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Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database
Manufacturing industries are undergoing a major paradigm shift towards more autonomy. Automated planning and scheduling then becomes a necessity. The Planning and Execution Competition for Logistics Robots in Simulation held at ICAPS is based on this scenario and provides an interesting testbed. However, the posed problem is challenging as also demonstrated by the somewhat weak results in 2017. The domain requires temporal reasoning and dealing with uncertainty. We propose a novel planning system based on Answer Set Programming and the Clingo solver to tackle these problems and incentivize robot cooperation. Our results show a significant performance improvement, both, in terms of lowering computational requirements and better game metrics.
With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment.
Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview.
Non-stationarities are ubiquitous in EEG signals. They are especially apparent in the use of EEG-based brain- computer interfaces (BCIs): (a) in the differences between the initial calibration measurement and the online operation of a BCI, or (b) caused by changes in the subject's brain processes during an experiment (e.g. due to fatigue, change of task involvement, etc). In this paper, we quantify for the first time such systematic evidence of statistical differences in data recorded during offline and online sessions. Furthermore, we propose novel techniques of investigating and visualizing data distributions, which are particularly useful for the analysis of (non-) stationarities. Our study shows that the brain signals used for control can change substantially from the offline calibration sessions to online control, and also within a single session. In addition to this general characterization of the signals, we propose several adaptive classification schemes and study their performance on data recorded during online experiments. An encouraging result of our study is that surprisingly simple adaptive methods in combination with an offline feature selection scheme can significantly increase BCI performance
Testability evaluation of sequential designs incorporating the multi-mode scannable memory element
(1999)
We construct a new RC phase shift network based Chua's circuit, which exhibits a period-doubling bifurcation route to chaos. Using coupled versions of such a phase-shift network based Chua's oscillators, we describe a new method for achieving complete synchronization (CS), approximate lag synchronization (LS), and approximate anticipating synchronization (AS) without delay or parameter mismatch. Employing the Pecora and Carroll approach, chaos synchronization is achieved in coupled chaotic oscillators, where the drive system variables control the response system. As a result, AS or LS or CS is demonstrated without using a variable delay line both experimentally and numerically.
The notion of coherence relations is quite widely accepted in general, but concrete proposals differ considerably on the questions of how they should be motivated, which relations are to be assumed, and how they should be defined. This paper takes a "bottom-up" perspective by assessing the contribution made by linguistic signals (connectives), using insights from the relevant literature as well as verification by practical text annotation. We work primarily with the German language here and focus on the realm of contrast. Thus, we suggest a new inventory of contrastive connective functions and discuss their relationship to contrastive coherence relations that have been proposed in earlier work.
Programmers make many changes to the program to eventually find a good solution for a given task. In this course of change, every intermediate development state can of value, when, for example, a promising ideas suddenly turn out inappropriate or the interplay of objects turns out more complex than initially expected before making changes. Programmers would benefit from tool support that provides immediate access to source code and run-time of previous development states of interest. We present IDE extensions, implemented for Squeak/Smalltalk, to preserve, retrieve, and work with this information. With such tool support, programmers can work without worries because they can rely on tools that help them with whatever their explorations will reveal. They no longer have to follow certain best practices only to avoid undesired consequences of changing code.
The use of neural networks is considered as the state of the art in the field of image classification. A large number of different networks are available for this purpose, which, appropriately trained, permit a high level of classification accuracy. Typically, these networks are applied to uncompressed image data, since a corresponding training was also carried out using image data of similar high quality. However, if image data contains image errors, the classification accuracy deteriorates drastically. This applies in particular to coding artifacts which occur due to image and video compression. Typical application scenarios for video compression are narrowband transmission channels for which video coding is required but a subsequent classification is to be carried out on the receiver side. In this paper we present a special H.264/Advanced Video Codec (AVC) based video codec that allows certain regions of a picture to be coded with near constant picture quality in order to allow a reliable classification using neural networks, whereas the remaining image will be coded using constant bit rate. We have combined this feature with the ability to run with lowest latency properties, which is usually also required in remote control applications scenarios. The codec has been implemented as a fully hardwired High Definition video capable hardware architecture which is suitable for Field Programmable Gate Arrays.
Background: The biological interpretation of large-scale gene expression data is one of the paramount challenges in current bioinformatics. In particular, placing the results in the context of other available functional genomics data, such as existing bio-ontologies, has already provided substantial improvement for detecting and categorizing genes of interest. One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group. Results: In this work, we suggest the information-theoretic concept of mutual information to investigate the relationship between groups of genes, as given by data-driven clustering, and their respective functional categories. Drawing upon related approaches (Gibbons and Roth, Genome Research 12: 1574-1581, 2002), we seek to quantify to what extent individual attributes are sufficient to characterize a given group or cluster of genes. Conclusion: We show that the mutual information provides a systematic framework to assess the relationship between groups or clusters of genes and their functional annotations in a quantitative way. Within this framework, the mutual information allows us to address and incorporate several important issues, such as the interdependence of functional annotations and combinatorial combinations of attributes. It thus supplements and extends the conventional search for overrepresented attributes within a group or cluster of genes. In particular taking combinations of attributes into account, the mutual information opens the way to uncover specific functional descriptions of a group of genes or clustering result. All datasets and functional annotations used in this study are publicly available. All scripts used in the analysis are provided as additional files.
And/Or reasoning graphs for determining prime implicants in multi-level combinational networks
(1997)
PLATON
(2019)
Lesson planning is both an important and demanding task—especially as part of teacher training. This paper presents the requirements for a lesson planning system and evaluates existing systems regarding these requirements. One major drawback of existing software tools is that most are limited to a text- or form-based representation of the lesson designs. In this article, a new approach with a graphical, time-based representation with (automatic) analyses methods is proposed and the system architecture and domain model are described in detail. The approach is implemented in an interactive, web-based prototype called PLATON, which additionally supports the management of lessons in units as well as the modelling of teacher and student-generated resources. The prototype was evaluated in a study with 61 prospective teachers (bachelor’s and master’s preservice teachers as well as teacher trainees in post-university teacher training) in Berlin, Germany, with a focus on usability. The results show that this approach proofed usable for lesson planning and offers positive effects for the perception of time and self-reflection.
A well-known result by Stein (1956) shows that in particular situations, biased estimators can yield better parameter estimates than their generally preferred unbiased counterparts. This letter follows the same spirit, as we will stabilize the unbiased generalization error estimates by regularization and finally obtain more robust model selection criteria for learning. We trade a small bias against a larger variance reduction, which has the beneficial effect of being more precise on a single training set. We focus on the subspace information criterion (SIC), which is an unbiased estimator of the expected generalization error measured by the reproducing kernel Hilbert space norm. SIC can be applied to the kernel regression, and it was shown in earlier experiments that a small regularization of SIC has a stabilization effect. However, it remained open how to appropriately determine the degree of regularization in SIC. In this article, we derive an unbiased estimator of the expected squared error, between SIC and the expected generalization error and propose determining the degree of regularization of SIC such that the estimator of the expected squared error is minimized. Computer simulations with artificial and real data sets illustrate that the proposed method works effectively for improving the precision of SIC, especially in the high-noise-level cases. We furthermore compare the proposed method to the original SIC, the cross-validation, and an empirical Bayesian method in ridge parameter selection, with good results
In recent years, many efforts have been made to apply image processing techniques for plant leaf identification. However, categorizing leaf images at the cultivar/variety level, because of the very low inter-class variability, is still a challenging task. In this research, we propose an automatic discriminative method based on convolutional neural networks (CNNs) for classifying 12 different cultivars of common beans that belong to three various species. We show that employing advanced loss functions, such as Additive Angular Margin Loss and Large Margin Cosine Loss, instead of the standard softmax loss function for the classification can yield better discrimination between classes and thereby mitigate the problem of low inter-class variability. The method was evaluated by classifying species (level I), cultivars from the same species (level II), and cultivars from different species (level III), based on images from the leaf foreside and backside. The results indicate that the performance of the classification algorithm on the leaf backside image dataset is superior. The maximum mean classification accuracies of 95.86, 91.37 and 86.87% were obtained at the levels I, II and III, respectively. The proposed method outperforms the previous relevant works and provides a reliable approach for plant cultivars identification.
Geocoder accuracy ranking
(2014)
Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address.
One of the goals of artificial intelligence is to develop agents that learn and act in complex environments. Realistic environments typically feature a variable number of objects, relations amongst them, and non-deterministic transition behavior. While standard probabilistic sequence models provide efficient inference and learning techniques for sequential data, they typically cannot fully capture the relational complexity. On the other hand, statistical relational learning techniques are often too inefficient to cope with complex sequential data. In this paper, we introduce a simple model that occupies an intermediate position in this expressiveness/efficiency trade-off. It is based on CP-logic (Causal Probabilistic Logic), an expressive probabilistic logic for modeling causality. However, by specializing CP-logic to represent a probability distribution over sequences of relational state descriptions and employing a Markov assumption, inference and learning become more tractable and effective. Specifically, we show how to solve part of the inference and learning problems directly at the first-order level, while transforming the remaining part into the problem of computing all satisfying assignments for a Boolean formula in a binary decision diagram. We experimentally validate that the resulting technique is able to handle probabilistic relational domains with a substantial number of objects and relations.
The usage of mobile devices is rapidly growing with Android being the most prevalent mobile operating system. Thanks to the vast variety of mobile applications, users are preferring smartphones over desktops for day to day tasks like Internet surfing. Consequently, smartphones store a plenitude of sensitive data. This data together with the high values of smartphones make them an attractive target for device/data theft (thieves/malicious applications).
Unfortunately, state-of-the-art anti-theft solutions do not work if they do not have an active network connection, e.g., if the SIM card was removed from the device. In the majority of these cases, device owners permanently lose their smartphone together with their personal data, which is even worse.
Apart from that malevolent applications perform malicious activities to steal sensitive information from smartphones. Recent research considered static program analysis to detect dangerous data leaks. These analyses work well for data leaks due to inter-component communication, but suffer from shortcomings for inter-app communication with respect to precision, soundness, and scalability.
This thesis focuses on enhancing users' privacy on Android against physical device loss/theft and (un)intentional data leaks. It presents three novel frameworks: (1) ThiefTrap, an anti-theft framework for Android, (2) IIFA, a modular inter-app intent information flow analysis of Android applications, and (3) PIAnalyzer, a precise approach for PendingIntent vulnerability analysis.
ThiefTrap is based on a novel concept of an anti-theft honeypot account that protects the owner's data while preventing a thief from resetting the device.
We implemented the proposed scheme and evaluated it through an empirical user study with 35 participants. In this study, the owner's data could be protected, recovered, and anti-theft functionality could be performed unnoticed from the thief in all cases.
IIFA proposes a novel approach for Android's inter-component/inter-app communication (ICC/IAC) analysis. Our main contribution is the first fully automatic, sound, and precise ICC/IAC information flow analysis that is scalable for realistic apps due to modularity, avoiding combinatorial explosion: Our approach determines communicating apps using short summaries rather than inlining intent calls between components and apps, which requires simultaneously analyzing all apps installed on a device.
We evaluate IIFA in terms of precision, recall, and demonstrate its scalability to a large corpus of real-world apps. IIFA reports 62 problematic ICC-/IAC-related information flows via two or more apps/components.
PIAnalyzer proposes a novel approach to analyze PendingIntent related vulnerabilities. PendingIntents are a powerful and universal feature of Android for inter-component communication. We empirically evaluate PIAnalyzer on a set of 1000 randomly selected applications and find 1358 insecure usages of PendingIntents, including 70 severe vulnerabilities.
Many Android applications embed webpages via WebView components and execute JavaScript code within Android. Hybrid applications leverage dedicated APIs to load a resource and render it in a WebView. Furthermore, Android objects can be shared with the JavaScript world. However, bridging the interfaces of the Android and JavaScript world might also incur severe security threats: Potentially untrusted webpages and their JavaScript might interfere with the Android environment and its access to native features.
No general analysis is currently available to assess the implications of such hybrid apps bridging the two worlds. To understand the semantics and effects of hybrid apps, we perform a large-scale study on the usage of the hybridization APIs in the wild. We analyze and categorize the parameters to hybridization APIs for 7,500 randomly selected and the 196 most popular applications from the Google Playstore as well as 1000 malware samples. Our results advance the general understanding of hybrid applications, as well as implications for potential program analyses, and the current security situation: We discovered thousands of flows of sensitive data from Android to JavaScript, the vast majority of which could flow to potentially untrustworthy code. Our analysis identified numerous web pages embedding vulnerabilities, which we exemplarily exploited. Additionally, we discovered a multitude of applications in which potentially untrusted JavaScript code may interfere with (trusted) Android objects, both in benign and malign applications.
Answer set planning
(2022)
Answer Set Planning refers to the use of Answer Set Programming (ASP) to compute plans, that is, solutions to planning problems, that transform a given state of the world to another state. The development of efficient and scalable answer set solvers has provided a significant boost to the development of ASP-based planning systems. This paper surveys the progress made during the last two and a half decades in the area of answer set planning, from its foundations to its use in challenging planning domains. The survey explores the advantages and disadvantages of answer set planning. It also discusses typical applications of answer set planning and presents a set of challenges for future research.
The submission and management of computational jobs is a traditional part of utility computing environments. End users and developers of domain-specific software abstractions often have to deal with the heterogeneity of such batch processing systems. This lead to a number of application programming interface and job description standards in the past, which are implemented and established for cluster and Grid systems. With the recent rise of cloud computing as new utility computing paradigm, the standardized access to batch processing facilities operated on cloud resources becomes an important issue. Furthermore, the design of such a standard has to consider a tradeoff between feature completeness and the achievable level of interoperability. The article discusses this general challenge, and presents some existing standards with traditional cluster and Grid computing background that may be applicable to cloud environments. We present OCCI-DRMAA as one approach for standardized access to batch processing facilities hosted in a cloud.
Monitoring virtual team collaboration : methods, applications and experiences in engineering design
(2010)
Computational analysis of virtual team collaboration in teh early stages of engineering design
(2010)
The concept of Linked Data has made its entrance in the cultural heritage sector due to its potential use for the integration of heterogeneous collections and deriving additional value out of existing metadata. However, practitioners and researchers alike need a better understanding of what outcome they can reasonably expect of the reconciliation process between their local metadata and established controlled vocabularies which are already a part of the Linked Data cloud. This paper offers an in-depth analysis of how a locally developed vocabulary can be successfully reconciled with the Library of Congress Subject Headings (LCSH) and the Arts and Architecture Thesaurus (AAT) through the help of a general-purpose tool for interactive data transformation (OpenRefine). Issues negatively affecting the reconciliation process are identified and solutions are proposed in order to derive maximum value from existing metadata and controlled vocabularies in an automated manner.
Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge network and the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in silico numerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A-B. (C) 2014 Elsevier B.V. All rights reserved.
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.
In recent years, named entity linking (NEL) tools were primarily developed in terms of a general approach, whereas today numerous tools are focusing on specific domains such as e.g. the mapping of persons and organizations only, or the annotation of locations or events in microposts. However, the available benchmark datasets necessary for the evaluation of NEL tools do not reflect this focalizing trend. We have analyzed the evaluation process applied in the NEL benchmarking framework GERBIL [in: Proceedings of the 24th International Conference on World Wide Web (WWW’15), International World Wide Web Conferences Steering Committee, Republic and Canton of Geneva, Switzerland, 2015, pp. 1133–1143, Semantic Web 9(5) (2018), 605–625] and all its benchmark datasets. Based on these insights we have extended the GERBIL framework to enable a more fine grained evaluation and in depth analysis of the available benchmark datasets with respect to different emphases. This paper presents the implementation of an adaptive filter for arbitrary entities and customized benchmark creation as well as the automated determination of typical NEL benchmark dataset properties, such as the extent of content-related ambiguity and diversity. These properties are integrated on different levels, which also enables to tailor customized new datasets out of the existing ones by remixing documents based on desired emphases. Besides a new system library to enrich provided NIF [in: International Semantic Web Conference (ISWC’13), Lecture Notes in Computer Science, Vol. 8219, Springer, Berlin, Heidelberg, 2013, pp. 98–113] datasets with statistical information, best practices for dataset remixing are presented, and an in depth analysis of the performance of entity linking systems on special focus datasets is presented.
Formalizing informal logic
(2015)
In this paper we investigate the extent to which formal argumentation models can handle ten basic characteristics of informal logic identified in the informal logic literature. By showing how almost all of these characteristics can be successfully modelled formally, we claim that good progress can be made toward the project of formalizing informal logic. Of the formal argumentation models available, we chose the Carneades Argumentation System (CAS), a formal, computational model of argument that uses argument graphs as its basis, structures of a kind very familiar to practitioners of informal logic through their use of argument diagrams.
Engineering of process-driven business applications can be supported by process modeling efforts in order to bridge the gap between business requirements and system specifications. However, diverging purposes of business process modeling initiatives have led to significant problems in aligning related models at different abstract levels and different perspectives. Checking the consistency of such corresponding models is a major challenge for process modeling theory and practice. In this paper, we take the inappropriateness of existing strict notions of behavioral equivalence as a starting point. Our contribution is a concept called behavioral profile that captures the essential behavioral constraints of a process model. We show that these profiles can be computed efficiently, i.e., in cubic time for sound free-choice Petri nets w.r.t. their number of places and transitions. We use behavioral profiles for the definition of a formal notion of consistency which is less sensitive to model projections than common criteria of behavioral equivalence and allows for quantifying deviation in a metric way. The derivation of behavioral profiles and the calculation of a degree of consistency have been implemented to demonstrate the applicability of our approach. We also report the findings from checking consistency between partially overlapping models of the SAP reference model.
In object-oriented programming, polymorphic dispatch of operations decouples clients from specific providers of services and allows implementations to be modified or substituted without affecting clients.
The Uniform Access Principle (UAP) tries to extend these qualities to resource access by demanding that access to state be indistinguishable from access to operations. Despite language features supporting the UAP, the overall goal of substitutability has not been achieved for either alternative resources such as keyed storage, files or web pages, or for alternate access mechanisms: specific kinds of resources are bound to specific access mechanisms and vice versa. Changing storage or access patterns either requires changes to both clients and service providers and trying to maintain the UAP imposes significant penalties in terms of code-duplication and/or performance overhead.
We propose introducing first class identifiers as polymorphic names for storage locations to solve these problems. With these Polymorphic Identifiers, we show that we can provide uniform access to a wide variety of resource types as well as storage and access mechanisms, whether parametrized or direct, without affecting client code, without causing code duplication or significant performance penalties.
With the success of wireless technologies in consumer electronics, standard wireless technologies are envisioned for the deployment in industrial environments as well. Industrial applications involving mobile subsystems or just the desire to save cabling make wireless technologies attractive. Nevertheless, these applications often have stringent requirements on reliability and timing. In wired environments, timing and reliability are well catered for by fieldbus systems (which are a mature technology designed to enable communication between digital controllers and the sensors and actuators interfacing to a physical process). When wireless links are included, reliability and timing requirements are significantly more difficult to meet, due to the adverse properties of the radio channels. In this paper we thus discuss some key issues coming up in wireless fieldbus and wireless industrial communication systems:1)fundamental problems like achieving timely and reliable transmission despite channel errors; 2) the usage of existing wireless technologies for this specific field of applications; and 3) the creation of hybrid systems in which wireless stations are included into existing wired systems
Independent component analysis of noninvasively recorded cortical magnetic DC-fields in humans
(2000)
Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.
Students beginning their studies at university face manifold problems such as orientation in a new environment and organizing their courses. This article presents the implementation and successful empirical evaluation of the pervasive browser-based educational game "FreshUP", which aims at helping to overcome the initial difficulties of freshmen. In contrast to a conventional scavenger hunt, mobile pervasive games like FreshUP, bridging in-game and real world activities, have the potential to provide help in a motivating manner using new technology which is currently becoming more and more common. (C) 2013 Elsevier B.V. All rights reserved.
We propose two methods that reduce the post-nonlinear blind source separation problem (PNL-BSS) to a linear BSS problem. The first method is based on the concept of maximal correlation: we apply the alternating conditional expectation (ACE) algorithm-a powerful technique from nonparametric statistics-to approximately invert the componentwise nonlinear functions. The second method is a Gaussianizing transformation, which is motivated by the fact that linearly mixed signals before nonlinear transformation are approximately Gaussian distributed. This heuristic, but simple and efficient procedure works as good as the ACE method. Using the framework provided by ACE, convergence can be proven. The optimal transformations obtained by ACE coincide with the sought-after inverse functions of the nonlinearitics. After equalizing the nonlinearities, temporal decorrelation separation (TDSEP) allows us to recover the source signals. Numerical simulations testing "ACE-TD" and "Gauss-TD" on realistic examples are performed with excellent results
This book presents an agile and model-driven approach to manage scientific workflows. The approach is based on the Extreme Model Driven Design (XMDD) paradigm and aims at simplifying and automating the complex data analysis processes carried out by scientists in their day-to-day work. Besides documenting the impact the workflow modeling might have on the work of natural scientists, this book serves three major purposes: 1. It acts as a primer for practitioners who are interested to learn how to think in terms of services and workflows when facing domain-specific scientific processes. 2. It provides interesting material for readers already familiar with this kind of tools, because it introduces systematically both the technologies used in each case study and the basic concepts behind them. 3. As the addressed thematic field becomes increasingly relevant for lectures in both computer science and experimental sciences, it also provides helpful material for teachers that plan similar courses.