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In this project I constructed a workflow that takes a DNA sequence as input and provides a phylogenetic tree, consisting of the input sequence and other sequences which were found during a database search. In this phylogenetic tree the sequences are arranged depending on similarities. In bioinformatics, constructing phylogenetic trees is often used to explore the evolutionary relationships of genes or organisms and to understand the mechanisms of evolution itself.
Spotlocator is a game wherein people have to guess the spots of where photos were taken. The photos of a defined area for each game are from panoramio.com. They are published at http://spotlocator. drupalgardens.com with an ID. Everyone can guess the photo spots by sending a special tweet via Twitter that contains the hashtag #spotlocator, the guessed coordinates and the ID of the photo. An evaluation is published for all tweets. The players are informed about the distance to the real photo spots and the positions are shown on a map.
Exploratory Data Analysis
(2014)
In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R.
The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins.
Lessons Learned
(2014)
This chapter summarizes the experience and the lessons we learned concerning the application of the jABC as a framework for design and execution of scientific workflows. It reports experiences from the domain modeling (especially service integration) and workflow design phases and evaluates the resulting models statistically with respect to the SIB library and hierarchy levels.
The Course's SIB Libraries
(2014)
This chapter gives a detailed description of the service framework underlying all the example projects that form the foundation of this book. It describes the different SIB libraries that we made available for the course “Process modeling in the natural sciences” to provide the functionality that was required for the envisaged applications. The students used these SIB libraries to realize their projects.
A major part of the scientific experiments that are carried out today requires thorough computational support. While database and algorithm providers face the problem of bundling resources to create and sustain powerful computation nodes, the users have to deal with combining sets of (remote) services into specific data analysis and transformation processes. Today’s attention to “big data” amplifies the issues of size, heterogeneity, and process-level diversity/integration. In the last decade, especially workflow-based approaches to deal with these processes have enjoyed great popularity. This book concerns a particularly agile and model-driven approach to manage scientific workflows that is based on the XMDD paradigm. In this chapter we explain the scope and purpose of the book, briefly describe the concepts and technologies of the XMDD paradigm, explain the principal differences to related approaches, and outline the structure of the book.
We summarize here the main characteristics and features of the jABC framework, used in the case studies as a graphical tool for modeling scientific processes and workflows. As a comprehensive environment for service-oriented modeling and design according to the XMDD (eXtreme Model-Driven Design) paradigm, the jABC offers much more than the pure modeling capability. Associated technologies and plugins provide in fact means for a rich variety of supporting functionality, such as remote service integration, taxonomical service classification, model execution, model verification, model synthesis, and model compilation. We describe here in short both the essential jABC features and the service integration philosophy followed in the environment. In our work over the last years we have seen that this kind of service definition and provisioning platform has the potential to become a core technology in interdisciplinary service orchestration and technology transfer: Domain experts, like scientists not specially trained in computer science, directly define complex service orchestrations as process models and use efficient and complex domain-specific tools in a simple and intuitive way.
Since spring 2014 the relations between the EU and Russia are stuck in an Ice Age. From a Western point of view, especially the annexation of Crimea by Russia and the intervention in the conflict in Ukraine are responsible. The EU has frozen their relations to Russia and applied sanctions against it. Russia reacted in the same way. Can this vicious circle be broken without betraying the values of the EU? This book presents the analysis and ideas of social scientists from Germany, Poland and Russia. The reasons for this crisis are seen quite differently but all try to find a way out of the current confrontation.
This volume is a novel approach to the corpus-based variationist sociolinguistic study of contemporary urban western Irish English. Based on qualitative data as well as on linguistic features extracted from the Corpus of Galway City Spoken English, this study approaches the major sociolinguistic characteristics of (th) and (dh) variability in Galway City English. It demonstrates the diverse local patterns of variability and change in the phonetic realisation of the dental fricatives and establishes a considerable degree of divergence from traditional accounts on Irish English. This volume suggests that the linguistic stratification of variants of (th) and (dh) in Galway correlates both with the social stratification of the city itself and with the stratification of speakers by social status, sex/gender and age group.
The current study investigates to what extent masked morphological priming is modulated by language-particular properties, specifically by its writing system. We present results from two masked priming experiments investigating the processing of complex Japanese words written in less common (moraic) scripts. In Experiment 1, participants performed lexical decisions on target verbs; these were preceded by primes which were either (i) a past-tense form of the same verb, (ii) a stem-related form with the epenthetic vowel -i, (iii) a semantically-related form, and (iv) a phonologically-related form. Significant priming effects were obtained for prime types (i), (ii), and (iii), but not for (iv). This pattern of results differs from previous findings on languages with alphabetic scripts, which found reliable masked priming effects for morphologically related prime/target pairs of type (i), but not for non-affixal and semantically-related primes of types (ii), and (iii). In Experiment 2, we measured priming effects for prime/target pairs which are neither morphologically, semantically, phonologically nor - as presented in their moraic scripts—orthographically related, but which—in their commonly written form—share the same kanji, which are logograms adopted from Chinese. The results showed a significant priming effect, with faster lexical-decision times for kanji-related prime/target pairs relative to unrelated ones. We conclude that affix-stripping is insufficient to account for masked morphological priming effects across languages, but that language-particular properties (in the case of Japanese, the writing system) affect the processing of (morphologically) complex words.
Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator–prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to pre-
vious studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.
Recombination of free charge is a key process limiting the performance of solar cells. For low mobility materials, such as organic semiconductors, the kinetics of non-geminate recombination (NGR) is strongly linked to the motion of charges. As these materials possess significant disorder, thermalization of photogenerated carriers in the inhomogeneously broadened density of state distribution is an unavoidable process. Despite its general importance, knowledge about the kinetics of NGR in complete organic solar cells is rather limited. We employ time delayed collection field (TDCF) experiments to study the recombination of photogenerated charge in the high-performance polymer:fullerene blend PCDTBT:PCBM. NGR in the bulk of this amorphous blend is shown to be highly dispersive, with a continuous reduction of the recombination coefficient throughout the entire time scale, until all charge carriers have either been extracted or recombined. Rapid, contact-mediated recombination is identified as an additional loss channel, which, if not properly taken into account, would erroneously suggest a pronounced field dependence of charge generation. These findings are in stark contrast to the results of TDCF experiments on photovoltaic devices made from ordered blends, such as P3HT:PCBM, where non-dispersive recombination was proven to dominate the charge carrier dynamics under application relevant conditions.
Application of hybridisation capture to investigate complete mitogenomes from ancient samples
(2015)
Two experiments examined how individuals respond to a restriction presented within an approach versus an avoidance frame. In Study 1, working on a problem-solving task, participants were initially free to choose their strategy, but for a second task were told to change their strategy. The message to change was embedded in either an approach or avoidance frame. When confronted with an avoidance compared to an approach frame, the participants’ reactance toward the request was greater and, in turn, led to impaired performance. The role of reactance as a response to threat to freedom was explicitly examined in Study 2, in which participants evaluated a potential change in policy affecting their program of study herein explicitly varying whether a restriction was present or absent and whether the message was embedded in an approach versus avoidance frame. When communicated with an avoidance frame and as a restriction, participants showed the highest resistance in terms of reactance, message agreement and evaluation of the communicator. The difference in agreement with the change was mediated by reactance only when a restriction was present. Overall, avoidance goal frames were associated with more resistance to change on different levels of experience (reactance, performance, and person perception). Reactance mediated the effect of goal frame on other outcomes only when a restriction was present.
Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several “onium” cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g|| and gK) of the tensors could be determined and information on the structural changes in the [CuBr4]2- anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids.
Compared to their inorganic counterparts, organic semiconductors suffer from relatively low charge carrier mobilities. Therefore, expressions derived for inorganic solar cells to correlate characteristic performance parameters to material properties are prone to fail when applied to organic devices. This is especially true for the classical Shockley-equation commonly used to describe current-voltage (JV)-curves, as it assumes a high electrical conductivity of the charge transporting material. Here, an analytical expression for the JV-curves of organic solar cells is derived based on a previously published analytical model. This expression, bearing a similar functional dependence as the Shockley-equation, delivers a new figure of merit α to express the balance between free charge recombination and extraction in low mobility photoactive materials. This figure of merit is shown to determine critical device parameters such as the apparent series resistance and the fill factor.