Geometric Surface Features Applied to Volumetric CAE Mesh Models

2005 ◽  
Author(s):  
Yifan Chen ◽  
Basavaraj Tonshal ◽  
Ali Saeed
Keyword(s):  
Large Scale ◽  
Geometric Feature ◽  
Direct Modeling ◽  
Modeling Paradigm ◽  
Model Independent ◽  
User Friendly ◽  
Geometric Surface ◽  
Mesh Models ◽  
Modeling Clay ◽  
Blending Function

In this paper, we discuss a way to extend a geometric surface feature framework known as Direct Surface Manipulation (DSM) into a volumetric mesh modeling paradigm that can be directly adopted by large-scale CAE applications involving models made of volumetric elements, multiple layers of surface elements or both. By introducing a polynomial-based depth-blending function, we extend the classic DSM mathematics into a volumetric form. The depth-blending function possesses similar user-friendly features as DSM basis functions permitting ease-of-control of the continuity and magnitude of deformation along the depth of deformation. Practical issues concerning the implementation of this technique are discussed in details and implementation results are shown demonstrating the versatility of this volumetric paradigm for direct modeling of complex CAE mesh models. In addition, the notion of a model-independent, volumetric-geometric feature is introduced. Motivated by modeling clay with sweeps and templates, a model-independent, catalog-able volumetric feature can be created. Deformation created by such a feature can be relocated, reoriented, duplicated, mirrored, pasted, and stored independent of the model to which it was originally applied. It can serve as a design template, thereby saving the time and effort to recreate it for repeated uses on different models (frequently seen in CAE-based Design of Experiments study).

Microcomputer Simulations of Presidential Elections

1983 ◽  
Vol 38 ◽  
pp. 20-20
Author(s):  
Robert S. Ross
Keyword(s):  
Social Sciences ◽  
Large Scale ◽  
Role Playing ◽  
Science Students ◽  
Instructional Programs ◽  
Santa Barbara ◽  
Large Scale Systems ◽  
The Social ◽  
User Friendly ◽  
Machine Interaction

Simulations have been an important adjunct to instructional programs for some time. These have ranged from games, or role playing exercises, such as SIMSOC or Internation Simulation, to student-machine interaction, such as the inter-school simulation run out of University of California, Santa Barbara in the early 70's, to the all machine activities found in some of the early SETUPS. Having social science students use the mainframe computer, however, always posed problems: it definitely was not user-friendly and most instructors had little if any training or interest in the use of large scale systems.The wide-spread use of the micro computer is not only revolutionizing areas traditionally relying upon the computer, but is going to have an impact on the social sciences as well.

scholarly journals fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy

2017 ◽  
Vol 33 (13) ◽  
pp. 2020-2028 ◽  
Author(s):  
Oliver Hilsenbeck ◽  
Michael Schwarzfischer ◽  
Dirk Loeffler ◽  
Sotiris Dimopoulos ◽  
Simon Hastreiter ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Segmentation ◽  
User Friendly

scholarly journals The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

2018 ◽  
Vol 2 ◽  
pp. 3 ◽  
Author(s):  
Heba Shaaban ◽  
David A. Westfall ◽  
Rawhi Mohammad ◽  
David Danko ◽  
Daniela Bezdan ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Large Scale ◽  
Research Effort ◽  
Gram Stain ◽  
Web Interface ◽  
Ongoing Effort ◽  
Student Researchers ◽  
User Friendly ◽  
Optimal Ph ◽  
Online Web

The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart (https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

scholarly journals 243 PREGNANCY RATES IN THE FIELD AFTER THE TRANSFER OF BOVINE IVP EMBRYOS VITRIFIED BY THE CRYOLOGIC VITRIFICATION METHOD

2005 ◽  
Vol 17 (2) ◽  
pp. 272 ◽  
Author(s):  
R. Fry ◽  
C. Earl ◽  
K. Fry ◽  
W. Lindemans
Keyword(s):  
Large Scale ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Pregnancy Rates ◽  
Chi Square ◽  
Full Field ◽  
Transfer Programs ◽  
Short Period ◽  
Rectal Palpation ◽  
User Friendly

Although large numbers of IVP embryos can be produced from donor cattle in a short period of time, commercial acceptance of the technology depends on the ability to cryopreserve these embryos and achieve a 50% pregnancy rate in large-scale embryo transfer programs. Many studies have reported low pregnancy rates of about 20% after the transfer of cryopreserved IVP embryos. We have developed the user friendly CryoLogic Vitrification Method (CVM) that vitrifies embryos on a solid surface at −196°C and warms them rapidly in a one-step procedure prior to transfer (Lindemans et al. 2004 Reprod. Fertil. Dev. 16, 174). We present an overview of the pregnancy rates in the field after vitrification of bovine IVP embryos by the CVM. The bos taurus IVP embryos in southern Australia (bT) and the bos indicus-based IVP embryos in northern Australia (bI) were produced by our standard TVR and IVP methodology (Fry et al., 2003 Theriogenology 59, 446). Pregnancy was determined by rectal palpation between Day 40 and Day 90 and differences between treatments were analyzed by chi-square. The development of the CVM has enabled the successful cryopreservation of bovine IVP embryos. In the laboratory the typical survival (90% re-expansion) and development (80% hatching) of IVP embryos post-vitrification is high and, as demonstrated here, the pregnancy rates after transfer are approaching commercially acceptable levels. However, further research is required to identify factors that may influence success under full field conditions, for both the IVP and the vitrification technologies. Table 1. Pregnancy rates for fresh IVP, CVM-vitrified IVP, and traditionally flushed embryos cryopreserved in glycerol

scholarly journals Analysis, identification and visualization of subgroups in genomics

2020 ◽  
Author(s):  
Gunnar Völkel ◽  
Simon Laban ◽  
Axel Fürstberger ◽  
Silke D Kühlwein ◽  
Nensi Ikonomi ◽  
...  
Keyword(s):  
Large Scale ◽  
Somatic Mutations ◽  
Target Selection ◽  
Gene Mutations ◽  
Use Case ◽  
The Past ◽  
Wide Availability ◽  
Approaches To Study ◽  
User Friendly ◽  
Personalized Intervention

Abstract Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact [email protected], phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502

scholarly journals A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Michelle Spoto ◽  
Changhui Guan ◽  
Elizabeth Fleming ◽  
Julia Oh
Keyword(s):  
Gene Function ◽  
Large Scale ◽  
Essential Gene ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Model Organisms ◽  
Design Parameters ◽  
Bacterial Genomes ◽  
Wide Range ◽  
User Friendly

ABSTRACT The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species. IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.

scholarly journals FastMM: an efficient toolbox for personalized constraint-based metabolic modeling

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Gong-Hua Li ◽  
Shaoxing Dai ◽  
Feifei Han ◽  
Wenxing Li ◽  
Jingfei Huang ◽  
...  
Keyword(s):  
Flux Balance Analysis ◽  
Large Scale ◽  
Computing Time ◽  
Metabolic Modeling ◽  
The Cancer Genome Atlas ◽  
Flux Balance ◽  
Mcmc Sampling ◽  
Genome Wide ◽  
Balance Analysis ◽  
User Friendly

Abstract Background Constraint-based metabolic modeling has been applied to understand metabolism related disease mechanisms, to predict potential new drug targets and anti-metabolites, and to identify biomarkers of complex diseases. Although the state-of-art modeling toolbox, COBRA 3.0, is powerful, it requires substantial computing time conducting flux balance analysis, knockout analysis, and Markov Chain Monte Carlo (MCMC) sampling, which may limit its application in large scale genome-wide analysis. Results Here, we rewrote the underlying code of COBRA 3.0 using C/C++, and developed a toolbox, termed FastMM, to effectively conduct constraint-based metabolic modeling. The results showed that FastMM is 2~400 times faster than COBRA 3.0 in performing flux balance analysis and knockout analysis and returns consistent outputs. When applied to MCMC sampling, FastMM is 8 times faster than COBRA 3.0. FastMM is also faster than some efficient metabolic modeling applications, such as Cobrapy and Fast-SL. In addition, we developed a Matlab/Octave interface for fast metabolic modeling. This interface was fully compatible with COBRA 3.0, enabling users to easily perform complex applications for metabolic modeling. For example, users who do not have deep constraint-based metabolic model knowledge can just type one command in Matlab/Octave to perform personalized metabolic modeling. Users can also use the advance and multiple threading parameters for complex metabolic modeling. Thus, we provided an efficient and user-friendly solution to perform large scale genome-wide metabolic modeling. For example, FastMM can be applied to the modeling of individual cancer metabolic profiles of hundreds to thousands of samples in the Cancer Genome Atlas (TCGA). Conclusion FastMM is an efficient and user-friendly toolbox for large-scale personalized constraint-based metabolic modeling. It can serve as a complementary and invaluable improvement to the existing functionalities in COBRA 3.0. FastMM is under GPL license and can be freely available at GitHub site: https://github.com/GonghuaLi/FastMM.

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