Issues

• Metabolic Pathway Data Collection

  Reed-CompBio/spras-benchmarking#80 · Filter by author annaritz opened on Jul 31, 2026

• Using PPI of yeast in SPRAS

  Reed-CompBio/spras-benchmarking#79 · Filter by author Sabah-hoq opened on Jul 31, 2026

• Running benchmarking jobs with HTCondor

  Reed-CompBio/spras-benchmarking#75 · Filter by author agitter opened on Jun 16, 2026

• Intermittent ModuleNotFoundError: No module named 'cache' when running workflows

  Bug

  Reed-CompBio/spras-benchmarking#74 · Filter by author ntalluri opened on May 15, 2026
  1

• Hook into loguru to warn for outdated datasets

  enhancement
  Reed-CompBio/spras-benchmarking#72 · Filter by author tristan-f-r opened on Mar 23, 2026
  2

• Pathway reconstruction with predicted PPI networks

  dataset
  Reed-CompBio/spras-benchmarking#63 · Filter by author agitter opened on Mar 6, 2026
  1

• Upsampling Panther Pathways for Performance Evaluation

  datasetenhancement
  Reed-CompBio/spras-benchmarking#62 · Filter by author ntalluri opened on Feb 27, 2026
  9

• Re-enable ML.

  bug
  Reed-CompBio/spras-benchmarking#60 · Filter by author tristan-f-r opened on Feb 24, 2026

• Document & cleanup website

  documentation
  Reed-CompBio/spras-benchmarking#36 · Filter by author tristan-f-r opened on Jul 24, 2025

• Interactive PR curve

  enhancement
  Reed-CompBio/spras-benchmarking#30 · Filter by author tristan-f-r opened on Jul 1, 2025

• Automatically suggest new gold standard nodes

  enhancement
  Reed-CompBio/spras-benchmarking#29 · Filter by author tristan-f-r opened on Jul 1, 2025

• Re-add config paramaters

  documentation
  Reed-CompBio/spras-benchmarking#28 · Filter by author tristan-f-r opened on Jul 1, 2025
  1

• Arabidopsis Thaliana Abscisic Acid Signaling Pathway

  dataset
  Reed-CompBio/spras-benchmarking#20 · Filter by author AMINOexe opened on Jun 11, 2025

• Core Pathways: MAPK

  dataset
  Reed-CompBio/spras-benchmarking#19 · Filter by author annaritz opened on Jun 9, 2025

• Logic Modeling Datasets

  dataset
  Reed-CompBio/spras-benchmarking#18 · Filter by author annaritz opened on Jun 6, 2025

• Edge Orienting Dataset

  dataset
  Reed-CompBio/spras-benchmarking#17 · Filter by author annaritz opened on Jun 6, 2025
  1

• More Synthetic Data (Gene Ontology)

  dataset
  Reed-CompBio/spras-benchmarking#16 · Filter by author annaritz opened on Jun 6, 2025

• More Synthetic Networks (Pathway Databases)

  dataset
  Reed-CompBio/spras-benchmarking#15 · Filter by author annaritz opened on Jun 6, 2025
  2

• Disease-specific data

  dataset
  Reed-CompBio/spras-benchmarking#14 · Filter by author annaritz opened on Jun 6, 2025
  3

• Benchmarking Dataset Ideas

  dataset
  Reed-CompBio/spras-benchmarking#13 · Filter by author annaritz opened on Jun 6, 2025

• State of the Interactomes: an evaluation of molecular networks for generating biological insights

  dataset
  Reed-CompBio/spras-benchmarking#31 · Filter by author agitter opened on May 7, 2024