Standardized Infinite plate reader section names for XML? about assaytools HOT 24 OPEN

It is not standardized. We have some rough things we do consistently, but nothing documented, and some things are still pretty sloppy. We should definitely refine this, but not sure it's a priority over getting the data.

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Can we at least standardize naming conventions for the remainder of the data we collect for the paper?

This is just a matter of saying "we'll name the different measurements X, Y, and Z in the XML file". We should release the XML files with the paper, so it would be optimal if the same naming convention is used throughout the collected datasets.

We don't need any standardization beyond this for now.

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I think this is a small piece of a much larger question... We've kind of been focusing on the data and the API separately, and now we are starting to merge them, which is great... Don't think it will be hard, we just need to hammer it out.

Right now the section names are tagged on to the end of the spectra output png files, and are: abs, em280,em280_Copy2,em340, and em340_Copy2. The 'Copy_2' sections are with a different gain, and this is not a great way of naming them, but we didn't realize this was happening until we'd already collected some data. Also all of this information (gain, emission wavelength, absorbance, and a lot of other things) are already in the metadata of each section, which we currently aren't storing and connecting to the data files themselves, other than appending as titles to the output png's.

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Also all of this information (gain, emission wavelength, absorbance, and a lot of other things) are already in the metadata of each section, which we currently aren't storing and connecting to the data files themselves, other than appending as titles to the output png's.

This would be an important part of the new API we keep talking about, I think.

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Ah, OK! As long as we can get this from the metadata, we're probably OK then.

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For now, as long as we have a consistent set of section names for each set of experimental data we might want to analyze together, we don't need a lot of new code engineering to get the job done.

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I'm curious what namign scheme you are using for the current set of single point experiments, where I think we want to collect

• absorbance at 280 nm, 350 nm, 450 nm
• excitation/emission for top/bottom with gains 100/120 at 280/350, 280/450, 350/450

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@Lucelenie and I are currently working on an updated version of the Spectra scripts. (Changing name from WIP to EXP, using newest D300 driver, adding comments, improving usage of variables, etc.) In this process we can also update the xml file Section names, since this is something our parsing scripts currently use (though it's not crucial as mentioned above, since this information is also in the metadata). The current names of sections are: abs, em280, em280_Copy2, em340, and em340_Copy2. Where the Copy2 suffix indicates that gain 120 rather than gain 100 was used. Any suggestions on the new names for these?

Maybe: abs, ex280_gain100, ex280_gain120, ex340_gain100, and ex340_gain120.

Since there has been some confusion in the past as to whether the wavelength is the excitation or emission wavelength, this also changes these headers to e.g. ex280 to indicate they are emission scans at an excitation of 280 nm.

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Any opinions on this @jchodera? We will be finalizing this tomorrow when Lucelenie runs the AZ ligands.

Also of note, right now our singlet assay section names are: 280_340_BOT_100, 280_340_TOP_100, 280_480_BOT_100, 280_480_TOP_100, 340_480_BOT_100, 340_480_TOP_100, 280_340_BOT_120, 280_340_TOP_120, 280_480_BOT_120, 280_480_TOP_120, 340_480_BOT_120, 340_480_TOP_120, ABS_280, ABS_340, and ABS_480.

We can definitely change this, but not sure which format is preferable, the equivalent for the spectra assay in this format would be: ABS, 280_TOP_100, 280_TOP_120, 340_TOP_100, and 340_TOP_120.

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Sounds great!

Can we stop calling it a "singlet assay", though? Maybe "Single wavelength assay"?

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Do you have a preference for one of those two formats?

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Sorry, I totally misread this. Just a moment.

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If we don't want to change the format of the single-wavelength assays too, what about:
ABS, 280_SCAN_TOP_100, 280_SCAN_TOP_120, etc., so that the difference between the single-wavelength and emission spectrum wavelength is just that we substitute the wavelength with SCAN to indicate we scanned this wavelength?

In general, I prefer the first suggestion (abs, ex280_gain100, ex280_gain120, ex340_gain100, ex340_gain120) since it is more comprehensible, but if you don't want to change the single-wavelength stuff to match style, maybe it's better to use a consistent format.

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The single wavelength assay is still being nailed down, so changing it will not be a big deal.

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The spectra assay format for singlet is a bit verbose: ex280_em340_bot_gain100. But maybe more intuitive?

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All the spectra assays at the moment are top fluorescence, so this is not currently included in the name, but maybe we would want to for consistency with the single wavelength assay?

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What is bot?

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Oh, bottom!

All the spectra assays at the moment are top fluorescence, so this is not currently included in the name, but maybe we would want to for consistency with the single wavelength assay?

I think it's best to be consistent and include it.

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It refers to whether fluorescence is being read from top or the bottom of the plate.

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Okay, so it seems like we've landed on:

Spectra sections: abs, ex280_top_gain100, ex280_top_gain120, ex340_top_gain100, ex340_top_gain120.

Single wavelength sections: ex280_em340_bot_gain100, ex280_em340_top_gain100, ex280_em480_bot_gain100, ex280_em480_top_gain100, ex340_em480_bot_gain100, ex340_em480_top_gain100, ex280_em340_bot_gain120, ex280_em340_top_gain120, ex280_em480_bot_gain120, ex280_em480_top_gain120, ex340_em480_bot_gain120, ex340_em480_top_gain120, abs_280, abs_340, and abs_480.

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How do you feel about ex280_top_scan_gain100 instead of ex280_top_gain100?

And ex280_em340_bottom_gain100 instead of ex280_em340_bot_gain100?

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Sounds great!

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Final section names (fluorescence has four fields, absorbance have two):

Spectra sections: abs_scan, ex280_scan_top_gain100, ex280_scan_top_gain120, ex340_scan_top_gain100, ex340_scan_top_gain120.

Single wavelength sections: ex280_em340_bottom_gain100, ex280_em340_top_gain100, ex280_em480_bottom_gain100, ex280_em480_top_gain100, ex340_em480_bottom_gain100, ex340_em480_top_gain100, ex280_em340_bottom_gain120, ex280_em340_top_gain120, ex280_em480_bottom_gain120, ex280_em480_top_gain120, ex340_em480_bottom_gain120, ex340_em480_top_gain120, abs_280, abs_340, and abs_480.

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Awesome!

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