From 85cdfa0694b57bd4950e5d4fe587eacadea7a270 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Wed, 29 Apr 2026 00:59:01 -0700 Subject: [PATCH 1/3] =?UTF-8?q?fix:=20label=2010=E2=81=BB=C2=B9=E2=81=B5?= =?UTF-8?q?=20m=C2=B3=20as=201=20pL=20not=201=20fL=20in=20stommel=5Fboyd20?= =?UTF-8?q?15=5Fvolumes?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The values 1.00E-15 m³ on rows 1, 2, and 3 (Gene & protein expression Space_max, Microbial growth (cellular) Space_max, Community metabolism (patch) Space_min) were labeled '1 fL' but 10⁻¹⁵ m³ = 1 pL = 1000 µm³. 1 fL = 10⁻¹⁸ m³ = 1 µm³, which is the Space_min value, not Space_max. Values unchanged; only the parenthetical unit labels are fixed. --- data/datasets/stommel_boyd2015_volumes.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/datasets/stommel_boyd2015_volumes.csv b/data/datasets/stommel_boyd2015_volumes.csv index af24815..8a67e43 100644 --- a/data/datasets/stommel_boyd2015_volumes.csv +++ b/data/datasets/stommel_boyd2015_volumes.csv @@ -1,8 +1,8 @@ ,Name,Time_min,Time_max,Space_min,Space_max,Color,Reference(s),Category,ProcessType,Notes,label_side,x_offset,y_offset,label_text,start_visible 0,Diffusion boundary layers,1.00E+01: ~10 seconds,1.00E+03: ~15 minutes,1.00E-13: ~100 µm × 100 µm × 10 µm,1.00E-06: 1 cm³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 1 mm – 1 cm (thin layers); V = L_h² × L_v.,left,-5,0,,True -1,Gene & protein expression,6.00E+01: ~1 minute,1.00E+04: ~3 hours,1.00E-18: 1 µm³,1.00E-15: 1 fL (single cell),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular only. Space_max = 10⁻¹⁵ m³. Number 1-2-3 in diagram.,left,-5,0,,True -2,Microbial growth (cellular),1.00E+02: ~2 minutes,1.73E+05: ~2 days,1.00E-18: 1 µm³,1.00E-15: 1 fL (single cell),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular & single-organism scale only. Space_max = 10⁻¹⁵ m³. Number 4 in diagram.,right,5,15,,True -3,Community metabolism (patch),3.60E+03: ~1 hour,3.00E+07: ~1 year,1.00E-15: 1 fL (biofilm base),1.00E-03: 1 L (small colony),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Community-level microbial metabolism at patch/colony scale.,right,5,-25,,True +1,Gene & protein expression,6.00E+01: ~1 minute,1.00E+04: ~3 hours,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular only. Space_max = 10⁻¹⁵ m³. Number 1-2-3 in diagram.,left,-5,0,,True +2,Microbial growth (cellular),1.00E+02: ~2 minutes,1.73E+05: ~2 days,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular & single-organism scale only. Space_max = 10⁻¹⁵ m³. Number 4 in diagram.,right,5,15,,True +3,Community metabolism (patch),3.60E+03: ~1 hour,3.00E+07: ~1 year,1.00E-15: 1 pL (biofilm base),1.00E-03: 1 L (small colony),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Community-level microbial metabolism at patch/colony scale.,right,5,-25,,True 4,Habitat-scale hydrodynamics,1.00E+03: ~15 minutes,1.00E+06: ~12 days,1.00E+05: 10⁵ m³,1.00E+10: 10¹⁰ m³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 10–100 m (mixed layer depth); V = L_h² × L_v. Number 5 in diagram.,right,5,-25,,False 5,Submesoscale eddies,1.00E+04: ~3 hours,1.00E+06: ~12 days,1.00E+08: 10⁸ m³,5.00E+12: 5×10¹² m³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 100–500 m; V = L_h² × L_v.,left,-5,0,,True 6,Mesoscale eddies,6.05E+05: ~1 week,1.00E+07: ~4 months,5.00E+10: 5×10¹⁰ m³,2.00E+15: 2×10¹⁵ m³,#7BA3B3,Boyd et al. (2015); Chelton et al. (2011); Dickey (2003),Physical processes,Physical,L_v = 500–2000 m (thermocline depth); V = L_h² × L_v. Number 7 in diagram.,left,-5,0,,True From 7eeda8af28f4445eecb54d9f4e4568cc8b017ec8 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Wed, 29 Apr 2026 00:59:36 -0700 Subject: [PATCH 2/3] =?UTF-8?q?docs:=20clarify=20Notes=20=E2=80=94=20upper?= =?UTF-8?q?=20bound=20covers=20eukaryotic=20microbes?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The upper bound of 10⁻¹⁵ m³ (1 pL ≈ 1000 µm³) on Gene & protein expression and Microbial growth (cellular) is too large for bacteria alone (~1-10 µm³). The values stay because the rows are meant to cover microbial diversity broadly — yeast (~30-50 µm³), small algae, etc. Notes column now states this explicitly. --- data/datasets/stommel_boyd2015_volumes.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/data/datasets/stommel_boyd2015_volumes.csv b/data/datasets/stommel_boyd2015_volumes.csv index 8a67e43..1343612 100644 --- a/data/datasets/stommel_boyd2015_volumes.csv +++ b/data/datasets/stommel_boyd2015_volumes.csv @@ -1,7 +1,7 @@ ,Name,Time_min,Time_max,Space_min,Space_max,Color,Reference(s),Category,ProcessType,Notes,label_side,x_offset,y_offset,label_text,start_visible 0,Diffusion boundary layers,1.00E+01: ~10 seconds,1.00E+03: ~15 minutes,1.00E-13: ~100 µm × 100 µm × 10 µm,1.00E-06: 1 cm³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 1 mm – 1 cm (thin layers); V = L_h² × L_v.,left,-5,0,,True -1,Gene & protein expression,6.00E+01: ~1 minute,1.00E+04: ~3 hours,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular only. Space_max = 10⁻¹⁵ m³. Number 1-2-3 in diagram.,left,-5,0,,True -2,Microbial growth (cellular),1.00E+02: ~2 minutes,1.73E+05: ~2 days,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular & single-organism scale only. Space_max = 10⁻¹⁵ m³. Number 4 in diagram.,right,5,15,,True +1,Gene & protein expression,6.00E+01: ~1 minute,1.00E+04: ~3 hours,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular only. Space_max = 10⁻¹⁵ m³ (1 pL); upper bound covers eukaryotic microbes (yeast ~30-50 µm³, small algae up to ~1000 µm³). Bacteria are ~1-10 µm³. Number 1-2-3 in diagram.,left,-5,0,,True +2,Microbial growth (cellular),1.00E+02: ~2 minutes,1.73E+05: ~2 days,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular & single-organism scale only. Space_max = 10⁻¹⁵ m³ (1 pL); upper bound covers eukaryotic microbes (yeast, small algae). Bacteria are ~1-10 µm³. Number 4 in diagram.,right,5,15,,True 3,Community metabolism (patch),3.60E+03: ~1 hour,3.00E+07: ~1 year,1.00E-15: 1 pL (biofilm base),1.00E-03: 1 L (small colony),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Community-level microbial metabolism at patch/colony scale.,right,5,-25,,True 4,Habitat-scale hydrodynamics,1.00E+03: ~15 minutes,1.00E+06: ~12 days,1.00E+05: 10⁵ m³,1.00E+10: 10¹⁰ m³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 10–100 m (mixed layer depth); V = L_h² × L_v. Number 5 in diagram.,right,5,-25,,False 5,Submesoscale eddies,1.00E+04: ~3 hours,1.00E+06: ~12 days,1.00E+08: 10⁸ m³,5.00E+12: 5×10¹² m³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 100–500 m; V = L_h² × L_v.,left,-5,0,,True From ae948fa68fb8b2b11b22527ba231ac28d6664556 Mon Sep 17 00:00:00 2001 From: madsCodeBuddy Date: Wed, 29 Apr 2026 01:25:09 -0700 Subject: [PATCH 3/3] =?UTF-8?q?fix:=20drop=20liter=20prefix=20from=20label?= =?UTF-8?q?s=20=E2=80=94=20keep=20cubic-distance=20throughout?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The legend tooltip labels mixed cubic-distance (m³, µm³, etc.) with liter prefix (1 pL), which jars against the m³ y-axis and the rest of the reference markers on the plot. Labels now use bare cubic-distance (1000 µm³). Disambiguating biological context moves to the Notes column where it belongs: - Row 3 now flags that 1000 µm³ ≈ 1000 cells (early biofilm cluster), not a single attached cell, since 'biofilm base' read as the latter. --- data/datasets/stommel_boyd2015_volumes.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/datasets/stommel_boyd2015_volumes.csv b/data/datasets/stommel_boyd2015_volumes.csv index 1343612..dece471 100644 --- a/data/datasets/stommel_boyd2015_volumes.csv +++ b/data/datasets/stommel_boyd2015_volumes.csv @@ -1,8 +1,8 @@ ,Name,Time_min,Time_max,Space_min,Space_max,Color,Reference(s),Category,ProcessType,Notes,label_side,x_offset,y_offset,label_text,start_visible 0,Diffusion boundary layers,1.00E+01: ~10 seconds,1.00E+03: ~15 minutes,1.00E-13: ~100 µm × 100 µm × 10 µm,1.00E-06: 1 cm³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 1 mm – 1 cm (thin layers); V = L_h² × L_v.,left,-5,0,,True -1,Gene & protein expression,6.00E+01: ~1 minute,1.00E+04: ~3 hours,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular only. Space_max = 10⁻¹⁵ m³ (1 pL); upper bound covers eukaryotic microbes (yeast ~30-50 µm³, small algae up to ~1000 µm³). Bacteria are ~1-10 µm³. Number 1-2-3 in diagram.,left,-5,0,,True -2,Microbial growth (cellular),1.00E+02: ~2 minutes,1.73E+05: ~2 days,1.00E-18: 1 µm³,1.00E-15: 1 pL (1000 µm³),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular & single-organism scale only. Space_max = 10⁻¹⁵ m³ (1 pL); upper bound covers eukaryotic microbes (yeast, small algae). Bacteria are ~1-10 µm³. Number 4 in diagram.,right,5,15,,True -3,Community metabolism (patch),3.60E+03: ~1 hour,3.00E+07: ~1 year,1.00E-15: 1 pL (biofilm base),1.00E-03: 1 L (small colony),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Community-level microbial metabolism at patch/colony scale.,right,5,-25,,True +1,Gene & protein expression,6.00E+01: ~1 minute,1.00E+04: ~3 hours,1.00E-18: 1 µm³,1.00E-15: 1000 µm³,#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular only. Space_max = 1000 µm³ covers eukaryotic microbes (yeast ~30-50 µm³, small algae up to ~1000 µm³); bacteria are ~1-10 µm³. Number 1-2-3 in diagram.,left,-5,0,,True +2,Microbial growth (cellular),1.00E+02: ~2 minutes,1.73E+05: ~2 days,1.00E-18: 1 µm³,1.00E-15: 1000 µm³,#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Intracellular & single-organism scale only. Space_max = 1000 µm³ covers eukaryotic microbes (yeast, small algae); bacteria are ~1-10 µm³. Number 4 in diagram.,right,5,15,,True +3,Community metabolism (patch),3.60E+03: ~1 hour,3.00E+07: ~1 year,1.00E-15: 1000 µm³,1.00E-03: 1 L (small colony),#6B9D9D,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Biological processes,Biological,Community-level microbial metabolism at patch/colony scale. Space_min = 1000 µm³ corresponds to an early biofilm cluster (~1000 cells), not a single attached cell.,right,5,-25,,True 4,Habitat-scale hydrodynamics,1.00E+03: ~15 minutes,1.00E+06: ~12 days,1.00E+05: 10⁵ m³,1.00E+10: 10¹⁰ m³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 10–100 m (mixed layer depth); V = L_h² × L_v. Number 5 in diagram.,right,5,-25,,False 5,Submesoscale eddies,1.00E+04: ~3 hours,1.00E+06: ~12 days,1.00E+08: 10⁸ m³,5.00E+12: 5×10¹² m³,#7BA3B3,"Boyd et al. (2015); cf. Dickey (2003), Haury et al. (1978)",Physical processes,Physical,L_v = 100–500 m; V = L_h² × L_v.,left,-5,0,,True 6,Mesoscale eddies,6.05E+05: ~1 week,1.00E+07: ~4 months,5.00E+10: 5×10¹⁰ m³,2.00E+15: 2×10¹⁵ m³,#7BA3B3,Boyd et al. (2015); Chelton et al. (2011); Dickey (2003),Physical processes,Physical,L_v = 500–2000 m (thermocline depth); V = L_h² × L_v. Number 7 in diagram.,left,-5,0,,True