Wire Twist Gene Pools into web calculator; simulate fold-sampling for 90% coverage#5
Open
micah-olivas wants to merge 1 commit into
Open
Wire Twist Gene Pools into web calculator; simulate fold-sampling for 90% coverage#5micah-olivas wants to merge 1 commit into
micah-olivas wants to merge 1 commit into
Conversation
…for 90% coverage - generate_cost_data.py: use Twist Gene Pools (skew=1.5, 300–1800 bp) for uSort-M synthesis cost when seq_length > 350 bp, replacing the prior $0 placeholder - generate_cost_data.py: call find_fold_sampling() once per synthesis method at startup to compute the fold required for 90% coverage (8.5× for Oligo Pools skew=4.0, 6.0× for Gene Pools skew=1.5), matching the estimate CLI's simulation approach - Regenerate all 29 cost_curve_*.json files and default_costs.json with updated synthesis costs, fold-sampling, and skew fields per data point - index.html: display simulated fold-sampling and skew from JSON data in the parameter strip below the plot (was hardcoded 4×) - index.html: pass fold-sampling through to updateTimeline() so well/plate counts in the timeline step are self-consistent - index.html: label >500 bp synthesis as "Twist Gene Pools (300–1800 bp)" (was "Instance Bio or custom synthesis") - index.html: update uSort-M footnote for long libraries to reflect Gene Pools pooled synthesis instead of substitution library language - twist_gene_pools.toml: skew 6.0 → 1.5 (tighter estimate from uniformity spec) - twist_cloned_mgf.toml: skew 3.0 → 2.0 - twist_multiplexed_gene_fragments.toml: skew 5.0 → 2.0
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
find_fold_sampling()once per synthesis method at startup to find the fold required for 90% coverage, matching whatusortm estimatedoes. Results: 8.5× for Twist Oligo Pools (skew=4.0) and 6.0× for Twist Gene Pools (skew=1.5). Previously hardcoded at 4×.default_costs.jsonregenerated.Test plan
docs/index.htmllocally and verify the plot renders for 300 bp (short) and 700 bp (long)