scholarly journals MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

2014 ◽  
Vol 42 (W1) ◽  
pp. W408-W415 ◽  
Author(s):  
Mads T. Bonde ◽  
Michael S. Klausen ◽  
Mads V. Anderson ◽  
Annika I.N. Wallin ◽  
Harris H. Wang ◽  
...  
Keyword(s):  
Genome Engineering ◽  
Design Tool ◽  
Web Based

scholarly journals Impact of CRISPR-Cas9-Based Genome Engineering in Farm Animals

2021 ◽  
Vol 8 (7) ◽  
pp. 122
Author(s):  
Parul Singh ◽  
Syed Azmal Ali
Keyword(s):  
Disease Resistance ◽  
Genome Engineering ◽  
Animal Health ◽  
Fundamental Principle ◽  
Farm Animals ◽  
Web Based ◽  
Knock Out ◽  
Guide Rna ◽  
Female Birth ◽  
Comprehensive Information

Humans are sorely over-dependent on livestock for their daily basic need of food in the form of meat, milk, and eggs. Therefore, genetic engineering and transgenesis provide the opportunity for more significant gains and production in a short span of time. One of the best strategies is the genetic alteration of livestock to enhance the efficiency of food production (e.g., meat and milk), animal health, and welfare (animal population and disease). Moreover, genome engineering in the bovine is majorly focused on subjects such as disease resistance (e.g., tuberculosis), eradicate allergens (e.g., beta-lactoglobulin knock-out), products generation (e.g., meat from male and milk from female), male or female birth specifically (animal sexing), the introduction of valuable traits (e.g., stress tolerance and disease resistance) and their wellbeing (e.g., hornlessness). This review addressed the impressive genome engineering method CRISPR, its fundamental principle for generating highly efficient target-specific guide RNA, and the accompanying web-based tools. However, we have covered the remarkable roadmap of the CRISPR method from its conception to its use in cattle. Additionally, we have updated the comprehensive information on CRISPR-based gene editing in cattle.

scholarly journals The Narrative Event Diagram

2009 ◽  
pp. 101-118
Author(s):  
Helyn Gould ◽  
Michael Hughes ◽  
Paul Maharg ◽  
Emma Nicol
Keyword(s):  
Professional Learning ◽  
Information Science ◽  
Further Education ◽  
Design Tool ◽  
Design History ◽  
Game Based Learning ◽  
Web Based ◽  
Design Iteration ◽  
The United Kingdom ◽  
Narrative Event

Game-based learning and simulation is a powerful mode of learning, used by industries as diverse as aviation and health sciences. While there are many generic Virtual Learning Environments available to further education and higher education in the United Kingdom, there is no widely available open-source Web-based simulation environment for professional learning. The SIMPLE (SIMulated Professional Learning Environment) project has designed, created, implemented and is in the process of evaluating such an environment in a range of disciplinary settings. The simulations that are being created place both undergraduates and postgraduates in a professional context where their work is, as it will be in the workplace, distributed between tools, colleagues, resources, anticipated, and unanticipated problems. One of the key tools that staff will use to create simulations is the “narrative event diagram”, a design tool as well as a means by which the narrative of the simulation is constructed. This chapter will describe the tool, its design history and context, its current use, and next design iteration. In particular it will show the interdisciplinary genesis of the tool’s design, arising from the confluence of computer science, information science, and narrative theory, and its power in designing professional educational simulations.

Web-Based Cad Tools for a Networked Manufacturing Service

1998 ◽  
Author(s):  
Fu-Chung F. Wang ◽  
Paul K. Wright
Keyword(s):  
New Product Development ◽  
Design Tool ◽  
Internet Technology ◽  
Machining Process ◽  
Global Network ◽  
The Internet ◽  
Distributed Design ◽  
Cad Tools ◽  
Web Based ◽  
Design And Manufacturing

Abstract New techniques in Information Technology are now changing not only our daily life, but also the professional practice of product design and manufacturing for new product development. Internet technology in particular opens up another domain for building future CAD/CAM environments. This environment will be a global, network-centric environment with various members providing different software tools, manufacturing facilities, and analysis services for distributed design and fabrication. In this paper, we first briefly describe a vision and current development in a distributed design and manufacturing environment. The paper then emphasizes how current CAD tools will evolve to facilitate the distributed design and fabrication process. In particular, the development of a set of Web-based design tools for fabricating parts using a machining process via the Internet is presented. Experiments on machining 2-1/2 D and freeform parts through this Java-based design tool have shown the feasibility for a networked machining service via the Internet.

scholarly journals Automated design of CRISPR prime editors for thousands of human pathogenic variants

2020 ◽  
Author(s):  
John A. Morris ◽  
Jahan A. Rahman ◽  
Xinyi Guo ◽  
Neville E. Sanjana
Keyword(s):  
Genetic Variants ◽  
Gene Editing ◽  
Genome Engineering ◽  
Disease Modeling ◽  
Automated Design ◽  
Common Variants ◽  
Therapeutic Gene ◽  
Web Based ◽  
Pathogenic Variants ◽  
Automated Pipeline

AbstractPrime editors (PEs) are CRISPR-based genome engineering tools that can introduce precise base-pair edits at specific locations in the genome. These programmable gene editors have been predicted to repair 89% of known human pathogenic variants in the ClinVar database, although these PE constructs do not presently exist. Towards this end, we developed an automated pipeline to correct (therapeutic editing) or introduce (disease modeling) human pathogenic variants that optimizes the design of several RNA constructs required for prime editing and avoids predicted off-targets in the human genome. However, using optimal PE design criteria, we find that only a small fraction of these pathogenic variants can be targeted. Through the use of alternative Cas9 enzymes and extended templates, we increase the number of targetable pathogenic variants to >50,000 variants and make these pre-designed PE constructs accessible through a web-based portal (http://primeedit.nygenome.org). Given the tremendous potential for therapeutic gene editing, we also assessed the possibility of developing universal PE constructs. By examining the overlap of different PE components with common human genetic variants in dbSNP, we find that common variants affect only a small minority of designed PEs.

scholarly journals PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation

2018 ◽  
Author(s):  
Moritz Schaefer ◽  
Dr. Djork-Arné Clevert ◽  
Dr. Bertram Weiss ◽  
Dr. Andreas Steffen
Keyword(s):  
Gene Editing ◽  
State Of The Art ◽  
Protein Structures ◽  
Design Tool ◽  
Protein Crystal ◽  
Functional Domain ◽  
Web Based ◽  
Domain Annotation ◽  
Sgrna Design ◽  
Processing Steps

AbstractSummary: sgRNAs targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state-of-the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports HDR template generation for gene editing experiments and the visualization of the mutated amino acids in 3D.Availability and Implementation: PAVOOC is available under https://pavooc.me and accessible using current browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend is implemented in Python 3 and ReactJS respectively. All components run in a simple Docker environment.Contact: [email protected]

E-Design Tool for Friction Stir Welding

2008 ◽  
Author(s):  
Harish Bagaitkar ◽  
Venkat Allada
Keyword(s):  
Friction Stir Welding ◽  
Experimental Studies ◽  
Lap Joints ◽  
Design Tool ◽  
Tool Geometry ◽  
Butt Joints ◽  
Web Based ◽  
Plunge Depth ◽  
Friction Stir ◽  
Input Parameters

This paper describes efforts to develop a web-based E-Design tool for the Friction Stir Welding (FSW) technique. The input parameters to the E-Design tool are the joint specifications. The output parameters of the E-Design tool are process parameters such as tool geometry details, tool rpm, and plunge depth. The heart of the E-Design tool is the FSW database. The FSW database contains mappings of various input parameters and output parameters that are captured by referring to various experimental studies cited in the literature. The proposed E-Design tool deals with lap joints and butt joints between similar aluminum alloys.

scholarly journals Establishment of expanded and streamlined pipeline of PITCh knock-in – a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO

Bioengineered ◽  
2017 ◽  
Vol 8 (3) ◽  
pp. 302-308 ◽  
Author(s):  
Kazuki Nakamae ◽  
Yuki Nishimura ◽  
Mitsumasa Takenaga ◽  
Shota Nakade ◽  
Naoaki Sakamoto ◽  
...  
Keyword(s):  
Design Tool ◽  
Web Based

MES—A Web-Based Design Tool for Microwave Engineering

2006 ◽  
Vol 49 (1) ◽  
pp. 67-73 ◽  
Author(s):  
R.M. Nelson ◽  
A.N.M.S. Islam
Keyword(s):  
Design Tool ◽  
Web Based ◽  
Microwave Engineering
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