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Simulation study #67

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XinsongDu opened this issue Aug 18, 2020 · 5 comments
Open

Simulation study #67

XinsongDu opened this issue Aug 18, 2020 · 5 comments
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@XinsongDu @xkcococo @ygillespie @nishachachad @hballard22
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enhancement New feature or request

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@XinsongDu XinsongDu added the enhancement New feature or request label Aug 18, 2020
@XinsongDu XinsongDu self-assigned this Aug 18, 2020
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Task: Use RUMP and UFRC to process your own data, suppose now this is your data: https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=ST000248

Report mistakes you experienced when you try to use RUMP to process this data.

@XinsongDu XinsongDu changed the title Think about unit tests Simulation study Sep 5, 2020
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See if we can find those peaks listed on this page

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XinsongDu commented Sep 6, 2020 •
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Scalability simulation study: https://github.com/lemaslab/RUMP/wiki/6.-Execution-time-estimation, also see if the result of using HPC and private computer is the same.

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Reproducibility study: 1) run without docker on two operating systems; run with docker on two operating systems; see the difference of detected metabolites. 2) run with different MZmine versions, see the difference of peak numbers.

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A great point brought by Dinish Kumar duing MANA meeting: Test on the largest dataset (e.g., more than one thousand files) and see if it works. One great selling point would be the data is not stored in the Docker container, but mounted to it.

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@XinsongDu XinsongDu

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@nishachachad nishachachad

@hballard22 hballard22

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@XinsongDu @xkcococo @ygillespie @nishachachad @hballard22