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

Requirements for Human Life01:26

Requirements for Human Life

13.7K
The Earth and its atmosphere have provided humans with air, water, and food, but these are not the only requirements for survival. Humans also require a specific range of temperature and pressure that the Earth and its atmosphere provides.
Oxygen
Atmospheric air is only about 20 percent oxygen, but that oxygen is a key component of the chemical reactions that keep the body alive, including the reactions that produce ATP. Brain cells are susceptible to a lack of oxygen because they require a...
13.7K
Trial and Error and Algorithm01:12

Trial and Error and Algorithm

424
A problem-solving strategy is a plan of action used to find a solution. Different strategies have distinct action plans. Trial and error involves trying different solutions until one works. For instance, to fix a broken printer, you might check ink levels, ensure the paper tray isn't jammed, and verify the printer's connection to your laptop. This method can be time-consuming but is commonly used. Thomas Edison, for example, used trial and error to find a suitable filament for the light...
424
Proteins: Dietary Sources and Requirements01:28

Proteins: Dietary Sources and Requirements

1.8K
Consuming animal-based products offers high-quality proteins that contain optimal levels and combinations of essential amino acids, crucial for tissue repair and growth. Foods like eggs, milk, fish, and most meats are a source of complete proteins. Legumes and cereals are abundant in proteins; however, they typically lack a full range of essential amino acids. As a result, they are considered incomplete protein sources. Some plant sources like soybeans, quinoa, and amaranth do contain complete...
1.8K
Oxygen Requirements and Growth Patterns01:29

Oxygen Requirements and Growth Patterns

1.4K
Microorganisms exhibit diverse oxygen requirements and growth patterns driven by their metabolic strategies and environmental adaptations. Oxygen, while essential for many organisms, can also be toxic under certain conditions, shaping how microorganisms grow and survive.Oxygen Requirements of MicroorganismsMicroorganisms are classified based on their ability to use or tolerate oxygen:● Obligate aerobes like Mycobacterium tuberculosis need oxygen for energy production, as it serves as the...
1.4K
Carbohydrates: Dietary Sources and Requirements01:15

Carbohydrates: Dietary Sources and Requirements

1.7K
Carbohydrates are predominantly obtained from plant sources. With the exception of lactose found in milk and insignificant glycogen amounts in meat, most consumed carbohydrates have plant origins. Monosaccharides and disaccharides, or sugars, can be sourced from fruits, honey, milk, sugar cane, and sugar beets. Grains and vegetables are rich in the polysaccharide starch. Two types of polysaccharides provide fiber: cellulose, which is abundant in many vegetables, forms undigestible roughage or...
1.7K
Lipids: Dietary Sources and Requirements01:18

Lipids: Dietary Sources and Requirements

2.0K
Lipids are an essential component of a balanced human diet. Triglycerides, which make up the majority of dietary lipids, are found in both saturated fats—commonly present in meat, dairy products, and certain tropical plants like coconut, and hydrogenated oils such as margarine and baking shortenings (trans fats)—and unsaturated fats, which are abundant in seeds, nuts, olive oil, and most vegetable oils. The main sources of cholesterol include egg yolks, various meats and organ...
2.0K

You might also read

Related Articles

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

Sort by
Same author

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

Journal of integrative bioinformatics·2026
Same author

Complementary Predictors for Asthma Attack Prediction in Children: Salivary Microbiome, Serum Inflammatory Mediators, and Past Attack History.

Allergy·2025
Same author

Preparedness for Visualization in the Next Pandemic.

IEEE computer graphics and applications·2025
Same author

Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

NPJ systems biology and applications·2025
Same author

FAIR assessment of Disease Maps fosters open science and scientific crowdsourcing in systems biomedicine.

Scientific data·2025
Same author

Repression of Connexin26 hemichannel activity protects the barrier function of respiratory airway epithelial cells against LPS-induced alteration.

Cell communication and signaling : CCS·2025
Same journal

STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.

Briefings in bioinformatics·2026
Same journal

A knowledge-guided deep learning framework for quantitative nucleic acid testing.

Briefings in bioinformatics·2026
Same journal

Optimal transport for label transfer in single-cell multi-omics integration.

Briefings in bioinformatics·2026
Same journal

Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.

Briefings in bioinformatics·2026
Same journal

Evaluating completeness, coherence, and consistency of genome-scale function annotations.

Briefings in bioinformatics·2026
Same journal

Transformers for single-cell RNA sequencing: a survey.

Briefings in bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Feb 4, 2026

Techniques for Imaging Ca2+ Signaling in Human Sperm
07:38

Techniques for Imaging Ca2+ Signaling in Human Sperm

Published on: June 16, 2010

17.6K

Human-like layout algorithms for signalling hypergraphs: outlining requirements.

Martin Siebenhaller1, Sune S Nielsen2, Fintan McGee2

  • 1yWorks GmbH,Vor dem Kreuzberg 28, 72070 Tübingen, Germany.

Briefings in Bioinformatics
|October 6, 2018
PubMed
Summary
This summary is machine-generated.

Automated layout for biological signalling pathway diagrams is crucial. This study enhances layout algorithms to produce high-quality diagrams comparable to manual drawings, addressing complex biological pathway representations.

Keywords:
layout algorithmsnetwork biologyprocess descriptionsystems biology

More Related Videos

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology
12:29

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology

Published on: May 3, 2017

11.1K
Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping
13:32

Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

Published on: June 26, 2012

26.9K

Related Experiment Videos

Last Updated: Feb 4, 2026

Techniques for Imaging Ca2+ Signaling in Human Sperm
07:38

Techniques for Imaging Ca2+ Signaling in Human Sperm

Published on: June 16, 2010

17.6K
Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology
12:29

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology

Published on: May 3, 2017

11.1K
Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping
13:32

Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

Published on: June 26, 2012

26.9K

Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Signalling pathway hypergraphs, visualized as process description diagrams, are increasingly used in biology.
  • Existing automated layout methods lack the sophistication to replicate high-quality manual diagrams due to complexity and user-specific needs.

Purpose of the Study:

  • To outline and examine requirements for effective automated layout of signalling pathway diagrams.
  • To introduce novel functionalities enhancing state-of-the-art layout techniques.
  • To address the need for automated layouts that meet the specific demands of biological researchers.

Main Methods:

  • Review and identification of requirements for automated biological pathway diagram layout.
  • Enhancement of existing layout algorithms with novel functionalities.
  • Demonstration of enhanced layout techniques on signalling pathway hypergraphs.

Main Results:

  • The enhanced algorithm produces results closely matching manually drawn layouts for smaller signalling pathways.
  • Identified key requirements beyond simple metrics for effective automated diagram generation.
  • Demonstrated the feasibility of improved automated layout for complex biological diagrams.

Conclusions:

  • Enhanced automated layout algorithms show promise in replicating the quality of manual biological pathway diagrams.
  • Further technical approaches are suggested to cover remaining requirements for comprehensive automated layout solutions.
  • Addressing these requirements will improve the usability and efficiency of biological pathway visualization tools.