scholarly journals Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows

2020 ◽  
Author(s):  
Melchior du Lac ◽  
Thomas Duigou ◽  
Joan Hérisson ◽  
Pablo Carbonell ◽  
Neil Swainston ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Computer Aided Design ◽  
Web Based ◽  
Workflow Systems ◽  
The Galaxy ◽  
Community Effort ◽  
Metabolic Pathway Design ◽  
Aided Design ◽  
Automation Tools

AbstractMany computer-aided design tools are available for synthetic biology and metabolic engineering. Yet, these tools can be difficult to apprehend, sometimes requiring a level of expertise that limits their use by a wider community. Furthermore, some of the tools, although complementary, rely on different input and output formats and cannot communicate with one another. Scientific workflows address these shortcomings while offering a novel design strategy. Among the workflow systems available, Galaxy is a web-based platform for performing findable and accessible data analyses for all scientists regardless of their informatics expertise, along with interoperable and reproducible computations regardless of the particular platform that is being used.Here, we introduce the Galaxy-SynBioCADa portal, the first Galaxy toolshed for synthetic biology and metabolic engineering. It allows one to easily create workflows or use those already developed by the community. The portal is a growing community effort where developers can add new tools and users can evaluate the tools performing design for their specific projects. The tools and workflows currently shared on the Galaxy-SynBioCAD portal cover an end-to-end metabolic pathway design process from the selection of strain and target to the calculation of DNA parts to be assembled to build libraries of strains to be engineered to produce the target.Standard formats are used throughout to enforce the compatibility of the tools. These include SBML for strain and pathway and SBOL for genetic layouts. The portal has been benchmarked on 81 literature pathways, overall, we find we have a 65% (and 88%) success rate in retrieving the literature pathways among the top 10 (50) pathways predicted and generated by the workflows.

A Web-based Product Structure Manager to Support Collaborative Assembly Modeling1

2004 ◽  
Vol 4 (1) ◽  
pp. 67-78 ◽  
Author(s):  
Li Chen, ◽  
Tingjin Wang, and ◽  
Zhijie Song
Keyword(s):  
Computer Aided Design ◽  
Product Structure ◽  
Web Based ◽  
Assembly Modeling ◽  
Product Structure Management ◽  
Cad System ◽  
Collaborative Assembly ◽  
3D Assembly ◽  
Function Module ◽  
Aided Design

Collaborative CAD systems enabling collaboration in computer-aided design processes among distributed designers are gaining more and more attention. Yet, such systems, especially in support of collaborative assembly modeling, are hardly achievable. In an effort to bridge this gap, we are dedicated to developing a collaborative CAD system with aim at 3D assembly modeling. As part of this effort, this paper addresses one function module of the system, a Web-based Product Structure Manager, which enables the Collaborative Product Structure Management (CPSM) in collaborative assembly modeling. In particular, CPSM facilitates product data sharing among distributed designers and supports collaboration in product structure creation and modification. A bench clamp assembly is used as an example to illustrate the Product Structure Manager for supporting collaborative assembly modeling.

A CAD Template Approach to Support Web-Based Customer Centric Product Design

2005 ◽  
Vol 5 (4) ◽  
pp. 381-387 ◽  
Author(s):  
Zahed Siddique ◽  
Karunakar Boddu
Keyword(s):  
Product Design ◽  
Design Process ◽  
Mass Customization ◽  
Computer Aided Design ◽  
Cad Model ◽  
Entire Family ◽  
Web Based ◽  
Computer Aided ◽  
Aided Design ◽  
Configurable Products

In order to provide products that can be tailored to the need of the customer, it is necessary to integrate the customer into the design process. In this paper we present a mass customization computer-aided design (CAD) framework that helps to integrate the customer into the design of user-configurable products. A template approach, which considers both modularity and scaling, is utilized to concisely represent a CAD model of the entire family. The system accepts user selections and parameters to automatically create a CAD model of the customized product in real time and then shows the model to the user. The system is implemented using PRO/ENGINEER and demonstrated through customization of bicycle frames.

scholarly journals Right the First Time

2008 ◽  
Vol 130 (06) ◽  
pp. 30-34 ◽  
Author(s):  
Brian MacCleery ◽  
Nipun Mathur
Keyword(s):  
Computer Aided Design ◽  
Integrated Design ◽  
Gear Ratio ◽  
Motion Simulation ◽  
Web Based ◽  
Trade Offs ◽  
Systems Software ◽  
Integrated Design Process ◽  
Aided Design ◽  
And Control

This paper discusses development of new tools that can help mechanical engineers avoid common pitfalls in designing complex mechatronic motion control systems. To help facilitate a more integrated design process for electromechanical systems, software developers are partnering with electrical and control design companies to add motion simulation capabilities to computer-aided design (CAD) environments to create a more unified mechatronics workflow. Integrating motion simulation with CAD simplifies design because the simulation uses information that already exists in the CAD model, such as assembly mates, couplings, and material mass properties. Simulations also simplify evaluating engineering trade-offs between different conceptual designs. The paper also highlights that several web-based motor-sizing tools have been designed to help sort through the thousands of choices, and some include motor data from multiple vendors. Using realistic multiaxis motion profiles to drive simulation can provide more accurate torque and velocity requirements, which depend on the acceleration characteristics of your motion profiles and the mass, friction, and gear ratio properties of the transmission.

Enhancement of Design and Manufacturing Curriculum Through Rapid Prototyping Practices

2004 ◽  
Author(s):  
Ismail Fidan ◽  
Ken Patton
Keyword(s):  
Rapid Prototyping ◽  
Computer Aided Design ◽  
Physical Models ◽  
Web Based ◽  
Capstone Courses ◽  
Computer Aided ◽  
Design And Manufacturing ◽  
Cad Cam ◽  
Industrial Projects ◽  
Aided Design

Advances in computer technology opened new horizons in teaching Computer Aided Design (CAD) and Computer Aided Manufacturing (CAM) technologies. This paper will report the outcomes of two current NSF grants, 0311586 and 0302314, funded on Rapid Prototyping (RP) curriculum development. The objective of these RP projects is to provide advanced instruction and laboratory practices in the areas of CAD/CAM/CAE through challenging laboratory assignments and industrial projects that are integrated into any engineering curriculum. These projects create web-based materials, and also adapt and implement RP experiences and educational practices following successful similar models at various engineering schools to enhance pedagogy in design and manufacturing curriculum. Enhanced RP capabilities enable the students to build physical models directly from CAD data, where the prototype communicates important information about parts, including engineering data such as fit and limited functional testing, labeling, highlighting, and appearance simulation. Developed RP labs are used in junior and senior level design and manufacturing courses, including the senior capstone courses.

Computer-Aided Modeling and Manufacturing of Spherical Mechanisms via a Novel Web Tool

2007 ◽  
Vol 7 (4) ◽  
pp. 339-346 ◽  
Author(s):  
J. Schuler ◽  
J. Ketchel ◽  
P. Larochelle
Keyword(s):  
Dynamic Simulation ◽  
Computer Aided Design ◽  
Geometric Modeling ◽  
Three Dimensional ◽  
Software Tool ◽  
Web Based ◽  
Spherical Mechanisms ◽  
Computer Aided ◽  
Manufacturing Software ◽  
Aided Design

In this paper, we present a novel web-based computer-aided modeling and manufacturing software tool for spherical mechanisms. Our purpose is to facilitate the analysis, dynamic simulation, and manufacture of one degree of freedom spherical four-bar mechanisms. First, a brief review of some of the current computer-aided design software for spherical four-bar mechanisms is presented. These software packages provide the three-dimensional visualization and computational capabilities necessary to synthesize and analyze spherical four-bar mechanisms. However, to date, no readily available and effective tools exist to aid in the modeling and manufacture of spherical mechanisms. Next, the kinematics of spherical four-bar mechanisms are reviewed as they pertain to their geometric modeling and manufacture. Finally, we present our web-based implementation of a computer-aided modeling, simulation, and manufacturing methodology for spherical four-bar mechanisms called SFBDESIGNER (for spherical four-bar designer). SFBDESIGNER facilitates the design, dynamic simulation, prototyping, and manufacture of spherical four-bar mechanisms.

Methodology and Tools to Support Knowledge Management in Topology Optimization

2010 ◽  
Vol 10 (4) ◽  
Author(s):  
Maurizio Muzzupappa ◽  
Loris Barbieri ◽  
Fabio Bruno ◽  
Umberto Cugini
Keyword(s):  
Design Automation ◽  
Computer Aided Design ◽  
Development Process ◽  
The Other ◽  
Topological Optimization ◽  
Product Development Process ◽  
Innovative Methodology ◽  
Original Procedure ◽  
Aided Design ◽  
Automation Tools

Topological optimization (TO) tools are today widely employed in several engineering fields (e.g., construction, aeronautics, aerospace, and automotive). The diffusion of these tools is due to their capacity to improve mechanical properties of products through a global optimization of the product in terms of weight, stiffness, strength, and cost. On the other hand, the adoption of TO tools still requires a sizeable organizational effort because, at present, these tools are mostly stand-alone and are not well integrated into the product development process (PDP). This paper presents an innovative methodology that supports designers and analysts in formalizing and transmitting design choices taken during project activities and in making the integration of TO tools in the PDP more efficient. The methodology clearly defines the roles, the activities, the data to exchange, and the software tools to be used in the process. Some custom computer-aided design automation tools have been implemented to improve the efficiency of the methodology. Moreover, this paper defines an original procedure to support the interpretation of the TO results.

scholarly journals Toward Engineering Synthetic Microbial Metabolism

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
George H. McArthur ◽  
Stephen S. Fong
Keyword(s):  
Synthetic Biology ◽  
Computer Aided Design ◽  
De Novo ◽  
Microbial Metabolism ◽  
Biological Design ◽  
Framework Design ◽  
Current State ◽  
Forward Engineering ◽  
Aided Design ◽  
Further Development

The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements inde novoDNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems from well-characterized parts. In this review we discuss the current state of synthetic biology within a four-stage framework (design, modeling, synthesis, analysis) and highlight areas requiring further advancement to facilitate true engineering of synthetic microbial metabolism.

SphinxCAM-Pro|E: Computer-Aided Modeling and Manufacturing of Spherical Mechanisms Via the Web

2006 ◽  
Author(s):  
Pierre M. Larochelle ◽  
Jason M. Schuler ◽  
John S. Ketchel
Keyword(s):  
Dynamic Simulation ◽  
Computer Aided Design ◽  
Geometric Modeling ◽  
Three Dimensional ◽  
Web Based ◽  
Modeling Simulation ◽  
Spherical Mechanisms ◽  
Software Packages ◽  
Computer Aided ◽  
Aided Design

In this paper we present a web-based computer-aided design modeling and manufacturing methodology for spherical mechanisms. Our purpose is to facilitate the analysis, dynamic simulation, and manufacture of one degree of freedom spherical four-bar mechanisms. First, a brief review of some of the current computer-aided design (CAD) software for spherical four-bar mechanisms, e.g. SPHINX, SPHINXPC, ISIS, and OSIRIS is presented. These software packages provide the three-dimensional visualization and computational capabilities necessary to design spherical four-bar mechanisms. However, to date no readily available and effective tools exist to aid in the modeling and manufacture of spherical mechanisms. Next, the kinematics of spherical four-bar mechanisms are reviewed as they pertain to their geometric modeling and manufacture. Finally, we present our web-based implementation of a computer-aided modeling, simulation, and manufacturing methodology for spherical four-bar mechanisms called SPHINXCAM-Pro|E. SPHINXCAM-Pro|E, when used with the CAD tools mentioned above, facilitates the design, dynamic simulation, prototyping, and manufacture of spherical four-bar mechanisms.

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