Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

What is an Experiment?

What is an Experiment?

An experiment is a planned activity carried out under controlled conditions. The purpose of an experiment is to investigate the relationship between two variables. When one variable causes change in another, we call the first variable the explanatory or independent variable. The affected variable is called the response or dependent variable. In a randomized experiment, the researcher manipulates values of the explanatory variable and measures the resulting changes in the response variable. The...

Randomized Experiments

Randomized Experiments

The randomization process involves assigning study participants randomly to experimental or control groups based on their probability of being equally assigned. Randomization is meant to eliminate selection bias and balance known and unknown confounding factors so that the control group is similar to the treatment group as much as possible. A computer program and a random number generator can be used to assign participants to groups in a way that minimizes bias.
Simple randomization
Simple...

Data Collection by Experiments

Data Collection by Experiments

Data collection is a systematic method of obtaining, observing, measuring, and analyzing accurate information. An experimental study is a standard method of data collection that involves the manipulation of the samples by applying some form of treatment prior to data collection. It refers to manipulating one variable to determine its changes on another variable. The sample subjected to treatment is known as “experimental units.”
An example of the experimental method is a public...

Experimental Designs

Experimental Designs

An experimental design is a systematic process that allows researchers to evaluate the relationship between dependent and independent variables. There are three widely used types of experimental design - pre-experimental design, true experimental design, and quasi-experimental design. In pre-experimental design, the researcher compares the data before and after some interventions or treatments. The true-experimental design has more than one purposefully created group, a commonly measured...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation.

Bioinformatics (Oxford, England)·2026

Same author

Meet NUM-ENRICH: A Collaborative National Effort to Extend and Harmonize Research Infrastructures Within the German Network University Medicine.

Studies in health technology and informatics·2026

Same author

From FAIR to CURE: guidelines for computational models of biological systems.

NPJ systems biology and applications·2026

Same author

PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems.

Bioinformatics (Oxford, England)·2026

Same author

Harmful anachronism: World Athletics reinstates gene testing to participate in women's competitions.

British journal of sports medicine·2026

Same author

Sex and Gender Differences in Chronic Kidney Disease-Explained by the Brenner-Luyckx Concept of Hyperfiltration.

Journal of clinical medicine·2026

Same journal

Updates and validation of the Compi RNA-seq pipeline with a case study in Alzheimer's disease.

Journal of integrative bioinformatics·2026

Same journal

Fragment-level FAIRness: annotating scientific data and its provenance using data fragment selectors.

Journal of integrative bioinformatics·2026

Same journal

Integrating cross-omics research through FAIR Digital Objects with DataPLANT.

Journal of integrative bioinformatics·2026

Same journal

Pheno-App 2.0 - a mobile app for collecting phenotypic data in plant research.

Journal of integrative bioinformatics·2026

Same journal

Evolving bioinformatics services - the journey of KPI metrics with Scorpion.

Journal of integrative bioinformatics·2026

Same journal

The community engagement and empowerment cycle: FAIRagro's framework to foster cultural change towards FAIR RDM practices in agrosystem science and beyond.

Journal of integrative bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 30, 2026

A Virtual Simulation Experiment of Mechanics: Material Deformation and Failure Based on Scanning Electron Microscopy

A Virtual Simulation Experiment of Mechanics: Material Deformation and Failure Based on Scanning Electron Microscopy

Published on: January 20, 2023

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Frank T Bergmann, Jonathan Cooper, Nicolas Le Novère

Journal of Integrative Bioinformatics

|November 4, 2015

Summary

This summary is machine-generated.

Computational models in biology are complex and require standardized descriptions for reproducibility. The Simulation Experiment Description Markup Language (SED-ML) provides a computer-readable XML format for encoding simulation experiments, enhancing model reuse and analysis.

More Related Videos

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction

Published on: February 26, 2014

Interactive and Visualized Online Experimentation System for Engineering Education and Research

Interactive and Visualized Online Experimentation System for Engineering Education and Research

Published on: November 24, 2021

Related Experiment Videos

Last Updated: Mar 30, 2026

A Virtual Simulation Experiment of Mechanics: Material Deformation and Failure Based on Scanning Electron Microscopy

A Virtual Simulation Experiment of Mechanics: Material Deformation and Failure Based on Scanning Electron Microscopy

Published on: January 20, 2023

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction

Published on: February 26, 2014

Interactive and Visualized Online Experimentation System for Engineering Education and Research

Interactive and Visualized Online Experimentation System for Engineering Education and Research

Published on: November 24, 2021

Area of Science:

Computational biology
Systems biology
Bioinformatics

Background:

Increasing complexity of biological models necessitates standardized methods for reproducibility.
Model structure alone is insufficient for replicating simulation outcomes.
Minimum Information About a Simulation Experiment (MIASE) guidelines highlight the need for procedural descriptions.

Framework:

Presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML).
SED-ML is an XML-based, computer-readable format for encoding simulation and analysis experiments.
Compatible with XML-based model formats like CellML and SBML.

Implementation:

SED-ML files detail model selection, pre-simulation modifications, simulation procedures, and analysis.
Specifies how to extract and present simulation results.
Level 1 Version 2 introduces encoding for repeated and chained procedures.

Implications:

Facilitates the reuse and adaptation of existing computational models.
Enhances the reproducibility of simulation experiments in systems biology.
Supports standardized reporting of simulation and analysis workflows.