Bioplate coordinates are numbers but it would be better to have character-number pairs

[Jari Häkkinen]

Bioplate row/col coordinates are numbers [0..n,0..m] whereas the physical plate uses character number pairs [A..Z,1..m]. I suppose the underlying database in BASE requires numbers but it is confusing for the users to see the numbers only coordinates. Also, starting the coordinates at 0 makes the life really hard to non computer science savvy users. Would it be possible to show character-number pairs in dialogues? Or at least show the coordinates with 1,1 as starting position rather than 0,0?

I suppose the coordinate system to use in batch importers also starts at 0,0 which may cause trouble for users.

[Nicklas Nordborg]

The same system is used for plates in the array lims section. Does this mean that the same change should be done there as well? I guess it is no problem to change what is displayed or to make the importer convert the values. One problem might be that filters on list pages still need to use the numerical values that are present in the database (0-based values). Is it common to filter on the coordinates? The simplest solution to the filtering problem would be to not allow filtering. Another option is to use enumerated values with a dropdown selection list.

Users should also be aware of that exports made with the Table exporter can only export the 0-based coordinates.

[Jari Häkkinen]

For consistency we should make the same change to the array LIMS plates as well.

I'll check for the use case on filtering on coordinates.

[Jari Häkkinen]

Replying to jari:

For consistency we should make the same change to the array LIMS plates as well.

I'll check for the use case on filtering on coordinates.

Filtering on coordinates is useful. The suggestion is to use dropdown selection lists where several values can be selected, i.e., one should not be restricted to only select A but to have A or B or E, ... The same goes for the other coordinate.

[Jari Häkkinen]

96-plates have [A..H,1..12]

384-plates have [A..P,1..24]

1536 is still unknown for us.

[Nicklas Nordborg]

The same system is used for plates in the array lims section.

This was not 100% true. The PlateFlatFileImporter assumes alphanumeric coordinates and translates A1->0,0; A2->0,1 and so on. But after that the 0-based numerical index is used on list pages and other places.

It should be fairly easy to do the same in the item batch importers as well. Does anyone mind if this is a backwards incompatible change with respect to coordinates? Eg. files that uses the internal (0-based) coordinate system will put things in incorrect wells.

This ticket should be divided into separate tickets for:

• Batch importer changes
• Filter and display changes in Bio Lims
• Filter and display changes in Array Lims

[Jari Häkkinen]

Replying to nicklas:

The same system is used for plates in the array lims section.

This was not 100% true. The PlateFlatFileImporter assumes alphanumeric coordinates and translates A1->0,0; A2->0,1 and so on.

The alphanumeric coordinates is what the user expects so I see this as a good thing.

It should be fairly easy to do the same in the item batch importers as well. Does anyone mind if this is a backwards incompatible change with respect to coordinates? Eg. files that uses the internal (0-based) coordinate system will put things in incorrect wells.

We have not started with importing coordinates yet so for us this is not an issue. We are developing our plate/batch importer procedures now so we'll just go for the new coordinates if they are adopted in the importers.

[Nicklas Nordborg]

Batch importer changes now has it's own ticket #1269. Since it is a backwards incompatible change it will go in 2.11. The other things will be handled in a later release.

[Nicklas Nordborg]

See ticket #1272 for a possible way to solve the table export issue.

[Nicklas Nordborg]

(In [4856]) References #1266, #1272: Bioplate coordinates are numbers but it would be better to have character-number pairs

A test of #1272. Fixes the export of wells from the Biomaterial LIMS -> Bioplates -> Biowell tab.

[Nicklas Nordborg]

(In [4858]) References #1266, #1272: Bioplate coordinates are numbers but it would be better to have character-number pairs

A test of #1272. Fixes the display of well coordinates in the list on Biomaterial LIMS -> Bioplates -> Biowell tab.

[Martin Svensson]

This ticket is split into two sub tickets

• Array LIMS ticket #1282
• Bio LIMS ticket #1281

[Martin Svensson]

See related tickets: #1281, #1282