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Related Concept Videos

Basic Continuous Time Signals01:22

Basic Continuous Time Signals

Basic continuous-time signals include the unit step function, unit impulse function, and unit ramp function, collectively referred to as singularity functions. Singularity functions are characterized by discontinuities or discontinuous derivatives.
The unit step function, denoted u(t), is zero for negative time values and one for positive time values, exhibiting a discontinuity at t=0. This function often represents abrupt changes, such as the step voltage introduced when turning a car's...
Basic Discrete Time Signals01:16

Basic Discrete Time Signals

The unit step sequence is defined as 1 for zero and positive values of the integer n. This sequence can be graphically displayed using a set of eight sample points, showing a step function starting from n=0 and remaining constant thereafter.
The unit impulse or sample sequence is mathematically expressed as zero for all n values except at n=0, where it is one. The unit impulse sequence, denoted by δ(n), is the first difference of the unit step sequence, while the unit step sequence u(n) is the...
Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...
Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...
Reconstruction of Signal using Interpolation01:10

Reconstruction of Signal using Interpolation

Signal processing techniques are essential for accurately converting continuous signals to digital formats and vice versa. When a continuous signal is sampled with a period T, the resulting sampled signal exhibits replicas of the original spectrum in the frequency domain, spaced at intervals equal to the sampling frequency. To handle this sampled signal, a zero-order hold method can be applied, which creates a piecewise constant signal by retaining each sample's value until the next sampling...
Biological Clocks and Seasonal Responses02:45

Biological Clocks and Seasonal Responses

The circadian—or biological—clock is an intrinsic, timekeeping, molecular mechanism that allows plants to coordinate physiological activities over 24-hour cycles called circadian rhythms. Photoperiodism is a collective term for the biological responses of plants to variations in the relative lengths of dark and light periods. The period of light-exposure is called the photoperiod.

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Related Experiment Video

Updated: May 19, 2026

Real-Time Proxy-Control of Re-Parameterized Peripheral Signals using a Close-Loop Interface
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Real-Time Proxy-Control of Re-Parameterized Peripheral Signals using a Close-Loop Interface

Published on: May 8, 2021

The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software

R R Adams, N Tsorman, K Stratford

    Journal of Biological Rhythms
    |August 3, 2012
    PubMed
    Summary

    A new Input Signal Step Function (ISSF) standardizes light input in computational circadian clock models. This improves reproducibility and reuse of Systems Biology Markup Language (SBML) models for chronobiology research.

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    Published on: November 4, 2025

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    Last Updated: May 19, 2026

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    Published on: May 8, 2021

    A User-friendly and Powerful R Analysis of Large-scale Datasets
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    Published on: November 4, 2025

    Area of Science:

    • Computational biology
    • Chronobiology
    • Systems biology

    Background:

    • Computational models of circadian rhythms require accurate time-dependent inputs, such as light-dark cycles.
    • Current Systems Biology Markup Language (SBML) models often lack standardized methods for encoding these inputs, hindering reproducibility and model reuse.
    • Existing methods for representing time-dependent inputs in SBML are inconsistent, complicating the integration and comparison of different models.

    Discussion:

    • The Input Signal Step Function (ISSF) provides a numerically continuous and configurable method for encoding periodic and transient inputs in SBML.
    • ISSF is broadly applicable to various experimental manipulations, including light-dark cycles, drug treatments, and temperature changes.
    • The function's flexibility allows for the reproduction of diverse waveforms, enhancing the utility of computational models.

    Key Insights:

    • ISSF enables standard simulation software to accurately reproduce specialized circadian protocols, such as phase-response curves.
    • Implementation of ISSF in SBML facilitates the modification of existing models to match published results, thereby improving reproducibility.
    • A user-friendly software tool has been developed to configure ISSF without requiring specialized SBML knowledge, promoting wider adoption.

    Outlook:

    • Establishing a community-standard approach for representing entraining inputs in circadian clock models is crucial for advancing chronobiology research.
    • Standardization through ISSF can accelerate the development and validation of computational models across different research groups.
    • Widespread adoption of ISSF will foster greater collaboration and facilitate the sharing of standardized, reusable circadian clock models.