Enabling the evolution of J2EE applications through reverse engineering and quality assurance

Enterprise Applications are complex software systems that manipulate much persistent data and interact with the user through a vast and complex user interface. In particular applications written for the Java 2 Platform, Enterprise Edition (J2EE) are composed using various technologies such as Enterprise Java Beans (EJB) or Java Server Pages (JSP) that in turn rely on languages other than Java, such as XML or SQL. In this heterogeneous context applying existing reverse engineering and quality assurance techniques developed for object-oriented systems is not enough. Because those techniques have been created to measure quality or provide information about one aspect of J2EE applications, they cannot properly measure the quality of the entire system. We intend to devise techniques and metrics to measure quality in J2EE applications considering all their aspects and to aid their evolution. Using software visualization we also intend to inspect to structure of J2EE applications and all other aspects that can be investigate through this technique. In order to do that we also need to create a unified meta-model including all elements composing a J2EE application.

Genetic Engineering of Induced Pluripotent Stem Cells and Reprogramming to Motor Neurons to Elucidate Selective Motor Neuron Death in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease, fatal within 1 to 5 years after onset of symptoms. About 3 out of 100’000 persons are diagnosed with ALS and there is still no cure available [1, 2]. 95% of all cases occur sporadically and the aetiology remains largely unknown [XXXX]. However, up to now 16 genes were identified to play a role in the development of familial ALS. One of these genes is FUS that encodes for the protein fused in sarcoma/translocated in liposarcoma (FUS/TLS). Mutations in this gene are responsible for some cases of sporadic as well as of inherited ALS [3]. FUS belongs to the family of heterogeneous nuclear ribonucleoproteins and is predicted to be involved in several cellular functions like transcription regulation [4], RNA splicing [5, 6], mRNA transport in neurons [7] and microRNA processing [8]. Aberrant accumulation of mutated FUS has been found in the cytoplasm of motor neurons from ALS patients [9]. The mislocalization of FUS is based on a mutation in the nuclear localization signal of FUS [10]. However, it is still unclear if the cytoplasmic localization of FUS leads to a toxic gain of cytoplasmic function and/or a loss of nuclear function that might be crucial in the course of ALS. The goal of this project is to characterize the impact of ALS-associated FUS mutations on in vitro differentiated motor neurons. To this end, we edit the genome of induced pluripotent stem cells (iPSC) using transcription activator-like effector nucleases (TALENs) [11,12] to create three isogenic cell lines, each carrying an ALS-associated FUS mutation (G156E, R244C and P525L). These iPSC’s will then be differentiated to motor neurons according to a recently establishe protocol (Ref Wichterle) and serve to study alterations in the transcriptome, proteome and metabolome upon the expression of ALS-associated FUS. With this approach, we hope to unravel the molecular mechanism leading to FUS-associated ALS and to provide new insight into the emerging connection between misregulation of RNA metabolism and neurodegeneration, a connection that is currently implied in a variety of additional neurological diseases, including spinocerebellar ataxia 2 (SCA-2), spinal muscular atrophy (SMA), fragile X syndrome, and myotonic dystrophy.

Genetic Engineering of Induced Pluripotent Stem Cells and Reprogramming to Motor Neurons to Elucidate Selective Motor Neuron Death in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease, fatal within 1 to 5 years after onset of symptoms. About 3 out of 100’000 persons are diagnosed with ALS and there is still no cure available [1, 2]. 95% of all cases occur sporadically and the aetiology remains largely unknown [3]. However, up to now 16 genes were identified to play a role in the development of familial ALS. One of these genes is FUS that encodes for the protein fused in sarcoma (FUS). Mutations in this gene are responsible for some cases of sporadic as well as of inherited ALS [4]. FUS belongs to the family of heterogeneous nuclear ribonucleoproteins and is predicted to be involved in several cellular functions like transcription regulation, RNA splicing, mRNA transport in neurons and microRNA processing [5] Aberrant accumulation of mutated FUS has been found in the cytoplasm of motor neurons from ALS patients [6]. The mislocalization of FUS is based on a mutation in the nuclear localization signal of FUS [7]. However, it is still unclear if the cytoplasmic localization of FUS leads to a toxic gain of cytoplasmic function and/or a loss of nuclear function that might be crucial in the course of ALS. The goal of this project is to characterize the impact of ALS-associated FUS mutations on in vitro differentiated motor neurons. To this end, we edit the genome of induced pluripotent stem cells (iPSC) using transcription activator-like effector nucleases (TALENs) [8,9] to create three isogenic cell lines, each carrying an ALS-associated FUS mutation (G156E, R244C and P525L). These iPSC’s will then be differentiated to motor neurons according to a recently established protocol [10] and serve to study alterations in the transcriptome, proteome and metabolome upon the expression of ALS-associated FUS. With this approach, we hope to unravel the molecular mechanism leading to FUS-associated ALS and to provide new insight into the emerging connection between misregulation of RNA metabolism and neurodegeneration, a connection that is currently implied in a variety of additional neurological diseases, including spinocerebellar ataxia 2 (SCA-2), spinal muscular atrophy (SMA), fragile X syndrome, and myotonic dystrophy. [1] Cleveland, D.W. et al. (2001) Nat Rev Neurosci 2(11): 806-819 [2] Sathasivam, S. (2010) Singapore Med J 51(5): 367-372 [3] Schymick, J.C. et al. (2007) Hum Mol Genet Vol 16: 233-242 [4] Pratt, A.J. et al. (2012). Degener Neurol Neuromuscul Dis 2012(2): 1-14 [5] Lagier-Tourenne, C. Hum Mol Genet, 2010. 19(R1): p. R46-64 [6] Mochizuki, Y. et al. (2012) J Neurol Sci 323(1-2): 85-92 [7] Dormann, D. et al. (2010) EMBO J 29(16): 2841-2857 [8] Hockemeyer, D. et al. (2011) Nat Biotech 29(8): 731-734 [9] Joung, J.K. and J.D. Sander (2013) Nat Rev Mol Cell Biol 14(1): 49-55 [10]Amoroso, M.W. et al. (2013) J Neurosci 33(2): 574-586.

Proceedings of the 13th Annual Biochemical Engineering Symposium

The symposium reported here was the thirteenth of a series devoted to talks by students on their biochemical engineering research. The first, third, fifth, ninth, and twelfth were at Kansas State University, the second and fourth were at the University of Nebraska–Lincoln, the sixth was in Kansas City and was hosted by Iowa State University, the seventh and tenth were at Iowa State, and the eighth and eleventh were at the University of Missouri–Columbia and Colorado State University, respectively. All symposia have been followed by proceedings edited by faculty of the host institution. Because final publication usually takes place elsewhere, papers here are brief, and often cover research in progress. ContentSequential Utilization of Mixed Sugars by Clostridium acetobutylicum, B. Hong, N. H. Choi, and L. T. Fan, Kansas State University The Effects of Dilution Rate on the Kinetics. of Anaerobic Acidogenesis, C. J. Huang, Colorado State University Ethanol Production by Zymomonas mobilis in Anaerobic Glucose-Limited Culture: A Yield Study, Mehmet D. Oner, Kansas State University Hydrolysis of Cellulosics by Enterobacteria, Michael R. Sierks, Iowa State University The Cellulase System of Chaetomium cellulolyticum, Nikhil Mehta, Colorado State University DNA Measurement as a Tool for Estimating Biomass Concentration in the Presence of Interfering Solids, Bamidele 0. Solomon, Kansas State University The Effect of Cellulose Crystallinity on Enzymatic Hydrolysis, Maria S. Bertran, Colorado State University High Performance Liquid Chromatography of Di- and Trisaccharides, Michael M. Meagher, Iowa State University Dynamics of Bubble Size .Distributions in Air-Lift Fermentors, c. H. Lee and Snehal A. Patel, Kansas State University A Thermal Coagulation Study of Alfalfa Leaf Proteins by Differential Scanning Calorimeter, Khalif Ahmed and Bruce Dale, Colorado State University Thermodynamic Efficiency of Photoautotrophic Growth, Hyeon Y. Lee, Kansas State University

The Risk of Using the Q Heterogeneity Estimator for Software Engineering Experiments

All meta-analyses should include a heterogeneity analysis. Even so, it is not easy to decide whether a set of studies are homogeneous or heterogeneous because of the low statistical power of the statistics used (usually the Q test). Objective: Determine a set of rules enabling SE researchers to find out, based on the characteristics of the experiments to be aggregated, whether or not it is feasible to accurately detect heterogeneity. Method: Evaluate the statistical power of heterogeneity detection methods using a Monte Carlo simulation process. Results: The Q test is not powerful when the meta-analysis contains up to a total of about 200 experimental subjects and the effect size difference is less than 1. Conclusions: The Q test cannot be used as a decision-making criterion for meta-analysis in small sample settings like SE. Random effects models should be used instead of fixed effects models. Caution should be exercised when applying Q test-mediated decomposition into subgroups.

Essentials in Ontology Engineering: Methodologies, Languages, and Tools

In the beginning of the 90s, ontology development was similar to an art: ontology developers did not have clear guidelines on how to build ontologies but only some design criteria to be followed. Work on principles, methods and methodologies, together with supporting technologies and languages, made ontology development become an engineering discipline, the so-called Ontology Engineering. Ontology Engineering refers to the set of activities that concern the ontology development process and the ontology life cycle, the methods and methodologies for building ontologies, and the tool suites and languages that support them. Thanks to the work done in the Ontology Engineering field, the development of ontologies within and between teams has increased and improved, as well as the possibility of reusing ontologies in other developments and in final applications. Currently, ontologies are widely used in (a) Knowledge Engineering, Artificial Intelligence and Computer Science, (b) applications related to knowledge management, natural language processing, e-commerce, intelligent information integration, information retrieval, database design and integration, bio-informatics, education, and (c) the Semantic Web, the Semantic Grid, and the Linked Data initiative. In this paper, we provide an overview of Ontology Engineering, mentioning the most outstanding and used methodologies, languages, and tools for building ontologies. In addition, we include some words on how all these elements can be used in the Linked Data initiative.

Integrated learning of computer applications for production engineering

A high productivity rate in Engineering is related to an efficient management of the flow of the large quantities of information and associated decision making activities that are consubstantial to the Engineering processes both in design and production contexts. Dealing with such problems from an integrated point of view and mimicking real scenarios is not given much attention in Engineering degrees. In the context of Engineering Education, there are a number of courses designed for developing specific competencies, as required by the academic curricula, but not that many in which integration competencies are the main target. In this paper, a course devoted to that aim is discussed. The course is taught in a Marine Engineering degree but the philosophy could be used in any Engineering field. All the lessons are given in a computer room in which every student can use each all the treated software applications. The first part of the course is dedicated to Project Management: the students acquire skills in defining, using Ms-PROJECT, the work breakdown structure (WBS), and the organization breakdown structure (OBS) in Engineering projects, through a series of examples of increasing complexity, ending up with the case of vessel construction. The second part of the course is dedicated to the use of a database manager, Ms-ACCESS, for managing production related information. A series of increasing complexity examples is treated ending up with the management of the pipe database of a real vessel. This database consists of a few thousand of pipes, for which a production timing frame is defined, which connects this part of the course with the first one. Finally, the third part of the course is devoted to the work with FORAN, an Engineering Production package of widespread use in the shipbuilding industry. With this package, the frames and plates where all the outfitting will be carried out are defined through cooperative work by the studens, working simultaneously in the same 3D model. In the paper, specific details about the learning process are given. Surveys have been posed to the students in order to get feed-back from their experience as well as to assess their satisfaction with the learning process. Results from these surveys are discussed in the paper

News in engineering education in Spain effective from 2010 in presence of external changes and mixed crisis, looking mostly to agro and civil engineers.

The engineering careers models were diverse in Europe, and are adopting now in Spain the Bolonia process for European Universities. Separated from older Universities, that are in part technically active, Civil Engineering (Caminos, Canales y Puertos) started at end of 18th century in Spain adopting the French models of Upper Schools for state civil servants with exam at entry. After 1800 intense wars, to conserve forest regions Ingenieros de Montes appeared as Upper School, and in 1855 also the Ingenieros Agrónomos to push up related techniques and practices. Other Engineers appeared as Upper Schools but more towards private factories. These ES got all adapted Lower Schools of Ingeniero Tecnico. Recently both grew much in number and evolved, linked also to recognized Professions. Spanish society, into European Community, evolved across year 2000, in part highly well, but with severe discordances, that caused severe youth unemployment with 2008-2011 crisis. With Bolonia process high formal changes step in from 2010-11, accepted with intense adaptation. The Lower Schools are changing towards the Upper Schools, and both that have shifted since 2010-11 various 4-years careers (Grado), some included into the precedent Professions, and diverse Masters. Acceptation of them to get students has started relatively well, and will evolve, and acceptation of new grades for employment in Spain, Europe or outside will be essential. Each Grado has now quite rigid curricula and programs, MOODLE was introduced to connect pupils, some specific uses of Personal Computers are taught in each subject. Escuela de Agronomos centre, reorganized with its old name in its precedent buildings at entrance of Campus Moncloa, offers Grados of Agronomic Engineering and Science for various public and private activities for agriculture, Alimentary Engineering for alimentary activities and control, Agro-Environmental Engineering more related to environment activities, and in part Biotechnology also in laboratories in Campus Monte-Gancedo for Biotechnology of Plants and Computational Biotechnology. Curricula include Basics, Engineering, Practices, Visits, English, ?project of end of career?, Stays. Some masters will conduce to specific professional diploma, list includes now Agro-Engineering, Agro-Forestal Biotechnology, Agro and Natural Resources Economy, Complex Physical Systems, Gardening and Landscaping, Rural Genie, Phytogenetic Resources, Plant Genetic Resources, Environmental Technology for Sustainable Agriculture, Technology for Human Development and Cooperation.

The Threads of Biosystems Engineering

The core concepts, or threads, of Biosystems Engineering (BSEN) are variously understood by those within the discipline, but have never been unequivocally defined due to its early stage of development. This makes communication and teaching difficult compared to other well established engineering subjects. Biosystems Engineering is a field of Engineering which int egrates engineering science and design with applied biological, environmental and agricultural sciences. It represents an evolution of the Agricultural Engineering discipline applied to all living organisms not including biomedical applications. The basic key element for the emerging EU Biosystems Engineering program of studies is to ensure that it offers essential minimum fundamental engine ering knowledge and competences . A core curriculum developed by Erasmus Thematic Networks is used as benchmark for Agr icultural and Biosystems Engineering studies in Europe. The common basis of the core curriculum for the discipline across the Atlantic , including a minimum of competences comprising the Biosystems Engineering core competencies, has been defined by an Atlan tis project , but this needs to be taken further by defining the threads linking courses together. This paper presents a structured approach to define the Threads of BSEN . The definition of the mid-level competences and the associated learning outcomes has been one of the objectives of the Atlantis programme TABE.NET. The mid-level competences and learning outcomes for each of six specializations of BSEN are defined while the domain-specific knowledge to be acquired for each outcome is proposed. Once the proposed definitions are adopted, these threads will be available for global development of the BSEN.

Configuration management and product lines to enhance the replication process in software engineering

This research is concerned with the experimental software engineering area, specifically experiment replication. Replication has traditionally been viewed as a complex task in software engineering. This is possibly due to the present immaturity of the experimental paradigm applied to software development. Researchers usually use replication packages to replicate an experiment. However, replication packages are not the solution to all the information management problems that crop up when successive replications of an experiment accumulate. This research borrows ideas from the software configuration management and software product line paradigms to support the replication process. We believe that configuration management can help to manage and administer information from one replication to another: hypotheses, designs, data analysis, etc. The software product line paradigm can help to organize and manage any changes introduced into the experiment by each replication. We expect the union of the two paradigms in replication to improve the planning, design and execution of further replications and their alignment with existing replications. Additionally, this research work will contribute a web support environment for archiving information related to different experiment replications. Additionally, it will provide flexible enough information management support for running replications with different numbers and types of changes. Finally, it will afford massive storage of data from different replications. Experimenters working collaboratively on the same experiment must all have access to the different experiments.

Survey on integration of Applied Geology and Geomorphology in Civil Engineering curricula in the framework of the European Higher Education Area (EHEA) by using practical trips

The engineer must have sufficient theoretical knowledge to be applied to solve specific problems, with the necessary capacity to simplify these approaches, and taking into account factors such as speed, simplicity, quality and economy. In Geology, its ultimate goal is the exploration of the history of the geological events through observation, deduction, reasoning and, in exceptional cases by the direct underground exploration or experimentation. Experimentation is very limited in Geology. Reproduction laboratory of certain phenomena or geological processes is difficult because both time and space become a large scale. For this reason, some Earth Sciences are in a nearly descriptive stage whereas others closest to the experimental, Geophysics and Geochemistry, have assimilated progress experienced by the physics and chemistry. Thus, Anglo-Saxon countries clearly separate Engineering Geology from Geological Engineering, i.e. Applied Geology to the Geological Engineering concepts. Although there is a big professional overlap, the first one corresponds to scientific approach, while the last one corresponds to a technological one. Applied Geology to Engineering could be defined as the Science and Applied Geology to the design, construction and performance of engineering infrastructures in and field geology discipline. There has been much discussion on the primacy of theory over practice. Today prevails the exaggeration of practice, but you get good workers and routine and mediocre teachers. This idea forgets too that teaching problem is a problem of right balance. The approach of the action lines on the European Higher Education Area (EHEA) framework provides for such balance. Applied Geology subject represents the first real contact with the physical environment with the practice profession and works. Besides, the situation of the topic in the first trace of Study Plans for many students implies the link to other subjects and topics of the career (tunnels, dams, groundwater, roads, etc). This work analyses in depth the justification of such practical trips. It shows the criteria and methods of planning and the result which manifests itself in pupils. Once practical trips experience developed, the objective work tries to know about results and changes on student’s motivation in learning perspective. This is done regardless of the outcome of their knowledge achievements assessed properly and they are not subject to such work. For this objective, it has been designed a survey about their motivation before and after trip. Survey was made by the Unidad Docente de Geología Aplicada of the Departamento de Ingeniería y Morfología del Terreno (Escuela Técnica Superior de Ingenieros de Caminos, Canales y Puertos, Universidad Politécnica de Madrid). It was completely anonymous. Its objective was to collect the opinion of the student as a key agent of learning and teaching of the subject. All the work takes place under new teaching/learning criteria approach at the European framework in Higher Education. The results are exceptionally good with 90% of student’s participation and with very high scores in a number of questions as the itineraries, teachers and visited places (range of 4.5 to 4.2 in a 5 points scale). The majority of students are very satisfied (average of 4.5 in a 5 points scale).

Integration of cooperation for development in Survey Engineering curricula at the European Higher Education Area (EHEA) framework

Survey Engineering curricula involves the integration of many formal disciplines at a high level of proficiency. The Escuela de Ingenieros en Topografía, Cartografía y Geodesia at Universidad Politécnica de Madrid (Survey Engineering) has developed an intense and deep teaching on so-called Applied Land Sciences and Technologies or Land Engineering. However, new approaches are encouraged by the European Higher Education Area (EHEA). This fact requires a review of traditional teaching and methods. Furthermore, the new globalization and international approach gives new ways to this discipline to teach and learn about how to bridge gap between cultures and regions. This work is based in two main needs. On one hand, it is based on integration of basic knowledge and disciplines involved in typical Survey Engineering within Land Management. On the other, there is an urgent need to consider territory on a social and ethical basis, as far as a part of the society, culture, idiosyncrasy or economy. The integration of appropriate knowledge of the Land Management is typically dominated by civil engineers and urban planners. It would be very possible to integrate Survey Engineering and Cooperation for Development in the framework of Land Management disciplines. Cooperation for Development is a concept that has changed since beginning of its use until now. Development projects leave an impact on society in response to their beneficiaries and are directed towards self-sustainability. Furthermore, it is the true bridge to reduce gap between societies when differences are immeasurable. The concept of development has also been changing and nowadays it is not a purely economic concept. Education, science and technology are increasingly taking a larger role in what is meant by development. Moreover, it is commonly accepted that Universities should transfer knowledge to society, and the transfer of knowledge should be open to countries most in need for developing. If the importance of the country development is given by education, science and technology, knowledge transfer would be one of the most clear of ways of Cooperation for Development. Therefore, university cooperation is one of the most powerful tools to achieve it, placing universities as agents of development. In Spain, the role of universities as agents of development and cooperation has been largely strengthened. All about this work deals to how to implement both Cooperation for Development and Land Management within Survey Engineering at the EHEA framework.

Introduction: Ontology Engineering in a Networked World

While ontology engineering is rapidly entering the mainstream, expert ontology engineers are a scarce resource. Hence, there is a need for practical methodologies and technologies, which can assist a variety of user types with ontology development tasks. To address this need, this book presents a scenario-based methodology, the NeOn Methodology, which provides guidance for all main activities in ontology engineering. The context in which we consider these activities is that of a networked world, where reuse of existing resources is commonplace, ontologies are developed collaboratively, and managing relationships between ontologies becomes an essential aspect of the ontological engineering process. The description of both the methodology and the ontology engineering activities is grounded in a comprehensive software environment, the NeOn Toolkit and its plugins, which provides integrated support for all the activities described in the book. Here we provide an introduction for the whole book, while the rest of the content is organized into 4 parts: (1) the NeOn Methodology Framework, (2) the set of ontology engineering activities, (3) the NeOn Toolkit and plugins, and (4) three use cases. Primary goals of this book are (a) to disseminate the results from the NeOn project in a structured and comprehensive form, (b) to make it easier for students and practitioners to adopt ontology engineering methods and tools, and (c) to provide a textbook for undergraduate and postgraduate courses on ontology engineering.