scholarly journals ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

2019 ◽  
Author(s):  
Niels Hulstaert ◽  
Timo Sachsenberg ◽  
Mathias Walzer ◽  
Harald Barsnes ◽  
Lennart Martens ◽  
...  
Keyword(s):  
File Format ◽  
Mass Spectrometers ◽  
Continuous Growth ◽  
Workflow Systems ◽  
File Formats ◽  
Standard File Format ◽  
Cross Platform ◽  
Quantitative Results ◽  
Cloud Infrastructures ◽  
User Friendly

AbstractThe field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we presented ThermoRawFileParser, an open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda and BioContainers containers around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.

scholarly journals Pydigree: a python library for manipulation and forward-time simulation and of genetic datasets

2017 ◽  
Author(s):  
James E. Hicks
Keyword(s):  
Population Genetics ◽  
Data Structures ◽  
Genetic Epidemiology ◽  
Genetic Data ◽  
Link Type ◽  
File Formats ◽  
Time Simulation ◽  
Cross Platform ◽  
User Friendly ◽  
Python Package

AbstractThe development of software for working with data from population genetics or genetic epidemiology often requires substantial time spent implementing common procedures. Pydigree is a cross-platform Python 3 library that contains efficient, user friendly implementations for many of these common functions, and support for input from common file formats. Developers can combine the functions and data structures to rapidly implement programs handling genetic data. Pydigree presents a useful environment for development of applications for genetic data or rapid prototyping before reimplementation in a higher-performance language.Pydigree is freely available under an open source license. Stable sources can be found in the Python Package Index at https://pypi.python.org/pypi/pydigree/, and development sources can be downloaded at https://github.com/jameshicks/pydigree/

An Extension to the JCAMP-DX Standard File Format, JCAMP-DX V.5.01

1999 ◽  
Vol 71 (8) ◽  
pp. 1549-1556 ◽  
Author(s):  
Peter Lampen ◽  
Jörg Lambert ◽  
R. J. Lancashire ◽  
R. S. McDonald ◽  
P. S. McIntyre ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Careful Consideration ◽  
File Format ◽  
Nmr Data ◽  
File Formats ◽  
Standard File Format ◽  
Good Laboratory ◽  
Year 2000

Version 5.00 of the JCAMP-DX specifications were published for NMR and Mass Spectrometry file formats in Appl. Spectrosc.47, 1093-1099, (1993) and Appl. Spectrosc.48, 1545-1552, (1994). Since publication of these protocols developments in spectroscopy have led to a large number of requests for additions for applications not originally covered. Following careful consideration, it has become apparent that a few minor modifications will significantly increase the range of possible applications.In addition, new data labels have been introduced to ensure that files are year 2000 compliant and allow for conformity with good laboratory practices (GLP). These modifications are detailed in this publication as well as examples of the official NTUPLE JCAMP-DX definition as applied to NMR data.

scholarly journals Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

2015 ◽  
Author(s):  
Antonino Ingargiola ◽  
Ted Laurence ◽  
Robert Boutelle ◽  
Shimon Weiss ◽  
Xavier Michalet
Keyword(s):  
Programming Languages ◽  
Single Molecule ◽  
Single Photon ◽  
Photon Counting ◽  
File Format ◽  
Single Molecule Fluorescence ◽  
File Formats ◽  
Photon Counting Detectors ◽  
User Friendly

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.

scholarly journals Examining Attributes of Open Standard File Formats for Long-term Preservation and Open Access

2012 ◽  
Vol 31 (4) ◽  
pp. 46 ◽  
Author(s):  
Eun G Park ◽  
Sam Oh
Keyword(s):  
Selection Criteria ◽  
Current Knowledge ◽  
File Format ◽  
Comprehensive Review ◽  
Common Criteria ◽  
File Formats ◽  
Open Standard ◽  
Standard File Format ◽  
Long Term Preservation

This study examines the attributes that have been used to assess file formats in literature and compiles the most frequently used attributes of file formats in order to establish open standard file format selection criteria.  A comprehensive review was undertaken to identify the current knowledge regarding file format selection criteria. The findings indicate that the most common criteria can be categorized into five major groups: functionality, metadata, openness, interoperability and independence. These attributes appear to be closely related. Additional attributes include presentation, authenticity, adoption, protection, preservation, reference and others. 

Pedigree and Pedigree Import Wizard

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 552g-553
Author(s):  
Shahrokh Khandizadeh
Keyword(s):  
Additional Data ◽  
File Format ◽  
Fruit Crops ◽  
Operating Environment ◽  
Agronomic Characteristics ◽  
Link Type ◽  
Plant Characteristics ◽  
User Friendly

Pedigree for Windows is a user-friendly program that allows the user to trace agronomic characteristics, draw pedigrees, and view images of several fruit crops, including more than 1400 apple, 800 strawberry, 800 almond, 100 blackberry, 80 blueberry, 790 pear, 200 raspberry examples. Pedigree Import Wizard®© for Windows is an add-on software for users who are interested in importing their research or breeding data records of fruit, flower, and plant characteristics and any related images into Pedigree for Windows. Pedigree for Windows and Pedigree Import Wizard have been designed so that a user familiar with the Windows operating environment should have little need to refer to the documentation provided with the program. Pedigree Import Wizard uses a comma-separated value (csv) file format under the MS Excel environment. This option allows the user to add or import additional data to the existing database that are already stored in other software such as Lotus, Excel, Access, QuattroPro, WordPerfect, and MS Word tables, etc., as long as they work under the Windows environment. A free demo version of Pedigree and Pedigree Import Wizard for Windows is available from http://www.pgris.com.

Research on the Three-Dimensional Displaying of STL ASCII and Binary File

2014 ◽  
Vol 940 ◽  
pp. 433-436 ◽  
Author(s):  
Ying Zhang ◽  
Xin Shi
Keyword(s):  
Detailed Analysis ◽  
Programming Language ◽  
Coordinate Transformation ◽  
Graphical Representation ◽  
Three Dimensional ◽  
File Format ◽  
Binary File ◽  
Stl File ◽  
File Formats ◽  
Three Dimensional Display

Based on the detailed analysis of the STL file format, VC++ 6.0 programming language was used to extract the STL ASCII and binary file information, at the same time, using the OpenGL triangle drawing technology for graphical representation of the STL file, with rendering functions such as material, coordinate transformation, lighting, et al, finally realizing the loading and three-dimensional display of STL ASCII and binary file formats.

scholarly journals PTRwid: a new widget-tool for processing PTR-TOF-MS data

2015 ◽  
Vol 8 (2) ◽  
pp. 1629-1669 ◽  
Author(s):  
R. Holzinger
Keyword(s):  
Comprehensive Evaluation ◽  
Time Of Flight ◽  
Proton Transfer Reaction ◽  
Mass Scale ◽  
Process Data ◽  
Mass Spectrometers ◽  
Scale Calibration ◽  
Field Campaigns ◽  
User Friendly ◽  
Tof Ms

Abstract. PTRwid is a fast and user friendly tool that has been developed to process data from proton-transfer-reaction time-of-flight mass-spectrometers (PTR-TOF-MS) that use HTOF time-of-flight mass-spectrometers from Tofwerk AG (Switzerland). PTRwid is designed for a comprehensive evaluation of whole laboratory or field based studies. All processing runs autonomously and whole laboratory or field campaigns can, in principle, be processed with a few mouse clicks. Unique features of PTRwid include (i) an autonomous and accurate mass scale calibration, (ii) the computation of an "Unified Mass list" that – in addition to an uniform data structure – provides a robust method to determine the precision of attributed peak masses, and (iii) fast data analysis due to well considered choices in data processing.

Recalculations between different expressions of stable HCNOS isotope results – is it easy?

2021 ◽  
Author(s):  
Grzegorz Skrzypek ◽  
Philip Dunn
Keyword(s):  
Mass Spectrometry ◽  
Stable Isotope ◽  
Isotope Ratio ◽  
Data Sets ◽  
Atom Fraction ◽  
Working Standard ◽  
Mass Spectrometers ◽  
User Friendly ◽  
Zero Points ◽  
Selection Of

<p>The stable HCNOS isotope compositions can be reported in various ways depending on scientific domain and needs. The most common notations are 1) the isotope ratio of two stable isotopes; 2) isotope delta value, and 3) atom fraction of one or more of the isotopes. Frequently recalculations between these notations are required for certain applications, particularly when merging different data sets. All these recalculations require using the absolute isotope ratio for the zero points of the stable isotope delta scales (<em>R<sub>std</sub></em>). However, several <em>R<sub>std</sub></em> with very contrasting values have been proposed over time and there is no common agreement on which values should be used word-wide (Skrzypek and Dunn, 2020a).</p><p>Differences in the selection of <em>R<sub>std</sub></em>value may lead to significant differences between different data sets recalculated from delta value to other notations. These differences in R<sub>std</sub> have a significant influence also on the normalization of raw values but only when the normalization is conducted versus the working standard gas value. We proposed a user-friendly EasyIsoCalculator (http://easyisocalculator.gskrzypek.com) that allows recalculation between the main expressions of isotope compositions using various <em>R<sub>std</sub></em> and aids for identification of potential inconsistencies in recalculations (Skrzypek and Dunn, 2020b).</p><p> </p><p>Skrzypek G., Dunn P. 2020a. Absolute isotope ratios defining isotope scales used in isotope ratio mass spectrometers and optical isotope instruments. Rapid Communications in Mass Spectrometry 34: e8890.</p><p>Skrzypek G., Dunn P., 2020b. The recalculation of the stable isotope expressions for HCNOS – EasyIsoCalculator. Rapid Communications in Mass Spectrometry 34: e8892.</p>

Digital File Formats for Digital Preservation

2018 ◽  
pp. 218-233
Author(s):  
Mayank Yuvaraj
Keyword(s):  
Digital Libraries ◽  
Digital Preservation ◽  
Institutional Repository ◽  
File Format ◽  
Institutional Repositories ◽  
File Formats ◽  
Digital File ◽  
The Common ◽  
Common Understanding

During the course of planning an institutional repository, digital library collections or digital preservation service it is inevitable to draft file format policies in order to ensure long term digital preservation, its accessibility and compatibility. Sincere efforts have been made to encourage the adoption of standard formats yet the digital preservation policies vary from library to library. The present paper is based against this background to present the digital preservation community with a common understanding of the common file formats used in the digital libraries or institutional repositories. The paper discusses both open and proprietary file formats for several media.

How Cross-Platform Technology Can Facilitate Easier Creation of Business Apps

2017 ◽  
pp. 104-140
Author(s):  
Tim A. Majchrzak ◽  
Jan C. Dageförde ◽  
Jan Ernsting ◽  
Christoph Rieger ◽  
Tobias Reischmann
Keyword(s):  
Mobile Computing ◽  
Mobile Devices ◽  
Web Technology ◽  
App Development ◽  
Long Run ◽  
Platform Technology ◽  
Cross Platform ◽  
Platform Development ◽  
User Friendly ◽  
Business Orientation

Applications for mobile devices – apps – have seen unprecedented growth in importance. Ever better apps keep propelling the proliferation of mobile computing. App development is rather easy, particularly if it is based on Web technology. However, implementing apps that are user friendly and useful in the long-run is cumbersome. Thereby, it typically is expensive for corporate developers. Nonetheless, business apps are embraced by enterprises. To overcome the overhead of developing separately for multiple platforms and to mitigate the problems of device fragmentation, cross-platform development approaches are employed. While many such approaches exist, few have found widespread usage. In this chapter, we argue what the path towards future solutions could look like. We thereby take a rather technological look, but always keep business-orientation in mind. Our findings suggest that much effort is needed to enable the next generations of business apps. However, such apps will provide many merits and possibilities. Moreover, they provide the chance to master several of today's challenges.

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