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

Correlation of Experimental Data01:23

Correlation of Experimental Data

482
Dimensional analysis simplifies complex physical problems and guides experimental investigations, but it does not provide complete solutions. It identifies the dimensionless groups that influence a phenomenon, but experimental data is needed to establish the specific relationships and validate theoretical predictions.
For example, a spherical particle moving through a viscous fluid experiences drag. Dimensional analysis shows that the drag force depends on the particle's diameter, velocity,...
482
Genomics02:02

Genomics

39.9K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
39.9K
What is Metabolism?00:52

What is Metabolism?

131.5K
Overview
131.5K
pH Scale02:41

pH Scale

79.1K
Hydronium and hydroxide ions are present both in pure water and in all aqueous solutions, and their concentrations are inversely proportional as determined by the ion product of water (Kw). The concentrations of these ions in a solution are often critical determinants of the solution’s properties and the chemical behaviors of its other solutes. Two different solutions can differ in their hydronium or hydroxide ion concentrations by a million, billion, or even trillion times. A common means of...
79.1K
Performing a Simple Data Analysis using MS-Excel Function01:17

Performing a Simple Data Analysis using MS-Excel Function

935
Microsoft Excel offers a suite of functions and tools ideal for statistical analysis, making it accessible to students and researchers. This article outlines fundamental Excel functions pivotal for data analysis.
SUM: This function calculates the total sum of a range of values. It's the foundation for aggregating data, essential for determining overall trends and totals in datasets.
AVERAGE: It computes the mean value of a given set of numbers, providing a quick insight into the central...
935
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

9.0K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
9.0K

You might also read

Related Articles

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

Sort by
Same author

EpiATLAS - a reference for human epigenomic research.

bioRxiv : the preprint server for biology·2026
Same author

A systems-level atlas of carbon-response transcriptional states in <i>Escherichia coli</i>.

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

Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.

Science advances·2026
Same author

Multi-ancestry, trans-generational GWAS meta-analysis of gestational diabetes and glycaemic traits during pregnancy reveals limited evidence of pregnancy-specific genetic effects.

Nature communications·2026
Same author

Spore-Based Biocomposite Thermoplastic Polyesters with Enhanced Toughness and Programmable Disintegration.

bioRxiv : the preprint server for biology·2026
Same author

Comparative analysis of gene importance in <i>Escherichia coli</i> across growth conditions.

mSystems·2026

Related Experiment Video

Updated: Jan 26, 2026

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.2K

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.

Jean-Christophe Lachance1, Colton J Lloyd2, Jonathan M Monk2

  • 1Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.

Plos Computational Biology
|April 23, 2019
PubMed
Summary

BOFdat is a new Python package that automates the creation of biomass objective functions (BOFs) for metabolic models. It provides accurate predictions for growth phenotypes and gene essentiality by using experimental data in an unbiased manner.

More Related Videos

Microalgae Cultivation and Biomass Quantification in a Bench-Scale Photobioreactor with Corrosive Flue Gases
08:41

Microalgae Cultivation and Biomass Quantification in a Bench-Scale Photobioreactor with Corrosive Flue Gases

Published on: December 19, 2019

10.8K
Author Spotlight: UAV Remote Sensing for Efficient Invasive Plant Biomass Estimation
08:47

Author Spotlight: UAV Remote Sensing for Efficient Invasive Plant Biomass Estimation

Published on: February 9, 2024

2.1K

Related Experiment Videos

Last Updated: Jan 26, 2026

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.2K
Microalgae Cultivation and Biomass Quantification in a Bench-Scale Photobioreactor with Corrosive Flue Gases
08:41

Microalgae Cultivation and Biomass Quantification in a Bench-Scale Photobioreactor with Corrosive Flue Gases

Published on: December 19, 2019

10.8K
Author Spotlight: UAV Remote Sensing for Efficient Invasive Plant Biomass Estimation
08:47

Author Spotlight: UAV Remote Sensing for Efficient Invasive Plant Biomass Estimation

Published on: February 9, 2024

2.1K

Area of Science:

  • Computational Biology
  • Systems Biology
  • Metabolic Engineering

Background:

  • Genome-scale metabolic models (GEMs) predict cellular phenotypes from genomic data.
  • Accurate biomass objective functions (BOFs) are crucial for reliable GEM predictions.
  • Current methods for BOF generation lack standardization and data-driven approaches.

Purpose of the Study:

  • To develop a standardized, data-driven computational platform for generating species-specific BOFs.
  • To address the gap in metabolic modeling software for unbiased BOF definition.
  • To improve the accuracy of phenotypic predictions from GEMs.

Main Methods:

  • Implementation of BOFdat, a Python package with a modular design.
  • BOFdat comprises three modules: macromolecule coefficient calculation, coenzyme/ion estimation, and species-specific precursor extraction.
  • Algorithmic extraction of biomass precursors from experimental data.

Main Results:

  • BOFdat successfully reconstructed the BOF for the Escherichia coli iML1515 model.
  • The BOF generated by BOFdat demonstrated superior concordance in biomass composition, growth rate, and gene essentiality predictions compared to other methods.
  • BOFdat provides an unbiased, data-driven approach to BOF definition.

Conclusions:

  • BOFdat offers a standardized and automated solution for generating accurate BOFs.
  • This tool enhances the reliability of GEM-based phenotypic predictions.
  • BOFdat is a valuable addition to the metabolic modeling software ecosystem, facilitating more precise biological insights.