Wire Badr/He/Wang MethodsX kinetic-model paper into Methylomicrobium-Chlorella#67
Merged
Merged
Conversation
…Chlorella doi:10.1016/j.mex.2022.101652 (Badr/He/Wang 2022 MethodsX, "Matlab implementation of a novel semi-structured kinetic model for methanotroph-photoautotroph cocultures") is an orphan cache and a companion to mrr.2023.70 already wired to this community. Add as PARTIAL evidence on the Methane and Carbon Dioxide Mitigation interaction: the kinetic-model paper's bullet "Explicitly models the exchange of in situ produced O2 and CO2 within the coculture" gives independent computational backing for the CO2/biomass dynamics curated here. PARTIAL because the modeled M-P system is generic rather than the specific M. alcaliphilum 20Z + Chlorella HS2 pairing. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
There was a problem hiding this comment.
Pull request overview
This PR adds a new computational evidence item (Badr/He/Wang 2022, MethodsX; doi:10.1016/j.mex.2022.101652) to the existing Methane and Carbon Dioxide Mitigation interaction within the Methylomicrobium–Chlorella methane sequestration coculture community record, capturing support for in situ O₂/CO₂ exchange dynamics in a methanotroph–photoautotroph coculture model.
Changes:
- Adds a new
evidenceentry referencing the MethodsX kinetic-model paper as PARTIAL computational support. - Provides a validated verbatim snippet describing explicit modeling of in situ O₂/CO₂ exchange.
- Adds a short explanation clarifying why support is partial (generic M-P system vs. the specific curated pairing).
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
2 tasks
realmarcin
added a commit
that referenced
this pull request
May 18, 2026
* Regenerate community HTML and UMAP Refresh docs/ to reflect community additions and evidence updates since the last regen (PR #54). UMAP grows from 252 -> 261 embedded communities; 7 existing community pages are refreshed with the evidence additions from PRs #55, #58, #60, #61, #62, #63, #66, #67; 9 new community pages are added (2 from this session: Alaska Tundra Permafrost Iron-Redox and Saccharomyces-Acinetobacter Lignocellulose Detox; 7 from other curation work merged in between). - gen-html: 264 community pages rendered without error - gen-umap: 261 communities embedded (3 host-only skipped because none of their taxa have NCBITaxon embeddings) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #71: render evidence everywhere it lives Three template/data fixes triggered by the Copilot review on the HTML/UMAP regen: - src/communitymech/templates/community.html: - Extend the interaction-network color map and legend with PREDATION, NICHE_PARTITIONING, STRAIN_COMPETITION, and COLONIZATION_FACILITATION. Previously these enum values fell back to generic gray on the force-directed graph and were omitted from the legend, making 5+ community pages (Cellulomonas-Rhodobacter, Sphingobium-Rhodococcus, Clostridium-Carboxidivorans-Kluyveri, Rhodopseudomonas- Geobacter-Magnetite, plus any others) hard to read. - Render evidence on taxonomy entries via an "evidence-row" span. The previous template only rendered evidence inside ecological_interactions and growth_media, so evidence wired onto taxon blocks in PRs like #61 and #62 was on-disk in the YAML but invisible in the rendered HTML. - Render evidence on environmental_factors with the same expanding-row pattern. This is where PR #62 wired the Ter Horst 2021 peat-virome evidence on the SPRUCE community; it now appears in the HTML. - Add an "External Resources" section (analogous to Associated Datasets) that renders external_resources entries including their per-resource evidence. This is where PR #66 wired the Smith 2025 BioModels reproducibility paper on the Kefir BioModels community; it now appears in the HTML. - kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml: add `metals_present: [IRON]`, `metal_relevance: SIGNIFICANT`, and metal_notes describing the Fe(III) reduction / Fe(II) oxidation cycle this community is built around. The community was previously absent from the iron/metal index filter despite being entirely iron-centric. - docs/: regenerate all 264 community pages with the new template + the Alaska_Tundra metals metadata. Many pages pick up the new evidence-row block; the four pages with NICHE_PARTITIONING interactions now render those nodes with the dedicated color and include the new legend entries. Verified after regen: - SPRUCE community page now shows PMID:38515239 and PMID:34836550 (zero matches before, two each after). - Kefir BioModels community page now shows PMID:41343683 (zero matches before, two after). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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
`doi:10.1016/j.mex.2022.101652` (Badr/He/Wang 2022 MethodsX, "Matlab implementation of a novel semi-structured kinetic model for methanotroph-photoautotroph cocultures") is an orphan cache and a methods companion to `doi:10.20517/mrr.2023.70` (the GEM paper) which was already wired into the same community in PR #63.
Wire as PARTIAL evidence on the Methane and Carbon Dioxide Mitigation interaction of `Methylomicrobium-Chlorella Methane Sequestration Coculture`. The kinetic-model paper's bullet "Explicitly models the exchange of in situ produced O2 and CO2 within the coculture" gives independent computational backing for the CO2 / biomass dynamics curated on this interaction.
PARTIAL because the modeled M-P system in the paper is generic, not the specific M. alcaliphilum 20Z + Chlorella HS2 pairing.
Test plan
🤖 Generated with Claude Code