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

Conversion of Units01:36

Conversion of Units

38.8K
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...
38.8K
Bioreactor Design and Operational System01:29

Bioreactor Design and Operational System

17
Bioreactors are engineered vessels designed to cultivate microorganisms under controlled conditions for industrial bioprocessing. They maintain sterility and allow precise regulation of pH, temperature, oxygen, and nutrient levels to optimize microbial growth and metabolite production. Bioreactors range from small laboratory units of 1 liter to industrial systems holding up to 500,000 liters, though only about 75% of their volume is actively used for fermentation. The remaining headspace...
17
Synthetic Biology02:55

Synthetic Biology

5.8K
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...
5.8K
Microbial Classification System01:24

Microbial Classification System

1.6K
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
1.6K
Cell Diagrams and IUPAC Conventions01:21

Cell Diagrams and IUPAC Conventions

52
Electrochemical cell notation is a standardized symbolic representation that communicates the structure and reaction pathway of galvanic and electrolytic cells. This notation plays a critical role in describing redox reactions and electrochemical cell configurations without the need for detailed diagrams.In electrochemical cell notation, a single vertical line “|” denotes a phase boundary, such as between a solid electrode and an aqueous solution. A double vertical line...
52
International System of Units01:29

International System of Units

5.5K
The International System of Units, known as the SI system, is a universally accepted measurement system recognized and used worldwide. The SI system is based on a set of three base units considered absolute, and their values do not change with location. These base units are meters, kilograms, and seconds.
Prefixes are used to define both larger and smaller quantities in the SI system. For example, milli, micro, and nano define smaller quantities, while kilo, mega, and giga are used to define...
5.5K

You might also read

Related Articles

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

Sort by
Same author

Molecular pathways of kidney development and their applications to clinical research.

Kidney international·2025
Same author

Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models.

Briefings in bioinformatics·2025
Same author

Multi-omics analysis in inclusion body myositis identifies mir-16 responsible for HLA overexpression.

Orphanet journal of rare diseases·2025
Same author

A collaborative network analysis for the interpretation of transcriptomics data in Huntington's disease.

Scientific reports·2025
Same author

Making PBPK models more reproducible in practice.

Briefings in bioinformatics·2024
Same author

The Virtual Human Platform for Safety Assessment (VHP4Safety) project: Next generation chemical safety assessment based on human data.

ALTEX·2024
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Mar 23, 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

18.7K

The systems biology format converter.

Nicolas Rodriguez1,2, Jean-Baptiste Pettit1, Piero Dalle Pezze2

  • 1EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.

BMC Bioinformatics
|April 6, 2016
PubMed
Summary
This summary is machine-generated.

The System Biology Format Converter (SBFC) offers a unified framework for converting computational models between various formats, addressing interoperability challenges in systems biology research. This Java-based tool enhances model accessibility for researchers and developers.

Keywords:
ConverterFormatSBMLSystems biology

More Related Videos

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities
09:57

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

12.6K
A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments
20:28

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

Published on: October 2, 2012

14.7K

Related Experiment Videos

Last Updated: Mar 23, 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

18.7K
Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities
09:57

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

12.6K
A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments
20:28

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

Published on: October 2, 2012

14.7K

Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Interoperability issues hinder progress in systems biology research due to diverse computational model formats.
  • Existing model conversion tools are often developed independently, leading to duplicated efforts and limited synergy.

Purpose of the Study:

  • To present a generic, extensible framework for converting computational models between different formats.
  • To address the need for a unified solution for systems biology model interoperability.

Main Methods:

  • Developed the System Biology Format Converter (SBFC) as a Java-based software.
  • Implemented a framework supporting multiple format conversions, including SBML, BioPAX, and Matlab.
  • Designed SBFC for use as a standalone executable or a web service.

Main Results:

  • SBFC provides a generic framework capable of converting between numerous systems biology model formats.
  • The framework currently supports conversions for SBML, BioPAX, SBGN-ML, Matlab, Octave, XPP, GPML, Dot, MDL, and APM.
  • The software is implemented in Java and offers flexible deployment options.

Conclusions:

  • SBFC is an evolving software project designed to be easily extended with new converters.
  • The framework benefits both systems biology modelers and software developers by improving accessibility and reducing redundancy.
  • Source code and documentation are freely available, promoting collaborative development and adoption.