“CodonWizard” – An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts

2019 ◽  
Vol 160 ◽  
pp. 84-93 ◽  
Author(s):  
Peter Rehbein ◽  
Jannik Berz ◽  
Patrick Kreisel ◽  
Harald Schwalbe
Keyword(s):  
User Interface ◽  
Protein Expression ◽  
Graphical User Interface ◽  
Codon Optimization ◽  
Software Tool

scholarly journals A Software Tool for Assisting Experimentation in Dynamic Environments

2015 ◽  
Vol 2015 ◽  
pp. 1-12
Author(s):  
Pavel Novoa-Hernández ◽  
Carlos Cruz Corona ◽  
David A. Pelta
Keyword(s):  
Statistical Analysis ◽  
User Interface ◽  
Graphical User Interface ◽  
Optimization Problems ◽  
Software Tool ◽  
Dynamic Environments ◽  
Experiment Management ◽  
And Performance ◽  
Main Components

In real world, many optimization problems are dynamic, which means that their model elements vary with time. These problems have received increasing attention over time, especially from the viewpoint of metaheuristics methods. In this context, experimentation is a crucial task because of the stochastic nature of both algorithms and problems. Currently, there are several technologies whose methods, problems, and performance measures can be implemented. However, in most of them, certain features that make the experimentation process easy are not present. Examples of such features are the statistical analysis of the results and a graphical user interface (GUI) that allows an easy management of the experimentation process. Bearing in mind these limitations, in the present work, we present DynOptLab, a software tool for experimental analysis in dynamic environments. DynOptLab has two main components: (1) an object-oriented framework to facilitate the implementation of new proposals and (2) a graphical user interface for the experiment management and the statistical analysis of the results. With the aim of verifying the benefits of DynOptLab’s main features, a typical case study on experimentation in dynamic environments was carried out.

A Software Tool for Simulating Motions and Loading in Planar Tensegrity Structures

2014 ◽  
Author(s):  
Carl A. Nelson
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Software Tool ◽  
Computational Tool ◽  
Tensegrity Structures ◽  
Indeterminate Structures

Tensegrity structures are unique in the sense that they tend to be overconstrained as mechanisms, yet they can be mobile due to the elastic nature of their tensile elements. The ability to easily visualize these motion properties would help designers to create new and useful tensegrity mechanisms. In this paper, a simple and interactive computational tool with a graphical user interface is presented for visualizing loading and displacements in tensegrity structures. This tool can also be extended for use with traditional static structures, including both determinate and indeterminate structures, as well as mechanisms.

scholarly journals Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Yide Huang ◽  
Ting Lin ◽  
Lingfang Lu ◽  
Fan Cai ◽  
Jie Lin ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Protein Expression ◽  
Codon Usage ◽  
Codon Optimization ◽  
Software Tool ◽  
Expression Levels ◽  
Gene Design ◽  
Codon Pair Bias ◽  
Codon Pair ◽  
Synthetic Gene Design

Abstract Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris.

scholarly journals AUTOMATIC IDENTIFICATION OF MINERALS IN IMAGES OF POLISHED SECTIONS

2021 ◽  
Vol XLIV-2/W1-2021 ◽  
pp. 113-118
Author(s):  
A. V. Khvostikov ◽  
D. M. Korshunov ◽  
A. S. Krylov ◽  
M. A. Boguslavskiy
Keyword(s):  
Neural Network ◽  
User Interface ◽  
Graphical User Interface ◽  
Software Tool ◽  
Semantic Segmentation ◽  
Automatic Analysis ◽  
Automatic Identification ◽  
Polished Section ◽  
High Quality ◽  
Mineral Associations

Abstract. Automatic identification of minerals in images of polished section is highly demanded in exploratory geology as it can provide a significant reduction in time spent in the study of ores and eliminate the factor of misdiagnosis of minerals. The development of algorithms for automatic analysis of images of polished sections makes it possible to create of a universal tool for comparing ores from different deposits, which is also much in demand. The main contribution of this paper can be summed up in three parts: i) creation of LumenStone dataset (https://imaging.cs.msu.ru/en/research/geology/lumenstone) which unites high-quality geological images of different mineral associations and provides pixel-level semantic segmentation masks, ii) development of CNN-based neural network for automatic identification of minerals in images of polished sections, iii) implementation of software tool with graphical user interface that can be used by expert geologists to perform an automatic analysis of polished sections images.

scholarly journals rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics

2018 ◽  
Author(s):  
Christian Trachsel ◽  
Christian Panse ◽  
Tobias Kockmann ◽  
Witold E. Wolski ◽  
Jonas Grossmann ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
User Interface ◽  
Graphical User Interface ◽  
Real World ◽  
Software Tool ◽  
R Package ◽  
Command Line ◽  
Diagnostic Plots ◽  
Method Optimization

AbstractOptimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) is a non-trivial task. Here we present rawDiag, a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots of scan level metadata. rawDiag is implemented as R package and can be executed on the command line, or through a graphical user interface (GUI) for less experienced users. The code runs platform independent and can process a hundred raw files in less than three minutes on current consumer hardware as we show by our benchmark. In order to demonstrate the functionality of our package, we included a real-world example taken from our daily core facility business.

scholarly journals iMet: A graphical user interface software tool to merge metabolic networks

Heliyon ◽  
2019 ◽  
Vol 5 (6) ◽  
pp. e01766
Author(s):  
Reza Mohammadi ◽  
Javad Zahiri ◽  
Mohammad Javad Niroomand
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Metabolic Networks ◽  
Software Tool

Development of a Web-Based Interactive Compressible Flow Solver

2005 ◽  
Author(s):  
H. Eletem ◽  
F. Young ◽  
K. Aung
Keyword(s):  
User Interface ◽  
Compressible Flow ◽  
Programming Language ◽  
Graphical User Interface ◽  
Mechanical Engineering ◽  
Software Tool ◽  
Ease Of Use ◽  
Web Based ◽  
Flow Solver ◽  
Java Programming

Compressible flow is an important subject in aerospace and mechanical engineering disciplines. This paper describes the development of a web-base interactive compressible flow solver using Java programming language. The main objective of the solver is to provide students with a software tool than can be used in the compressible flow course offered in the Department of Mechanical Engineering at Lamar University. The solver has a graphical user interface (GUI) for ease of use and interactivity. The solver was developed with the intention of free distribution to the educational community and other interested users.

scholarly journals MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

2019 ◽  
Vol 36 (7) ◽  
pp. 2258-2259 ◽  
Author(s):  
Gurjit S Randhawa ◽  
Kathleen A Hill ◽  
Lila Kari
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Dna Sequences ◽  
Software Tool ◽  
Digital Signal ◽  
Disease Classification ◽  
Supplementary Information ◽  
Alignment Free ◽  
Comparison And Analysis

Abstract Summary Machine Learning with Digital Signal Processing and Graphical User Interface (MLDSP-GUI) is an open-source, alignment-free, ultrafast, computationally lightweight, and standalone software tool with an interactive GUI for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others. Availability and implementation MLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/. Supplementary information Supplementary data are available at Bioinformatics online.

Sign in / Sign up

Export Citation Format

Share Document