Opened 14 years ago

Last modified 13 years ago

#979 closed enhancement

Biomaterial LIMS (BioLIMS) — at Initial Version

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


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 will have Plate type that in turn will have Geometry.
  • 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.
  • Manage biomaterial by BioPlate, i.e., mapping an entire BioPlate to a daughter BioPlate and in the process evoke processing events applied to biomaterials in the wells. The processing events should include regular transformations applicable to biomaterials, e.g., samples can be processed into new samples or into extracts. When a transformation is performed, the user can specify properties, e.g., Protocol, Original quantity, and Created date, which are then applied to all well biomaterials (child name can follow current naming procedures). NOTE: when processing biomaterials by BioPlate a limitation could be set that only a BioPlates holding a single biomaterial type, e.g., samples or extracts, can be transformed (or defaults/parameters would have to be set per biomaterial type).
  • Mapping of labeled extracts in BioPlate to array indices of Hybridization. One or more wells form a BioPlate holding labeled extracts could be mapped to a specified Hybridization. By specifying the source wells, the destination hybridization, and how mapping should be performed, labeled extracts could be associated to hybridizations. For example, from a 96-well BioPlate, all labeled extracts could be mapped to a Hybridization having 96 arrays. Correspondingly, from a 96-well BioPlate, labeled extracts from wells 1-6 could be mapped to array indices 1-6 of a Hybridization having 6 arrays.

Creating geometries, plate types, plates and mappings:
From a BioLIMS menu one would access functionality to create BioPlate types, BioPlate geometries, and corresponding 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). Possibly, functions from ArrayLIMS could be reused to a certain extent.

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, events, and wells. Additional action button (BioPlateAct) to remove/add biomaterials would be needed. This interface could perhaps be similar to that of how items are shared to other users/groups/projects (in that biomaterials could be considered members of a well). A similar BioPlateAct button could be placed in the biomaterial table views. 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.

Track tab - tracking biomaterial lineage:
Currently, the single biomaterial item view holds a tab with events. The events tab list events for the appropriate single item. An additional tab “Track” could be added. This tab would hold an overview, presenting the lineage for the item, i.e., the chain of items backwards starting with parents and downwards starting with children. In this overview, the BioLIMS should be included and for lineage items harbored in BioPlates the BioPlates and BioPlateWells should be indicated.

Experimental overview:
As BioLIMS mearly constitutes optional biomaterial management functionality, BioPlates should not appear or affect the current experimental overview. Naturally, biomaterials are tracked trough the experiment overview irrespectively of whether they exist in BioPlates or not, and irrespectively of whether they were created by BioPlate. Thus, biomaterial properties are not linked to BioPlate transformations, rather BioPlate transformations set biomaterial properties.

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