Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Networks

Protein Networks

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

Plant Tissue Culture

Plant Tissue Culture

Plant tissue culture is widely used in both primary and applied science. Applications range from plant development studies to functional gene studies, crop improvement, commercial micropropagation, virus elimination, and conservation of rare species.

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

You might also read

Related Articles

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

Sort by

Same author

Diurnal rhythms of choice: a novel state-dependent drift diffusion model uncovers time-dependent changes in rat decision making.

Research square·2026

Same author

Diurnal rhythms of choice: a novel state-dependent drift diffusion model uncovers time-dependent changes in rat decision making.

bioRxiv : the preprint server for biology·2026

Same author

A feature-based generalizable prediction model for both perceptual and abstract reasoning.

Cognitive neuroscience·2025

Same author

Tetanus Severity Classification in Low-Middle Income Countries through ECG Wearable Sensors and a 1D-Vision Transformer.

BioMedInformatics·2025

Same author

Wearable remote monitoring for patients with COVID-19 in low-resource settings: case study.

BMJ innovations·2025

Same author

Vital sign monitoring using wearable devices in a Vietnamese intensive care unit.

BMJ innovations·2025

Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026

Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026

Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026

Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026

Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026

Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 13, 2025

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

PyRice: a Python package for querying Oryza sativa databases.

Quan Do^1,2, Ho Bich Hai³, Pierre Larmande^1,2,4

¹University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam.

Bioinformatics (Oxford, England)

|August 1, 2020

Summary

This summary is machine-generated.

PyRice offers a unified Python API for accessing diverse Oryza sativa gene information. This tool simplifies data retrieval for researchers, enabling faster and more logical scientific discovery.

More Related Videos

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Repeatable Stair-step Assay to Access the Allelopathic Potential of Weedy Rice Oryza sativa ssp.

Repeatable Stair-step Assay to Access the Allelopathic Potential of Weedy Rice Oryza sativa ssp.

Published on: January 28, 2020

Related Experiment Videos

Last Updated: Dec 13, 2025

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Repeatable Stair-step Assay to Access the Allelopathic Potential of Weedy Rice Oryza sativa ssp.

Repeatable Stair-step Assay to Access the Allelopathic Potential of Weedy Rice Oryza sativa ssp.

Published on: January 28, 2020

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Gene information for Oryza sativa is fragmented across multiple online databases.
Current data access methods are diverse and can be challenging for domain experts.
Efficiently collecting and integrating this information is crucial for scientific advancement.

Purpose of the Study:

To develop a unified programming interface for accessing Oryza sativa gene databases.
To simplify data retrieval and integration for researchers.
To enhance the efficiency of scientific research in rice genomics.

Main Methods:

Developed PyRice, a Python package providing a consistent API.
Implemented a modular design with a smart query system.
Optimized query speed by adapting to available computing resources.

Main Results:

PyRice enables simultaneous access to multiple supported databases.
The package ensures consistent output formats across different data sources.
The smart query system optimizes data retrieval performance.

Conclusions:

PyRice provides an easy-to-use and intuitive solution for accessing rice gene data.
The tool facilitates faster and more integrated scientific research.
PyRice streamlines the process of querying heterogeneous biological databases.