CASAT-HOOMT: Computer Aided Software Analysis Tool Based on High Order Object-Oriented Modeling Technique

2013 ◽  
Author(s):  
Fan Zhang ◽  
Jinwu Wang ◽  
Xiaoqing Frank Liu ◽  
Buqing Cao ◽  
Mingdong Tang
Keyword(s):  
Object Oriented ◽  
High Order ◽  
Modeling Technique ◽  
Analysis Tool ◽  
Software Analysis ◽  
Computer Aided

scholarly journals 423. SARS-CoV-2 NGS Assay Powered by Biotia COVID-DX Software

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S278-S279
Author(s):  
Dorottya Nagy-Szakal ◽  
Mara Couto-Rodriguez ◽  
Joseph Barrows ◽  
Heather L Wells ◽  
Marilyne Debieu ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Viral Genome ◽  
Board Member ◽  
Limit Of Detection ◽  
Clinical Samples ◽  
Analysis Tool ◽  
Viral Titer ◽  
Target Enrichment ◽  
Library Preparation ◽  
Software Analysis

Abstract Background COVID-19 had spread quickly, causing an international public health emergency with an alarming global shortage of COVID-19 diagnostic tests. We developed and clinically validated a next-generation sequencing (NGS)-based target enrichment assay with the COVID-DX Software tailored for the detection, characterization, and surveillance of the SARS-CoV-2 viral genome. Methods The SARS-CoV-2 NGS assay consists of components including library preparation, target enrichment, sequencing, and a COVID-DX Software analysis tool. The NGS library preparation starts with extracted RNA from nasopharyngeal (NP) swabs followed by cDNA synthesis and conversion to Illumina TruSeq-compatible libraries using the Twist Library Preparation Kit via Enzymatic Fragmentation and Unique Dual Indices (UDI). The library is then enriched for SARS-CoV-2 sequences using a panel of dsDNA biotin-labeled probes, specifically designed to target the SARS-CoV-2 genome, then sequenced on an Illumina NextSeq 550 platform. The COVID-DX Software analyzes sequence results and provides a clinically oriented report, including the presence/absence of SARS-CoV-2 for diagnostic use. An additional research use only report describes the assay performance, estimated viral titer, coverage across the viral genome, genetic variants, and phylogenetic analysis. Results The SARS-CoV-2 NGS Assay was validated on 30 positive and 30 negative clinical samples. To measure the sensitivity and specificity of the assay, the positive and negative percent agreement (PPA, NPA) was defined in comparison to an orthogonal EUA RT-PCR assay (PPA [95% CI]: 96.77% [90.56%-100%] and NPA [95% CI]: 100% [100%-100%]). Data reported using our assay defined the limit of detection to be 40 copies/ml using heat-inactivated SARS-CoV-2 viral genome in clinical matrices. In-silico analysis provided >99.9% coverage across the SARS-CoV-2 viral genome and no cross-reactivity with evolutionarily similar respiratory pathogens. Conclusion The SARS-CoV-2 NGS Assay powered by the COVID-DX Software can be used to detect the SARS-CoV-2 virus and provide additional insight into viral titer and genetic variants to track transmission, stratify risk, predict outcome and therapeutic response, and control the spread of infectious disease. Disclosures Dorottya Nagy-Szakal, MD PhD, Biotia (Employee) Mara Couto-Rodriguez, MS, Biotia (Employee) Joseph Barrows, MS, Biotia, Inc. (Employee, Shareholder) Heather L. Wells, MPH, Biotia (Consultant) Marilyne Debieu, PhD, Biotia (Employee) Courteny Hager, BS, Biotia (Employee) Kristin Butcher, MS, Twist Bioscience (Employee) Siyuan Chen, PhD, Twist Bioscience (Employee) Christopher Mason, PhD, Biotia (Board Member, Employee, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder)Twist (Other Financial or Material Support, I am CEO of Biotia and Biotia has business partnership with Twist)

scholarly journals NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR

2020 ◽  
Author(s):  
Fangyan Yu ◽  
Ka Wai Leong ◽  
Alexander Makrigiorgos ◽  
Viktor A Adalsteinsson ◽  
Ioannis Ladas ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Analysis Tool ◽  
Circulating Dna ◽  
Liquid Biopsies ◽  
Software Analysis ◽  
Multiplexed Pcr ◽  
Human Genomes ◽  
Custom Made ◽  
Alu Element ◽  
Next Generation Sequencing Ngs

Abstract Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new approach to detect MSI using inter-Alu-PCR followed by targeted NGS, that combines the practical advantages of multiplexed-PCR with the breadth of information provided by NGS. Inter-Alu-PCR employs poly-adenine repeats of variable length present in every Alu element and provides a massively-parallel, rapid approach to capture poly-A-rich genomic fractions within short 80–150bp amplicons generated from adjacent Alu-sequences. A custom-made software analysis tool, MSI-tracer, enables Alu-associated MSI detection from tissue biopsies or MSI-tracing at low-levels in circulating-DNA. MSI-associated indels at somatic-indel frequencies of 0.05–1.5% can be detected depending on the availability of matching normal tissue and the extent of instability. Due to the high Alu copy-number in human genomes, a single inter-Alu-PCR retrieves enough information for identification of MSI-associated-indels from ∼100 pg circulating-DNA, reducing current limits by ∼2-orders of magnitude and equivalent to circulating-DNA obtained from finger-sticks. The combined practical and informational advantages of inter-Alu-PCR make it a powerful tool for identifying tissue-MSI-status or tracing MSI-associated-indels in liquid biopsies.

HyperGear: An Object Oriented Design Program for Single Stage Gear Box Design

1991 ◽  
Author(s):  
Gary A. Gabriele ◽  
Agustî Maria I. Serrano
Keyword(s):  
Computer Aided Design ◽  
Object Oriented ◽  
Design Tool ◽  
Single Stage ◽  
Design Tools ◽  
Object Oriented Design ◽  
Computer Aided ◽  
Gear Box ◽  
Aided Design ◽  
Object Oriented Languages

Abstract The need for superior design tools has lead to the development of better and more complex computer aided design programs. Two of the more important new developments in application tools being investigation are Object Oriented Languages, and HyperMedia. Object Oriented Languages allow the development of CAD tools where the parts being designed and the design procedures specified are conceptualized as objects. This allows for the development of design aids that are non-procedural and more readily manipulated by the user trying to accomplish a design task. HyperMedia allows for the easy inclusion of many different types of data, such as design charts and graphs, into the tool that are normally difficult to include in design tools programmed with more conventional programming languages. This paper explores the development of a computer aided design tool for the design of a single stage gear box using the development HyperCard® environment and the HyperTalk® programming language. The resulting program provides a user friendly interface, the ability to handle several kinds of design information including graphic and textual, and a non-procedural design tool to help the user design simple, one stage gear boxes. Help facilities in the program make it suitable for undergraduate instruction in a machine elements design course.

Automated Reuse of Solutions in Manufacturing Process Planning Through a Case-Based Approach

1996 ◽  
Author(s):  
M. Marefat ◽  
J. Britanik
Keyword(s):  
Process Planning ◽  
Manufacturing Process ◽  
Object Oriented ◽  
Process Plan ◽  
Primary Mechanism ◽  
Prismatic Parts ◽  
Manufacturing Process Planning ◽  
Computer Aided ◽  
Effective Use ◽  
Case Based

Abstract This research focuses on the development of an object-oriented case-based process planner which combines the advantages of the variant and generative approaches to process planning. The case-based process planner operates on general 3D prismatic parts, represented by a collection of features (eg: slots, pockets, holes, etc.). Each feature subplan is developed by the case-based planner. Then the feature subplans are combined into the global process plan for the part via a hierarchical plan merging mechanism. Abstracted feature subplans correspond to cases, which are used in subsequent planning operations to solve new problems. The abstracting and storing of feature subplans as cases is the primary mechanism by which the planner learns from its previous experiences to become more effective and efficient. The computer-aided process planner is designed to be extensible and flexible through the effective use of object-oriented principles.

An object‐oriented approach to computer aided composition

Interface ◽  
1990 ◽  
Vol 19 (2-3) ◽  
pp. 185-196 ◽  
Author(s):  
Bruno Fagarazzi ◽  
Carla Saraggiotto
Keyword(s):  
Object Oriented ◽  
Computer Aided ◽  
Object Oriented Approach ◽  
Oriented Approach
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