Reconstruction of an in silico metabolic model of _Arabidopsis thaliana_ through database integration

The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.

Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant _Arabidopsis thaliana_, including over 2300 reactions and compounds. Our reconstruction was performed using a semi-automatic methodology based on the integration of two public genome-wide databases, significantly accelerating the process. Database entries were compared and integrated with each other, allowing us to resolve discrepancies and enhance the quality of the reconstruction. This process lead to the construction of three models based on different quality and validation standards, providing users with the possibility to choose the standard that is most appropriate for a given application. First, a _core metabolic model_ containing only consistent data provides a high quality model that was shown to be stoichiometrically consistent. Second, an _intermediate metabolic model_ attempts to fill gaps and provides better continuity. Third, a _complete metabolic model_ contains the full set of known metabolic reactions and compounds in _Arabidopsis thaliana_.

We provide an annotated SBML file of our core model to enable the maximum level of compatibility with existing tools and databases. We eventually discuss a series of principles to raise awareness of the need to develop coordinated efforts and common standards for the reconstruction of genome-scale metabolic models, with the aim of enabling their widespread diffusion, frequent update, maximum compatibility and convenience of use by the wider research community and industry

Standards and practices necessary to implement a successful security review program for intrusion management systems

Thesis (Master)--Izmir Institute of Technology, Computer Engineering, Izmir, 2002Includes bibliographical references (leaves: 84-85)Text in English; Abstract: Turkish and Englishviii, 91 leavesIntrusion Management Systems are being used to prevent the information systems from successful intrusions and their consequences. They also have detection features. They try to detect intrusions, which have passed the implemented measures. Also the recovery of the system after a successful intrusion is made by the Intrusion Management Systems. The investigation of the intrusion is made by Intrusion Management Systems also. These functions can be existent in an intrusion management system model, which has a four layers architecture. The layers of the model are avoidance, assurance, detection and recovery. At the avoidance layer necessary policies, standards and practices are implemented to prevent the information system from successful intrusions. At the avoidance layer, the effectiveness of implemented measures are measured by some test and reviews. At the detection layer the identification of an intrusion or intrusion attempt is made in the real time. The recovery layer is responsible from restoring the information system after a successful intrusion. It has also functions to investigate the intrusion. Intrusion Management Systems are used to protect information and computer assets from intrusions. An organization aiming to protect its assets must use such a system. After the implementation of the system, continuous reviews must be conducted in order to ensure the effectiveness of the measures taken. Such a review can achieve its goal by using principles and standards. In this thesis, the principles necessary to implement a successful review program for Intrusion Management Systems have been developed in the guidance of Generally Accepted System Security Principles (GASSP). These example principles are developed for tools of each Intrusion Management System layer. These tools are firewalls for avoidance layer, vulnerability scanners for assurance layer, intrusion detection systems for detection layer and integrity checkers for recovery layer of Intrusion Management Systems

Software Engineering Methodologies and Life

The paradigms of design patterns and software engineering methodologies are methods that apply to areas outside the software space. As a business owner and student, I implement many software principles daily in both my work and personal life. After experiencing the power of Agile methodologies outside the scope of software engineering, I always think about how I can integrate the computer science skills that I am learning at Columbia in my life. For my study, I seek to learn about other software engineering development processes that can be useful in life. I theorize that if a model such as Agile can provide me with useful tools, then a model that the government and most of the world trusts should have paradigms I can learn with as well. The software model I will study is open source software (OSS). My research examines the lateral software standards of (OSS) and closed source software (CSS). For the scope of this paper, I will focus on research primarily on Linux as the OSS model and Agile as the CSS model. OSS has had an extraordinary impact on the software revolution [1], and CSS models have gained such popularity that its paradigms extend far beyond the software engineering space. Before delving into research, I thought the methodologies of OSS and CSS would be radically different. My study shall describe the similarities that exist between these two methodologies. In the process of my research, I was able to implement the values and paradigms that define the OSS development model to work more productively in my business. Software engineering core values and models can be used as a tool to improve our lives

Navigating The Leading Edge: A Prototype Curriculum for Software Systems Management

This article presents a meaningful and advantageous new direction for information technology education, embodying principles for systematically optimizing the functioning of the business. Our curriculum was built on the thesis that every aspect of software systems management can be understood and described as a component of four universal, highly correlated behaviors: abstraction, product creation, product verification and validation, and process optimization. Given this, our model curriculum was structured to provide the maximum exposure to current best practice in six thematic areas, which taken together as an integrated set, makes-up the attributes that differentiate us from the other computer disciplines: Abstraction: understanding and description of the problem space Design: models for framing artifact to meet criteria 3, 4, 5, and 6 Process Engineering: application of large models such as IEEE 12207 Organizational Control Systems: SQA and configuration management Evaluation with Measurement: with an emphasis on testing and metrics Construction: professional programming languages with emphasis on reusability Our teaching strategy approaches this as a hierarchy of similar activities. In every course we require the student to define and implement all three interfaces and be able to clearly communicate this as a logically consistent model before working out the details of the solution. The focus of all understanding is top-down from the information interface. Our curriculum centers on the application of software engineering standards (such as those promulgated by IEEE) and the software process improvement, or quality standards (such as those promulgated by SEI and ISO) under the assumption that this embodies the common body of knowledge and state of best practice in software production and management. The practical realization of this is an integration of the large subject areas of: software engineering (methods, models and criteria), process and product quality management (software quality assurance and metrics), software project management (work decomposition, planning, sizing and estimating), and software configuration management. Reconciliation of project and configuration management is accomplished by cross-referencing the problems, tools, notations and solutions (through explicit identification, authorization and validation procedures). As a side agenda, we have also stressed the need for re-engineering the vast number of software products currently on the shelves. This model plus germane simulated real-world experience introduces all of the relevant principles to the student within the (currently understood) framework. It allows them to develop and internalize their own comprehensive understanding and formulate a personal model of the disciplinary body of knowledge

Examining perceptions of agility in software development practice

This is the post-print version of the final published article that is available from the link below. Copyright @ 2010 ACM.Organizations undertaking software development are often reminded that successful practice depends on a number of non-technical issues that are managerial, cultural and organizational in nature. These issues cover aspects from appropriate corporate structure, through software process development and standardization to effective collaborative practice. Since the articulation of the 'software crisis' in the late-1960s, significant effort has been put into addressing problems related to the cost, time and quality of software development via the application of systematic processes and management practices for software engineering. Early efforts resulted in prescriptive structured methods, which have evolved and expanded over time to embrace consortia/ company-led initiatives such as the Unified Modeling Language and the Unified Process alongside formal process improvement frameworks such as the International Standards Organization's 9000 series, the Capability Maturity Model and SPICE. More recently, the philosophy behind traditional plan-based initiatives has been questioned by the agile movement, which seeks to emphasize the human and craft aspects of software development over and above the engineering aspects. Agile practice is strongly collaborative in its outlook, favoring individuals and interactions over processes and tools, working software over comprehensive documentation, customer collaboration over contract negotiation, and responding to change over following a plan (see Sidebar 1). Early experience reports on the use of agile practice suggest some success in dealing with the problems of the software crisis, and suggest that plan-based and agile practice are not mutually exclusive. Indeed, flexibility may arise from this unlikely marriage in an aim to strike a balance between the rigor of traditional plan-based approaches and the need for adaptation of those to suit particular development situations. With this in mind, this article surveys the current practice in software engineering alongside perceptions of senior development managers in relation to agile practice in order to understand the principles of agility that may be practiced implicitly and their effects on plan-based approach

An integrated product and process information modelling system for on-site construction

The inadequate infrastructure that exists for seamless project team communications has its roots in the problems arising from fragmentation, and the lack of effective co-ordination between stages of the construction process. The use of disparate computer-aided engineering (CAE) systems by most disciplines is one of the enduring legacies of this problem and makes information exchange between construction team members difficult and, in some cases, impossible. The importance of integrating modelling techniques with a view to creating an integrated product and process model that is applicable to all stages of a construction project's life cycle, is being recognised by the Construction Industry. However, improved methods are still needed to assist the developer in the definition of information model structures, and current modelling methods and standards are only able to provide limited assistance at various stages of the information modelling process. This research investigates the role of system integration by reviewing product and process information models, current modelling practices and modelling standards in the construction industry, and draws conclusions with similar practices from other industries, both in terms of product and process representation, and model content. It further reviews various application development tools and information system requirements to support a suitable integrated information structure, for developing an integrated product and process model for design and construction, based on concurrent engineering principles. The functional and information perspectives of the integrated model, which were represented using IDEFO and the unified modelling language (UML), provided the basis for developing a prototype hyper-integrated product and process information modelling system (HIPPY). Details of the integrated conceptual model's implementation, practical application of the prototype system, using house-building as an example, and evaluation by industry practitioners are also presented. It is concluded that the effective integration of product and process information models is a key component of the implementation of concurrent engineering in construction, and is a vital step towards providing richer information representation, better efficiency, and the flexibility to support life cycle information management during the construction stage of small to medium sized-building projects

Development of a quality assurance prototype for intrusion detection systems

Thesis (Master)-- Izmir Institute of Technology, Computer Engineering, Izmir, 2002Includes bibliographical references (leaves: 75-79)Text in English; Abstract: Turkish and Englishix, 97 leavesQuality assurance is an essential activity for any business interacting with consumers. There are considerable number of projects going on to develop intrusion detection systems (IDSs). However, efforts to establish standards and practices to ensure the quality of such systems are comparatively less significant. The quality assurance activities for IDSs should ensure the conformance of explicitly stated functional and performance requirements as well as implicit characteristics that are expected from information security tools. This dissertation establishes guidelines to review, evaluate and possibly to develop an IDS. To establish guidelines, generic IDS and software requirements, software quality factors and design principles are used which are available in related literature and these requirements are presented both on developed generic IDS model and in Common Criteria Protection Profile format. First, the guidelines are developed, then they are implemented on a specific IDS product evaluation

SYSML4TA: A SysML Profile for Consistent Tolerance Analysis in a Manufacturing System Case Application

Tolerance analysis is a key engineering task that is usually supported by domain-specific analysis models and tools that are generally not connected to the system functionality. The model-based system engineering (MBSE) approach is a potential solution to this limitation, but it has not yet been deeply explored in this type of mechanical analysis, for which some problems need to be explored. One of these issues is the capacity of languages such as SysML to describe solution principles based on active surfaces that participate in functionality and are present for tolerance analysis. Thus, this study explored the possibilities that enable SysML to represent these geometries and their mathematical relationships based on Topologically and Technologically Related Surfaces (TTRS) theory and aligned with Geometric Dimensioning and Tolerancing (GD&T) standards. Additionally, the capacity of SysML to assure the consistency of tolerance analysis models is also explored, due to the limitations identified in analysis languages like Modelica. In this context, this paper presents a SysML profile for tolerance analysis modeling (SysML4TA), containing domain-specific semantics (concepts and constraints) to assure the completeness of the analysis models and consistency between the different models considered in the integrated model of the system. Finally, a case study applied to a manufacturing context is presented to validate the capacity of SysML to solve the identified problems.La herencia reconstruida. Crecimiento agrario y transformaciones del paisaje tras las conquistas de al-Andalus (siglos XII-XV

A quality management based on the Quality Model life cycle

Managing quality is a hard and expensive task that involves the execution and control of processes and techniques. For a good quality management, it is important to know the current state and the objective to be achieved. It is essential to take into account with a Quality Model that specifies the purposes of managing quality. QuEF (Quality Evaluation Framework) is a framework to manage quality in MDWE (Model-driven Web Engineering). This paper suggests managing quality but pointing out the Quality Model life cycle. The purpose is to converge toward a quality continuous improvement by means of reducing effort and time.Ministerio de Ciencia e Innovación TIN2010-20057-C03-02Ministerio de Ciencia e Innovación TIN 2010-12312-EJunta de Andalucía TIC-578

Standardization Framework for Sustainability from Circular Economy 4.0

The circular economy (CE) is widely known as a way to implement and achieve sustainability, mainly due to its contribution towards the separation of biological and technical nutrients under cyclic industrial metabolism. The incorporation of the principles of the CE in the links of the value chain of the various sectors of the economy strives to ensure circularity, safety, and efficiency. The framework proposed is aligned with the goals of the 2030 Agenda for Sustainable Development regarding the orientation towards the mitigation and regeneration of the metabolic rift by considering a double perspective. Firstly, it strives to conceptualize the CE as a paradigm of sustainability. Its principles are established, and its techniques and tools are organized into two frameworks oriented towards causes (cradle to cradle) and effects (life cycle assessment), and these are structured under the three pillars of sustainability, for their projection within the proposed framework. Secondly, a framework is established to facilitate the implementation of the CE with the use of standards, which constitute the requirements, tools, and indicators to control each life cycle phase, and of key enabling technologies (KETs) that add circular value 4.0 to the socio-ecological transition