Developing sustainable research data management services: an institutional collaboration

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Case study of the use of remotely sensed data for modeling flood inundation on the river Severn, UK.

A methodology for using remotely sensed data to both generate and evaluate a hydraulic model of floodplain inundation is presented for a rural case study in the United Kingdom: Upton-upon-Severn. Remotely sensed data have been processed and assembled to provide an excellent test data set for both model construction and validation. In order to assess the usefulness of the data and the issues encountered in their use, two models for floodplain inundation were constructed: one based on an industry standard one-dimensional approach and the other based on a simple two-dimensional approach. The results and their implications for the future use of remotely sensed data for predicting flood inundation are discussed. Key conclusions for the use of remotely sensed data are that care must be taken to integrate different data sources for both model construction and validation and that improvements in ground height data shift the focus in terms of model uncertainties to other sources such as boundary conditions. The differences between the two models are found to be of minor significance.

En beskrivning av manuellt test : Svagheter och styrkor med och utan stöd avett testverktyg

Test is an area in system development. Test can be performed manually or automated. Test activities can be supported by Word documents and Excel sheets for documenting and executing test cases and as well for follow up, but there are also new test tools designed to support and facilitate the testing process and the activities of the test. This study has described manual test and identified strengths and weaknesses of manual testing with a testing tool called Microsoft Test Manager (MTM) and of manual testing using test cases and test log templates developed by the testers at Sogeti. The result that emerged from the problem and strength analysis and the analysis of literature studies and firsthand experiences (in terms of creating, documenting and executing test cases) addresses the issue of the following weaknesses and strengths. Strengths of the test tool is that it contains needed functionality all in one place and it is available when needed without having to open up other programs which saves many steps of activity. Strengths with test without the support of test tools is mainly that it is easy to learn and gives a good overview, easy to format text as desired and flexible to changes during execution of a test case. Weaknesses in test with the support of test tools include that it is difficult to get a good overview of the entire test case, that it is not possible to format the text in the test steps. It is as well not possible to modify the test steps during execution. It is also difficult to use some of the test design techniques of TMap, for example a checklist, when using the test tool MTM. Weaknesses with test without the support of the testing tool MTM is that the tester gets many more steps of activities to do compared to doing the same activities with the support of the testing tool MTM. There is more to remember because the documents the tester use are not directly linked. Altogether the strengths of the test tool stands out when it comes to supporting the testing process.

Beta: uma ferramenta para geração de testes de unidade a partir de especificações B

Formal methods and software testing are tools to obtain and control software quality. When used together, they provide mechanisms for software specification, verification and error detection. Even though formal methods allow software to be mathematically verified, they are not enough to assure that a system is free of faults, thus, software testing techniques are necessary to complement the process of verification and validation of a system. Model Based Testing techniques allow tests to be generated from other software artifacts such as specifications and abstract models. Using formal specifications as basis for test creation, we can generate better quality tests, because these specifications are usually precise and free of ambiguity. Fernanda Souza (2009) proposed a method to define test cases from B Method specifications. This method used information from the machine s invariant and the operation s precondition to define positive and negative test cases for an operation, using equivalent class partitioning and boundary value analysis based techniques. However, the method proposed in 2009 was not automated and had conceptual deficiencies like, for instance, it did not fit in a well defined coverage criteria classification. We started our work with a case study that applied the method in an example of B specification from the industry. Based in this case study we ve obtained subsidies to improve it. In our work we evolved the proposed method, rewriting it and adding characteristics to make it compatible with a test classification used by the community. We also improved the method to support specifications structured in different components, to use information from the operation s behavior on the test case generation process and to use new coverage criterias. Besides, we have implemented a tool to automate the method and we have submitted it to more complex case studies

Decreasing pH of mammary gland secretions is associated with parturition and is correlated with electrolyte concentrations in prefoaling mares

The objectives of this study were to determine pH of the mammary gland secretions and the corresponding electrolyte concentrations in prefoaling mares. Pregnant mares (seven primiparous and seven multiparous) were monitored daily from 310.320 days of gestation until parturition. Prefoaling mammary gland secretions were collected, and pH was immediately determined with a pH meter and pH strip test. An aliquot of prefoaling mammary secretions was frozen and stored until further analyses. After parturition, samples from day .4 to 0 (day of foaling) were thawed and electrolyte concentrations (ie, Ca2+, Mg2+, Na+, K+ and Cl-) were determined with an automated analyser. Data were analysed via a mixed model with the mare as a random effect. Correlations were determined between pH and electrolyte concentrations by the Pearson product-moment for each pair. There was significant reduction in pH of mammary secretions on the day of foaling (P<0.0001), and most mares (11/14) with a pH .7 foaled within 24 hours. There was high correlation between the two pH methods (r=0.93). Additionally, there were significant (P<0.05) increases in Ca2+ and K+ concentrations, and significant decreases in Na+ and Cl- concentrations from one day before to the day of foaling. The pH of mammary secretions was highly and significantly (P<0.001) correlated with Na + (r=0.87), Cl- (r=0.85), Ca2+ (r=-0.88); and K+(r=.0.80) concentrations, and moderately correlated with Mg 2+ (r=-0.58). Daily evening pH measure of the mammary gland secretions can predict foaling in most mares.

HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples

HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes.

MODEL PARTITIONS AND COMPACT TEST CASE SUITES

We present a generalized test case generation method, called the G method. Although inspired by the W method, the G method, in contrast, allows for test case suite generation even in the absence of characterization sets for the specification models. Instead, the G method relies on knowledge about the index of certain equivalences induced at the implementation models. We show that the W method can be derived from the G method as a particular case. Moreover, we discuss some naturally occurring infinite classes of FSM models over which the G method generates test suites that are exponentially more compact than those produced by the W method.

Dynamic distance analysis : new geometric data structures and algorithms for the real-time calculation of tolerance violating regions in the digital mockup process

In vielen Industriezweigen, zum Beispiel in der Automobilindustrie, werden Digitale Versuchsmodelle (Digital MockUps) eingesetzt, um die Konstruktion und die Funktion eines Produkts am virtuellen Prototypen zu überprüfen. Ein Anwendungsfall ist dabei die Überprüfung von Sicherheitsabständen einzelner Bauteile, die sogenannte Abstandsanalyse. Ingenieure ermitteln dabei für bestimmte Bauteile, ob diese in ihrer Ruhelage sowie während einer Bewegung einen vorgegeben Sicherheitsabstand zu den umgebenden Bauteilen einhalten. Unterschreiten Bauteile den Sicherheitsabstand, so muss deren Form oder Lage verändert werden. Dazu ist es wichtig, die Bereiche der Bauteile, welche den Sicherhabstand verletzen, genau zu kennen. rnrnIn dieser Arbeit präsentieren wir eine Lösung zur Echtzeitberechnung aller den Sicherheitsabstand unterschreitenden Bereiche zwischen zwei geometrischen Objekten. Die Objekte sind dabei jeweils als Menge von Primitiven (z.B. Dreiecken) gegeben. Für jeden Zeitpunkt, in dem eine Transformation auf eines der Objekte angewendet wird, berechnen wir die Menge aller den Sicherheitsabstand unterschreitenden Primitive und bezeichnen diese als die Menge aller toleranzverletzenden Primitive. Wir präsentieren in dieser Arbeit eine ganzheitliche Lösung, welche sich in die folgenden drei großen Themengebiete unterteilen lässt.rnrnIm ersten Teil dieser Arbeit untersuchen wir Algorithmen, die für zwei Dreiecke überprüfen, ob diese toleranzverletzend sind. Hierfür präsentieren wir verschiedene Ansätze für Dreiecks-Dreiecks Toleranztests und zeigen, dass spezielle Toleranztests deutlich performanter sind als bisher verwendete Abstandsberechnungen. Im Fokus unserer Arbeit steht dabei die Entwicklung eines neuartigen Toleranztests, welcher im Dualraum arbeitet. In all unseren Benchmarks zur Berechnung aller toleranzverletzenden Primitive beweist sich unser Ansatz im dualen Raum immer als der Performanteste.rnrnDer zweite Teil dieser Arbeit befasst sich mit Datenstrukturen und Algorithmen zur Echtzeitberechnung aller toleranzverletzenden Primitive zwischen zwei geometrischen Objekten. Wir entwickeln eine kombinierte Datenstruktur, die sich aus einer flachen hierarchischen Datenstruktur und mehreren Uniform Grids zusammensetzt. Um effiziente Laufzeiten zu gewährleisten ist es vor allem wichtig, den geforderten Sicherheitsabstand sinnvoll im Design der Datenstrukturen und der Anfragealgorithmen zu beachten. Wir präsentieren hierzu Lösungen, die die Menge der zu testenden Paare von Primitiven schnell bestimmen. Darüber hinaus entwickeln wir Strategien, wie Primitive als toleranzverletzend erkannt werden können, ohne einen aufwändigen Primitiv-Primitiv Toleranztest zu berechnen. In unseren Benchmarks zeigen wir, dass wir mit unseren Lösungen in der Lage sind, in Echtzeit alle toleranzverletzenden Primitive zwischen zwei komplexen geometrischen Objekten, bestehend aus jeweils vielen hunderttausend Primitiven, zu berechnen. rnrnIm dritten Teil präsentieren wir eine neuartige, speicheroptimierte Datenstruktur zur Verwaltung der Zellinhalte der zuvor verwendeten Uniform Grids. Wir bezeichnen diese Datenstruktur als Shrubs. Bisherige Ansätze zur Speicheroptimierung von Uniform Grids beziehen sich vor allem auf Hashing Methoden. Diese reduzieren aber nicht den Speicherverbrauch der Zellinhalte. In unserem Anwendungsfall haben benachbarte Zellen oft ähnliche Inhalte. Unser Ansatz ist in der Lage, den Speicherbedarf der Zellinhalte eines Uniform Grids, basierend auf den redundanten Zellinhalten, verlustlos auf ein fünftel der bisherigen Größe zu komprimieren und zur Laufzeit zu dekomprimieren.rnrnAbschießend zeigen wir, wie unsere Lösung zur Berechnung aller toleranzverletzenden Primitive Anwendung in der Praxis finden kann. Neben der reinen Abstandsanalyse zeigen wir Anwendungen für verschiedene Problemstellungen der Pfadplanung.

Investigation of the effect of using data collection technology on students' attitudes to science instruction

The purpose of this project was to investigate the effect of using of data collection technology on student attitudes towards science instruction. The study was conducted over the course of two years at Madison High School in Adrian, Michigan, primarily in college preparatory physics classes, but also in one college preparatory chemistry class and one environmental science class. A preliminary study was conducted at a Lenawee County Intermediate Schools student summer environmental science day camp. The data collection technology used was a combination of Texas Instruments TI-84 Silver Plus graphing calculators and Vernier LabPro data collection sleds with various probeware attachments, including motion sensors, pH probes and accelerometers. Students were given written procedures for most laboratory activities and were provided with data tables and analysis questions to answer about the activities. The first year of the study included a pretest and posttest measuring student attitudes towards the class they were enrolled in. Pre-test and post-test data were analyzed to determine effect size, which was found to be very small (Coe, 2002). The second year of the study focused only on a physics class and used Keller’s ARCS model for measuring student motivation based on the four aspects of motivation: Attention, Relevance, Confidence and Satisfaction (Keller, 2010). According to this model, it was found that there were two distinct groups in the class, one of which was motivated to learn and the other that was not. The data suggest that the use of data collection technology in science classes should be started early in a student’s career, possibly in early middle school or late elementary. This would build familiarity with the equipment and allow for greater exploration by the student as they progress through high school and into upper level science courses.

Variability of in vivo fish acute toxicity data

The variability of toxicity data contained within databases was investigated using the widely used US EPA ECOTOX database as an example. Fish acute lethality (LC50) values for 44 compounds (for which at least 10 data entries existed) were extracted from the ECOTOX database yielding a total of 4654 test records. Significant variability of LC50 test results was observed, exceeding several orders of magnitude. In an attempt to systematically explore potential causes of the data variability, the influence of biological factors (such as test species or life stages) and physical factors (such as water temperature, pH or water hardness) were examined. Even after eliminating the influence of these inherent factors, considerable data variability remained, suggesting an important role of factors relating to technical and measurement procedures. The analysis, however, was limited by pronounced gaps in the test documentation. Of the 4654 extracted test reports, 66.5% provided no information on the fish life stage used for testing. Likewise, water temperature, hardness or pH were not recorded in 19.6%, 48.2% and 41.2% of the data entries, respectively. From these findings, we recommend the rigorous control of data entries ensuring complete recording of testing conditions. A more consistent database will help to better discriminate between technical and natural variability of the test data, which is of importance in ecological risk assessment for extrapolation from laboratory tests to the field, and also might help to develop correction factors that account for systematic differences in test results caused by species, life stage or test conditions.

NETWORK TOPOLOGY IN HUMAN PROTEIN INTERACTION DATA PREDICTS FUNCTIONAL ASSOCIATION

High-throughput assays, such as yeast two-hybrid system, have generated a huge amount of protein-protein interaction (PPI) data in the past decade. This tremendously increases the need for developing reliable methods to systematically and automatically suggest protein functions and relationships between them. With the available PPI data, it is now possible to study the functions and relationships in the context of a large-scale network. To data, several network-based schemes have been provided to effectively annotate protein functions on a large scale. However, due to those inherent noises in high-throughput data generation, new methods and algorithms should be developed to increase the reliability of functional annotations. Previous work in a yeast PPI network (Samanta and Liang, 2003) has shown that the local connection topology, particularly for two proteins sharing an unusually large number of neighbors, can predict functional associations between proteins, and hence suggest their functions. One advantage of the work is that their algorithm is not sensitive to noises (false positives) in high-throughput PPI data. In this study, we improved their prediction scheme by developing a new algorithm and new methods which we applied on a human PPI network to make a genome-wide functional inference. We used the new algorithm to measure and reduce the influence of hub proteins on detecting functionally associated proteins. We used the annotations of the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as independent and unbiased benchmarks to evaluate our algorithms and methods within the human PPI network. We showed that, compared with the previous work from Samanta and Liang, our algorithm and methods developed in this study improved the overall quality of functional inferences for human proteins. By applying the algorithms to the human PPI network, we obtained 4,233 significant functional associations among 1,754 proteins. Further comparisons of their KEGG and GO annotations allowed us to assign 466 KEGG pathway annotations to 274 proteins and 123 GO annotations to 114 proteins with estimated false discovery rates of <21% for KEGG and <30% for GO. We clustered 1,729 proteins by their functional associations and made pathway analysis to identify several subclusters that are highly enriched in certain signaling pathways. Particularly, we performed a detailed analysis on a subcluster enriched in the transforming growth factor β signaling pathway (P<10-50) which is important in cell proliferation and tumorigenesis. Analysis of another four subclusters also suggested potential new players in six signaling pathways worthy of further experimental investigations. Our study gives clear insight into the common neighbor-based prediction scheme and provides a reliable method for large-scale functional annotations in this post-genomic era.

datos.bne.es and MARiMbA: an insight into Library Linked Data

Purpose – Linked data is gaining great interest in the cultural heritage domain as a new way for publishing, sharing and consuming data. The paper aims to provide a detailed method and MARiMbA a tool for publishing linked data out of library catalogues in the MARC 21 format, along with their application to the catalogue of the National Library of Spain in the datos.bne.es project. Design/methodology/approach – First, the background of the case study is introduced. Second, the method and process of its application are described. Third, each of the activities and tasks are defined and a discussion of their application to the case study is provided. Findings – The paper shows that the FRBR model can be applied to MARC 21 records following linked data best practices, librarians can successfully participate in the process of linked data generation following a systematic method, and data sources quality can be improved as a result of the process. Originality/value – The paper proposes a detailed method for publishing and linking linked data from MARC 21 records, provides practical examples, and discusses the main issues found in the application to a real case. Also, it proposes the integration of a data curation activity and the participation of librarians in the linked data generation process.

A semantic middleware architecture focused on data and heterogeneity management within the Smart Grid

There is an increasing tendency of turning the current power grid, essentially unaware of variations in electricity demand and scattered energy sources, into something capable of bringing a degree of intelligence by using tools strongly related to information and communication technologies, thus turning into the so-called Smart Grid. In fact, it could be considered that the Smart Grid is an extensive smart system that spreads throughout any area where power is required, providing a significant optimization in energy generation, storage and consumption. However, the information that must be treated to accomplish these tasks is challenging both in terms of complexity (semantic features, distributed systems, suitable hardware) and quantity (consumption data, generation data, forecasting functionalities, service reporting), since the different energy beneficiaries are prone to be heterogeneous, as the nature of their own activities is. This paper presents a proposal on how to deal with these issues by using a semantic middleware architecture that integrates different components focused on specific tasks, and how it is used to handle information at every level and satisfy end user requests.

Influence apart from Adoption: How Interaction between Programming and Scientific Practices Shapes Modes of Inquiry in Four Oceanography Teams

Thesis (Ph.D.)--University of Washington, 2016-06

Computational methods for the detection of facial palsy

We are developing a telemedicine application which offers automated diagnosis of facial (Bell's) palsy through a Web service. We used a test data set of 43 images of facial palsy patients and 44 normal people to develop the automatic recognition algorithm. Three different image pre-processing methods were used. Machine learning techniques (support vector machine, SVM) were used to examine the difference between the two halves of the face. If there was a sufficient difference, then the SVM recognized facial palsy. Otherwise, if the halves were roughly symmetrical, the SVM classified the image as normal. It was found that the facial palsy images had a greater Hamming Distance than the normal images, indicating greater asymmetry. The median distance in the normal group was 331 (interquartile range 277-435) and the median distance in the facial palsy group was 509 (interquartile range 334-703). This difference was significant (P