What Was Observed? (Introduction)

• The goal of regenerative biology is to understand how some organisms can regrow lost body parts or organs, like limbs or even the brain.
• Planarian worms are special because they can regenerate entire worms from small pieces of their body. Even if you cut them into many parts, each part can grow into a full worm.
• Despite numerous studies on planarian regeneration, there is no single model that fully explains how regeneration works.
• The research team created a new way to organize and study data about planarian regeneration using a tool called Planform.
• Planform helps scientists access, understand, and analyze over a thousand experiments about planarian regeneration.

Why Planarian Worms? (Why They’re Special)

• Planarians have a complex body with a brain, eyes, digestive system, muscles, and more.
• They are known for their incredible ability to regenerate. Even when cut into pieces, they can regrow all their missing parts.
• This ability makes them a great model for studying how regeneration works in biology.

The Need for a New Approach

• Researchers realized that despite many studies on regeneration, there was no database that clearly organized all the experimental data.
• The existing databases were not helpful because they only used text to describe experiments, and computers cannot easily understand text descriptions.
• To solve this, the research team introduced Planform, which uses a mathematical system called “graphs” to represent data, making it easier for computers to analyze.

What is Planform? (The New Tool)

• Planform is a software tool and database that organizes experimental data about planarian regeneration into graphs.
• A graph is a system of nodes (points) connected by edges (lines). In Planform, these nodes represent different body parts or actions in the experiment, and the edges represent relationships between them.
• This makes it possible to compare different experiments more easily and extract valuable insights.
• Planform includes over 1,000 experiments from scientific publications, and it’s constantly being updated.

How Planform Works (Methods)

• Planform uses graphs to represent the body structures of planarians and the manipulations done in experiments (like cutting or irradiating the worms).
• The body parts are divided into regions, which are linked together to represent the connections between them.
• Each experiment is represented as a tree structure showing the order and type of manipulations done (like cutting or transplanting parts of the worm).

Key Features of Planform (What Makes It Special)

• Planform allows users to create, view, and edit experimental data easily.
• The software provides a graphical interface where users can visualize the planarian’s morphology (body shape) and experiment manipulations.
• It helps users see how different manipulations affect the regeneration process by automatically generating diagrams of the worm’s changes.
• Users can query the database to find specific experiments, manipulations, or results they are interested in.

What Was the Result? (Results)

• At the time of the study, Planform contained 1,139 experiments from 74 scientific papers.
• The software includes a search feature that helps users find experiments based on specific criteria, like the type of manipulation or the resulting body shape.
• Planform also allows users to add new data, helping the database grow as new research is published.

What Did We Learn? (Discussion and Conclusions)

• Planform is the first database focused specifically on planarian regeneration experiments, and it is a valuable resource for researchers in the field.
• The database and software tool will help researchers understand the patterns of regeneration in planarians, and could be useful for studying other organisms as well.
• By organizing experimental data in a standardized way, Planform makes it easier for scientists to analyze and compare results, helping them to develop a better understanding of how regeneration works.
• Planform represents a step toward using artificial intelligence to analyze and extract knowledge from large datasets in regenerative biology.

Key Takeaways

• Planform is a groundbreaking tool for studying the regeneration of planarians, and it organizes experimental data using a mathematical graph system.
• The database contains over 1,000 experiments and continues to grow.
• Planform helps scientists explore and compare regeneration experiments more effectively, which could lead to a better understanding of how regeneration works in other animals, including humans.

Acknowledgements

• We thank Emma Marshall for beta testing, and the Levin Lab members for valuable feedback.
• Funding: National Science Foundation (EF-1124651), National Institutes of Health (GM078484), US Army Medical Research and Materiel Command (#W81XWH-10-2-0058), G. Harold and Leila Y. Mathers Charitable Foundation.

什么被观察到？（引言）

• 再生生物学的主要目标是了解一些有机体如何再生丢失的身体部分或器官，例如肢体甚至大脑。
• 计划虫因其令人惊叹的再生能力而特别：即使将它们切成许多部分，每个部分都可以再生为完整的虫子。
• 尽管关于计划虫再生的许多研究，尚未有单一模型可以完全解释再生的机制。
• 研究小组创建了一种新方法来组织和研究计划虫再生的数据，使用了一个名为Planform的工具。
• Planform帮助科学家访问、理解和分析关于计划虫再生的超过一千个实验。

为什么选择计划虫？（它们的特别之处）

• 计划虫拥有复杂的身体结构，包括大脑、眼睛、消化系统、肌肉等。
• 它们因能够再生缺失的部分而著名，即使被切成小块，它们也能再生为完整的虫子。
• 这种能力使它们成为研究再生机制的理想模型。

为什么需要新的方法？

• 研究人员意识到，尽管有许多关于再生的研究，但没有一个数据库能清晰地组织所有实验数据。
• 现有的数据库无法有效使用，因为它们仅通过文本描述实验，而计算机无法轻松理解文本描述。
• 为了弥补这一点，研究小组推出了Planform，它使用一种数学系统叫做“图形”来表示数据，使得计算机能够分析这些数据。

什么是Planform？（新工具）

• Planform是一个软件工具和数据库，用图形的方式组织计划虫再生的实验数据。
• 图形是由节点（点）和边（线）组成的系统。在Planform中，这些节点代表不同的身体部位或实验中的操作，而边表示它们之间的关系。
• 这种方式使得比较不同实验结果变得更加简单，帮助提取有价值的见解。
• Planform包含了来自科学文献的超过1,000个实验，且不断更新。

Planform如何工作（方法）

• Planform使用图形表示计划虫的身体结构和实验中的操作（如切割或照射虫子）。
• 身体部分被划分为不同区域，这些区域通过连接来表示它们之间的联系。
• 每个实验都用一个树状结构表示，显示操作的顺序和类型（如切割或移植虫子的部分）。

Planform的主要特点（为什么它特别）

• Planform允许用户轻松创建、查看和编辑实验数据。
• 该软件提供了一个图形界面，用户可以可视化计划虫的形态和实验操作。
• 它通过自动生成虫子变化的图示，帮助用户看到不同操作对再生过程的影响。
• 用户可以查询数据库，找到自己感兴趣的特定实验、操作或结果。

结果是什么？（结果）

• 截至目前，Planform包含了来自74篇科学论文的1,139个实验。
• 该软件包括了一个搜索功能，帮助用户根据特定标准查找实验数据。
• Planform还允许用户添加新的数据，使得数据库随着新研究的发布而增长。

我们学到了什么？（讨论和结论）

• Planform是第一个专门针对计划虫再生实验的数据库，它为研究人员提供了一个宝贵的资源。
• 数据库和软件工具将帮助研究人员更好地理解计划虫的再生模式，也可能对研究其他生物有帮助。
• 通过以标准化的方式组织实验数据，Planform使科学家们能够更有效地分析和比较实验结果，从而加深对再生机制的理解。
• Planform代表了朝着使用人工智能分析和提取再生生物学领域数据的新工具迈出的第一步。

关键要点

• Planform是一个开创性的工具，用于研究计划虫的再生，通过图形系统组织实验数据。
• 该数据库包含超过1,000个实验，并持续更新。
• Planform帮助科学家们更有效地探索和比较再生实验，可能会有助于更好地理解其他动物（包括人类）的再生机制。

致谢

• 感谢Emma Marshall的beta测试帮助，以及Levin实验室成员的宝贵反馈。
• 资助：美国国家科学基金会（EF-1124651），美国国立卫生研究院（GM078484），美国陆军医学研究与物资指挥部（#W81XWH-10-2-0058），G. Harold和Leila Y. Mathers慈善基金会。