Module: Submission::ScrnaCoreCdnaPrepFeasibilityCalculator

Included in:
ScrnaCoreCdnaPrepFeasibilityValidator
Defined in:
app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb

Overview

This module provides methods for calculating the full allowance volume and the final resuspension volume for scRNA core cDNA prep feasibility validations. NB. Search for 'scRNA Core Pooling Developer Documentation' page in Confluence (public) for a more verbose explanation of the calculations used here.

Constant Summary collapse

SCRNA_CORE_CDNA_PREP_GEM_X_5P = 
'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p'
HEADER_BARCODE =

Constants for the headers in the bulk submission for scRNA core cDNA prep.

'barcode'
HEADER_PLATE_WELL = 
'plate well'
HEADER_NUMBER_OF_POOLS = 
'scrna core number of pools'
HEADER_CELLS_PER_CHIP_WELL = 
'scrna core cells per chip well'
ALLOWANCE_BANDS = 
{
  two_pools_two_counts: '2 pool attempts, 2 counts',
  two_pools_one_count: '2 pool attempts, 1 count',
  one_pool_two_counts: '1 pool attempt, 2 counts',
  one_pool_one_count: '1 pool attempt, 1 count'
}.freeze

Instance Method Summary collapse

Instance Method Details

#calculate_allowance_bands ⇒ Hash

Calculates the allowance band for each study and project combination. This method evaluates the final resuspension volume for each study-project group and assigns an appropriate allowance band based on predefined thresholds. Example output: { { study: "Study A", project: "Project X" } => "2 pool attempts, 2 counts", { study: "Study B", project: "Project Y" } => "1 pool attempt, 2 counts" }

Returns:

  • (Hash) —

    A hash where the keys are hashes containing :study and :project, and the values are the corresponding allowance bands as strings.



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# File 'app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb', line 62

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#calculate_chip_loading_volume(number_of_cells_per_chip_well) ⇒ Float

This method calculates the chip loading volume (in microlitres) for the specified number of cells per chip well, which is typically specified in in a bulk submission per study and project. It uses the pooling settings from the scRNA config.

Parameters:

  • number_of_cells_per_chip_well (Integer) —

    the number of cells per chip well from the bulk submission

Returns:

  • (Float) —

    the chip loading volume



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# File 'app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb', line 81

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#calculate_resuspension_volume(count_of_samples_in_pool) ⇒ Float

This method calculates the resuspension volume (in microlitres) for the specified number of samples in a pool, which is typically taken as the number of samples in the smallest pool for a study and project. It uses the pooling settings from the scRNA config. It first calculates the total cells in 300ul for the given number of samples in the pool, and then the resuspension volume for that total cell count.

Parameters:

  • count_of_samples_in_pool (Integer) —

    the number of samples in the pool

Returns:

  • (Float) —

    the resuspension volume



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# File 'app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb', line 95

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#calculate_total_cells_in_300ul(count_of_samples_in_pool) ⇒ Integer

This method calculates the total cells in 300ul for the specified number of samples in a pool, which is typically taken as the number of samples in the smallest pool for a study and project. It uses the pooling settings from the scRNA config.

Parameters:

  • count_of_samples_in_pool (Integer) —

    the number of samples in the pool

Returns:

  • (Integer) —

    the total cells in 300ul



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# File 'app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb', line 107

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#calculate_volume_needed(number_of_cells_per_chip_well, number_runs, number_cell_counts) ⇒ Float

Calculates the total volume needed (in microliters) for a given number of cells per chip well.

This method is used in bulk submissions per study and project, leveraging pooling settings from the scRNA configuration. It first calculates the chip loading volume for the specified number of cells per chip well and then determines the total volume required, including allowances for cell counting and wastage.

The total volume needed is calculated as:

- The volume required for loading chips, based on the number of pool attempts (`number_runs`).
- The volume taken for cell counting, based on the number of cell counts (`number_cell_counts`).
- An additional wastage volume (`scrna_config[:wastage_volume]`).

Band Allowance Calculations:

- If `number_runs = 2` and `number_cell_counts = 2`, it calculates `2 pool attempts, 2 counts` (Full allowance).
- If `number_runs = 2` and `number_cell_counts = 1`, it calculates `2 pool attempts, 1 count`.
- If `number_runs = 1` and `number_cell_counts = 2`, it calculates `1 pool attempt, 2 counts`.
- If `number_runs = 1` and `number_cell_counts = 1`, it calculates `1 pool attempt, 1 count`.

Parameters:

  • number_of_cells_per_chip_well (Integer) —

    The number of cells per chip well.

  • number_runs (Integer) —

    The number of pool attempts (runs) to be performed.

  • number_cell_counts (Integer) —

    The number of times cell counting is performed.

Returns:

  • (Float) —

    The total volume required for the experiment.



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# File 'app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb', line 45

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end