The authors of this article include scholars such as Chenchengjie, Hao Chen, Yi Zhang, Hannah R. Thomas, Margaret Frank, and Ye Hua. Chenchengjie has in-depth research in banana wilt resistance breeding and bioinformatics, and has received multiple honors and research grants; Hao Chen focuses on gene families, big data analysis, and the development of bioinformatics tools; Yi Zhang's research direction is the protection and utilization of subtropical agricultural biological resources; Hannah R. Thomas and Margaret Frank are from Cornell University, studying plant science and plant biology, respectively; Ye Hua's research involves pineapple genomics and embryonic development. Rui Xia is a national-level talent program awardee, engaged in the research of horticultural plant genomics and small molecule RNAs, has published multiple highly cited papers, and has developed various bioinformatics data analysis tools.

TBtools - An Integrated Toolkit for Bio-Big Data Interactive Analysis

Abstract

• The development of high-throughput sequencing technology has propelled biology into the era of big data.
• TBtools is an independent software with a user-friendly interface, integrating more than 100 functions.
• It incorporates a variety of functions from sequence processing to data visualization, including the new plotting engine JIGplot.

Introduction

Developed for Wet-Lab Biologists

• The rapid development of HTS technology has led to an exponential increase in biological data.
• TBtools is designed to provide wet-lab biologists with ready-to-use data processing solutions.

Developed as an Integrated Toolkit

• TBtools integrates a variety of functions, avoiding the need to use multiple independent tools in a command-line environment.
• It covers functions from big data preview to data format conversion, sequence management, interactive data visualization, and more.

Development of Interactive Data Presentation

• TBtools' JIGplot engine allows for quick modifications to chart features, enabling interactive presentation of data.

Functional Overview

• The functions of TBtools are divided into five main directories:

1. Sequence Toolkit
2. BLAST
3. GO&KEGG Enrichment Analysis
4. Graphics
5. Other Functions

Outstanding Features

• TBtools is continuously optimized, expanded, and upgraded based on user needs and feedback.
• Several functions are widely used and have been featured in the results and/or graphics of hundreds of peer-reviewed publications.

Q: What research methods were specifically used in the paper?

The paper primarily employed software development methods, including:

• Designed and developed an integrated toolkit named TBtools, which contains over 100 functions for handling biological big data.
• Developed a new plotting engine "JIGplot" to enhance the interactivity of charts.
• Integrated existing bioinformatics tools and programs, and wrote original Java code to implement the toolkit's various functions.
• Continuously optimized and updated the toolkit's functions based on user feedback and needs.

Q: What are the main research findings and outcomes?

The main research findings and outcomes include:

• Successfully developed TBtools, an integrated toolkit with a user-friendly graphical interface that enables wet-lab biologists to easily handle and analyze biological big data.
• TBtools integrates over 100 functions, covering aspects from sequence management to data visualization, significantly simplifying the bioinformatics analysis process.
• Developed the JIGplot drawing engine, providing highly interactive charts that allow users to quickly modify chart features and export high-resolution bitmap and vector format charts.
• TBtools has received positive feedback from over 15,000 stable users, with its functions and features significantly enhanced.
• Results and charts generated using TBtools have been applied in hundreds of peer-reviewed publications.

Q: What are the current limitations of this research?

The limitations mentioned in the paper may include:

• Although TBtools integrates various functions, it may not cover all the needs of bioinformatics analysis, especially for highly specialized or specific field research that may require additional tools.
• While the toolkit aims to simplify the bioinformatics analysis process, some advanced features may still be challenging for users without programming backgrounds.
• TBtools' interactivity, although powerful, may require significant computational resources, potentially leading to performance limitations on lower-end computer systems.
• Although the toolkit has attracted a large number of users, it may still require more user feedback and testing to ensure its stability and reliability.
• With the rapid development of the bioinformatics field, TBtools needs to be continuously updated and optimized to maintain its functionality and technological advancement.