Tier 0 · open
acid mine drainage -> recover ZnS
SINGLE-ORGANISM
corpus v0.3.0 · hash 3574ed92836e…
Model licensing
This run includes model(s) we cannot re-serve. They are named and cited so you can obtain them directly from the source. Naming a model in a result is not redistribution.
- link-only: Unconfirmed (repo MIT; vmh.life data license not confirmed, preprint noted CC-BY-NC 4.0) -- obtain a license from the source before reuse; source: https://vmh.life/files/reconstructions/AGORA2/version2.01/
- link-only: Unconfirmed (no repo license file; vmh.life data license not confirmed) -- obtain a license from the source before reuse; source: https://vmh.life/files/reconstructions/AGORA/
The remaining models are openly redistributable (CC-BY).
Provenanced sample report (Syntropa discovery, role-aware Stage-1). Corpus v0.3.0 (15717 models, fingerprint 3574ed92836e) · tools v0.1.0 (git 38fbc04, code 7965284a0cdb) · env py3.13.13 win32 swiglpk5.0.13+osqp1.1.3+highspy1.15.1+pyscipopt6.2.1+optlang1.9.1 (deps fec80ac6eed5). Feed={'ethanol': 10, 'sulfate': 10, 'zn2': 1} target=ZnS__precip mode=produce. Report id 11f4932284c6 (content-addressed to config + EXACT corpus + EXACT tools -> reproducible/auditable). Honest-by-construction: read the caveats.
Verdict: SINGLE-ORGANISM
the target is achieved by a single organism -- no consortium is required.
Super-additivity + honest scope
- Best SINGLE organism reaches 1.000; best CONSORTIUM reaches 1.000 (~1.0x) -- a real multi-member effect.
- The 10055 feedstock-dependent candidates are COMBINATIONS over a diverse front-end core and largely SHARE the finisher(s) ['agora2_desulfovibrio_desulfuricanssubsp', 'agora_desulfovibrio', 'cme_gcf000186885'] -- they are variations on a small number of core relays, NOT 10055 independent discoveries. The biological finding is the finisher + its best partners, not the raw count.
Ranked feedstock-dependent candidates (top 10 of 10055)
| rank | n | production | emergence | members |
|---|---|---|---|---|
| 1 | 1 | 1.000 | additive | agora2_desulfovibrio_desulfuricanssubsp (AGORA2 v2.01 (Heinken 2023)/semi-curated) |
| 2 | 1 | 1.000 | additive | agora_desulfovibrio (AGORA v1.03 (Magnusdottir 2017)/semi-curated) |
| 3 | 1 | 1.000 | additive | cme_gcf000186885 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 4 | 2 | 1.000 | additive | agora2_acidaminococcus_intestinirycmr95 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + embl_desulfovibrio_alaskensis_g20 (embl_gems (CarveMe RefSeq, Machado 2018)/draft) |
| 5 | 2 | 1.000 | additive | agora2_acidaminococcus_intestinirycmr95 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + embl_desulfovibrio_dechloracetivorans_beroc1 (embl_gems (CarveMe RefSeq, Machado 2018)/draft) |
| 6 | 2 | 1.000 | additive | agora2_acidaminococcus_massiliensismarsei (AGORA2 v2.01 (Heinken 2023)/semi-curated) + agora2_desulfovibrio_desulfuricanssubsp (AGORA2 v2.01 (Heinken 2023)/semi-curated) |
| 7 | 2 | 1.000 | additive | agora2_acidaminococcus_spd21 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000186885 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 8 | 2 | 1.000 | additive | agora2_acidaminococcus_spd21 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + agora_desulfovibrio (AGORA v1.03 (Magnusdottir 2017)/semi-curated) |
| 9 | 2 | 1.000 | additive | agora2_acinetobacter_baumannii6013113 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + agora_desulfovibrio (AGORA v1.03 (Magnusdottir 2017)/semi-curated) |
| 10 | 2 | 1.000 | additive | agora2_acidaminococcus_massiliensismarsei (AGORA2 v2.01 (Heinken 2023)/semi-curated) + embl_desulfovibrio_alaskensis_g20 (embl_gems (CarveMe RefSeq, Machado 2018)/draft) |
Attribution
Every model above is credited by id + source. Model authors: your reconstruction appears in this result. (Impact-ledger stamping = flywheel, pending.)
Caveats (disclosed up front)
- FBA proves a route is stoichiometrically POSSIBLE, not that a living cell will do it.
- Every consortium here is a HYPOTHESIS until cultured; nothing is wet-lab validated.
- Feedstock-dependence is the anti-medium-artifact control: withdraw the feed and the product must collapse (a NOT-feedstock-dependent result is flagged SUSPECT, not a discovery).
- The ranking score is a documented heuristic for human review, not a truth or biology claim.
- Stage-1 selects finisher x diverse front-ends; multi-finisher relays are out of scope. Stage-2 expansion of winners is pending -- these are PRELIMINARY until it runs.