Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

SBAR II: Application of SBAR01:14

SBAR II: Application of SBAR

SBAR is an effective communication tool used by healthcare professionals to communicate patient information accurately. SBAR stands for Situation, Background, Assessment, and Recommendation. For a better understanding, an example is given below.
SBAR Report from a Nurse to a Health Care Provider
S: "Hello, Dr. Smith. This is Jane, RN, from the Med Surg unit. I am calling to tell you about Ms. White in Room 210, who is experiencing increased pain and redness at her incision site. Her recent...
SBAR I: Understanding the Concept01:29

SBAR I: Understanding the Concept

Effective communication among healthcare professionals during hand-off reporting is essential to delivering safe and continuous patient care. Common professional interactions include reports to healthcare team members, hand-off, and transfer reports. Nurses routinely report information to other healthcare team members and also urgently contact healthcare providers to report changes in patient status.
Standardized methods of communication have been developed to ensure that information is...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
NMR Spectroscopy of Benzene Derivatives01:37

NMR Spectroscopy of Benzene Derivatives

Simple unsubstituted benzene has six aromatic protons, all chemically equivalent. Therefore, benzene exhibits only a singlet peak at δ 7.3 ppm in the 1H NMR spectrum. The observed shift is far downfield because the aromatic ring current strongly deshields the protons. Any substitution on the benzene ring makes the aromatic protons nonequivalent, and the protons split each other. The peak is, therefore, no longer a singlet and the splitting pattern and their associated coupling constants depend...
Singularity Functions for Bending Moment01:18

Singularity Functions for Bending Moment

Singularity functions simplify the representation of bending moments in beams subjected to discontinuous loading, allowing the use of a single mathematical expression. For a supported beam AB, with uniform loading from its midpoint M to the right side end B, the approach involves conceptual 'cuts' at specific points to determine the bending moment in each segment. By cutting the beam at a point between A and M, the bending moment for the segment before reaching midpoint M is represented using a...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

You might also read

Related Articles

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

Sort by
Same author

Transient pores account for cell-penetrating peptide and homeoprotein translocation.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Local Perceptions and Discourses on Pesticide Health Risks in a Rural Community in Paysandú, Uruguay.

New solutions : a journal of environmental and occupational health policy : NS·2026
Same author

Heartbeat: a multimodal dataset of fetal echocardiography and clinical metadata for early detection of congenital heart disease.

Frontiers in cardiovascular medicine·2026
Same author

Vertex (Buenos Aires, Argentina)·2026
Same author

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

NPJ systems biology and applications·2026
Same author

Asymmetric Phosphoinositide Lipid Bilayers Generated by Spontaneous Lipid Insertion.

Langmuir : the ACS journal of surfaces and colloids·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: May 31, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

JSBML: a flexible Java library for working with SBML.

Andreas Dräger1, Nicolas Rodriguez, Marine Dumousseau

  • 1Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany. jsbml-team@sbml.org

Bioinformatics (Oxford, England)
|June 24, 2011
PubMed
Summary
This summary is machine-generated.

JSBML provides a Java-based in-memory representation for Systems Biology Markup Language (SBML) models, facilitating simulations and software manipulations across platforms. It ensures compatibility with SBML standards and offers modularity for plugin development.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: May 31, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • The Systems Biology Markup Language (SBML) is a standard for representing biological models in text files.
  • An in-memory representation is crucial for performing simulations, visualizations, and software manipulations of SBML models.
  • Existing SBML APIs may not be optimized for specific programming environments.

Purpose of the Study:

  • To develop a robust in-memory representation of SBML models specifically for the Java programming language.
  • To provide a platform-independent solution for handling SBML models in Java applications.
  • To ensure compatibility with existing SBML standards and facilitate integration with other tools.

Main Methods:

  • Developed JSBML, a new API designed from the ground up in Java for SBML.
  • Ensured support for all SBML Levels and Versions up to Level 3 Version 1.
  • Focused on maintaining high compatibility with the established libSBML library.
  • Incorporated modular design principles to support plugin development.

Main Results:

  • JSBML offers a Java-native solution for in-memory SBML model representation.
  • The library is compatible with all major SBML versions and levels.
  • JSBML provides benefits for Java users, including easier distribution via Java Web Start.
  • The modular architecture facilitates the creation of plugins and migration from libSBML.

Conclusions:

  • JSBML is a comprehensive Java API for Systems Biology Markup Language (SBML) model manipulation.
  • It offers cross-platform compatibility and supports all SBML versions, enhancing usability for Java developers.
  • The library's design promotes extensibility and interoperability within the systems biology software ecosystem.