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Related Concept Videos

Indirect Motor Pathways01:22

Indirect Motor Pathways

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The indirect motor or extrapyramidal pathways originate in the brainstem, the lower portion of the brain that connects it to the spinal cord. They consist of several distinct tracts, each with specialized functions. The four main tracts of the indirect motor pathways are the vestibulospinal tract, the reticulospinal tract, the tectospinal tract, and the rubrospinal tract.
The vestibulospinal tract originates in the vestibular nuclei of the brainstem. The vestibular system detects changes in...
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Direct Motor Pathways01:11

Direct Motor Pathways

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The direct motor pathways, also known as the pyramidal tracts, are a group of neural pathways that originate in the brain and descend through the spinal cord. They control the voluntary movement of the body. There are two major direct motor pathways: the corticospinal and the corticobulbar tracts.
The corticospinal tract is responsible for the voluntary movement of the limbs and trunk. It originates in the cerebral cortex of the brain and descends through the cerebrum's internal capsule and...
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C4 Pathway and CAM01:27

C4 Pathway and CAM

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Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
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Photoreceptors and Visual Pathways01:22

Photoreceptors and Visual Pathways

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At the molecular level, visual signals trigger transformations in photopigment molecules, resulting in changes in the photoreceptor cell's membrane potential. The photon's energy level is denoted by its wavelength, with each specific wavelength of visible light associated with a distinct color. The spectral range of visible light, classified as electromagnetic radiation, spans from 380 to 720 nm. Electromagnetic radiation wavelengths exceeding 720 nm fall under the infrared category,...
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IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

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Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
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ER Retrieval Pathway01:45

ER Retrieval Pathway

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In the secretory pathway, vesicles transport proteins from one cellular compartment to another in forward transport to deliver the protein to its correct location. Occasionally, misfolded proteins and incorrect proteins escape their original compartments, and a retrieval pathway is used to return the escaped proteins to their original compartment.
The ER uses many checkpoints to prevent the entry of incorrectly folded or a resident protein as cargo onto a transport vesicle. These mechanisms...
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Related Experiment Video

Updated: Apr 13, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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A Web Tool for Generating High Quality Machine-readable Biological Pathways

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Pathways with PathWhiz.

Allison Pon1, Timothy Jewison1, Yilu Su1

  • 1Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada.

Nucleic Acids Research
|May 3, 2015
PubMed
Summary
This summary is machine-generated.

PathWhiz is a web server for creating interactive biological pathway diagrams. It simplifies the generation of complex pathways, supporting various data formats for easy sharing and viewing.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Biological pathway visualization is crucial for understanding complex cellular processes.
  • Existing tools may lack comprehensive features for creating accurate and interactive diagrams.

Purpose of the Study:

  • To introduce PathWhiz, a web server for generating biologically accurate and interactive pathway diagrams.
  • To provide a user-friendly platform for visualizing and sharing biological pathways.

Main Methods:

  • PathWhiz utilizes a specialized drawing palette for rendering metabolites, proteins, nucleic acids, and cellular components.
  • It supports the construction of both small-molecule and protein/gene pathways through various biological processes.
  • Pathway replication and propagation functions enable cross-species pathway generation.

Main Results:

  • PathWhiz generates colorful, visually appealing, and machine-readable pathway diagrams.
  • The server supports multiple data exchange formats (BioPAX, SBGN-ML, SBML) and image formats (PNG, SVG).
  • Over 700 pathway diagrams have been generated for databases like HMDB, DrugBank, and SMPDB.

Conclusions:

  • PathWhiz offers a versatile and accessible solution for biological pathway visualization and data integration.
  • Its features facilitate the creation and dissemination of complex pathway information for research and database applications.