Plans

Current as of 2026-06-03.

Current State

  • AgentOS developer-project scaffold has been added: AGENTS.md, prompts/README.md, prompts/architecture.md, and prompts/plans.md.
  • The site remains a Jekyll/GitHub Pages static website; no site behavior or content was changed by the scaffold.
  • A durable local Ruby setup has been installed with rbenv under /Users/benbfly/.rbenv; this repo is pinned to Ruby 3.3.4 via .ruby-version, and ~/.zshrc initializes rbenv for fresh zsh shells.
  • Local rbenv, ruby-build, compiled Ruby, installed gems, and shell initialization affect Ben’s Mac only. GitHub Pages hosting continues to use GitHub’s own Pages runtime.

Maintenance Guidance

  • Read prompts/architecture.md before changing _config.yml, collections, layouts/includes, data formats, dependencies, build behavior, or deployment behavior.
  • For content-only edits, update the relevant top-level page or collection Markdown and validate with a Jekyll build when practical.
  • Keep active prompt files brief; move dated historical detail into prompts/*_deep_records_*.md.

Validation

  • Typography base-size preview validated on 2026-06-03: _sass/_variables.scss now sets $font-size-base to 1rem; _site/assets/main.css rendered body { font-size: 1rem; }; in-app browser verification at http://127.0.0.1:4001/ computed body and ordinary paragraph text as 16px with 24px line-height and no page console errors. /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing missing project layout and Bootstrap deprecation warnings.
  • Publications header link update validated on 2026-06-03: pubs.md now defines web_of_science_researcher and links “Web of Science Researcher page” after the Google Scholar link; _site/pubs.html rendered https://www.webofscience.com/wos/author/record/AAT-3720-2021; /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing missing project layout and Bootstrap deprecation warnings.
  • People page photo update validated on 2026-06-03: Ben Berman’s member photo front matter now points to Berman2026.jpg; _site/people/index.html rendered /assets/images/Berman2026.jpg; /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing missing project layout and Bootstrap deprecation warnings.
  • Research page update validated on 2026-06-03: _projects/022_ctdna.md was moved to _projects/010_ctdna.md so “Characterizing tumor DNA in circulation using Oxford Nanopore sequencing” renders first on _site/research.html; the project copy now links to Berman, Genome Biology 2026 (10.1186/s13059-026-04060-8) and Katsman, bioRxiv 2026 (10.64898/2026.04.15.718632) while preserving the short Research-page style. /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing missing project layout and Bootstrap deprecation warnings.
  • Publications update validated on 2026-06-03: removed _data/pubs/ref0107.json, the 2024 bioRxiv preprint “Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer”; added _data/pubs/ref0120.json for the 2026 Genome Biology article “Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer” (10.1186/s13059-026-04060-8); added _data/pubs/ref0125.json for the 2026 Efrat Katsman bioRxiv preprint “Improved deconvolution of circulating tumor DNA from ultra-low-pass whole-genome methylation sequencing using CelFiE-ISH” (10.64898/2026.04.15.718632); updated the static peer-reviewed publication count in pubs.md from 80 to 81. JSON parsing succeeded for all _data/pubs/*.json; _site/pubs.html rendered both new DOIs and no longer contained the old preprint title/DOI; /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
  • People page roster update validated on 2026-06-03: Amit Levin, Dolev Revivo, and Yonatan Berg member files were removed; Efrat Katsman was moved to past members; Rohi, Ofri, Efrat, Irene, Devorah, Lior, and Dror titles/current-address/photo metadata were updated; _site/people/index.html rendered the requested names, titles, image, and current-address links, and omitted the removed names. /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
  • People page metadata-field update validated on 2026-06-03: people.md now conditionally renders optional website, orcid, and current_address member front matter. Unambiguous ORCIDs were added for Ben Berman, Efrat Katsman, Shari Orlanski, and Irene Unterman from public article/ORCID evidence; no ORCID was added for other listed members where search results were absent or ambiguous. _site/people/index.html rendered the four expected ORCID links and no empty Website/Current address rows; /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
  • People page content update validated on 2026-06-03: _members/current/030_rohi.md and _members/current/040_ofri.md were added, Efrat/Shari photo front matter was updated to their new images, _site/people/index.html contained the expected names and image paths, and /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
  • bundle exec jekyll build was attempted on 2026-06-03. It did not reach a Jekyll build because the local Bundler environment is missing http_parser.rb, required through github-pages -> jekyll-seo-tag -> jekyll -> em-websocket.
  • Local preview diagnosis on 2026-06-03: Apple system Ruby 2.6.10 and Bundler 1.17.2 are active. The global gems under /Library/Ruby/Gems/2.6.0 have broken/stale native extensions for commonmarker, eventmachine, http_parser.rb, and racc; ffi is also installed as an incompatible x86_64 native gem. A disposable temp bundle succeeded with the project Gemfile plus gem "ffi", "< 1.17.3", then BUNDLE_GEMFILE=/private/tmp/methylgrammarlab-jekyll-preview-test/Gemfile bundle exec jekyll build --source /Users/benbfly/Documents/benbfly.github.io --destination /private/tmp/methylgrammarlab-jekyll-preview-build.
  • Jekyll preview was verified on 2026-06-03 with BUNDLE_GEMFILE=/private/tmp/methylgrammarlab-jekyll-preview-test/Gemfile bundle exec jekyll serve --source /Users/benbfly/Documents/benbfly.github.io --destination /private/tmp/methylgrammarlab-jekyll-preview-serve --host 127.0.0.1 --port 4000; localhost returned HTTP 200 and the in-app browser loaded http://127.0.0.1:4000/.
  • Public DNS diagnosis on 2026-06-03: methylgrammarlab.org uses Hover nameservers and resolves to the four GitHub Pages apex A records; www.methylgrammarlab.org is a CNAME to benbfly.github.io; HTTP and HTTPS both return 200 from GitHub Pages. benbermanlab.com uses Hover nameservers but has no apex A record and no www CNAME, so HTTP/HTTPS resolution fails. A forced Host-header test against a GitHub Pages IP for benbermanlab.com returned GitHub 404, consistent with this repo’s single-domain CNAME (methylgrammarlab.org). To use benbermanlab.com as a secondary entry point, configure it as a redirect domain rather than a second direct GitHub Pages alias.
  • Existing non-blocking build warnings: _projects/015_PMDs.md and _projects/022_ctdna.md request missing layout project; Bootstrap emits a deprecated text-hide() mixin warning.
  • Durable preview setup completed on 2026-06-03: rbenv and ruby-build were installed under /Users/benbfly/.rbenv; Ruby 3.3.4 was compiled with local OpenSSL and libyaml; .ruby-version was added; ~/.zshrc initializes rbenv; bundle install resolved github-pages 232 and Jekyll 3.10.0; a fresh interactive shell successfully ran bundle exec jekyll build.
  • Current verified server command: bundle exec jekyll serve --host 127.0.0.1 --port 4000 from a fresh shell in the repo; HTTP response reported WEBrick with Ruby 3.3.4.

Local Jekyll Preview

  • Open a fresh zsh shell, cd /Users/benbfly/Documents/benbfly.github.io, then run bundle exec jekyll serve.
  • The current preview server was verified at http://127.0.0.1:4000 using WEBrick with Ruby 3.3.4.
  • Gemfile.lock is still ignored by .gitignore; do not treat the local lockfile as a source-controlled artifact unless Ben explicitly changes that convention.
  • If bundle unexpectedly uses /usr/bin/ruby, open a fresh shell or confirm ~/.zshrc still contains the rbenv PATH/init lines.

Safe Resume

  • Start with git status --short.
  • Use a fresh shell so rbenv initialization in ~/.zshrc is active.
  • If preview is already running on port 4000, stop the existing Jekyll process or choose another port.
  • Do not revert unrelated worktree changes such as .DS_Store or newly added content assets unless Ben explicitly asks.
Creative Commons License

The Ben Berman lab at Hebrew University