Skip to content

Navigation Menu

Appearance settings

- AI CODE CREATION
  GitHub CopilotWrite better code with AI
  GitHub Copilot appDirect agents from issue to merge
  MCP Registry^NewIntegrate external tools
- DEVELOPER WORKFLOWS
  ActionsAutomate any workflow
  CodespacesInstant dev environments
  IssuesPlan and track work
  Code ReviewManage code changes
- APPLICATION SECURITY
  GitHub Advanced SecurityFind and fix vulnerabilities
  Code securitySecure your code as you build
  Secret protectionStop leaks before they start
- EXPLORE
  Why GitHub
  Documentation
  Blog
  Changelog
  Marketplace
View all features
- BY COMPANY SIZE
  Enterprises
  Small and medium teams
  Startups
  Nonprofits
- BY USE CASE
  App Modernization
  DevSecOps
  DevOps
  CI/CD
  View all use cases
- BY INDUSTRY
  Healthcare
  Financial services
  Manufacturing
  Government
  View all industries
View all solutions
- EXPLORE BY TOPIC
  AI
  Software Development
  DevOps
  Security
  View all topics
- EXPLORE BY TYPE
  Customer stories
  Events & webinars
  Ebooks & reports
  Business insights
  GitHub Skills
- SUPPORT & SERVICES
  Documentation
  Customer support
  Community forum
  Trust center
  Partners
View all resources
- COMMUNITY
  GitHub SponsorsFund open source developers
- PROGRAMS
  Security Lab
  Maintainer Community
  Accelerator
  GitHub Stars
  Archive Program
- REPOSITORIES
  Topics
  Trending
  Collections
- ENTERPRISE SOLUTIONS
  Enterprise platformAI-powered developer platform
- AVAILABLE ADD-ONS
  GitHub Advanced SecurityEnterprise-grade security features
  Copilot for BusinessEnterprise-grade AI features
  Premium SupportEnterprise-grade 24/7 support
Pricing

Search code, repositories, users, issues, pull requests...

Search

Clear

Search syntax tips

Provide feedback

We read every piece of feedback, and take your input very seriously.

Include my email address so I can be contacted

Saved searches

Use saved searches to filter your results more quickly

Name

Query

To see all available qualifiers, see our documentation.

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

SysBioChalmers / raven-python Public

Notifications You must be signed in to change notification settings
Fork 0
Star 0

Code
Issues
Pull requests 1
Actions
Projects
Security and quality
Insights

Additional navigation options

Code
Issues
Pull requests
Actions
Projects
Security and quality
Insights

Subcellular localisation prediction and yeast-GEM validation#9

Merged

edkerk merged 23 commits into

developSysBioChalmers/raven-python:developfrom

feature/localizationSysBioChalmers/raven-python:feature/localizationCopy head branch name to clipboard

May 30, 2026

Conversation Commits23 (23)Checks Files changed

Merged

Subcellular localisation prediction and yeast-GEM validation#9
edkerk merged 23 commits into
developfrom
feature/localization

Commits

Commits on May 29, 2026

Project scaffold: pyproject + package skeleton + README + LICENSE
edkerk
committed
Add GitHub Actions CI and the maintainer-scripts README
edkerk
committed
Add the foundation utilities: GPR, balance, parse, sort, validate
edkerk
committed
Add the model-manipulation layer (add, remove, transport, merge, etc.)
edkerk
committed
Add binary + data resolvers for external tools and published artefacts
edkerk
committed
Add YAML and SIF model I/O
edkerk
committed
Add Excel export and the Standard-GEM git-layout export
edkerk
committed
Add BLAST and DIAMOND wrappers for protein-homology searches
edkerk
committed
Add the homology-based draft model builder (getModelFromHomology port)
edkerk
committed
Add KEGG download, dump parser and taxonomy parser
edkerk
committed
Add KEGG HMM-library build and HMM-based KO assignment
edkerk
committed
Add KEGG species-model assembly (per-organism reconstruction)
edkerk
committed
Add KEGG artefact-build scripts and HMM-cutoff calibration docs
edkerk
committed
Add metabolic-task parsing and the check_tasks validator
edkerk
committed
Add connectivity gap-filling (MILP) against template models
edkerk
committed
Add the tINIT (INIT) MILP and its supporting machinery
edkerk
committed
Add the ftINIT pipeline and task-aware gap-filling
edkerk
committed
Add Human-GEM validation, parameter studies and cross-solver tests
edkerk
committed
Add HPA omics ingestion (proteomics + RNA-seq)
edkerk
committed
Add FSEOF, reporter metabolites and flux sampling
edkerk
committed
Add N-model comparison (presence + Jaccard + optional task check)
edkerk
committed
Add subcellular-localisation prediction (MILP) with pluggable predictors
edkerk
committed
Add the yeast-GEM localization benchmark (real-data validation)
edkerk
committed

Footer

© 2026 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.