Counter (LOPC, Rolls Royce Canada Ltd.) that was mounted on a carousel water sampler together with a Conductivity-Temperature-Depth sensor (CTD, SBE19plusV2, Seabird Electronics, Inc., USA) and a fluorescence sensor (F, ECO Puck chlorophyll a fluorometer, WET Labs Inc., USA). Based on the LOPC data, abundance (individuals/m**3) and biovolume (mm3/m**3) were calculated as described in the LOPC Software Operation Manual [(Anonymous, 2006), http://www.brooke-ocean.com/index.html]. LOPC data were regrouped into 49 size groups of equal log10(body volume) increments, see Edvardsen et al. (2002, doi:10.3354/meps227205). LOPC data quality was checked as described in Basedow et al. (2013, doi:10.1016/j.pocean.2012.10.005). Fluorescence was roughly converted into chlorophyll based on filtered chlorophyll values obtained from station 10 in the Labrador Sea. Due to the low number of filtered samples that was used for the conversion the resulting chlorophyll values should be considered with care. CTD data were screened for erroneous (out of range) values and then averaged to the same frequency as the LOPC data (2 Hz). All data were processed using especially developed scripts in the python programming language. The LOPC is an optical instrument designed to count and measure particles (0.1 to 30 mm equivalent spherical diameter) in the water column, see Herman et al., (2004, doi:10.1093/plankt/fbh095). The size of particles as equivalent spherical diameter (ESD) was computed as described in the manual (Anonymous, 2006), and in more detail in Checkley et al. (2008, doi:10.4319/lo.2008.53.5_part_2.2123) and Gaardsted et al. (2010, doi:10.1111/j.1365-2419.2010.00558.x).

Zooplankton abundance and size structure in the North Atlantic from MSM26_127-22

Data on zooplankton abundance and biovolume were collected in concert with data on the biophysical environment at 9 stations in the North Atlantic, from the Iceland Basin in the East to the Labrador Sea in the West. The data were sampled along vertical profiles by a Laser Optical Plankton Counter (LOPC, Rolls Royce Canada Ltd.) that was mounted on a carousel water sampler together with a Conductivity-Temperature-Depth sensor (CTD, SBE19plusV2, Seabird Electronics, Inc., USA) and a fluorescence sensor (F, ECO Puck chlorophyll a fluorometer, WET Labs Inc., USA). Based on the LOPC data, abundance (individuals/m**3) and biovolume (mm3/m**3) were calculated as described in the LOPC Software Operation Manual [(Anonymous, 2006), http://www.brooke-ocean.com/index.html]. LOPC data were regrouped into 49 size groups of equal log10(body volume) increments, see Edvardsen et al. (2002, doi:10.3354/meps227205). LOPC data quality was checked as described in Basedow et al. (2013, doi:10.1016/j.pocean.2012.10.005). Fluorescence was roughly converted into chlorophyll based on filtered chlorophyll values obtained from station 10 in the Labrador Sea. Due to the low number of filtered samples that was used for the conversion the resulting chlorophyll values should be considered with care. CTD data were screened for erroneous (out of range) values and then averaged to the same frequency as the LOPC data (2 Hz). All data were processed using especially developed scripts in the python programming language. The LOPC is an optical instrument designed to count and measure particles (0.1 to 30 mm equivalent spherical diameter) in the water column, see Herman et al., (2004, doi:10.1093/plankt/fbh095). The size of particles as equivalent spherical diameter (ESD) was computed as described in the manual (Anonymous, 2006), and in more detail in Checkley et al. (2008, doi:10.4319/lo.2008.53.5_part_2.2123) and Gaardsted et al. (2010, doi:10.1111/j.1365-2419.2010.00558.x).