Organizing large-scale biological data around standardized projects

Nathan Sheffield, PhD
www.databio.org/slides
Data is becoming more...

abundant
available
powerful
So why are the world's problems not solved?


First step in bioinformatics analysis:

pipeline

Papers with
"bioinformatics pipeline"
in title
Problem solved?
Problem solved?
Problem solved?

Data munging

Then, downstream tools need a different organization

What if?

Why is this hard to do?
Because of microwave syndrome....

Microwave syndrome

In user interface design, prioritizing easy access to integrated functions over their individual components.

The UNIX philosophy

[T]he power of a system comes more from the relationships among programs than from the programs themselves.

Many UNIX programs do quite trivial tasks in isolation, but, combined with other programs, become general and useful tools.

- Kernighan and Pike, The UNIX Programming Environment (1983, p. viii)

Problem

Solution

PEP: Portable Encapsulated Projects

PEP format

project_config.yaml
metadata:
  sample_annotation: /path/to/samples.csv
  output_dir: /path/to/output/folder

samples.csv
sample_name, protocol, organism, data_source
frog_0h, RNA-seq, frog, /path/to/frog0.gz
frog_1h, RNA-seq, frog, /path/to/frog1.gz
frog_2h, RNA-seq, frog, /path/to/frog2.gz
frog_3h, RNA-seq, frog, /path/to/frog3.gz

PEP portability features

Derived attributes
Implied attributes
Subprojects
Derived attributes
Automatically build new sample attributes from existing attributes.
Without derived attribute:
| sample_name | t | protocol | organism | data_source | | ------------- | ---- | :-------------: | -------- | ---------------------- | | frog_0h | 0 | RNA-seq | frog | /path/to/frog0.gz | | frog_1h | 1 | RNA-seq | frog | /path/to/frog1.gz | | frog_2h | 2 | RNA-seq | frog | /path/to/frog2.gz | | frog_3h | 3 | RNA-seq | frog | /path/to/frog3.gz |
Using derived attribute:
| sample_name | t | protocol | organism | data_source | | ------------- | ---- | :-------------: | -------- | ---------------------- | | frog_0h | 0 | RNA-seq | frog | my_samples | | frog_1h | 1 | RNA-seq | frog | my_samples | | frog_2h | 2 | RNA-seq | frog | my_samples | | frog_3h | 3 | RNA-seq | frog | my_samples | | crab_0h | 0 | RNA-seq | crab | your_samples | | crab_3h | 3 | RNA-seq | crab | your_samples |
| sample_name | t | protocol | organism | data_source | | ------------- | ---- | :-------------: | -------- | ---------------------- | | frog_0h | 0 | RNA-seq | frog | my_samples | | frog_1h | 1 | RNA-seq | frog | my_samples | | frog_2h | 2 | RNA-seq | frog | my_samples | | frog_3h | 3 | RNA-seq | frog | my_samples | | crab_0h | 0 | RNA-seq | crab | your_samples | | crab_3h | 3 | RNA-seq | crab | your_samples |
Project config file:
derived_columns: [data_source]
data_sources:
  my_samples: "/path/to/my/samples/{organism}_{t}h.gz"
  your_samples: "/path/to/your/samples/{organism}_{t}h.gz"
{variable} identifies sample annotation columns
Benefit: Enables distributed files, portability
Implied attributes
Add new sample attributes conditioned on values of existing attributes
Before:
| sample_name | protocol | organism | | ------------- | :-------------: | -------- | | human_1 | RNA-seq | human | | human_2 | RNA-seq | human | | human_3 | RNA-seq | human | | mouse_1 | RNA-seq | mouse |
After:
| sample_name | protocol | organism | genome | | ------------- | :-------------: | -------- | ------ | | human_1 | RNA-seq | human | hg38 | | human_2 | RNA-seq | human | hg38 | | human_3 | RNA-seq | human | hg38 | | mouse_1 | RNA-seq | mouse | mm10 |
| sample_name | protocol | organism | | ------------- | :-------------: | -------- | | human_1 | RNA-seq | human | | human_2 | RNA-seq | human | | human_3 | RNA-seq | human | | mouse_1 | RNA-seq | mouse |
Project config file:
implied_columns:
  organism:
    human:
      genome: hg38
    mouse:
      genome: mm10
Benefit: Divides project from sample metadata
Subprojects
Define activatable project attributes.
subprojects:
  diverse:
    metadata:
      sample_annotation: psa_rrbs_diverse.csv
  cancer:
    metadata:
      sample_annotation: psa_rrbs_intracancer.csv
Benefit: Defines multiple similar projects in a single file
How is this portable and encapsulated?

Encapsulated:
A project is an extensible object, with samples and settings as attributes.
Portable:
  1. A project can be moved from one analysis tool to another
  2. A project can be moved from one computing environment to another

geofetch

Connects the Gene Expression Omnibus (GEO)
and Sequence Read Archive (SRA)
with PEP format

$ geofetch -i GSE502503
peppy package
import peppy

prj = Project("pep_config.yaml")
samples = prj.get_samples()

for sample in samples:
	print(sample.name)
	# do further analysis to each sample
Project API
pepr package
library("pepr")

prj = pepr::Project("pep_config.yaml")
samples = pepr::pepSamples(prj)

for (sample in samples) {
	message(pepr::sampleName(sample))
	# do further analysis to each sample
	}

Looper

Deploys pipelines across samples by connecting
samples to any command-line tool
pipeline_interface.yaml
protocol_mappings:
  RNA-seq: rna-seq 

pipelines:
  rna-seq:
    name: RNA-seq_pipeline
    path: path/to/rna-seq.py
    arguments:
      "--option1": sample_attribute
      "--option2": sample_attribute2
  • maps protocols to pipelines
  • maps sample attributes (columns) to pipeline arguments
  • Looper features

    Single-input runs
    Flexible pipelines
    Flexible resources
    Flexible compute
    Job status-aware
    Single-input runs
    Run your entire project with one line:
    looper run project_config.yaml
    Flexible pipelines
    protocol_mappings:
      RRBS: rrbs
      WGBS: wgbs
      EG: wgbs.py
      SMART-seq: rnaBitSeq -f; rnaTopHat -f
      ATAC-SEQ: atacseq
      DNase-seq: atacseq
      CHIP-SEQ: chipseq
    Many-to-many mappings
    Flexible resources
    pipeline_key:
      name: pipeline_name
      arguments:
        "--option" : value
      resources:
        default:
          file_size: "0"
          cores: "2"
          mem: "6000"
          time: "01:00:00"
        large_input:
          file_size: "2000"
          cores: "4"
          mem: "12000"
          time: "08:00:00"
    Resources can vary by input file size
    Flexible compute
    compute:
      slurm:
        submission_template: templates/slurm_template.sub
        submission_command: sbatch
      localhost:
        submission_template: templates/localhost_template.sub
        submission_command: sh

    Adjust compute package on-the-fly:
    > looper run project_config.yaml --compute localhost
    Job status-aware
    Looper only submits jobs for samples not already flagged as running, completed, or failed.
    looper check project_config.yaml
    looper summarize project_config.yaml

    Conclusion

    • PEP format is a novel approach to standardize projects.
    • Initial tools like geofetch and looper build PEP projects and connect them to pipelines
    • Python and R packages provide a universal interface to PEP metadata for tools and analysis
    More information at pepkit.github.io.

    Thank You


    nsheff · databio.org · nsheffield@virginia.edu
    Postdoc positions available!