Computational Biology Tools
Browse all available computational biology tools.
Available tools
- Biological Delay Interpolation Weight Tool Linear interpolation between explicit history anchors for a delay-model query; no extrapolation or delay-equation solve.
- Biological Model Event Priority Tie Tag Compare explicit model event priorities using a supplied higher-number-first convention without scheduling events.
- Biological Model Parameter Unit Label Label a supplied biological-model parameter value and explicit unit without validating a biological model.
- Biological ODE Local Residual Compare explicit observed and modeled derivatives of the same biological state in compatible units without fitting model parameters.
- Birth Death One Event Count Step Tool Apply a supplied discrete count event; no stochastic event time or event type is sampled.
- Boolean Network One Node Update Tool Evaluate one supplied Boolean node rule; empty AND is true, empty OR and XOR are false.
- Boolean Regulator Inhibition Token Tool Evaluate an explicit Boolean gating rule; no gene network or biological effect is inferred.
- Cell Barcode Ambiguity Count Tool Calculate cell barcode ambiguity count from explicit caller-supplied inputs.
- Cell State Probability Mass Gap Tool Calculate cell state probability mass gap from explicit caller-supplied inputs.
- Cellular Potts One Contact Energy Term Tool One Cellular Potts interfacial J*(1-delta(cellId1,cellId2)) contribution; coefficient is supplied, including its sign.
- Chemostat Washout Growth Gap Tool Local Monod growth-minus-dilution term, without solving substrate balance or predicting stable operation.
- Compartment Concentration Volume Factor Tool Compute amount from a supplied compatible concentration-volume pair.
- Compartment Dilution Reference Base Tool Calculate compartment dilution reference base from explicit caller-supplied inputs.
- Compartment Flow Sign Crosswalk Apply an explicit compartment inflow-positive bookkeeping convention to a nonnegative flow magnitude.
- Compartment Transfer One Timestep Term Tool One nonnegative explicit Euler transfer between closed compartments with conserved total amount.
- Flux Objective Single Reaction Contribution Multiply a supplied reaction flux by its signed linear objective coefficient for one metabolic objective contribution.
- Gene Logic Two Regulator Truth Row Evaluate one explicit Boolean AND, OR or XOR gene-regulator truth-table row without inferring biological regulation.
- Gene Set Universe Intersection Count Tool Count distinct exact supplied identifiers; no gene alias database is consulted.
- Hill Repression One State Evaluation Tool Calculate hill repression one state evaluation from explicit caller-supplied inputs.
- Lattice Population One Migration Balance Tool Calculate lattice population one migration balance from explicit caller-supplied inputs.
- Lineage Node Generation Depth Label Keep explicitly supplied biological generation and graph-depth indices distinct in a lineage-node label.
- Logistic Growth One Euler Step Tool One explicit Euler update of the logistic ODE; no clipping or numerical-stability guarantee is added.
- Lotka Volterra One Species Rate Tool Calculate lotka volterra one species rate from explicit caller-supplied inputs.
- Mass Action Bimolecular One Propensity Term Tool Stochastic mass-action pair count; identical reactants use n choose 2 and a supplied per-pair propensity coefficient.
- Metabolic Bound Flux Slack Report signed flux slack to explicit inclusive metabolic bounds without solving an optimization problem.
- Metabolic Flux One Constraint Residual Tool One stoichiometric row constraint S*v=accumulation; signed reaction fluxes are permitted.
- Metabolic Reaction Direction Sign Apply an explicit forward-positive sign convention to a nonnegative recorded metabolic reaction-rate magnitude.
- Model Observation Normalized Time Point Place an explicit observation time on a model’s supplied origin and positive reference-duration scale, allowing pre-origin observations.
- Morphogen Boundary Flux Sign Tool One-dimensional Fick flux sign under a supplied outward-normal convention.
- Neutral Model Mutant Frequency Step Tool Apply a supplied net replacement change at fixed population size; no neutral-process sampling distribution is inferred.
- Phylogeny Edge Transition Probability Term Tool Jukes-Cantor four-state DNA model where rate is total expected substitutions per site per time; oneOtherBaseProbability is for one specified other base.
- Population Step Birth Death Balance Balance explicitly supplied population events over one step without projecting growth or selecting an organism model.
- Predator Functional Response One Prey Point Tool Holling type II instantaneous rate with caller-supplied parameters; depletion during a finite feeding interval is excluded.
- Propensity Molecularity Volume Factor Calculate the explicit V^(1-molecularity) factor used in a supplied stochastic mass-action convention, excluding rate and combinatorial factors.
- Reaction Network One Species Drift Tool Expected instantaneous count drift from explicit reaction propensities; no random trajectory is sampled.
- Reaction Rate Temperature Reference Label Record explicit reaction-rate reference temperature metadata without applying a temperature law.
- Reaction Species Count Residual Tool Calculate reaction species count residual from explicit caller-supplied inputs.
- Regulatory Edge Activation Inhibition Label Label an explicitly recorded regulatory edge and its sign without inferring biological interactions.
- Sequence Fitness One Locus Contribution Tool Diploid additive-on-fitness coding gives heterozygote h*s and variant homozygote s; parameters are supplied rather than inferred from sequence.
- Sequence Kmer Edge Loss Tool Calculate sequence kmer edge loss from explicit caller-supplied inputs.
- Simulation Population Fraction Residual Tool Compare supplied simulation counts with independently supplied candidate fractions without fitting a biological model.
- Stochastic Propensity Noninteger Flag Tool Validate the supplied count domain for a combinatorial propensity term without simulating a reaction.
- Stoichiometric Column Conservation Residual Tool Weighted conservation residual for one reaction column, without deriving conserved moieties.
- Stoichiometric Species Balance Gap Tool Check one supplied species row against explicit reaction extents without constructing a biological mechanism.
- Time Course Observation Censor Token Preserve explicit biological time-course censoring metadata without imputing values.