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README.md

@@ -1,3 +1,115 @@
 ---
 license: mit
+language:
+- en
+tags:
+- rna
+- biology
+- diffusion
+- generative
+- sequence-design
 ---
+
+# yakRNA Design: A semantic multimodal RNA composer
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/YousufAKhan/yakRNA/main/mascot.png" width="160"/>
+</p>
+
+**yakRNA Design** is a 110M-parameter discrete diffusion language model for conditional RNA sequence design. It can generate RNA sequences conditioned on any combination of secondary structure, consensus sequence, and Gene Ontology (GO) terms — or unconditionally from a target length.
+
+---
+
+## Model Details
+
+| | |
+|---|---|
+| **Architecture** | ModernBERT-based discrete diffusion |
+| **Parameters** | 110M |
+| **Training data** | Full Rfam database |
+| **Max sequence length** | 636 nt |
+| **Supported GO terms** | 280 |
+
+---
+
+## Quickstart
+
+The easiest way to use yakRNA Design is via the **[Google Colab notebook](https://colab.research.google.com/github/YousufAKhan/yakRNA/blob/main/yakRNA_colab.ipynb)** — no setup required.
+
+For local use, see the **[GitHub repository](https://github.com/YousufAKhan/yakRNA)**.
+
+---
+
+## Download the Weights
+
+**CLI:**
+```bash
+pip install huggingface_hub
+huggingface-cli download MasterYster/yakRNA-Design yakRNA_110M.pt --local-dir checkpoints/
+```
+
+**Python:**
+```python
+from huggingface_hub import hf_hub_download
+hf_hub_download(repo_id="MasterYster/yakRNA-Design", filename="yakRNA_110M.pt", local_dir="checkpoints/")
+```
+
+---
+
+## Generation Modes
+
+| Mode | Description |
+|------|-------------|
+| Unconditional | Generate from a target length |
+| Structure-conditioned | Dot-bracket secondary structure |
+| Consensus-conditioned | Mixed-case IUPAC consensus |
+| GO term-conditioned | Up to 12 GO terms |
+| Sequence infilling | Fixed positions + `*` masks |
+| Multimodal | Any combination of the above |
+
+---
+
+## Example Usage
+
+```bash
+# Install
+git clone https://github.com/YousufAKhan/yakRNA.git
+cd yakRNA
+pip install -r requirements.txt
+
+# Generate 5 sequences conditioned on a hairpin structure
+python inference/rna_sequence_generator.py \
+    --config configs/inference.yaml \
+    --checkpoint checkpoints/yakRNA_110M.pt \
+    --secondary_structure "((((....))))" \
+    --num_sequences 5
+
+# Generate with all three modalities
+python inference/rna_sequence_generator.py \
+    --config configs/inference.yaml \
+    --checkpoint checkpoints/yakRNA_110M.pt \
+    --secondary_structure ":::::::<<<<<<<<<-:::--[[[[[-->>>>>>>>><<<<<<<<<<_________>>>->>>>>>>::::]]]]]::::" \
+    --consensus "GAGUaaGGGGuuCuAGU...gcaGCcCgcCUaGaaCCCUGcgacacuGGuucuaaaaCagAugucgUuuuaAGgGCuUUUG" \
+    --go_terms "GO:0075523" \
+    --num_sequences 5
+```
+
+---
+
+## Links
+
+- **GitHub**: [YousufAKhan/yakRNA](https://github.com/YousufAKhan/yakRNA)
+- **Colab**: [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/YousufAKhan/yakRNA/blob/main/yakRNA_colab.ipynb)
+
+---
+
+## Citation
+
+```bibtex
+@software{yakrna2026,
+  author = {Khan, Yousuf},
+  title  = {yakRNA Design: A semantic multimodal RNA composer},
+  year   = {2026},
+  url    = {https://github.com/YousufAKhan/yakRNA}
+}
+```