Biology

punnett

The Punnett square of two parents and their offspring's genotypes and phenotypes, as exact probabilities and as a ratio. A genotype is two alleles for each gene, up to six genes: "Aa", "AaBb"; a superscript after ^ for multiple alleles and the sex chromosomes: "I^AI^B", "I^Ai", "X^AX^a", "X^aY" (braced when longer: "X^{w+}"). An allele whose letter (its superscript's, if any) is upper case is dominant. Gives gametes_1, gametes_2 (each distinct gamete once), grid (a row for each gamete of the first parent), genotypes and phenotypes (each {name, probability, parts}, in the order they first appear in the grid) and genotype_ratio, phenotype_ratio ("9:3:3:1"). Complete dominance shows each gene as A_ or aa; I^AI^B shows both; a male's X^AY is his phenotype.

• parent1 (string) -- the first parent's genotype
• parent2 (string) -- the second parent's genotype, its genes in any order
• mode (string) -- optional: "complete" (the default), or "incomplete" or "codominant", where each genotype is its own phenotype

hardyWeinberg

Hardy-Weinberg from genotype counts: p = (2 AA + Aa)/2N and q = 1 - p, observed_frequencies, expected_frequencies (p^2, 2pq, q^2), expected_counts, test_result (chiSquareTest of the counts against the expected counts; df = 2, the sheet's rule of outcomes minus one) and in_equilibrium (the test does not reject at 0.05).

• AA (number) -- homozygous dominant count
• Aa (number) -- heterozygous count
• aa (number) -- homozygous recessive count

hardyWeinbergFromQ2

Hardy-Weinberg from the frequency of the recessive phenotype q^2: q (exact when the fraction is a square), p, p2, two_pq and q2.

• q2 (number) -- the frequency of the homozygous recessive, 0 to 1

alleleFrequencies

The frequency p of allele A over generations of selection with fitnesses wAA, wAa, waa: p' = (p^2 wAA + pq wAa)/w, w = p^2 wAA + 2pq wAa + q^2 waa. An array of p for generations 0 to n; exact while the fractions fit, decimals after.

• p0 (number) -- p in generation 0
• wAA (number) -- fitness of AA
• wAa (number) -- fitness of Aa
• waa (number) -- fitness of aa
• n (number) -- the number of generations

complementStrand Apas Cloud

The partner strand of a DNA strand: strand (read 5' to 3') and aligned (as it stands under the given strand, "3'-TACG-5'").

• strand (string) -- a DNA or RNA strand: A T G C or A U G C; the ends may be marked "5'-ATG-3'" (marked 3' first, it is read as written 3' to 5')

transcribe Apas Cloud

The mRNA (5' to 3') made from a DNA strand: of the coding strand, the strand with U for T; of the template strand, its complement read 5' to 3'.

• strand (string) -- a DNA or RNA strand: A T G C or A U G C; the ends may be marked "5'-ATG-3'" (marked 3' first, it is read as written 3' to 5')
• role (string) -- optional: "coding" (the default) or "template"

translation Apas Cloud

Translates an mRNA (or the coding strand) by the standard genetic code from the first AUG to the first stop codon, or from base 1, 2 or 3 of a reading frame. Gives codons, protein ("Met-Phe-Gly"), one_letter ("MFG"), length (amino acids made), start (the first codon's base, from 1) and stop (the stop codon, or none).

• strand (string) -- a DNA or RNA strand: A T G C or A U G C; the ends may be marked "5'-ATG-3'" (marked 3' first, it is read as written 3' to 5')
• frame (number) -- optional: 1, 2 or 3, to read from that base without looking for AUG

aminoAcid Apas Cloud

One codon of the standard genetic code: three_letter, one_letter, name, is_start (AUG), is_stop (UAA, UAG, UGA). A DNA codon (ATG) is read as its mRNA.

• codon (string) -- three bases

codonsFor Apas Cloud

Every mRNA codon of an amino acid (three letters, one letter or name; or Stop), in the table's order: six for Leu, Ser and Arg, one for Met and Trp.

• aminoAcid (string) -- "Leu", "L", "leucine" or "Stop"

compareSequences Apas Cloud

A mutation, by translating both sequences from the original's first AUG: change (substitution, insertion, deletion or none), bases (how many), position (the first base that differs, from 1), effect (silent, missense, nonsense, frameshift, in frame insertion, in frame deletion or no change), original_protein, mutated_protein.

• original (string) -- the original coding strand or mRNA
• mutated (string) -- the mutated one

restrictionDigest Apas Cloud

Where restriction enzymes cut a DNA strand and the fragments: cuts (the cut falls after this many bases), fragments (lengths in order along the molecule) and bands (longest first, the order on a gel from the wells). Enzymes by name (EcoRI, BamHI, HindIII, PstI, SmaI, XhoI, SalI, XbaI, NotI, KpnI, SacI, NdeI, EcoRV, BglII, ClaI, NcoI, SpeI, SphI, AluI, HaeIII) or a site with ^ at the cut ("G^AATTC").

• strand (string) -- a DNA or RNA strand: A T G C or A U G C; the ends may be marked "5'-ATG-3'" (marked 3' first, it is read as written 3' to 5')
• enzymes (string or array) -- one enzyme or a list
• shape (string) -- optional: "linear" (the default) or "circular" (a plasmid: n cuts give n pieces)

fragmentLengths Apas Cloud

The fragments of a molecule from its length and cut positions only (a plasmid map): cuts, fragments, bands.

• length (number) -- base pairs
• cuts (array) -- cut positions
• shape (string) -- optional: "linear" (the default) or "circular"

gelSize Apas Cloud

A band's size from a ladder: log10(size) is a straight line in the distance run (least squares through the ladder). Gives size, slope, intercept and r_squared.

• ladderSizes (array) -- the ladder's sizes
• ladderDistances (array) -- how far each ran
• distance (number) -- how far the unknown band ran

pcrCopies Apas Cloud

Double-stranded DNA after n PCR cycles: total (2^n a template) and target_length (2^n - 2n a template: those exactly the target's length).

• cycles (number) -- 0 to 120
• templates (number) -- optional: starting molecules, 1 by default

dnaFacts Apas Cloud

The double helix of a strand (its partner pairs every base): base_pairs, the counts a, t, g, c in the duplex, gc_content, hydrogen_bonds (A-T two, G-C three), length_nm (0.34 nm a pair) and turns (10 pairs a turn).

• strand (string) -- a DNA or RNA strand: A T G C or A U G C; the ends may be marked "5'-ATG-3'" (marked 3' first, it is read as written 3' to 5')

chargaff Apas Cloud

Chargaff's rule: in double-stranded DNA A = T and G = C, so one base's percentage gives the four: a, t, g, c.

• percent (number) -- 0 to 50
• base (string) -- "A", "T", "G" or "C"

gel Apas Cloud

A picture of an agarose gel: a lane for each list of sizes (or a digest), wells at the top, each band where its size runs (distance a straight line in log10(size)); an optional ladder is the first lane with its sizes written beside it.

• lanes (array) -- a list of lanes, each a list of sizes or a digest
• labels (array) -- optional: a label for each lane
• ladder (array) -- optional: the ladder's sizes

surfaceToVolume

Surface area, volume and their ratio for the AP Biology sheet's solids, exact (pi kept): "sphere" (r), "cube" (s), "cylinder" (r, h), "rectangular solid" (l, w, h). A smaller cell has the larger ratio.

• solid (string) -- "sphere", "cube", "cylinder" or "rectangular solid"
• dims (number) -- the lengths: r; s; r, h; or l, w, h

solutePotential

The solute potential psi_S = -iCRT in bars, with the sheet's R = 0.0831 L bar/(mol K) and T = t + 273.

• i (number) -- the ionization constant: 1 for sucrose, 2 for NaCl
• C (number) -- molar concentration
• t (number) -- temperature, degrees C

waterPotential

Water potential psi = psi_P + psi_S, bars.

• pressure (number) -- pressure potential (0 in an open container)
• solute (number) -- solute potential

waterMovement

Which way water moves between a cell and its solution, from the higher water potential to the lower: direction (into the cell, out of the cell, no net movement), solution (hypotonic, isotonic or hypertonic to the cell) and difference (the solution's minus the cell's).

• cell (number) -- the cell's water potential
• solution (number) -- the solution's water potential

twoPointCross Apas Cloud

A two-point test cross: parental (the largest class and its reciprocal), recombinant, recombinants, total, frequency (recombinants/total), map_units (cM, 100 x frequency) and linked (frequency under 1/2).

• classes (array) -- the offspring classes as strings, one letter a gene in one gene order, each with its reciprocal
• counts (array) -- a count for each class

threePointCross Apas Cloud

A three-point test cross of eight classes: order ("V-P-B", the middle gene the one the double crossovers swap), parental, double_crossovers (the smallest pair), first_distance and second_distance (cM between neighbours, double crossovers counted in both), total_distance, coincidence (observed/expected double crossovers) and interference (1 - coincidence).

• classes (array) -- the offspring classes as strings, one letter a gene in one gene order, each with its reciprocal
• counts (array) -- a count for each class

geneOrder Apas Cloud

Genes on a line from the map distances between pairs: order ("A-C-B"), genes and positions (cM from the first). The farthest pair are the ends; distances that do not fit one line are refused.

• pairs (array) -- pairs of gene letters: ["AB", "BC", "AC"]
• distances (array) -- a map distance for each pair

chromosomeMap Apas Cloud

A picture of a gene map: the chromosome as a bar, each gene at its position, the distance between neighbours below in cM. From a geneOrder result, or from genes and positions in order.

• map (record or array) -- a geneOrder result, or the genes in order
• positions (array) -- optional (with genes): their positions, cM

tonicity Apas Cloud

A picture of a cell in a hypotonic, isotonic or hypertonic solution with the net movement of water: an animal cell swells, keeps its shape or shrinks (crenates); a plant cell is turgid, flaccid or plasmolysed.

• solution (string) -- "hypotonic", "isotonic" or "hypertonic"
• cell (string) -- optional: "animal" (the default) or "plant"

errorBars

Error bars as the AP Biology sheet gives them: n, mean, sd (sample, n - 1), se (sd / sqrt(n)), and lower, upper = mean -/+ 2 SE (about 95% confidence); exact while the square roots are.

• xs (array) -- the values, two or more

compareErrorBars

Two samples' error bars (first, second), whether they overlap, and the course's reading: overlapping bars mean the difference may not be significant; bars that do not overlap, that it likely is.

• xs (array) -- the first sample
• ys (array) -- the second sample

percentChange

(new - old) / old x 100.

• old (number) -- the starting value, not 0
• new (number) -- the new value

rateTable

Rates from a table, dY/dt over each interval (rates), the average rate over the whole (average) and the interval of the fastest rate (fastest, from 1).

• ts (array) -- the times, rising
• ys (array) -- a value at each time

michaelisMenten

The rate of an enzyme reaction v = Vmax S / (Km + S): half of Vmax when S = Km.

• vmax (number) -- the maximum rate
• km (number) -- the Michaelis constant
• s (number) -- substrate concentration

inhibitedEnzyme

The apparent vmax and km with an inhibitor at concentration i: a competitive one raises Km to km (1 + i/ki), Vmax unchanged; a noncompetitive one lowers Vmax to vmax / (1 + i/ki), Km unchanged.

• vmax (number) -- Vmax
• km (number) -- Km
• i (number) -- inhibitor concentration
• ki (number) -- the inhibitor's constant
• kind (string) -- "competitive", "noncompetitive" or "none"

populationRate

dN/dt on the sheet: exponential rmax N, or logistic rmax N (K - N)/K with a carrying capacity; exact.

• r (number) -- rmax, the maximum per capita growth rate
• N (number) -- population size
• K (number) -- optional: carrying capacity

populationSize

N(t) of continuous growth: N0 e^(rt), or logistic K / (1 + (K - N0)/N0 e^(-rt)).

• N0 (number) -- population at t = 0
• r (number) -- rmax
• t (number) -- time
• K (number) -- optional: carrying capacity

populationSteps

N over n generations of discrete growth, N + rN (or + rN (K - N)/K): an array from generation 0; exact while the fractions fit.

• N0 (number) -- starting population
• r (number) -- growth rate a generation
• n (number) -- generations
• K (number) -- optional: carrying capacity

simpsonIndex

Simpson's diversity index on the sheet, 1 - sum (n/N)^2, exact: index, total (N) and dominance (sum (n/N)^2).

• counts (array) -- organisms of each species

energyPyramid

The energy at each trophic level, producers first, each level the efficiency (10% by default) of the one below.

• producers (number) -- energy of the producers
• levels (number) -- how many levels, 1 to 12
• efficiency (number) -- optional: the fraction passed up, 0.1 by default

netPrimaryProductivity

NPP = GPP - R: what the producers keep after their own respiration.

• gpp (number) -- gross primary productivity
• respiration (number) -- respiration of the producers

foodWeb Apas Cloud

A food web from its links: species, producers (eat nothing), top_predators (eaten by nothing) and levels (each species' trophic level, 1 + the shortest chain from a producer, and highest_level, by the longest).

• links (array) -- links "food>eater" as energy flows: ["grass>rabbit", "rabbit>hawk"]

removeSpecies Apas Cloud

What follows from losing a species: lost (consumers left with no food, the cascade included), lose_a_food_source (survivors that ate it or a species lost with it) and may_increase (survivors that it, or a species lost with it, ate).

• links (array) -- links "food>eater" as energy flows: ["grass>rabbit", "rabbit>hawk"]
• species (string) -- the species removed

foodWebDiagram Apas Cloud

A picture of a food web: each species in a row by its highest trophic level, producers at the bottom, an arrow from each food to its eater.

• links (array) -- links "food>eater" as energy flows: ["grass>rabbit", "rabbit>hawk"]

trophicPyramid Apas Cloud

A picture of an ecological pyramid, the first value at the bottom, widths on a logarithmic scale so ten-fold steps stay readable.

• values (array) -- a value for each level, producers first
• labels (array) -- optional: a name for each level

enzymeCurve Apas Cloud

The course's enzyme curves as a graph: "temperature" (gentle rise to the optimum, steep fall as the enzyme denatures; optimum 37 C by default), "pH" (a bell round the optimum, 7 by default), "substrate" (Michaelis-Menten, Vmax dashed) or "inhibitors" (no, competitive and noncompetitive inhibitor). A model for drawing, not measured data.

• kind (string) -- "temperature", "pH", "substrate" or "inhibitors"
• optimum (number) -- optional: the optimum temperature or pH

growthCurve Apas Cloud

A graph of N(t) (populationSize): exponential, or logistic with the carrying capacity K dashed.

• N0 (number) -- population at t = 0
• r (number) -- rmax
• tmax (number) -- the end of the time axis
• K (number) -- optional: carrying capacity

errorBarChart Apas Cloud

A bar chart of each group's mean with whiskers to mean +/- 2 SE (errorBars).

• groups (array) -- a list of samples
• labels (array) -- a name for each

cladogram Apas Cloud

A cladogram from a table of shared characters, by the fewest changes. A character's derived state is the one the outgroup lacks (the outgroup is named, or is the taxon with the fewest 1s). When the characters nest, each is gained once, and taxa that nothing splits stay on one branching. When they conflict, every tree is tried (up to 9 taxa) and one with the fewest changes is kept; homoplasy names the characters that change more than once, and equally_good counts the trees that are just as short. Gives newick (the tree, its characters in square brackets), outgroup, changes, homoplasy, equally_good and clades (each group with the characters gained on the branch into it).

• taxa (array) -- the taxa, one a row of the table
• characters (array) -- the characters, one a column
• table (array) -- rows of 0 (absent) and 1 (present)
• outgroup (string) -- optional: the taxon the others are compared with

cladogramDiagram Apas Cloud

Draws a tree sideways: the root at the left, the taxa in a column at the right, and each character over the branch where it is gained, with a tick across it. A tree with branch lengths (from treeFromSequences or treeFromDifferences) is drawn to scale.

• tree (record) -- the result of cladogram, treeFromSequences or treeFromDifferences, or Newick text

closestRelative Apas Cloud

The taxa that branch off together with a taxon: its closest relatives, all equally close. Also the characters it shares with them (gained on the way from the root).

• tree (record) -- a tree (a cladogram's result, or Newick text)
• taxon (string) --

commonAncestor Apas Cloud

The most recent common ancestor of some taxa: every taxon descended from it, and the characters they all share.

• tree (record) -- a tree (a cladogram's result, or Newick text)
• taxa (array) -- two or more taxa

treeChanges Apas Cloud

The fewest character changes a given tree needs for a table (Fitch's count; a branching may have more than two branches). Use it to compare trees: the one with fewer changes is the more parsimonious.

• tree (string) -- Newick text, (out,(A,(B,C)));
• taxa (array) --
• characters (array) --
• table (array) -- rows of 0 and 1, one a taxon

treeFromSequences Apas Cloud

A tree from aligned sequences. The differences between each pair are counted, and the tree is built by UPGMA: the two closest groups are joined first, meeting at half their difference, and a joined group's difference from the others is the average over its members. Gives differences (the table), newick (with branch lengths) and joins (each join and its height, exact).

• taxa (array) --
• sequences (array) -- aligned DNA or protein sequences, all of one length

treeFromDifferences Apas Cloud

A tree by UPGMA from a table of differences (amino acids or bases that differ, between each pair of taxa). Gives newick and joins, as treeFromSequences does.

• taxa (array) --
• differences (array) -- a square table: 0 down the middle, the same both ways

molecularClock

The molecular clock: differences build up at a steady rate. molecularClock(d, rate) gives the time since two lineages split, d / rate. molecularClock(d, D, T) sets the clock from a pair whose split is known (D differences in time T) and gives d x T / D. Exact.

• differences (number) -- between the two lineages
• rate or D (number) -- differences per unit of time, or the known pair's differences
• T (number) -- optional: the known pair's time

clockRate

The molecular clock's rate: differences / time. Exact.

• differences (number) --
• time (number) --

cellDivision

What a cell holds at each stage of mitosis or meiosis, for a species with 2n chromosomes. Each row gives cells, chromosomes per cell (counted by centromeres), dna_molecules (each chromatid one), dna (in C, where G1 is 2C), homologous_pairs, haploid and tetrads. At anaphase the sister chromatids have parted and each counts as a chromosome. Telophase is counted before cytokinesis. Give a stage to get only its row.

• 2n (number) -- the diploid number: 46 for humans
• division (string) -- "mitosis" or "meiosis"
• stage (string) -- optional: "G1", "S", "G2", "prophase", ..., "metaphase I", ..., "cytokinesis II"

gameteCombinations

The kinds of gamete that independent assortment of n chromosome pairs can make, 2^n, and the kinds of zygote two parents can make, (2^n)^2. Exact.

• n (number) -- the chromosome pairs: 23 for humans

divisionStage Apas Cloud

Draws a stage of mitosis or meiosis for 2n up to 8. Each pair has its own length; the copy from the mother is in a red and the copy from the father in a blue. Duplicated chromosomes are drawn as two sister chromatids. The number drawn in each cell is cellDivision's count for that stage, and the picture is not drawn otherwise. The caption gives the counts.

• 2n (number) -- 2, 4, 6 or 8
• division (string) -- "mitosis" or "meiosis"
• stage (string) -- as in cellDivision

cellCycle Apas Cloud

The cell cycle as a ring, clockwise: G1, S and G2 (interphase), then M (mitosis and cytokinesis). It marks the G1, G2 and M checkpoints and G0 for cells that stop dividing. The shares of the ring are schematic.

membrane Apas Cloud

A stretch of the phospholipid bilayer with up to 6 features in the order given. Channels and carriers show passive movement down the gradient; a pump shows active transport against it, with ATP. In a mitochondrion's inner membrane or a thylakoid's, the electron transport chain pumps protons to the upper side (the intermembrane space or the thylakoid space). ATP synthase lets the protons back down and makes ATP on the lower side (the matrix or the stroma).

• features (array) -- "channel", "aquaporin", "carrier", "pump", "receptor", "glycoprotein", "cholesterol", "peripheral", "electron transport", "ATP synthase"
• place (string) -- optional: "cell" (the default; outside the cell above, the cytoplasm below), "mitochondrion" or "thylakoid"

signalPathway Apas Cloud

A signal-transduction pathway: the signal (the first step) outside the cell, its receptor (the second) in the membrane, each relay inside with an arrow to the next, and the cell's response (the last) at the bottom. The stages are marked reception, transduction and response.

• steps (array) -- 3 to 9 steps: the signal, the receptor, the relays, the response

metabolismOverview Apas Cloud

The overview of photosynthesis (light reactions and the Calvin cycle, with what passes between them) or of cellular respiration (glycolysis, pyruvate oxidation, the Krebs cycle, electron transport and chemiosmosis). Each stage shows where in the cell it happens and what goes in and comes out, with the yields per glucose that the biology bank verifies: glycolysis 2 ATP (net) and 2 NADH, the Krebs cycle 2 ATP, 6 NADH and 2 FADH2, and oxidative phosphorylation most of the ATP (the bank gives no number).

• process (string) -- "photosynthesis" or "respiration"

punnettSquare Apas Cloud

Draws the Punnett square as a textbook does. The first parent's gametes run down the left and the second's across the top, repeated gametes included (AA × Aa is 2 by 2). Each cell shows its genotype on the colour of its phenotype class. Below the square are the classes with their exact chances and the phenotype and genotype ratios (punnett's). Works for up to three genes, with X and Y for sex-linked genes and ^ for multiple alleles (I^A, I^B, i).

• parent1 (string) -- "Aa", "AaBb", "X^AX^a", "I^Ai"
• parent2 (string) --
• mode (string) -- optional: "complete" (the default), "incomplete" or "codominant"

pedigreeModes Apas Cloud

Which modes of inheritance fit a pedigree: autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, Y-linked and mitochondrial. A mode fits when some genotype for each person gives every child from its parents (full penetrance, no new mutations), and every assignment is tried. Gives fits, ruled_out and modes: each mode with the reason it does not fit (the course's, such as "II-1 is affected but neither parent is") or each person's genotypes and their chances.

• people (array) -- each "id sex [affected|carrier] [parent parent]": "II-3 f affected I-1 I-2"; sex m or f; both parents or neither
• q (number) -- optional: the disease allele's frequency. People who married in are then weighed by Hardy-Weinberg; otherwise they carry no more disease alleles than the family makes them carry

pedigreeGenotypes Apas Cloud

Each person's possible genotypes under one mode, with exact chances. For example, the unaffected brother of an affected girl with unaffected parents is a carrier with chance 2/3 (autosomal recessive).

• people (array) -- as in pedigreeModes
• mode (string) -- "autosomal recessive", "X-linked recessive", ...
• q (number) -- optional, as in pedigreeModes

pedigreeChild Apas Cloud

The chance that a child of two people in the pedigree is affected, under one mode: affected (either sex), son_affected, daughter_affected, and carrier (an unaffected heterozygote).

• people (array) -- as in pedigreeModes
• mode (string) --
• parent1 (string) -- an id
• parent2 (string) -- an id
• q (number) -- optional, as in pedigreeModes

pedigreeChart Apas Cloud

Draws the pedigree in the usual symbols: a square for a male, a circle for a female, filled when affected and half filled for a carrier. Partners are joined by a line, and their children hang from a line under them. Each generation is a row, numbered I, II, III at the left.

• people (array) -- as in pedigreeModes

bioTerm Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. A term from the glossary: its definition in our own words, the record's id (topic/id), the topic, its state and the source pages. Either name of a term with two works ("citric acid cycle").

• term (string) --

bioFact Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. A claim judged against the facts: supported, contradicted, conflict (the records disagree), unknown (no record bears on it) or overstated (the records state it only as usual or possible: "usually", "can", "may"), with the records that decide it. A one-valued relation (takes place in) contradicts any other value. Give "not" to judge the negated claim.

• subject (string) -- a thing, by name or id
• relation (string) -- "takes place in", "produces", "needs" ... (the notes show them)
• object (string) --
• not (string) -- optional: "not"

bioFacts Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. Every fact the bank holds about a thing, as a sentence with its record's id.

• thing (string) --

bioSteps Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. A process's stages in order, with what goes in and comes out of each and how many times it runs.

• process (string) -- an id or words of its name: "aerobic respiration"

bioCount Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. A molecule counted over a process, exactly: each stage's amount times its repeats, with the parts. A stage with no fixed number ("the number varies") makes the count not a fixed number unless that stage is left out. With ATP, "ATP (or GTP)" counts too.

• process (string) --
• molecule (string) -- "ATP", "NADH", "CO2" ...
• side (string) -- optional: "out" (the default), "in" or "net"
• stages (array) -- optional: only these stages

bioEffect Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. What a change does, found by following the bank's signed cause-and-effect links. The answer is increases, decreases, unknown (no chain links them) or ambiguous (chains disagree, so no answer is given). Each chain is given as steps with its records, to serve as the explanation.

• change (string) -- a quantity, by name or id
• direction (string) -- "up" or "down"
• target (string) --
• context (string) -- optional: a context that some links need

bioCompare Apas Cloud

From the biology knowledge bank's verified records (us-content/biology, exported into the engine), never from a model's memory. A comparison table, each cell with the records it comes from; a cell with no record says so.

• table (string) -- an id or words of its title

bioBankCheck Apas Cloud

The biology bank's logic checks: - every id named exists; - no fact is contradicted by another; - each process balances (carbons, loaded and empty carriers) and gives the counts its source states; - every course topic has terms and facts. The notes list topics with no process or table, and links whose chains disagree. The quotes are checked against their pages by the bank's own tool (bio_bank.py check).