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

Gene Conversion02:08

Gene Conversion

2.8K
2.8K
Gene Conversion02:08

Gene Conversion

10.5K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.5K
SBAR II: Application of SBAR01:14

SBAR II: Application of SBAR

5.5K
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...
5.5K
Conversion of Units01:36

Conversion of Units

33.4K
Sometimes, there is a need to convert from one unit to another one. For instance, reading a cookbook in which quantities are expressed in units of liters or ounces may require conversion of quantities to cups. Or, when looking up directions on how to get to a location, we may be interested to know how many miles we are going to walk. In this case, we would have to convert units of feet or meters to miles.
The first step in the unit conversion is to list the given units and the units required...
33.4K
Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

4.1K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
4.1K
SBAR I: Understanding the Concept01:29

SBAR I: Understanding the Concept

5.7K
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...
5.7K

You might also read

Related Articles

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

Sort by
Same author

Multilayer network approaches to omics data integration in digital twins for cancer research.

Frontiers in systems biology·2026
Same author

Mesenchymal to epithelial transition (MET) in cancer progression: insights from logical modeling.

Scientific reports·2026
Same author

Perspective of using <i>in vitro</i> models to understand immunotherapy-induced cytokine release syndrome.

Frontiers in immunology·2026
Same author

Systems biology graphical notation: process description language level 1 version 2.1.

Journal of integrative bioinformatics·2026
Same author

Multiomic integration reveals tumoral heterogeneity of lipid dependence within lethal group 3 medulloblastoma.

Cancer cell·2026
Same author

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

NPJ systems biology and applications·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

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

Related Experiment Video

Updated: Dec 31, 2025

Streamlined 3D Cerebellar Differentiation Protocol with Optional 2D Modification
10:15

Streamlined 3D Cerebellar Differentiation Protocol with Optional 2D Modification

Published on: December 9, 2017

7.9K

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.

Irina Balaur1, Ludovic Roy2,3,4, Alexander Mazein1,5,6

  • 1European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France.

Bioinformatics (Oxford, England)
|January 7, 2020
PubMed
Summary
This summary is machine-generated.

A new library, cd2sbgnml, enables bidirectional conversion between CellDesigner's Systems Biology Markup Language (SBML) extensions and Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML). This facilitates interoperability for large-scale biological network analysis.

More Related Videos

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
07:00

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

Published on: May 25, 2015

17.8K
Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology
21:47

Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology

Published on: December 19, 2010

13.1K

Related Experiment Videos

Last Updated: Dec 31, 2025

Streamlined 3D Cerebellar Differentiation Protocol with Optional 2D Modification
10:15

Streamlined 3D Cerebellar Differentiation Protocol with Optional 2D Modification

Published on: December 9, 2017

7.9K
qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
07:00

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

Published on: May 25, 2015

17.8K
Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology
21:47

Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology

Published on: December 19, 2010

13.1K

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • CellDesigner is a widely used biological map editor.
  • Interoperability challenges exist between CellDesigner's proprietary SBML extensions and the standardized SBGN-ML format.

Purpose of the Study:

  • To develop a solution for bidirectional conversion between CellDesigner's SBML extensions and SBGN-ML.
  • To improve data exchange and integration in systems biology research.

Main Methods:

  • Introduction of the cd2sbgnml library and a web service for format conversion.
  • Development in Java and distribution under GNU GPL v3.0.
  • Testing with large-scale biological networks like the RECON Human Metabolic network.

Main Results:

  • Successful bidirectional conversion between CellDesigner's SBML extension and SBGN-ML formats.
  • Demonstrated functionality on comprehensive datasets, including the Atlas of Cancer Signalling Network.
  • The cd2sbgnml tool and web service are publicly available on GitHub.

Conclusions:

  • The cd2sbgnml library and web service effectively address the interoperability challenge between CellDesigner and SBGN-ML.
  • Facilitates the use of CellDesigner files in systems biology workflows requiring SBGN-ML.
  • Promotes wider adoption and integration of systems biology models.