golfy 2.5.2

Heuristic peptide pool optimization for ELISpot and other immunological assays

Golfy

Golfy is a heuristic solver for experimental designs using pools of peptides, such as combinatorial ELISpot epitope mapping. Golfy constructs experimental designs which assign peptides to pools with a fixed specified "coverage" (number of pools that each peptide occurs in) while trying to avoid having any pair of peptides occur together in a pool more than once.

More formally, Golfy is a collection of heuristic search techniques for partially balanced incomplete block designs, where block design means that it's an experimental design where peptides are tested in groups, incomplete means that each block is smaller than the full set of peptides, and partially balanced means that a pair of peptides can occur together in a group 0 or 1 times.

Golfy also includes a deconvolution algorithm which attempts to find a sparse set of "hit peptides" to best explain ELISpot counts observed after using a Golfy generated experimental design.

Installation

pip install golfy

Also, scikit-learn is an requirement for the deconvolution module:

pip install scikit-learn

Usage

Assignments of peptides to pools are called golfy.Design objects, which can be constructed and optimized using several different strategies.

Designs for single round ESLIpot experiments

If all you care about is finding the best design for a fixed number of peptides and a maximum number of pools (eg 96 wells on a plate) then use thing function:

from golfy import best_design_for_pool_budget

design = best_design_for_pool_budget(num_peptides=200, max_pools=96)

It will loop over a very large configuration space, try to make the best design for each configuration, simulate ELISpot counts under a simplistic model, and score each design by its ability to deconvolve hits out of pooled results in a single round of experimentation (without a second round of validation for individual peptides).

More control over design parameters

If you want to control parameters such as the number of replicates or the maximum peptides per pool, you can call find_best_design, which tries multiple different initialization strategies to create multiple designs, optimizes each one, and returns the design which fewest constraint violations and fewest number of total pools.

from golfy import find_best_design

design = find_best_design(
    num_peptides=100,
    max_peptides_per_pool=5,
    num_replicates=3,
    invalid_neighbors=[(0,1), (1,2)],
    preferred_neighbors=[(0,3),(1,5)],
    allow_extra_pools=False,
    verbose=False)

A key parameter to find_best_design is allow_extra_pools, which determines whether Golfy is allowed to expand the number of total pools beyond the minimum by the ceil(num_peptides * num_replicates / max_peptides_per_pool). If Golfy cannot add extra pools then it may not be able to find a valid solution for every combination of parameters (but will still give you the design with the least constraint violations that it could construct and optimize).

Initialization and optimization of designs

If you want more control over the way that desgins are initialized and optimized you can use the golfy.init and golfy.optimize functions directly.

from golfy import init, is_valid, optimize

# create a random initial assignment of peptides to pools
s = init(num_peptides=100, peptides_per_pool=5, num_replicates=3, strategy='random', allow_extra_pools=False)

# the random assignment probably isn't yet a valid design
assert not is_valid(s)

# iteratively swap peptides which violate constraints until
# a valid configuration is achieved
optimize(s, allow_extra_pools=False)

assert is_valid(s)

Deconvolution of hit peptides from ELISpot counts

from golfy.deconvolution import create_linear_system, solve_linear_system

# s is a golfy.Design object containing the mapping of peptides to pools
# counts is a dictionary from (replicate, pool) index pairs to ELISpot counts or activity values
linear_system = create_linear_system(s, counts)

# result type has an array of individual peptide activity estimates (result.activity_per_peptide)
# and a set of high confidence hit peptides (result.high_confidence_peptides)
result = solve_linear_system(linear_system)
print(result.high_confidence_hits)