Update README.md

README.md

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-<p style="text-align: center;">Developed by DanLing on Earth</p>
+# [MultiMolecule](https://multimolecule.danling.org)
 
-We are a community of scientists, researchers, engineers, and others who are working together to push the boundaries of what is possible with Deep Learning.
+> [!TIP]
+> Accelerate Molecular Biology Research with Machine Learning
 
-We are a community of individuals from around the world who seek to make Deep Learning more accessible.
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15119050.svg)](https://doi.org/10.5281/zenodo.15119050)
 
-We are passionate about Deep Learning and the people who use it.
+[![Codacy - Quality](https://app.codacy.com/project/badge/Grade/ad5fd8904c2e426bb0a865a9160d6c69)](https://app.codacy.com/gh/DLS5-Omics/multimolecule/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![Codacy - Coverage](https://app.codacy.com/project/badge/Coverage/ad5fd8904c2e426bb0a865a9160d6c69)](https://app.codacy.com/gh/DLS5-Omics/multimolecule/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
+[![CodeCov - Coverage](https://codecov.io/gh/DLS5-Omics/multimolecule/graph/badge.svg?token=G9WGWCOFQE)](https://codecov.io/gh/DLS5-Omics/multimolecule)
 
-We are DanLing.
+[![PyPI - Version](https://img.shields.io/pypi/v/multimolecule)](https://pypi.org/project/multimolecule)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/multimolecule)](https://pypi.org/project/multimolecule)
+[![Downloads Statistics](https://static.pepy.tech/badge/multimolecule/month)](https://multimolecule.danling.org)
+
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
+
+## 🧬 Introduction
+
+MultiMolecule is a framework that bridges molecular biology and machine learning. It offers machine learning tools specifically designed for biomolecular data (RNA, DNA, and protein).
+
+MultiMolecule serves as a foundation for advancing research at the intersection of molecular biology and machine learning.
+
+## 🚀 Features
+
+### 📑 Resources
+
+- **[Model Hub](https://multimolecule.danling.org/models)**: Models designed for biomolecular data.
+- **[Dataset Hub](https://multimolecule.danling.org/datasets)**: Processed biomolecular datasets.
+
+### 🛠️ Tools
+
+- **[`pipelines`](pipelines)**: End-to-end workflows for applying models.
+- **[`runner`](runner)**: Automatic Runner for training models.
+
+### ⚙️ Infrastructure
+
+- **[`data`](data)**: Smart [`Dataset`][multimolecule.data.Dataset] that automatically infer tasks—including their level (sequence, token, contact) and type (classification, regression).
+- **[`tokenisers`](tokenisers)**: Tokenizers for biomolecular sequences.
+- **[`module`](module)**: Neural network building blocks.
+
+## 🔧 Installation
+
+=== "Install the stable release from PyPI"
+
+    ```bash
+    pip install multimolecule
+    ```
+
+=== "Install the latest development version"
+
+    ```bash
+    pip install git+https://github.com/DLS5-Omics/multimolecule
+    ```
+
+## 📜 Citation
+
+If you use MultiMolecule in your research, please cite us as follows:
+
+```bibtex
+@software{chen_2024_12638419,
+  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
+  title     = {MultiMolecule},
+  doi       = {10.5281/zenodo.12638419},
+  publisher = {Zenodo},
+  url       = {https://doi.org/10.5281/zenodo.12638419},
+  year      = 2024,
+  month     = may,
+  day       = 4
+}
+```
+
+## 📄 License
+
+We believe openness is the Foundation of Research.
+
+MultiMolecule is licensed under the [GNU Affero General Public License](license.md).
+
+For additional terms and clarifications, please refer to our [License FAQ](license-faq.md).
+
+Please join us in building an open research community.
+
+`SPDX-License-Identifier: AGPL-3.0-or-later`