From 5ef89a19a6a86027f1cb974b23f64a216ef95612 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:19:24 -0700 Subject: [PATCH 1/9] Resolve R1-R8 data issues for desert_farm_leverage_points MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit R1: CO2 fixation Time_min 7.69E-03 → 6.67E-02 (Bar-On natural kcat ceiling, 15/s) R2: Replace Moore et al. 2013 mis-citations on Nutrient transport, Biochemical synthesis, and Cell growth with Milo & Phillips (2015) Cell Biology by the Numbers R3: Rename Growth → Cell growth; tighten bounds to single algal cell scope (Time 1e3-1e5 s, Space 1e-18 to 1e-14 m³). Population scales remain covered by Community Ecology row. R4: MD Space_max 1e-27 → 1e-22 m³ (modern atomistic-MD reach) R5: Community Metabolic Models Time_min 99 → 1.00E+02 (formatting consistency) R6: Fill empty Reference cells: - Molecular Dynamics Models: Karplus & McCammon (2002) Nat Struct Biol 9:646 - Community Metabolic Models: Zakem et al. (2020) ISME J 14:288 - Biogeochemical Circulation Models: Levine et al. (2025) Annu Rev Earth Planet Sci 53:595 R7: Rename Extraction → Fossil-fuel formation; Time bounds 3.16E+13 to 3.16E+15 s reflect formation duration rather than deposit age R8: Extend CO2 fixation Reference text to justify both time and space bounds --- data/datasets/desert_farm_leverage_points.csv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/data/datasets/desert_farm_leverage_points.csv b/data/datasets/desert_farm_leverage_points.csv index 16f307c..a78a86c 100644 --- a/data/datasets/desert_farm_leverage_points.csv +++ b/data/datasets/desert_farm_leverage_points.csv @@ -1,13 +1,13 @@ Prefix,ShortName,Time_min,Time_max,Space_min,Space_max,Color,Reference -model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-27,#013333, -process,CO2 fixation,7.69E-03,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat dependent on HCO3- pool via carbonic anhydrase (Igamberdiev 2015) -process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Moore et al. (2013) Nature Geosci 6:701 -process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Moore et al. (2013) Nature Geosci 6:701 -process,Growth,1.00E+05,1.00E+06,1.00E-20,1.00E-10,#006666,Moore et al. (2013) Nature Geosci 6:701 -model,Community Metabolic Models,99,1.00E+07,1.00E-18,1.00E-03,#013333, +model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-22,#013333,Karplus & McCammon (2002) Nat Struct Biol 9:646 +process,CO2 fixation,6.67E-02,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat = 3-15/s natural RuBisCO; space = 0.1×–1.7× RuBisCO L8S8 enzyme volume (~7e-25 m³) +process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers +process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers +process,Cell growth,1.00E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers +model,Community Metabolic Models,1.00E+02,1.00E+07,1.00E-18,1.00E-03,#013333,Zakem et al. (2020) ISME J 14:288 leverage point,Community Ecology,1.00E+06,1.00E+08,1.00E-09,1.00E+00,#FF9900,Moore et al. (2013) Nature Geosci 6:701 leverage point,Flocculation,1.00E+03,86400,1.00E-15,1.00E-09,#FF9900,Salim et al. (2011) J Appl Phycol; Vandamme et al. (2013) Biotechnol Adv 31:1680 leverage point,Ponds,86400,3.15E+07,2000,2.00E+04,#FF9900,Design basis: 10x100x3m deep ponds (3000 m3); depth for photoinhibition protection and floc settling -model,Biogeochemical Circulation Models,1.00E+05,1.00E+10,1.00E+09,1.00E+16,#013333, +model,Biogeochemical Circulation Models,1.00E+05,1.00E+10,1.00E+09,1.00E+16,#013333,Levine et al. (2025) Annu Rev Earth Planet Sci 53:595 leverage point,Sequestration,3.15E+08,1.00E+11,3.12E+09,2.91E+10,#FF9900,40 GtCO2/yr: Space_min=C as diamond (3.5 t/m3) Space_max=biomass+salt+sand (rho~1.5 t/m3) per year -process,Extraction,3.16E+14,6.31E+15,2.03E+12,2.05E+14,#006666,Carboniferous coal (~300 Mya) + Mesozoic petroleum (~252-66 Mya); Tissot & Welte (1984) +process,Fossil-fuel formation,3.16E+13,3.16E+15,2.03E+12,2.05E+14,#006666,Kerogen→petroleum maturation (~1-10 My) + coalification (~10-100 My); Tissot & Welte (1984) From 6ca77aed19f815a711304d0676a414ba7e45a867 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:19:24 -0700 Subject: [PATCH 2/9] Add curated BioNumbers subset for Milo & Phillips citations 25 entries justifying time/space bounds for Cell growth (8), Biochemical synthesis (8), and Nutrient transport (9) rows. Phototroph-specific where available; generic-organism proxies (E. coli, Xenopus, generic) used where phototroph data was unavailable. Each entry includes direct URL to BioNumbers page. --- data/references/bionumbers_subset.csv | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 data/references/bionumbers_subset.csv diff --git a/data/references/bionumbers_subset.csv b/data/references/bionumbers_subset.csv new file mode 100644 index 0000000..1315984 --- /dev/null +++ b/data/references/bionumbers_subset.csv @@ -0,0 +1,26 @@ +bion_id,Properties,Organism,Value,Range,Units,URL,Cited_in_row +100289,Generation time,Cyanobacteria Synechocystis PCC 6803,6.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100289,Cell growth +102211,Mean generation time (on acetate),Green algae chlorella,20.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102211,Cell growth +102212,mean generation time (photoautotrophic growth),Green algae chlorella,11.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102212,Cell growth +104195,Generation time,Diatom Phaeodactylum tricornutum,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104195,Cell growth +104196,Generation time,Green algae Dunaliella tertiolecta,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104196,Cell growth +105638,Generation time at 30°C,Green algae Dunaliella salina,20.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105638,Cell growth +111252,Doubling time,Cyanobacteria Synechocystis PCC 6803,12.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111252,Cell growth +111335,Fastest generation time,Cyanobacteria Synechocystis PCC 6803,5.13,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111335,Cell growth +100233,Translation rate of beta-galactosidase in E. coli,Bacteria Escherichia coli,14.5,'13-16,aa/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100233,Biochemical synthesis +105067,Translation rate for short peptides,Bacteria Escherichia coli,22.0,'Table link - http://bionumbers.hms.harvard.edu/files/Maximal%20translation%20rate.pdf,1/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105067,Biochemical synthesis +104300,Translation rate on culture of nitrogen bases and glucose,Budding yeast Saccharomyces cerevisiae,9.3,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104300,Biochemical synthesis +104598,Translation rate,Human Homo sapiens,5.0,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104598,Biochemical synthesis +100060,RNA polymerase transcription rate of stable RNA,Bacteria Escherichia coli,85.0,'Table link - http://bionumbers.hms.harvard.edu/files/Parameters%20pertaining%20to%20the%20macromolecular%20synthesis%20rates%20in%20exponentially%20growing%20E.%20coli%20Br%20as%20a%20function%20of%20growth%20rate%20at%2037%20degrees%20celsius.pdf,nt/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100060,Biochemical synthesis +101904,Transcription elongation rate of rRNA operons,Bacteria Escherichia coli,42.0,'±2,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=101904,Biochemical synthesis +100664,Single molecule RNA polymerase II transcription rates,Bacteria Escherichia coli,12.8,'±4.9,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100664,Biochemical synthesis +100662,Maximum RNA polymerase II transcription elongation rate,Mammalian tissue culture cell,71.6,,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100662,Biochemical synthesis +104089,Diffusion coefficient of glucose in water,Generic,600.0,'Table link - http://bionumbers.hms.harvard.edu/files/Diffusion%20coefficients%20of%20various%20substances%20in%20Water.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104089,Nutrient transport +104437,Diffusion coefficient of ammonium in water,Generic,1860.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104437,Nutrient transport +104439,Diffusion coefficient of nitrate in water,Generic,1700.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104439,Nutrient transport +109504,Diffusion coefficient glucose in water at 25°C,Generic,673.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109504,Nutrient transport +110618,Diffusion coefficient of CO2 in red blood cell,Human Homo sapiens,650.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=110618,Nutrient transport +117305,Diffusion coefficient of CO2 in air,air,1.4e-05,,m2/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=117305,Nutrient transport +102428,Intracellular diffusion coefficient for glucose transporter,African clawed frog Xenopus laevis,100.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102428,Nutrient transport +109673,Highest glucose uptake rate that still allows the maximal NADH formation rate,Bacteria Escherichia coli,2.4,,mmol/(gCDW·…h),https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109673,Nutrient transport +109686,Glucose uptake rate of strain C-3000 in minimal M9 media,Bacteria Escherichia coli,12.0,'±0.5,mmol/gDW/h,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109686,Nutrient transport From 284727202b105aab127a41342260987726963800 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:19:25 -0700 Subject: [PATCH 3/9] Add data/references/README documenting BioNumbers subset Schema, curation criteria, known gaps (including the Cell growth Time_min mismatch flagged by phototroph data), update procedure, and BioNumbers attribution per Milo et al. (2010) Nucleic Acids Res 38:D750. --- data/references/README.md | 74 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 data/references/README.md diff --git a/data/references/README.md b/data/references/README.md new file mode 100644 index 0000000..69628b9 --- /dev/null +++ b/data/references/README.md @@ -0,0 +1,74 @@ +# References + +## BioNumbers subset — `bionumbers_subset.csv` + +This file contains a curated subset of entries from the +[BioNumbers database](https://bionumbers.hms.harvard.edu/) (Milo & Phillips, +*Cell Biology by the Numbers*) that justify the time and space bounds for +specific rows in `data/datasets/desert_farm_leverage_points.csv`. + +### Why a subset + +The full BioNumbers database contains ~14,300 entries (~27 MB as HTML export). +Most are irrelevant to the desert farm Stommel diagram. Including only the +cited subset keeps this repo lean and provides explicit per-number provenance. +Each entry links back to its canonical BioNumbers page via the `URL` column. + +### Schema + +| Column | Description | +|---|---| +| `bion_id` | BioNumbers entry ID (stable identifier) | +| `Properties` | Description of the measured quantity | +| `Organism` | Organism the measurement is from | +| `Value` | Reported value | +| `Range` | Reported range (often empty) | +| `Units` | Units of `Value` | +| `URL` | Direct link to the BioNumbers entry | +| `Cited_in_row` | Which `desert_farm_leverage_points.csv` row uses this entry | + +### Curation criteria + +- **Cell growth**: phototroph generation/doubling times (cyanobacteria, green + algae, diatoms). Excluded: heterotrophic bacteria, fungi, mammalian cells. +- **Biochemical synthesis**: translation and transcription elongation rates + across model organisms. Used to bound time per peptide/RNA elongation. +- **Nutrient transport**: diffusion coefficients of small molecules (CO2, + glucose, nitrate, ammonium) in water and intracellular environments, plus + representative uptake rates. + +### Known gaps and caveats + +- Several BioNumbers entries with relevant `Properties` strings have + `NaN` in the `Value` column (record exists but no scalar). Those were + excluded from this subset. +- Phototroph-specific data is sparse for some categories (e.g., transporter + kinetics). Where a phototroph entry was unavailable, generic or + representative organism data (E. coli, Xenopus, generic) was used as a + proxy. This is documented per-entry in `Organism`. +- **Cell growth Time_min mismatch**: the row's `Time_min = 1.00E+03` s + (~17 min) is faster than any documented phototroph cell division in this + subset. The fastest entry is Synechocystis PCC 6803 at 5.13 h (~1.85e4 s) + — about 18× slower than the lower bound. Either the row should be + tightened to ~1e4 s, or it should be re-scoped to include + cell-growth-adjacent sub-processes (ribosome biogenesis, replication + initiation) which can occur on shorter timescales than full division. + +### Updating + +When new rows are added to `desert_farm_leverage_points.csv` that cite +Milo & Phillips, append matching BioNumbers entries to this subset and +add a corresponding `Cited_in_row` value. Avoid duplication — a single +entry can be `Cited_in_row` for multiple rows by listing them +semicolon-separated. + +### Attribution + +BioNumbers is a project of the Milo Lab (Weizmann Institute) and the Harvard +Medical School. Cite as: Milo R, Jorgensen P, Moran U, Weber G, Springer M +(2010). *BioNumbers — the database of key numbers in molecular and cell +biology*. Nucleic Acids Res. 38:D750–D753. +DOI: [10.1093/nar/gkp889](https://doi.org/10.1093/nar/gkp889). + +For the broader synthesis: Milo R, Phillips R (2015). *Cell Biology by the +Numbers*. Garland Science. From e952ecb351db6ef5ecfe0ae55518df8ac39482f0 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:36:38 -0700 Subject: [PATCH 4/9] =?UTF-8?q?Rename=20Cell=20growth=20=E2=86=92=20Photoa?= =?UTF-8?q?utotroph=20cell=20growth;=20tighten=20Time=5Fmin?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The Time bound for cell division varies by ~3 OOM across phyla. The previous 'Cell growth' label silently scoped to phototrophs (since Time_min was set based on phototroph cell-cycle data). Rename makes the implicit organism scope explicit. Time_min 1.00E+03 → 7.56E+03 s (2.1 h, Synechococcus elongatus UTEX 2973 — currently fastest known photoautotroph). Anchored to Yu et al. (2015) Sci Rep 5:8132. Reference cell extended to cite both Milo & Phillips and Yu et al. --- data/datasets/desert_farm_leverage_points.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/datasets/desert_farm_leverage_points.csv b/data/datasets/desert_farm_leverage_points.csv index a78a86c..f200bf8 100644 --- a/data/datasets/desert_farm_leverage_points.csv +++ b/data/datasets/desert_farm_leverage_points.csv @@ -3,7 +3,7 @@ model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-22,#013333,Karp process,CO2 fixation,6.67E-02,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat = 3-15/s natural RuBisCO; space = 0.1×–1.7× RuBisCO L8S8 enzyme volume (~7e-25 m³) process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers -process,Cell growth,1.00E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers +process,Photoautotroph cell growth,7.56E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers; Yu et al. (2015) Sci Rep 5:8132 (UTEX 2973 fastest) model,Community Metabolic Models,1.00E+02,1.00E+07,1.00E-18,1.00E-03,#013333,Zakem et al. (2020) ISME J 14:288 leverage point,Community Ecology,1.00E+06,1.00E+08,1.00E-09,1.00E+00,#FF9900,Moore et al. (2013) Nature Geosci 6:701 leverage point,Flocculation,1.00E+03,86400,1.00E-15,1.00E-09,#FF9900,Salim et al. (2011) J Appl Phycol; Vandamme et al. (2013) Biotechnol Adv 31:1680 From 3c50a44d55c125cfb3f0dba013ba2cdb49ee30ac Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:36:54 -0700 Subject: [PATCH 5/9] Add supplementary phototroph-growth references (non-BioNumbers) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Sibling file to bionumbers_subset.csv for entries from primary literature where BioNumbers either has no value (NaN) or no entry. Initial entry: Synechococcus elongatus UTEX 2973 doubling time 2.1 h from Yu et al. (2015) Sci Rep 5:8132 — anchors the Time_min for the Photoautotroph cell growth row. BioNumbers entry 112484 exists for this strain but has NaN Value, hence the supplementary citation. --- data/references/phototroph_growth_supplementary.csv | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 data/references/phototroph_growth_supplementary.csv diff --git a/data/references/phototroph_growth_supplementary.csv b/data/references/phototroph_growth_supplementary.csv new file mode 100644 index 0000000..5ef6f98 --- /dev/null +++ b/data/references/phototroph_growth_supplementary.csv @@ -0,0 +1,2 @@ +Properties,Organism,Value,Range,Units,Reference,URL,Cited_in_row +Doubling time under high light and high CO2 (38°C; 1500 µmol photons/m²/s; 5% CO2),Cyanobacteria Synechococcus elongatus UTEX 2973,2.1,,hours,Yu et al. (2015) Sci Rep 5:8132,https://doi.org/10.1038/srep08132,Photoautotroph cell growth From 865408332684d6d5f46332f161fff0f6d3481f45 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:37:30 -0700 Subject: [PATCH 6/9] Update README: document supplementary file; resolve Time_min gap MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Add phototroph_growth_supplementary.csv documentation and schema - Remove the 'Cell growth Time_min mismatch' known gap (now resolved by anchoring to UTEX 2973 in supplementary file) - Update curation criteria to reflect Photoautotroph cell growth rename and the BioNumbers-NaN → supplementary workflow - Restructure 'Known gaps' to reflect current state --- data/references/README.md | 100 +++++++++++++++++++------------------- 1 file changed, 51 insertions(+), 49 deletions(-) diff --git a/data/references/README.md b/data/references/README.md index 69628b9..5cdc295 100644 --- a/data/references/README.md +++ b/data/references/README.md @@ -1,20 +1,22 @@ # References -## BioNumbers subset — `bionumbers_subset.csv` +This directory contains curated reference data backing the Stommel-diagram +row bounds in `data/datasets/desert_farm_leverage_points.csv`. -This file contains a curated subset of entries from the -[BioNumbers database](https://bionumbers.hms.harvard.edu/) (Milo & Phillips, -*Cell Biology by the Numbers*) that justify the time and space bounds for -specific rows in `data/datasets/desert_farm_leverage_points.csv`. +## Files -### Why a subset +- `bionumbers_subset.csv` — entries from the [BioNumbers database](https://bionumbers.hms.harvard.edu/) (Milo & Phillips, *Cell Biology by the Numbers*) with stable `bion_id` identifiers. +- `phototroph_growth_supplementary.csv` — entries from primary literature where BioNumbers has no entry or no scalar value (e.g., entries with `NaN` in the BioNumbers `Value` column). + +Each file uses `Cited_in_row` to map back to the row(s) in `desert_farm_leverage_points.csv` that the entry justifies. + +## Why a curated subset The full BioNumbers database contains ~14,300 entries (~27 MB as HTML export). Most are irrelevant to the desert farm Stommel diagram. Including only the cited subset keeps this repo lean and provides explicit per-number provenance. -Each entry links back to its canonical BioNumbers page via the `URL` column. -### Schema +## `bionumbers_subset.csv` schema | Column | Description | |---|---| @@ -27,47 +29,47 @@ Each entry links back to its canonical BioNumbers page via the `URL` column. | `URL` | Direct link to the BioNumbers entry | | `Cited_in_row` | Which `desert_farm_leverage_points.csv` row uses this entry | -### Curation criteria - -- **Cell growth**: phototroph generation/doubling times (cyanobacteria, green - algae, diatoms). Excluded: heterotrophic bacteria, fungi, mammalian cells. -- **Biochemical synthesis**: translation and transcription elongation rates - across model organisms. Used to bound time per peptide/RNA elongation. -- **Nutrient transport**: diffusion coefficients of small molecules (CO2, - glucose, nitrate, ammonium) in water and intracellular environments, plus - representative uptake rates. - -### Known gaps and caveats - -- Several BioNumbers entries with relevant `Properties` strings have - `NaN` in the `Value` column (record exists but no scalar). Those were - excluded from this subset. -- Phototroph-specific data is sparse for some categories (e.g., transporter - kinetics). Where a phototroph entry was unavailable, generic or - representative organism data (E. coli, Xenopus, generic) was used as a - proxy. This is documented per-entry in `Organism`. -- **Cell growth Time_min mismatch**: the row's `Time_min = 1.00E+03` s - (~17 min) is faster than any documented phototroph cell division in this - subset. The fastest entry is Synechocystis PCC 6803 at 5.13 h (~1.85e4 s) - — about 18× slower than the lower bound. Either the row should be - tightened to ~1e4 s, or it should be re-scoped to include - cell-growth-adjacent sub-processes (ribosome biogenesis, replication - initiation) which can occur on shorter timescales than full division. - -### Updating - -When new rows are added to `desert_farm_leverage_points.csv` that cite -Milo & Phillips, append matching BioNumbers entries to this subset and -add a corresponding `Cited_in_row` value. Avoid duplication — a single -entry can be `Cited_in_row` for multiple rows by listing them -semicolon-separated. - -### Attribution - -BioNumbers is a project of the Milo Lab (Weizmann Institute) and the Harvard -Medical School. Cite as: Milo R, Jorgensen P, Moran U, Weber G, Springer M -(2010). *BioNumbers — the database of key numbers in molecular and cell -biology*. Nucleic Acids Res. 38:D750–D753. +## `phototroph_growth_supplementary.csv` schema + +Same as above but `bion_id` replaced with a `Reference` column containing the full citation, since these entries are not in BioNumbers. + +| Column | Description | +|---|---| +| `Properties` | Description of the measured quantity | +| `Organism` | Organism the measurement is from | +| `Value` | Reported value | +| `Range` | Reported range (often empty) | +| `Units` | Units of `Value` | +| `Reference` | Full citation (author, year, journal, volume, page) | +| `URL` | Direct link to the article (DOI preferred) | +| `Cited_in_row` | Which `desert_farm_leverage_points.csv` row uses this entry | + +## Curation criteria + +- **Photoautotroph cell growth**: cell division/generation times for cyanobacteria, green algae, and diatoms. Excluded: heterotrophic bacteria, fungi, mammalian cells. The row `Time_min` is anchored to *Synechococcus elongatus* UTEX 2973 (the fastest known photoautotroph, ~2.1 h doubling), sourced from `phototroph_growth_supplementary.csv` since BioNumbers entry 112484 for this strain has no scalar value. +- **Biochemical synthesis**: translation and transcription elongation rates across model organisms. Bound by time per peptide/RNA elongation event. +- **Nutrient transport**: diffusion coefficients of small molecules (CO2, glucose, nitrate, ammonium) in water and intracellular environments, plus representative uptake rates. + +## Known gaps + +- Some BioNumbers entries with relevant `Properties` strings have `NaN` in `Value` (record exists but no scalar). These were excluded from `bionumbers_subset.csv`. Where the row's bound depends on such an entry, the data is moved to `phototroph_growth_supplementary.csv` with primary-literature citation (e.g., UTEX 2973). +- Phototroph-specific data is sparse for some categories (e.g., transporter kinetics). Where a phototroph entry was unavailable, generic or representative organism data (E. coli, Xenopus, generic) was used as a proxy. This is documented per-entry in `Organism`. + +## Updating + +When new rows are added to `desert_farm_leverage_points.csv` that cite Milo & Phillips (or other primary literature): + +1. Search the full BioNumbers database for relevant entries. +2. Add matching entries to `bionumbers_subset.csv` with the appropriate `Cited_in_row` value. +3. If a needed value is not in BioNumbers (or has `NaN`), add a primary-literature entry to `phototroph_growth_supplementary.csv`. +4. Avoid duplication — a single entry can be `Cited_in_row` for multiple rows by listing them semicolon-separated. + +## Attribution + +BioNumbers is a project of the Milo Lab (Weizmann Institute) and Harvard Medical +School. Cite as: Milo R, Jorgensen P, Moran U, Weber G, Springer M (2010). +*BioNumbers — the database of key numbers in molecular and cell biology*. +Nucleic Acids Res. 38:D750–D753. DOI: [10.1093/nar/gkp889](https://doi.org/10.1093/nar/gkp889). For the broader synthesis: Milo R, Phillips R (2015). *Cell Biology by the From 7e81569821949350a4e15c276ba7d2af62136c58 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:56:49 -0700 Subject: [PATCH 7/9] Fix Cited_in_row='Cell growth' -> 'Photoautotroph cell growth' (8 rows) Matches the R3 rename in desert_farm_leverage_points.csv. The supplementary file already used the new name; this aligns the BioNumbers subset so the Cited_in_row join key works for all 26 entries. --- data/references/bionumbers_subset.csv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/data/references/bionumbers_subset.csv b/data/references/bionumbers_subset.csv index 1315984..c144293 100644 --- a/data/references/bionumbers_subset.csv +++ b/data/references/bionumbers_subset.csv @@ -1,12 +1,12 @@ bion_id,Properties,Organism,Value,Range,Units,URL,Cited_in_row -100289,Generation time,Cyanobacteria Synechocystis PCC 6803,6.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100289,Cell growth -102211,Mean generation time (on acetate),Green algae chlorella,20.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102211,Cell growth -102212,mean generation time (photoautotrophic growth),Green algae chlorella,11.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102212,Cell growth -104195,Generation time,Diatom Phaeodactylum tricornutum,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104195,Cell growth -104196,Generation time,Green algae Dunaliella tertiolecta,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104196,Cell growth -105638,Generation time at 30°C,Green algae Dunaliella salina,20.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105638,Cell growth -111252,Doubling time,Cyanobacteria Synechocystis PCC 6803,12.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111252,Cell growth -111335,Fastest generation time,Cyanobacteria Synechocystis PCC 6803,5.13,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111335,Cell growth +100289,Generation time,Cyanobacteria Synechocystis PCC 6803,6.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100289,Photoautotroph cell growth +102211,Mean generation time (on acetate),Green algae chlorella,20.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102211,Photoautotroph cell growth +102212,mean generation time (photoautotrophic growth),Green algae chlorella,11.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102212,Photoautotroph cell growth +104195,Generation time,Diatom Phaeodactylum tricornutum,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104195,Photoautotroph cell growth +104196,Generation time,Green algae Dunaliella tertiolecta,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104196,Photoautotroph cell growth +105638,Generation time at 30°C,Green algae Dunaliella salina,20.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105638,Photoautotroph cell growth +111252,Doubling time,Cyanobacteria Synechocystis PCC 6803,12.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111252,Photoautotroph cell growth +111335,Fastest generation time,Cyanobacteria Synechocystis PCC 6803,5.13,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111335,Photoautotroph cell growth 100233,Translation rate of beta-galactosidase in E. coli,Bacteria Escherichia coli,14.5,'13-16,aa/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100233,Biochemical synthesis 105067,Translation rate for short peptides,Bacteria Escherichia coli,22.0,'Table link - http://bionumbers.hms.harvard.edu/files/Maximal%20translation%20rate.pdf,1/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105067,Biochemical synthesis 104300,Translation rate on culture of nitrogen bases and glucose,Budding yeast Saccharomyces cerevisiae,9.3,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104300,Biochemical synthesis From b2d7145cd7706352fb05e234bb6b029c73d7708e Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Mon, 27 Apr 2026 23:57:26 -0700 Subject: [PATCH 8/9] Add (see data/references/) markers to 3 Reference cells MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Discoverable cross-link from main CSV to data/references/ for the rows backed by curated BioNumbers / primary-literature data: Nutrient transport, Biochemical synthesis, Photoautotroph cell growth. Non-breaking — Reference column is free-form display text. --- data/datasets/desert_farm_leverage_points.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/datasets/desert_farm_leverage_points.csv b/data/datasets/desert_farm_leverage_points.csv index f200bf8..546e870 100644 --- a/data/datasets/desert_farm_leverage_points.csv +++ b/data/datasets/desert_farm_leverage_points.csv @@ -1,9 +1,9 @@ Prefix,ShortName,Time_min,Time_max,Space_min,Space_max,Color,Reference model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-22,#013333,Karplus & McCammon (2002) Nat Struct Biol 9:646 process,CO2 fixation,6.67E-02,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat = 3-15/s natural RuBisCO; space = 0.1×–1.7× RuBisCO L8S8 enzyme volume (~7e-25 m³) -process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers -process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers -process,Photoautotroph cell growth,7.56E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers; Yu et al. (2015) Sci Rep 5:8132 (UTEX 2973 fastest) +process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers (see data/references/) +process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers (see data/references/) +process,Photoautotroph cell growth,7.56E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers; Yu et al. (2015) Sci Rep 5:8132 (UTEX 2973 fastest) (see data/references/) model,Community Metabolic Models,1.00E+02,1.00E+07,1.00E-18,1.00E-03,#013333,Zakem et al. (2020) ISME J 14:288 leverage point,Community Ecology,1.00E+06,1.00E+08,1.00E-09,1.00E+00,#FF9900,Moore et al. (2013) Nature Geosci 6:701 leverage point,Flocculation,1.00E+03,86400,1.00E-15,1.00E-09,#FF9900,Salim et al. (2011) J Appl Phycol; Vandamme et al. (2013) Biotechnol Adv 31:1680 From 98d31e38bd2a7dcd09350857e7616a25d190c5ea Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Tue, 28 Apr 2026 00:07:24 -0700 Subject: [PATCH 9/9] Decouple BioNumbers subset from desert_farm_leverage_points.csv Per Madison's clarification: BioNumbers data is meant as a standalone resource for future work, not as a backing-data layer for the main CSV. Changes: - Drop (see data/references/) markers from 3 Reference cells in desert_farm_leverage_points.csv (main CSV stands alone) - Drop Cited_in_row column from bionumbers_subset.csv (no longer a join key into the main CSV) - Delete phototroph_growth_supplementary.csv (its only entry was UTEX 2973 / Yu 2015 / 2.1h doubling, already inline-cited in the main CSV's Photoautotroph cell growth Reference cell) - Rewrite README.md to describe bionumbers_subset.csv as a standalone phototroph reference set, removing all cross-linking schema docs --- data/datasets/desert_farm_leverage_points.csv | 6 +- data/references/README.md | 59 +++---------------- data/references/bionumbers_subset.csv | 52 ++++++++-------- .../phototroph_growth_supplementary.csv | 2 - 4 files changed, 36 insertions(+), 83 deletions(-) delete mode 100644 data/references/phototroph_growth_supplementary.csv diff --git a/data/datasets/desert_farm_leverage_points.csv b/data/datasets/desert_farm_leverage_points.csv index 546e870..f200bf8 100644 --- a/data/datasets/desert_farm_leverage_points.csv +++ b/data/datasets/desert_farm_leverage_points.csv @@ -1,9 +1,9 @@ Prefix,ShortName,Time_min,Time_max,Space_min,Space_max,Color,Reference model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-22,#013333,Karplus & McCammon (2002) Nat Struct Biol 9:646 process,CO2 fixation,6.67E-02,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat = 3-15/s natural RuBisCO; space = 0.1×–1.7× RuBisCO L8S8 enzyme volume (~7e-25 m³) -process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers (see data/references/) -process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers (see data/references/) -process,Photoautotroph cell growth,7.56E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers; Yu et al. (2015) Sci Rep 5:8132 (UTEX 2973 fastest) (see data/references/) +process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers +process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers +process,Photoautotroph cell growth,7.56E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers; Yu et al. (2015) Sci Rep 5:8132 (UTEX 2973 fastest) model,Community Metabolic Models,1.00E+02,1.00E+07,1.00E-18,1.00E-03,#013333,Zakem et al. (2020) ISME J 14:288 leverage point,Community Ecology,1.00E+06,1.00E+08,1.00E-09,1.00E+00,#FF9900,Moore et al. (2013) Nature Geosci 6:701 leverage point,Flocculation,1.00E+03,86400,1.00E-15,1.00E-09,#FF9900,Salim et al. (2011) J Appl Phycol; Vandamme et al. (2013) Biotechnol Adv 31:1680 diff --git a/data/references/README.md b/data/references/README.md index 5cdc295..c77c110 100644 --- a/data/references/README.md +++ b/data/references/README.md @@ -1,20 +1,10 @@ # References -This directory contains curated reference data backing the Stommel-diagram -row bounds in `data/datasets/desert_farm_leverage_points.csv`. +Standalone reference data — not coupled to any specific dataset in this repo. ## Files -- `bionumbers_subset.csv` — entries from the [BioNumbers database](https://bionumbers.hms.harvard.edu/) (Milo & Phillips, *Cell Biology by the Numbers*) with stable `bion_id` identifiers. -- `phototroph_growth_supplementary.csv` — entries from primary literature where BioNumbers has no entry or no scalar value (e.g., entries with `NaN` in the BioNumbers `Value` column). - -Each file uses `Cited_in_row` to map back to the row(s) in `desert_farm_leverage_points.csv` that the entry justifies. - -## Why a curated subset - -The full BioNumbers database contains ~14,300 entries (~27 MB as HTML export). -Most are irrelevant to the desert farm Stommel diagram. Including only the -cited subset keeps this repo lean and provides explicit per-number provenance. +- `bionumbers_subset.csv` — curated phototroph-relevant entries from the [BioNumbers database](https://bionumbers.hms.harvard.edu/) (Milo & Phillips, *Cell Biology by the Numbers*) with stable `bion_id` identifiers and direct URLs. ## `bionumbers_subset.csv` schema @@ -27,50 +17,15 @@ cited subset keeps this repo lean and provides explicit per-number provenance. | `Range` | Reported range (often empty) | | `Units` | Units of `Value` | | `URL` | Direct link to the BioNumbers entry | -| `Cited_in_row` | Which `desert_farm_leverage_points.csv` row uses this entry | - -## `phototroph_growth_supplementary.csv` schema - -Same as above but `bion_id` replaced with a `Reference` column containing the full citation, since these entries are not in BioNumbers. - -| Column | Description | -|---|---| -| `Properties` | Description of the measured quantity | -| `Organism` | Organism the measurement is from | -| `Value` | Reported value | -| `Range` | Reported range (often empty) | -| `Units` | Units of `Value` | -| `Reference` | Full citation (author, year, journal, volume, page) | -| `URL` | Direct link to the article (DOI preferred) | -| `Cited_in_row` | Which `desert_farm_leverage_points.csv` row uses this entry | - -## Curation criteria - -- **Photoautotroph cell growth**: cell division/generation times for cyanobacteria, green algae, and diatoms. Excluded: heterotrophic bacteria, fungi, mammalian cells. The row `Time_min` is anchored to *Synechococcus elongatus* UTEX 2973 (the fastest known photoautotroph, ~2.1 h doubling), sourced from `phototroph_growth_supplementary.csv` since BioNumbers entry 112484 for this strain has no scalar value. -- **Biochemical synthesis**: translation and transcription elongation rates across model organisms. Bound by time per peptide/RNA elongation event. -- **Nutrient transport**: diffusion coefficients of small molecules (CO2, glucose, nitrate, ammonium) in water and intracellular environments, plus representative uptake rates. - -## Known gaps - -- Some BioNumbers entries with relevant `Properties` strings have `NaN` in `Value` (record exists but no scalar). These were excluded from `bionumbers_subset.csv`. Where the row's bound depends on such an entry, the data is moved to `phototroph_growth_supplementary.csv` with primary-literature citation (e.g., UTEX 2973). -- Phototroph-specific data is sparse for some categories (e.g., transporter kinetics). Where a phototroph entry was unavailable, generic or representative organism data (E. coli, Xenopus, generic) was used as a proxy. This is documented per-entry in `Organism`. -## Updating +## Scope -When new rows are added to `desert_farm_leverage_points.csv` that cite Milo & Phillips (or other primary literature): +Curated to phototroph-relevant entries (cyanobacteria, green algae, diatoms) across three categories: cell generation/doubling times, biochemical synthesis rates (transcription/translation elongation), and nutrient transport (small-molecule diffusion, transporter kinetics). Where phototroph-specific entries were unavailable, generic or model-organism data (e.g., E. coli, Xenopus) was kept as a proxy and noted in `Organism`. -1. Search the full BioNumbers database for relevant entries. -2. Add matching entries to `bionumbers_subset.csv` with the appropriate `Cited_in_row` value. -3. If a needed value is not in BioNumbers (or has `NaN`), add a primary-literature entry to `phototroph_growth_supplementary.csv`. -4. Avoid duplication — a single entry can be `Cited_in_row` for multiple rows by listing them semicolon-separated. +The full BioNumbers database has ~14,300 entries (~27 MB HTML export); this is a focused subset kept as a resource for future work. ## Attribution -BioNumbers is a project of the Milo Lab (Weizmann Institute) and Harvard Medical -School. Cite as: Milo R, Jorgensen P, Moran U, Weber G, Springer M (2010). -*BioNumbers — the database of key numbers in molecular and cell biology*. -Nucleic Acids Res. 38:D750–D753. -DOI: [10.1093/nar/gkp889](https://doi.org/10.1093/nar/gkp889). +BioNumbers is a project of the Milo Lab (Weizmann Institute) and Harvard Medical School. Cite as: Milo R, Jorgensen P, Moran U, Weber G, Springer M (2010). *BioNumbers — the database of key numbers in molecular and cell biology*. Nucleic Acids Res. 38:D750–D753. DOI: [10.1093/nar/gkp889](https://doi.org/10.1093/nar/gkp889). -For the broader synthesis: Milo R, Phillips R (2015). *Cell Biology by the -Numbers*. Garland Science. +For the broader synthesis: Milo R, Phillips R (2015). *Cell Biology by the Numbers*. Garland Science. diff --git a/data/references/bionumbers_subset.csv b/data/references/bionumbers_subset.csv index c144293..2db5ed5 100644 --- a/data/references/bionumbers_subset.csv +++ b/data/references/bionumbers_subset.csv @@ -1,26 +1,26 @@ -bion_id,Properties,Organism,Value,Range,Units,URL,Cited_in_row -100289,Generation time,Cyanobacteria Synechocystis PCC 6803,6.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100289,Photoautotroph cell growth -102211,Mean generation time (on acetate),Green algae chlorella,20.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102211,Photoautotroph cell growth -102212,mean generation time (photoautotrophic growth),Green algae chlorella,11.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102212,Photoautotroph cell growth -104195,Generation time,Diatom Phaeodactylum tricornutum,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104195,Photoautotroph cell growth -104196,Generation time,Green algae Dunaliella tertiolecta,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104196,Photoautotroph cell growth -105638,Generation time at 30°C,Green algae Dunaliella salina,20.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105638,Photoautotroph cell growth -111252,Doubling time,Cyanobacteria Synechocystis PCC 6803,12.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111252,Photoautotroph cell growth -111335,Fastest generation time,Cyanobacteria Synechocystis PCC 6803,5.13,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111335,Photoautotroph cell growth -100233,Translation rate of beta-galactosidase in E. coli,Bacteria Escherichia coli,14.5,'13-16,aa/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100233,Biochemical synthesis -105067,Translation rate for short peptides,Bacteria Escherichia coli,22.0,'Table link - http://bionumbers.hms.harvard.edu/files/Maximal%20translation%20rate.pdf,1/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105067,Biochemical synthesis -104300,Translation rate on culture of nitrogen bases and glucose,Budding yeast Saccharomyces cerevisiae,9.3,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104300,Biochemical synthesis -104598,Translation rate,Human Homo sapiens,5.0,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104598,Biochemical synthesis -100060,RNA polymerase transcription rate of stable RNA,Bacteria Escherichia coli,85.0,'Table link - http://bionumbers.hms.harvard.edu/files/Parameters%20pertaining%20to%20the%20macromolecular%20synthesis%20rates%20in%20exponentially%20growing%20E.%20coli%20Br%20as%20a%20function%20of%20growth%20rate%20at%2037%20degrees%20celsius.pdf,nt/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100060,Biochemical synthesis -101904,Transcription elongation rate of rRNA operons,Bacteria Escherichia coli,42.0,'±2,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=101904,Biochemical synthesis -100664,Single molecule RNA polymerase II transcription rates,Bacteria Escherichia coli,12.8,'±4.9,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100664,Biochemical synthesis -100662,Maximum RNA polymerase II transcription elongation rate,Mammalian tissue culture cell,71.6,,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100662,Biochemical synthesis -104089,Diffusion coefficient of glucose in water,Generic,600.0,'Table link - http://bionumbers.hms.harvard.edu/files/Diffusion%20coefficients%20of%20various%20substances%20in%20Water.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104089,Nutrient transport -104437,Diffusion coefficient of ammonium in water,Generic,1860.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104437,Nutrient transport -104439,Diffusion coefficient of nitrate in water,Generic,1700.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104439,Nutrient transport -109504,Diffusion coefficient glucose in water at 25°C,Generic,673.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109504,Nutrient transport -110618,Diffusion coefficient of CO2 in red blood cell,Human Homo sapiens,650.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=110618,Nutrient transport -117305,Diffusion coefficient of CO2 in air,air,1.4e-05,,m2/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=117305,Nutrient transport -102428,Intracellular diffusion coefficient for glucose transporter,African clawed frog Xenopus laevis,100.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102428,Nutrient transport -109673,Highest glucose uptake rate that still allows the maximal NADH formation rate,Bacteria Escherichia coli,2.4,,mmol/(gCDW·…h),https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109673,Nutrient transport -109686,Glucose uptake rate of strain C-3000 in minimal M9 media,Bacteria Escherichia coli,12.0,'±0.5,mmol/gDW/h,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109686,Nutrient transport +bion_id,Properties,Organism,Value,Range,Units,URL +100289,Generation time,Cyanobacteria Synechocystis PCC 6803,6.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100289 +102211,Mean generation time (on acetate),Green algae chlorella,20.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102211 +102212,mean generation time (photoautotrophic growth),Green algae chlorella,11.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102212 +104195,Generation time,Diatom Phaeodactylum tricornutum,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104195 +104196,Generation time,Green algae Dunaliella tertiolecta,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104196 +105638,Generation time at 30°C,Green algae Dunaliella salina,20.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105638 +111252,Doubling time,Cyanobacteria Synechocystis PCC 6803,12.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111252 +111335,Fastest generation time,Cyanobacteria Synechocystis PCC 6803,5.13,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111335 +100233,Translation rate of beta-galactosidase in E. coli,Bacteria Escherichia coli,14.5,'13-16,aa/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100233 +105067,Translation rate for short peptides,Bacteria Escherichia coli,22.0,'Table link - http://bionumbers.hms.harvard.edu/files/Maximal%20translation%20rate.pdf,1/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105067 +104300,Translation rate on culture of nitrogen bases and glucose,Budding yeast Saccharomyces cerevisiae,9.3,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104300 +104598,Translation rate,Human Homo sapiens,5.0,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104598 +100060,RNA polymerase transcription rate of stable RNA,Bacteria Escherichia coli,85.0,'Table link - http://bionumbers.hms.harvard.edu/files/Parameters%20pertaining%20to%20the%20macromolecular%20synthesis%20rates%20in%20exponentially%20growing%20E.%20coli%20Br%20as%20a%20function%20of%20growth%20rate%20at%2037%20degrees%20celsius.pdf,nt/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100060 +101904,Transcription elongation rate of rRNA operons,Bacteria Escherichia coli,42.0,'±2,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=101904 +100664,Single molecule RNA polymerase II transcription rates,Bacteria Escherichia coli,12.8,'±4.9,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100664 +100662,Maximum RNA polymerase II transcription elongation rate,Mammalian tissue culture cell,71.6,,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100662 +104089,Diffusion coefficient of glucose in water,Generic,600.0,'Table link - http://bionumbers.hms.harvard.edu/files/Diffusion%20coefficients%20of%20various%20substances%20in%20Water.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104089 +104437,Diffusion coefficient of ammonium in water,Generic,1860.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104437 +104439,Diffusion coefficient of nitrate in water,Generic,1700.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104439 +109504,Diffusion coefficient glucose in water at 25°C,Generic,673.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109504 +110618,Diffusion coefficient of CO2 in red blood cell,Human Homo sapiens,650.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=110618 +117305,Diffusion coefficient of CO2 in air,air,1.4e-05,,m2/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=117305 +102428,Intracellular diffusion coefficient for glucose transporter,African clawed frog Xenopus laevis,100.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102428 +109673,Highest glucose uptake rate that still allows the maximal NADH formation rate,Bacteria Escherichia coli,2.4,,mmol/(gCDW·…h),https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109673 +109686,Glucose uptake rate of strain C-3000 in minimal M9 media,Bacteria Escherichia coli,12.0,'±0.5,mmol/gDW/h,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109686 diff --git a/data/references/phototroph_growth_supplementary.csv b/data/references/phototroph_growth_supplementary.csv deleted file mode 100644 index 5ef6f98..0000000 --- a/data/references/phototroph_growth_supplementary.csv +++ /dev/null @@ -1,2 +0,0 @@ -Properties,Organism,Value,Range,Units,Reference,URL,Cited_in_row -Doubling time under high light and high CO2 (38°C; 1500 µmol photons/m²/s; 5% CO2),Cyanobacteria Synechococcus elongatus UTEX 2973,2.1,,hours,Yu et al. (2015) Sci Rep 5:8132,https://doi.org/10.1038/srep08132,Photoautotroph cell growth