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Voltage sonification maps −100 to +40 mV onto a logarithmic 110–1760 Hz pitch range."},{"scene":"neural","citation":"Howarth, Gleeson & Attwell (2012) · rodent cortex model","url":"https://doi.org/10.1038/jcbfm.2012.35","limitations":"ATP demand calculated from the Howarth et al. cortical budget. Ribbons split process totals into receptor types, neuronal compartments and resting costs; width follows absolute demand. Gray ribbons show the 4 Hz reference. Firing rate, release probability and Na⁺ overlap update exported Python coefficients. Source assumptions include doubled vesicle costs and spreadsheet glial scaling. Housekeeping is one third of signaling demand. Source parameter uncertainty is unspecified. Sonification assigns a pitch to each process and maps demand to bounded oscillator gain. Optional vesicle depletion uses a reduced mean-field resource model and effective release U×R. Recovery time is an illustrative control; facilitation and activity-dependent recovery are omitted."},{"scene":"hh","citation":"Hodgkin–Huxley equations · membrane_report synthetic model","url":"https://pubmed.ncbi.nlm.nih.gov/12991237/","limitations":"A single-compartment Hodgkin–Huxley simulation with C = 1 µF/cm², gNa = 120, gK = 36 and gL = 0.3 mS/cm², and reversal potentials +50, −77 and −54.387 mV. The current step lasts from 50 to 250 ms. Controls vary current density and maximal channel conductance. Effective channel conductance is gNa × m³h or gK × n⁴, shown in the meters. Spike counts use upward 0 mV crossings. Browser integration uses RK4 at 0.01 ms and is checked against SciPy DOP853. Geometry is schematic. Audio clicks follow model spike times. This is the classic squid-axon model at 6.3 °C. Temperature scales all gate rates by 3^((T−6.3)/10), while reversal potentials remain fixed. Paired-pulse mode applies two 2 ms pulses; the interval is measured onset to onset."}],"access":{"mcp":"/mcp","rest":"/api/catalog","behavior":"/api/behavior","source":"/api/source?path=visualization/atlas.js","experiment":"/api/experiment","views":"/api/views/{id}","browser":"window.livingSystems.inspect()"},"data":{"thermal":"/data/thermal.json","neural":"/data/neural.json","recordings":"See traces; pinned NWB binary source URLs remain with DANDI."},"research":{"reviewed_at":"2026-10-14","method":"Consensus searches and fetched paper records; bibliographic and implementation checks against PubMed, original-paper PDF and NEURON hh.mod.","papers":[{"authors":"Kingsolver, Higgins & Augustine","year":2015,"title":"Fluctuating temperatures and ectotherm growth: distinguishing non-linear and time-dependent effects","journal":"Journal of Experimental Biology","doi":"10.1242/jeb.120733","pmid":"25987738","pubmed":"https://pubmed.ncbi.nlm.nih.gov/25987738/","consensus":"https://consensus.app/papers/fluctuating-temperatures-and-ectotherm-growth-kingsolver-higgins/80ca2657425d502297c2eac7e45d874e/?utm_source=chatgpt","citation_count_at_review":185,"scenes":["thermal"],"supports":"Nonlinear rate curves can yield different time-averaged responses at equal mean temperature.","limit":"The study concerns Manduca growth, not Chlorella oxygen flux. Exposure duration and thermal history can invalidate instantaneous averaging. The atlas demonstrates the mathematical effect conditional on its fitted rate curve."},{"authors":"Hodgkin & Huxley","year":1952,"title":"A quantitative description of membrane current and its application to conduction and excitation in nerve","journal":"Journal of Physiology","doi":"10.1113/jphysiol.1952.sp004764","pmid":"12991237","pubmed":"https://pubmed.ncbi.nlm.nih.gov/12991237/","consensus":"https://consensus.app/papers/a-quantitative-description-of-membrane-current-and-its-hodgkin-huxley/455037f923405f5390c7441952ec4b88/?utm_source=chatgpt","citation_count_at_review":18920,"scenes":["membrane"],"implementation_reference":"https://github.com/neuronsimulator/nrn/blob/master/src/nrnoc/hh.mod","supports":"Voltage-dependent channel gating, sodium inactivation, recovery and the classic temperature factor 3^((T-6.3)/10).","limit":"A spatially uniform squid-axon model. Temperature changes gating rates only; ion concentrations, reversal potentials and maximal conductances stay fixed. It does not fit the recorded mouse cells."},{"authors":"Tsodyks & Markram","year":1997,"title":"The neural code between neocortical pyramidal neurons depends on neurotransmitter release probability","journal":"PNAS","doi":"10.1073/pnas.94.2.719","pmid":"9012851","pubmed":"https://pubmed.ncbi.nlm.nih.gov/9012851/","full_text":"https://www.cns.nyu.edu/csh/csh04/Articles/Tsodyks-Markram-97.pdf","consensus":"https://consensus.app/papers/the-neural-code-between-neocortical-pyramidal-neurons-tsodyks-markram/651903c31cb752e2a737aabdf7b0a12a/?utm_source=chatgpt","citation_count_at_review":1763,"scenes":["neural"],"supports":"Release-dependent resource depletion, exponential recovery and saturation of mean synaptic output with firing rate.","limit":"The atlas uses a reduced one-pool mean-field approximation, R′=(1−R)/τ−U f R. Coupling U×R to the Howarth per-event ATP accounting is an illustrative extension, not an experimentally validated whole-cortex ATP trajectory."},{"authors":"Fuhrmann, Cowan, Segev, Tsodyks & Stricker","year":2004,"title":"Multiple mechanisms govern the dynamics of depression at neocortical synapses of young rats","journal":"Journal of Physiology","doi":"10.1113/jphysiol.2003.058107","pmid":"15020700","pubmed":"https://pubmed.ncbi.nlm.nih.gov/15020700/","consensus":"https://consensus.app/papers/multiple-mechanisms-govern-the-dynamics-of-depression-at-fuhrmann-cowan/3acd0660edda5c0d8c870ad9715ecfd9/?utm_source=chatgpt","citation_count_at_review":68,"scenes":["neural"],"supports":"An explicit limit on the simplified depletion model: real cortical synapses also exhibit release-independent depression and activity-dependent recovery.","limit":"These mechanisms are not represented by the atlas's fixed recovery time."}],"extensions":[{"id":"thermal-cycle","scene":"thermal","control":"thermal-amplitude","python":"thermal_response.derived.cycle_average","calculation":"Uniform time average over mean+amplitude*sin(phase)","checks":"Convex/concave/linear known answers and independent SciPy adaptive quadrature versus browser periodic quadrature."},{"id":"hh-temperature","scene":"membrane","control":"hh-temperature","python":"membrane_report.hh.simulate_hh","calculation":"Multiply gate kinetics by 3^((T-6.3)/10)","checks":"Gate-derivative factor identity and browser RK4 versus DOP853 voltage/gate trajectories."},{"id":"hh-pulse-pair","scene":"membrane","control":"hh-protocol","python":"membrane_report.hh.simulate_hh","calculation":"Two 2 ms pulses separated by a 4–30 ms onset interval","checks":"Exact current transitions, 1 versus 2 spike recovery cases, sodium block and independent integrators."},{"id":"vesicle-depletion","scene":"neural","control":"depletion-toggle","python":"neural_budget.synapse.resource_state/depleted_budget","calculation":"R′=(1−R)/τ−U*f*R; effective release U*R","checks":"Analytic solution versus independent ODE, zero-firing recovery and per-component Python/browser ATP parity."}]}}