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 Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

2015 ◽  
Vol 14 ◽  
pp. CIN.S26470 ◽  
Author(s):  
Richard P. Finney ◽  
Qing-Rong Chen ◽  
Cu V. Nguyen ◽  
Chih Hao Hsu ◽  
Chunhua Yan ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Reference Genome ◽  
Source Code ◽  
Software Tool ◽  
Command Line ◽  
Sequencing Data ◽  
Genome Data ◽  
Command Line Tool ◽  
Portable Software ◽  
Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

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.

scholarly journals LexOPS: An R package and user interface for the controlled generation of word stimuli

2020 ◽  
Vol 52 (6) ◽  
pp. 2372-2382
Author(s):  
Jack E. Taylor ◽  
Alistair Beith ◽  
Sara C. Sereno
Keyword(s):  
User Interface ◽  
Factorial Design ◽  
Graphical User Interface ◽  
R Package ◽  
Psycholinguistic Research ◽  
Link Type ◽  
Control Current ◽  
Word Lists ◽  
And Control ◽  
Manipulation And Control

AbstractLexOPS is an R package and user interface designed to facilitate the generation of word stimuli for use in research. Notably, the tool permits the generation of suitably controlled word lists for any user-specified factorial design and can be adapted for use with any language. It features an intuitive graphical user interface, including the visualization of both the distributions within and relationships among variables of interest. An inbuilt database of English words is also provided, including a range of lexical variables commonly used in psycholinguistic research. This article introduces LexOPS, outlining the features of the package and detailing the sources of the inbuilt dataset. We also report a validation analysis, showing that, in comparison to stimuli of existing studies, stimuli optimized with LexOPS generally demonstrate greater constraint and consistency in variable manipulation and control. Current instructions for installing and using LexOPS are available at https://JackEdTaylor.github.io/LexOPSdocs/.

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