Dataset Information

An Understandable, Extensible, and Reusable Implementation of the Hodgkin-Huxley Equations Using Modelica.

ABSTRACT: The Hodgkin-Huxley model of the squid giant axon has been used for decades as the basis of many action potential models. These models are usually communicated using just a list of equations or a circuit diagram, which makes them unnecessarily complicated both for novices and for experts. We present a modular version of the Hodgkin-Huxley model that is more understandable than the usual monolithic implementations and that can be easily reused and extended. Our model is written in Modelica using software engineering concepts, such as object orientation and inheritance. It retains the electrical analogy, but names and explains individual components in biological terms. We use cognitive load theory to measure understandability as the amount of items that have to be kept in working memory simultaneously. The model is broken down into small self-contained components in human-readable code with extensive documentation. Additionally, it features a hybrid diagram that uses biological symbols in an electrical circuit and that is directly tied to the model code. The new model design avoids many redundancies and reduces the cognitive load associated with understanding the model by a factor of 6. Extensions can be easily applied due to an unifying interface and inheritance from shared base classes. The model can be used in an educational context as a more approachable introduction to mathematical modeling in electrophysiology. Additionally the modeling approach and the base components can be used to make complex Hodgkin-Huxley-type models more understandable and reusable.

SUBMITTER: Scholzel C

PROVIDER: S-EPMC7566415 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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An Understandable, Extensible, and Reusable Implementation of the Hodgkin-Huxley Equations Using Modelica.

Schölzel Christopher C Blesius Valeria V Ernst Gernot G Dominik Andreas A

Frontiers in physiology 20201002

The Hodgkin-Huxley model of the squid giant axon has been used for decades as the basis of many action potential models. These models are usually communicated using just a list of equations or a circuit diagram, which makes them unnecessarily complicated both for novices and for experts. We present a modular version of the Hodgkin-Huxley model that is more understandable than the usual monolithic implementations and that can be easily reused and extended. Our model is written in Modelica using s ...[more]

PMID: 33117198

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Project description:BackgroundThere has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized graphical outputs. A number of systems have emphasized custom development of ChIP-seq pipelines. These systems are primarily based on custom programming of a single, complex pipeline or supply libraries of modules and do not produce the full range of outputs commonly produced for ChIP-seq datasets. It is desirable to have more comprehensive pipelines, in particular ones addressing common metadata tasks, such as pathway analysis, and pipelines producing standard complex graphical outputs. It is advantageous if these are highly modular systems, available as both turnkey pipelines and individual modules, that are easily comprehensible, modifiable and extensible to allow rapid alteration in response to new analysis developments in this growing area. Furthermore, it is advantageous if these pipelines allow data provenance tracking.ResultsWe present a set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The turnkey pipelines in Kepler allow data provenance tracking. Implementation emphasized use of common R packages and widely-used external tools (e.g., MACS for peak finding), along with custom programming. This software presents comprehensive solutions and easily repurposed code blocks for ChIP-seq analysis and pipeline creation. Tasks include mapping raw reads, peakfinding via MACS, summary statistics, peak location statistics, summary plots centered on the transcription start site (TSS), gene ontology, pathway analysis, and de novo motif finding, among others.ConclusionsThese pipelines range from those performing a single task to those performing full analyses of ChIP-seq data. The pipelines are supplied as both Kepler workflows, which allow data provenance tracking, and, in the majority of cases, as standalone R scripts. These pipelines are designed for ease of modification and repurposing.

Dataset Information

An Understandable, Extensible, and Reusable Implementation of the Hodgkin-Huxley Equations Using Modelica.

Publications

An Understandable, Extensible, and Reusable Implementation of the Hodgkin-Huxley Equations Using Modelica.

Similar Datasets

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