Opened 14 years ago

Closed 13 years ago

Last modified 13 years ago

#979 closed enhancement (fixed)

Biomaterial LIMS

Reported by: Johan Vallon-Christersson Owned by: Martin Svensson
Priority: critical Milestone: BASE 2.10
Component: core Version:
Keywords: Cc:

Description (last modified by Jari Häkkinen)

Enhancing biomaterial management in BASE by adding Biomaterial LIMS (BioLIMS) functionality. Shortly, the BioLIMS functionality would comprise the capability to organize biomaterial items into plates, broadly corresponding to how reporters can be organized in plates under Array LIMS.

Main features:

  • Create BioPlates with wells that can hold Biomaterial items.
  • BioPlates have a Geometry (re-use from Array LIMS).
  • Organize Biomaterials in BioPlates by moving/removing them to/from a well of a BioPlate, i.e., a biomaterial item can exist outside of a well or in a well. NOTE: in the regular table views of biomaterials all items should be viewable (both those in and outside of BioPlate wells). BioPlate and BioPlateWell could be columns in the view tables.
  • Create new biomaterial directly into a BioPlate well. For example, from an existing biomaterial, pointing to a BioPlate well can create a child biomaterial in that well. Thus, a user has the option to move a biomaterial into a well or to create a child biomaterial in a well.

Creating plates:
From a BioLIMS menu one would access functionality to create BioPlates that can hold biomaterials. Essentially, for these functions one would have the same interface as for ArrayLIMS with the exception that users should be able to create individual plates by clicking a “New…” button (for Array LIMS plates are always uploaded from file).

Managing BioPlates:
Table views for BioPlates should be available and can basically have the same layout as table view for ArrayLIMS plates. BioPlate view table can be available from the BioLIMS menu or from the regular view menu. Single BioPlate view could share layout with single ArrayLIMS plate view with tabs for properties, annotations, and wells. Additional action button (BioPlateAct) to remove/add biomaterials would be needed. Importantly, in the regular table views of biomaterials all items should be viewable (both those in and outside of BioPlate wells). BioPlate and BioPlateWell could be columns in the view tables.

UML Diagram
Added BioPlate and BioWell to the existing biomaterials diagram: source:trunk/doc/src/docbook/figures/uml/datalayer.biomaterials.png

Change History (23)

comment:1 Changed 14 years ago by Jari Häkkinen

Milestone: BASE 2.8
Owner: changed from everyone to Johan Vallon-Christersson

comment:2 Changed 14 years ago by Jari Häkkinen

Priority: majorcritical

comment:3 Changed 14 years ago by Johan Vallon-Christersson

Milestone: BASE 2.8BASE 2.x+

comment:4 Changed 14 years ago by Johan Vallon-Christersson

Owner: Johan Vallon-Christersson deleted

comment:5 Changed 13 years ago by Nicklas Nordborg

Description: modified (diff)
Milestone: BASE 2.x+BASE 2.10

comment:6 Changed 13 years ago by Nicklas Nordborg

(In [4658]) References #979: Biomaterial LIMS

Added BioLIMS to UML diagram.

comment:7 Changed 13 years ago by Nicklas Nordborg

Description: modified (diff)
Summary: Biomaterial LIMS (BioLIMS)Biomaterial LIMS

comment:8 Changed 13 years ago by Martin Svensson

Owner: set to Martin Svensson
Status: newassigned

comment:9 Changed 13 years ago by Jari Häkkinen

Description: modified (diff)

comment:10 Changed 13 years ago by Martin Svensson

(In [4670]) References #979 Added data- and item classes needed by BioMaterial? LIMS. Also created a test-class to test BioPlate? functionallity.

comment:11 Changed 13 years ago by Martin Svensson

(In [4671]) References #979 Added keyword to svn-properties

comment:12 Changed 13 years ago by Martin Svensson

(In [4672]) References #979 Missed some files in the last commit.

comment:13 Changed 13 years ago by Martin Svensson

(In [4677]) References #979 Updated schema_version, implemented the last methods to the classes and re-arranged in BioPlate?. Tests and documentation will be written next.

comment:14 Changed 13 years ago by Martin Svensson

(In [4678]) References #979 Removed compling error in test-class

comment:15 Changed 13 years ago by Martin Svensson

(In [4685]) References #979 Added some more comments for javadoc and finished the test.

comment:16 Changed 13 years ago by Martin Svensson

(In [4704]) References #979 First commit of bioplates-support in the webbinterface.

comment:17 Changed 13 years ago by Martin Svensson

(In [4729]) References #979 Removed edit and view pages for biowells because they are not needed. Added support to view/edit a sample's bioplate/biowell

comment:18 Changed 13 years ago by Martin Svensson

(In [4730]) References #979 A labeledextract's or extract's bioplate/biowell are now available in the webclient. The pages has gone through some testings but can still have some bugs.

comment:19 Changed 13 years ago by Martin Svensson

(In [4731]) References #979 The implementation of bioplates/biowells in the webclient is now done.

comment:20 Changed 13 years ago by Martin Svensson

Resolution: fixed
Status: assignedclosed

(In [4732]) Fixes #979 Biomaterial LIMS

comment:21 Changed 13 years ago by Martin Svensson

(In [4734]) References #979 A biowell's coordinates are split into two columns on biomaterial list-pages.

comment:22 Changed 13 years ago by Martin Svensson

(In [4735]) References #979 Images for the documentation about biomaterial LIMS

comment:23 Changed 13 years ago by Nicklas Nordborg

(In [4781]) References #979: Biomaterial LIMS

Made 'ok' and 'cancel' buttons fixed on page so we don't have to scroll every time.

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