Jove
Visualize
Contact Us

Related Concept Videos

Bioreactor Design and Operational System01:29

Bioreactor Design and Operational System

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...

You might also read

Related Articles

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

Sort by
Same author

Comprehensive mapping of the 5' and 3' untranslated regions of <i>Aspergillus fumigatus</i> reveals diverse mechanisms of mRNA processing including premature transcription termination.

RNA (New York, N.Y.)·2025
Same author

Translon: a single term for translated regions.

Nature methods·2025
Same author

The GATA-like transcription factor Gat201 determines alkaline-restricted growth in <i>Cryptococcus neoformans</i>.

mSphere·2025
Same author

Improved gene editing and fluorescent-protein tagging in <i>Aspergillus nidulans</i> using a Golden Gate-based CRISPR-Cas9 plasmid system.

Wellcome open research·2024
Same author

Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs.

bioRxiv : the preprint server for biology·2024
Same author

A trade-off between proliferation and defense in the fungal pathogen <i>Cryptococcus</i> at alkaline pH is controlled by the transcription factor GAT201.

bioRxiv : the preprint server for biology·2023
Same journal

DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.

PLoS computational biology·2026
Same journal

Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.

PLoS computational biology·2026
Same journal

Optimized phenotype definitions boost GWAS power.

PLoS computational biology·2026
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
See all related articles
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 Experiment Video

Updated: Jun 18, 2026

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus
12:10

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Published on: November 30, 2014

13.6K

Using prototyping to choose a bioinformatics workflow management system.

Michael Jackson1, Kostas Kavoussanakis1, Edward W J Wallace2

  • 1EPCC, The University of Edinburgh, Edinburgh, United Kingdom.

Plos Computational Biology
|February 25, 2021
PubMed
Summary
This summary is machine-generated.

Workflow management systems streamline computational biology. Nextflow was chosen for the RiboViz package after evaluating several systems, demonstrating prototyping

More Related Videos

Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

12.7K
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

18.2K

Related Experiment Videos

Last Updated: Jun 18, 2026

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus
12:10

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Published on: November 30, 2014

13.6K
Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

12.7K
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

18.2K

Area of Science:

  • Computational biology
  • Bioinformatics
  • Genomics

Background:

  • Workflow management systems (WMS) are crucial for reproducible and efficient computational analysis in bioinformatics.
  • They offer features like incremental builds, re-entrancy, and portability across different computing environments (containers, HPC, cloud).
  • RiboViz, a package for analyzing ribosome profiling data, initially used a Python script for its core workflow.

Purpose of the Study:

  • To reimplement the RiboViz analysis workflow within a WMS to adhere to scientific computing best practices.
  • To evaluate and select an appropriate WMS for the RiboViz project.
  • To demonstrate the utility of prototyping in software selection for scientific projects.

Main Methods:

  • A rapid survey of available WMS, shortlisting Snakemake, cwltool, Toil, and Nextflow.
  • Prototyping a subset of the RiboViz workflow on each shortlisted candidate system.
  • Selection of Nextflow based on evaluation and prototyping results.

Main Results:

  • Nextflow was selected as the WMS for the RiboViz workflow.
  • The selection process, including prototyping, required 10 person-days.
  • Prototyping provided assurance that Nextflow met the project's specific requirements.

Conclusions:

  • Reimplementing the RiboViz workflow in a WMS enhances reproducibility and code reuse.
  • Nextflow is a suitable WMS for complex bioinformatics workflows like RiboViz.
  • Prototyping is a cost-effective method for informed software selection in scientific research.