Integrated Suite Of Tools Research Articles

Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints

The powerful CRISPR genome editing system is hindered by its off-target effects, and existing computational tools achieved limited performance in genome-wide off-target prediction due to the lack of deep understanding of the CRISPR molecular mechanism. In this study, we propose to incorporate molecular dynamics (MD) simulations in the computational analysis of CRISPR system, and present CRISOT, an integrated tool suite containing four related modules, i.e., CRISOT-FP, CRISOT-Score, CRISOT-Spec, CRISORT-Opti for RNA-DNA molecular interaction fingerprint generation, genome-wide CRISPR off-target prediction, sgRNA specificity evaluation and sgRNA optimization of Cas9 system respectively. Our comprehensive computational and experimental tests reveal that CRISOT outperforms existing tools with extensive in silico validations and proof-of-concept experimental validations. In addition, CRISOT shows potential in accurately predicting off-target effects of the base editors and prime editors, indicating that the derived RNA-DNA molecular interaction fingerprint captures the underlying mechanisms of RNA-DNA interaction among distinct CRISPR systems. Collectively, CRISOT provides an efficient and generalizable framework for genome-wide CRISPR off-target prediction, evaluation and sgRNA optimization for improved targeting specificity in CRISPR genome editing.

Expected Credit Loss Modeling from a Top-Down Stress Testing Perspective

The objective of this paper is to present an integrated tool suite for IFRS 9- and CECL-compatible estimation in top-down solvency stress tests. The tool suite serves as an illustration for institutions wishing to include accounting-based approaches for credit risk modeling in top-down stress tests.

Expected Credit Loss Modeling from a Top-Down Stress Testing Perspective

The objective of this paper is to present an integrated tool suite for IFRS 9- and CECL-compatible estimation in top-down solvency stress tests. The tool suite serves as an illustration for institutions wishing to include accounting-based approaches for credit risk modeling in top-down stress tests.

Formalizing and appling compliance patterns for business process compliance

Today's enterprises demand a high degree of compliance of business processes to meet diverse regulations and legislations. Several industrial studies have shown that compliance management is a daunting task, and organizations are still struggling and spending billions of dollars annually to ensure and prove their compliance. In this paper, we introduce a comprehensive compliance management framework with a main focus on design-time compliance management as a first step towards a preventive lifetime compliance support. The framework enables the automation of compliance-related activities that are amenable to automation, and therefore can significantly reduce the expenditures spent on compliance. It can help experts to carry out their work more efficiently, cut the time spent on tedious manual activities, and reduce potential human errors. An evident candidate compliance activity for automation is the compliance checking, which can be achieved by utilizing formal reasoning and verification techniques. However, formal languages are well known of their complexity as only versed users in mathematical theories and formal logics are able to use and understand them. However, this is generally not the case with business and compliance practitioners. Therefore, in the heart of the compliance management framework, we introduce the Compliance Request Language (CRL), which is formally grounded on temporal logic and enables the abstract pattern-based specification of compliance requirements. CRL constitutes a series of compliance patterns that spans three structural facets of business processes; control flow, employed resources and temporal perspectives. Furthermore, CRL supports the specification of compensations and non-monotonic requirements, which permit the relaxation of some compliance requirements to handle exceptional situations. An integrated tool suite has been developed as an instantiation artefact, and the validation of the approach is undertaken in several directions, which includes internal validity, controlled experiments, and functional testing.

RCOS: a formal model-driven engineering method for component-based software

Model-driven architecture (MDA) has become a main stream technology for software-intensive system design. The main engineering principle behind it is that the inherent complexity of software development can only be mastered by building, analyzing and manipulating system models. MDA also deals with system complexity by providing component-based design techniques, allowing independent component design, implementation and deployment, and then system integration and reconfiguration based on component interfaces. The model of a system in any stage is an integration of models of different viewpoints. Therefore, for a model-driven method to be applied effectively, it must provide a body of techniques and an integrated suite of tools for model construction, validation, and transformation. This requires a number of modeling notations for the specification of different concerns and viewpoints of the system. These notations should have formally defined syntaxes and a unified theory of semantics. The underlying theory of the method is needed to underpin the development of tools and correct use of tools in software development, as well as to formally verify and reason about properties of systems in mission-critical applications. The modeling notations, techniques, and tools must be designed so that they can be used seamlessly in supporting development activities and documentation of artifacts in software design processes. This article presents such a method, called the rCOS, focusing on the models of a system at different stages in a software development process, their semantic integration, and how they are constructed, analyzed, transformed, validated, and verified.

The Chamois Reconfigurable Data-Mining Architecture.

The process of knowledge discovery in data (KDD) stored in computers in general requires iterations of three stages: data preparation, data mining, and results analysis. A variety of software tools are available for each of the stages. KDD environments, objectives of KDD, and types of data to be mined affect the choice of software tools in each stage. This article proposes a component-based architecture for an “end-to-end” integrated suite of KDD software tools that supports the entire KDD process. The architecture allows the configuring of an integrated tool suite with software tools appropriate for a given KDD environment and a given set of KDD objectives. The architecture is a part of the Chamois component-based knowledge-engineering framework under development at Ewha Women’s University in Korea.

TOOLS INTEGRATION INTEREST GROUP REPORT: SCENARIOS FOR A CONCEPT OF OPERATIONS FOR AN INTEGRATED SYSTEMS ENGINEERING ENVIRONMENT, Part II

ABSTRACTThe Tools Integration and Interoperability Working Group (TIWG) is developing a Concept of Operations and a Specification for an Integrated Systems Engineering Environment (ISEE). Last year's TIWG Report (Reference 1) focused on the development of an initial set of scenarios leading toward the development of the full Concepts of Operations. This paper collects the next set of three scenarios which have been developed. The scenarios presented address: (1) the process of defining an organizational systems engineering process; (2) the set of processes associated with administration of an ISEE as part of an organization's information infrastructure; and (3) the process of assessing an organization's systems engineering capability. Based on these process oriented scenarios, we discuss the requirements which an integrated tool suite will have to meet to provide user's with the desired capabilities. The discussion also addresses the technological needs and feasibility of developing an ISEE.