TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation

Choi, Inho; Abeysinghe, Eroma; Coulter, Eric; Marru, Suresh; Pierce, Marlon; Liu, Xiaowen

doi:10.1145/3311790.3400853

Cited by 2 publications

(2 citation statements)

References 21 publications

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“…The installation is as simple as downloading and running the containerised application (Supplementary Material Section 4). However, unlike other available computing environments for TD data processing like the web browser-based TDPortal or TopPIC Gateway [23,24], or the stand-alone tool MASH explorer [25] (which needs the Windows operating system to run), the workflows themselves are not reconfigurable via a graphical user interface. Instead, high-throughput analysis can be conducted on a huge variety of compute infrastructures through the application of the underlying Nextflow workflows.…”

Section: Datasetmentioning

confidence: 99%

TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data

Walzer,

Jeong,

Tabb

et al. 2023

Proteomics

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Although Top‐down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise their adoption. In this context, there are numerous improvements that are possible in the area of open science practices, including a greater application of the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. These include, for example, increased data sharing practices and readily available open data standards. Additionally, the field would benefit from the development of open data analysis workflows that can enable data reuse of public datasets, something that is increasingly common in other proteomics fields.

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Section: Datasetmentioning

confidence: 99%

TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data

Walzer,

Jeong,

Tabb

et al. 2023

Proteomics

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show abstract

“…Our TopDownApp is free and open to use, and can be used on a local computer or institutional server-setup, installation as simple as downloading and running the containerised app. However, unlike other computing environments for TD data processing like TDPortal or TopPIC Gateway [22,23], the workflows themselves are not reconfigurable via GUI. Instead, high-throughput analysis can be conducted on a huge variety of compute infrastructures through application of the underlying nextflows.…”

Section: Main Textmentioning

confidence: 99%

TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data

Walzer

Jeong

Tabb

et al. 2023

Preprint

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Although Top-down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise its adoption. In this context, there are numerous improvements that are possible in the area of open science including the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include e.g. increased data sharing practices and availability of tailored open data standards. Additionally, the field would benefit from the development of open analysis workflows that can enable e.g. data reuse of public datasets, something that is increasingly common in other proteomics fields. We present an open and modular platform for the analysis and visualisation of TD proteomics data called TopDownApp. It can be used as a flexible analysis platform, through the use of a common workflow engine, common data formats for input/output, and software containerisation. It can also serve as a tool for visual inspection through its simple setup. As a key point, it can also be used as a development platform for new tools through the use of Python, a modular design, software containerisation and common data formats. TopDownApp is open source and freely available at: https://github.com/mwalzer/TopDownApp.

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TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation

Cited by 2 publications

References 21 publications

TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data

TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data

TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data

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