TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure

Executable system architecting using systems modeling language in conjunction with Colored Petri Nets - a demonstration using the GEOSS network centric system

Models and simulation furnish abstractions to manage complexities allowing engineers to visualize the proposed system and to analyze and validate system behavior before constructing it. Unified Modeling Language (UML) and its systems engineering extension, Systems Modeling Language (SysML), provide a rich set of diagrams for systems specification. However, the lack of executable semantics of such notations limits the capability of analyzing and verifying defined specifications. This research has developed an executable system architecting framework based on SysML-CPN transformation, which introduces dynamic model analysis into SysML modeling by mapping SysML notations to Colored Petri Net (CPN), a graphical language for system design, specification, simulation, and verification. A graphic user interface was also integrated into the CPN model to enhance the model-based simulation. A set of methodologies has been developed to achieve this framework. The aim is to investigate system wide properties of the proposed system, which in turn provides a basis for system reconfiguration --Abstract, page iii

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Toward a conceptual framework for designing sustainable cyber-physical system architectures: A systematic mapping study

Cyber-physical systems (CPS) represent devices whose components enable interaction between machines and processes. One of the biggest challenges of these systems today is the ability to adjust to changes at the time of execution as they are implemented in environments with a multidimensional complexity, this challenge is currently addressed from the design of the systems themselves by integrating sustainability. With this problem in mind, the present document describes a systematic mapping study of the literature with the goal of demonstrating the current panorama of the frameworks, designs, and/or models used at the time of initiating the development of a cyber-physical system. As a result, it has been concluded that there is a lack of guidelines to construct sustainable, and evolvable cyber-physical systems. To address these issues, a framework for designing sustainable CPS architectures is outlined

Integrated testing and verification system for research flight software design document

The NASA Langley Research Center is developing the MUST (Multipurpose User-oriented Software Technology) program to cut the cost of producing research flight software through a system of software support tools. The HAL/S language is the primary subject of the design. Boeing Computer Services Company (BCS) has designed an integrated verification and testing capability as part of MUST. Documentation, verification and test options are provided with special attention on real time, multiprocessing issues. The needs of the entire software production cycle have been considered, with effective management and reduced lifecycle costs as foremost goals. Capabilities have been included in the design for static detection of data flow anomalies involving communicating concurrent processes. Some types of ill formed process synchronization and deadlock also are detected statically

User driven modelling: Visualisation and systematic interaction for end-user programming with tree-based structures

This thesis addresses certain problems encountered by teams of engineers when modelling complex structures and processes subject to cost and other resource constraints. The cost of a structure or process may be ‘read off’ its specifying model, but the language in which the model is expressed (e.g. CAD) and the language in which resources may be modelled (e.g. spreadsheets) are not naturally compatible. This thesis demonstrates that a number of intermediate steps may be introduced which enable both meaningful translation from one conceptual view to another as well as meaningful collaboration between team members. The work adopts a diagrammatic modelling approach as a natural one in an engineering context when seeking to establish a shared understanding of problems.Thus, the research question to be answered in this thesis is: ‘To what extent is it possible to improve user-driven software development through interaction with diagrams and without requiring users to learn particular computer languages?’ The goal of the research is to improve collaborative software development through interaction with diagrams, thereby minimising the need for end-users to code directly. To achieve this aim a combination of the paradigms of End-User Programming, Process and Product Modelling and Decision Support, and Semantic Web are exploited and a methodology of User Driven Modelling and Programming (UDM/P) is developed, implemented, and tested as a means of demonstrating the efficacy of diagrammatic modelling.In greater detail, the research seeks to show that diagrammatic modelling eases problems of maintenance, extensibility, ease of use, and sharing of information. The methodology presented here to achieve this involves a three step translation from a visualised ontology, through a modelling tool, to output to interactive visualisations. An analysis of users groups them into categories of system creator, model builder, and model user. This categorisation corresponds well with the three-step translation process where users develop the ontology, modelling tool, and visualisations for their problem.This research establishes and exemplifies a novel paradigm of collaborative end-user programming by domain experts. The end-user programmers can use a visual interface where the visualisation of the software exactly matches the structure of the software itself, making translation between user and computer, and vice versa, much more direct and practical. The visualisation is based on an ontology that provides a representation of the software as a tree. The solution is based on translation from a source tree to a result tree, and visualisation of both. The result tree shows a structured representation of the model with a full visualisation of all parts that leads to the computed result.In conclusion, it is claimed that this direct representation of the structure enables an understanding of the program as an ontology and model that is then visualised, resulting in a more transparent shared understanding by all users. It is further argued that our diagrammatic modelling paradigm consequently eases problems of maintenance, extensibility, ease of use, and sharing of information. This method is applicable to any problem that lends itself to representation as a tree. This is considered a limitation of the method to be addressed in a future project