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

Search research articles

Related Experiment Video

Updated: Jun 16, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

BioExtract server--an integrated workflow-enabling system to access and analyze heterogeneous, distributed

Carol Lushbough¹, Michael K Bergman, Carolyn J Lawrence

¹Department of Computer Science, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA. Carol.Lushbough@usd.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|February 13, 2010

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by

Same author

Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.

Briefings in bioinformatics·2024

Same author

Global challenges and microbial biofilms: Identification of priority questions in biofilm research, innovation and policy.

Biofilm·2024

Same author

Convergence research and training in computational bioengineering: a case study on AI/ML driven biofilm-material interaction discovery.

Research square·2023

Same author

Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria.

Frontiers in microbiology·2023

Same author

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow.

Microorganisms·2023

Same author

BASIN: A Semi-automatic Workflow, with Machine Learning Segmentation, for Objective Statistical Analysis of Biomedical and Biofilm Image Datasets.

Journal of molecular biology·2022

Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024

See all related articles

BioExtract Server integrates diverse bioinformatics data and tools for researchers. This web-based application simplifies data access and analysis, enabling workflow creation for reproducible research.

Area of Science:

Bioinformatics and Computational Biology
Biomolecular Data Integration
Scientific Workflow Management

Background:

Bioinformatics research necessitates accessing multiple, distributed data sources and analytical tools.
Heterogeneous data sources use distinct query languages and formats, complicating data retrieval.
Analytical tools often have specific input/output requirements, hindering the integration of results.

Purpose of the Study:

To present the BioExtract Server, a web-based application for data integration in bioinformatics.
To enable researchers to consolidate, analyze, and serve data from heterogeneous biomolecular databases.
To simplify the process of querying diverse data sources and applying analytical tools.

Main Methods:

The BioExtract Server provides a web interface for researchers to interact with data sources and tools.

More Related Videos

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Related Experiment Videos

Last Updated: Jun 16, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Users can specify data sources, query them flexibly, and apply analytical tools.

The system automatically saves user actions as steps, which can be preserved as workflows.

Main Results:

The BioExtract Server consolidates data from heterogeneous biomolecular databases into a mash-up.
It allows flexible querying of data sources and application of analytic tools.
User interactions are saved, facilitating the creation of reusable workflows.

Conclusions:

The BioExtract Server simplifies data integration and analysis for in silico bioinformatics investigations.
It empowers researchers to overcome challenges associated with disparate data formats and tool incompatibilities.
The workflow preservation feature promotes reproducibility and efficiency in bioinformatics research.