Deprecated features in El-MAVEN

ElucidataInc / ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.

https://resources.elucidata.io/elmaven/

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Deprecated features in El-MAVEN #586

Open shubhra-agrawal opened 6 years ago

shubhra-agrawal commented 6 years ago

We are planning to deprecate certain features of El-MAVEN that are either no longer useful to the community or fall outside the scope of El-MAVEN. See discussion We propose:

[x] NA correction (except C13 abundance )
[ ] ~~Statistics module~~
[ ] Pathway visualization module
[ ] Peptide Fragmentation widget
[x] Loess Fit alignment
[x] mzroll format

We would like to hear from our users before implementing any of these changes. Suggestions for other modules that are no longer useful are also welcome.

sp-eldata commented 6 years ago

@lparsons @chubukov Please chime in.

@shubhra-agrawal We should also discuss how to clearly labels issues which are or are going to be deprecated.

chubukov commented 6 years ago

What do you mean by the statistics module? If you mean the scatter/volcano plots, I would not get rid of them. They work ok, and people do use them.

lparsons commented 6 years ago

@shubhra-agrawal Perhaps make this a checklist with links to specific issues if they exist (e.g.)

[ ] Item 1 - Link to Issue
[ ] Item 2 - Link to issue
[x] Item 3 - Link to issue (closed)

lparsons commented 6 years ago

Remove one of the duplicate Group Filtering options (not really deprecate, just remove)

Minimum Quality and At least x peaks above min qualilty
Min. Good Peak / Group

lparsons commented 6 years ago

Poly Fit alignment algorithm
External Programs interfaces (ProteoWizard and R)

sahil21 commented 6 years ago

[ ] Remove or update 'Method Summary' in the peaks dialog as we have dump & load settings feature implemented.
[ ] We have 3 alignment visualizations. Do we need all 3 of them?
[ ] Gallery widget? Not sure people use it or not.

chubukov commented 6 years ago

@sahil21

We have 3 alignment visualizations. Do we need all 3 of them?

I don't find the one with the within-group RT deviation as a function of RT time particularly useful. But I wouldn't rush to get rid of these -- perhaps they will turn out to be useful (maybe with small modifications) as you try out different alignment algorithms.

Gallery widget? Not sure people use it or not.

I don't think anyone in our group uses it.

sahil21 commented 6 years ago

@chubukov Sure. We can think of removing that particular alignment visualization after we are done finalizing the new alignment algorithm. At least for the next release, let's not remove it.

shubhra-agrawal commented 6 years ago

@surbhipoddar FYI

shubhra-agrawal commented 5 years ago

@lparsons @chubukov We have added the 'deprecated' tag to the following features as of v0.7.0:

mzroll format
Loess fit alignment
NA correction

We will not be fixing issues related to the above features anymore. These will be available for the next 2 releases after which we will gradually remove them from the software.

Please let us know if there are any questions/concerns.

chubukov commented 5 years ago

@shubhra-agrawal Will the ability to read old mzroll files be kept?

shubhra-agrawal commented 5 years ago

@chubukov We're largely in favour of retaining that functionality for at least 2 more releases to give our users enough time to convert their old mzrolls to the new emDB format. If not, they can always use an older version of El-MAVEN to convert their mzrolls and use the resulting emDB in the latest version of El-MAVEN. Does that sound acceptable?

saifulbkhan commented 5 years ago

With release v0.8.0 (and forward), Loess Fit alignment and mzroll export abilities have been removed.