scholarly journals Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening

2020 ◽  
Author(s):  
Rick Helmus ◽  
Thomas Ter laak ◽  
Pim de Voogt ◽  
Annemarie van Wezel ◽  
Emma Schymanski
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Open Source Software ◽  
Current Data ◽  
Environmental Data ◽  
Software Platform ◽  
Environmental Sciences ◽  
Target Analysis ◽  
Usage Evaluation ◽  
Target Screening

Abstract Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailoredand straightforwardnon-target analysis workflows. This platform makes the usage, evaluation and mixing of well-tested algorithms seamless by harmonizing various commonly (primarily open) software tools under a consistent interface. In addition, patRoonoffersvarious functionality and strategies tosimplify and perform automated processing of complex (environmental) data effectively.patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform a straightforward and effective non-target analysis was demonstrated with real-world environmental samples, showing thatpatRoonmakes comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.

scholarly journals patRoon: open source software platform for environmental mass spectrometry based non-target screening

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Rick Helmus ◽  
Thomas L. ter Laak ◽  
Annemarie P. van Wezel ◽  
Pim de Voogt ◽  
Emma L. Schymanski
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Open Source Software ◽  
Treatment Plant ◽  
Drinking Water Treatment ◽  
Current Data ◽  
Environmental Data ◽  
Software Platform ◽  
Environmental Sciences ◽  
Target Analysis

AbstractMass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.

scholarly journals patRoon: Open source software platform for environmental mass spectrometry based non-target screening

2020 ◽  
Author(s):  
Rick Helmus ◽  
Thomas Ter laak ◽  
Annemarie van Wezel ◽  
Pim de Voogt ◽  
Emma Schymanski
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Open Source Software ◽  
Treatment Plant ◽  
Drinking Water Treatment ◽  
Current Data ◽  
Environmental Data ◽  
Software Platform ◽  
Environmental Sciences ◽  
Target Analysis

Abstract Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.

scholarly journals OpenMS: a flexible open-source software platform for mass spectrometry data analysis

2016 ◽  
Vol 13 (9) ◽  
pp. 741-748 ◽  
Author(s):  
Hannes L Röst ◽  
Timo Sachsenberg ◽  
Stephan Aiche ◽  
Chris Bielow ◽  
Hendrik Weisser ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Mass Spectrometry Data ◽  
Software Platform

scholarly journals Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware

2021 ◽  
Author(s):  
Jonathan Shapey ◽  
Thomas Dowrick ◽  
Rémi Delaunay ◽  
Eleanor C. Mackle ◽  
Stephen Thompson ◽  
...  
Keyword(s):  
Skull Base ◽  
Open Source ◽  
Open Source Software ◽  
Skull Base Surgery ◽  
Patient Specific ◽  
Software Platform ◽  
Image Guided ◽  
Phantom Model ◽  
Technical Requirements ◽  
Navigated Ultrasound

Abstract Purpose Image-guided surgery (IGS) is an integral part of modern neuro-oncology surgery. Navigated ultrasound provides the surgeon with reconstructed views of ultrasound data, but no commercial system presently permits its integration with other essential non-imaging-based intraoperative monitoring modalities such as intraoperative neuromonitoring. Such a system would be particularly useful in skull base neurosurgery. Methods We established functional and technical requirements of an integrated multi-modality IGS system tailored for skull base surgery with the ability to incorporate: (1) preoperative MRI data and associated 3D volume reconstructions, (2) real-time intraoperative neurophysiological data and (3) live reconstructed 3D ultrasound. We created an open-source software platform to integrate with readily available commercial hardware. We tested the accuracy of the system’s ultrasound navigation and reconstruction using a polyvinyl alcohol phantom model and simulated the use of the complete navigation system in a clinical operating room using a patient-specific phantom model. Results Experimental validation of the system’s navigated ultrasound component demonstrated accuracy of $$<4.5\,\hbox {mm}$$ < 4.5 mm and a frame rate of 25 frames per second. Clinical simulation confirmed that system assembly was straightforward, could be achieved in a clinically acceptable time of $$<15\,\hbox {min}$$ < 15 min and performed with a clinically acceptable level of accuracy. Conclusion We present an integrated open-source research platform for multi-modality IGS. The present prototype system was tailored for neurosurgery and met all minimum design requirements focused on skull base surgery. Future work aims to optimise the system further by addressing the remaining target requirements.

scholarly journals OptFlux: an open-source software platform for in silico metabolic engineering

2010 ◽  
Vol 4 (1) ◽  
Author(s):  
Isabel Rocha ◽  
Paulo Maia ◽  
Pedro Evangelista ◽  
Paulo Vilaça ◽  
Simão Soares ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Open Source ◽  
Open Source Software ◽  
In Silico ◽  
Software Platform

Pulse Physiology Engine: an Open-Source Software Platform for Computational Modeling of Human Medical Simulation

2019 ◽  
Vol 1 (5) ◽  
pp. 362-377 ◽  
Author(s):  
Aaron Bray ◽  
Jeffrey B. Webb ◽  
Andinet Enquobahrie ◽  
Jared Vicory ◽  
Jerry Heneghan ◽  
...  
Keyword(s):  
Computational Modeling ◽  
Open Source ◽  
Open Source Software ◽  
Medical Simulation ◽  
Software Platform

scholarly journals OPEN SCIENCE, KNOWLEDGE SHARING AND REPRODUCIBILITY AS DRIVERS FOR THE ADOPTION OF FOSS4G IN ENVIRONMENTAL RESEARCH

2019 ◽  
Vol XLII-4/W14 ◽  
pp. 107-110
Author(s):  
I. Iosifescu Enescu ◽  
G-K. Plattner ◽  
L. Bont ◽  
M. Fraefel ◽  
R. Meile ◽  
...  
Keyword(s):  
Knowledge Sharing ◽  
Open Source ◽  
Open Source Software ◽  
Academic Research ◽  
Open Science ◽  
Environmental Data ◽  
Environmental Research ◽  
Data Repository ◽  
User Requirement ◽  
Data Portal

<p><strong>Abstract.</strong> Support for open science is a highly relevant user requirement for the environmental data portal EnviDat. EnviDat, the institutional data portal and publication data repository of the Swiss Federal Research Institute WSL, actively implements the FAIR (Findability, Accessibility, Interoperability and Reusability) principles and provides a range of services in the area of research data management. Open science, with its requirements for improved knowledge sharing and reproducibility, is driving the adoption of free and open source software for geospatial (FOSS4G) in academic research. Open source software can play a key role in the proper documentation of data sets, processes and methodologies, because it supports the transparency of methods and the precise documentation of all steps needed to achieve the published results. EnviDat actively supports these activities to enhance its support for open science. With EnviDat, WSL contributes to the ongoing cultural evolution in research towards open science and opportunities for distant collaboration.</p>

scholarly journals A brief introduction to Open Data, Open Source Software and Collective Intelligence for environmental data creators and users

2018 ◽  
Author(s):  
Tomislav Hengl ◽  
Ichsani Wheeler ◽  
Robert A MacMillan
Keyword(s):  
Open Access ◽  
Open Source ◽  
Open Source Software ◽  
Collective Intelligence ◽  
Open Data ◽  
Open Science ◽  
Environmental Data ◽  
Key Aspects

Using the term "Open data" has become a bit of a fashion, but using it without clear specifications is misleading i.e. it can be considered just an empty phrase. Probably even worse is the term "Open Science" — can science be NOT open at all? Are we reinventing something that should be obvious from start? This guide tries to clarify some key aspects of Open Data, Open Source Software and Crowdsourcing using examples of projects and business. It aims at helping you understand and appreciate complexity of Open Data, Open Source software and Open Access publications. It was specifically written for producers and users of environmental data, however, the guide will likely be useful to any data producers and user.

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