Update readme

Fix links
Polish phrasing

README.md

@@ -2,6 +2,8 @@
 license: mit
 tags:
 - METL
+- biology
+- protein
 ---
 
 # METL
@@ -11,19 +13,21 @@ Mutational Effect Transfer Learning (METL) is a framework for pretraining and fi
 
 ## Model Details
 
-This 🤗 repository contains a wrapper meant to facilitate the ease of use of METL models. Usage of this wrapper will be provided below. Models are hosted on (Zenodo)[https://zenodo.org/records/11051645] and will be downloaded by this wrapper when used.
+This repository contains a wrapper meant to facilitate the ease of use of METL models.
+Usage of this wrapper will be provided below.
+Models are hosted on [Zenodo](https://zenodo.org/doi/10.5281/zenodo.11051644) and will be downloaded by this wrapper when used.
 
 ### Model Description
 
-METL is discussed in the (paper)[https://www.biorxiv.org/content/10.1101/2024.03.15.585128v1] in further detail. The github contains more documentation and includes scripts for training and predicting with METL. A google colab notebook for finetuning and predicting on publically available METL models is made available as well [here](https://github.com/gitter-lab/metl/tree/main/notebooks).
+METL is discussed in the [paper](https://doi.org/10.1101/2024.03.15.585128) in further detail.
+The GitHub [repo](https://github.com/gitter-lab/metl) contains more documentation and includes scripts for training and predicting with METL.
+Google Colab notebooks for finetuning and predicting on publicly available METL models are available as well [here](https://github.com/gitter-lab/metl/tree/main/notebooks).
 
-### Model Sources [optional]
+### Model Sources
 
-<!-- Provide the basic links for the model. -->
-
-- **Repository:** [METL Repo](https://github.com/gitter-lab/metl)
-- **Paper:** [METL bio archrive](https://www.biorxiv.org/content/10.1101/2024.03.15.585128v1)
-- **Demo:** [Huggingface demo space for METL](https://huggingface.co/spaces/gitter-lab/METL_demo)
+- **Repository:** [METL repo](https://github.com/gitter-lab/metl)
+- **Paper:** [METL preprint](https://doi.org/10.1101/2024.03.15.585128)
+- **Demo:** [Hugging Face Spaces demo](https://huggingface.co/spaces/gitter-lab/METL_demo)
 
 ## How to Get Started with the Model
 
@@ -38,9 +42,10 @@ scipy>=1.9.1
 biopandas>=0.2.7
 ```
 
-In order to run the example, a PDB file must be installed. It is provided (here)[https://github.com/gitter-lab/metl-pretrained/blob/main/pdbs/2qmt_p.pdb] and in raw format (here)[https://raw.githubusercontent.com/gitter-lab/metl-pretrained/main/pdbs/2qmt_p.pdb].
+In order to run the example, a PDB file for the GB1 protein structure must be installed.
+It is provided [here](https://github.com/gitter-lab/metl-pretrained/blob/main/pdbs/2qmt_p.pdb) and in raw format [here](https://raw.githubusercontent.com/gitter-lab/metl-pretrained/main/pdbs/2qmt_p.pdb).
 
-After installing those packages and the above file, you may run METL with the following code example (assuming the downloaded file is in the same place as the script):
+After installing those packages and downloading the above file, you may run METL with the following code example (assuming the downloaded file is in the same place as the script):
 
 ```python
 from transformers import AutoModel
@@ -67,10 +72,10 @@ with torch.no_grad():
 
 ## Citation
 
-Biophysics-based protein language models for protein engineering
-Sam Gelman, Bryce Johnson, Chase Freschlin, Sameer D’Costa, Anthony Gitter, Philip A. Romero
+Biophysics-based protein language models for protein engineering  
+Sam Gelman, Bryce Johnson, Chase Freschlin, Sameer D’Costa, Anthony Gitter, Philip A. Romero  
 bioRxiv 2024.03.15.585128; doi: https://doi.org/10.1101/2024.03.15.585128
 
 ## Model Card Contact
 
-For questions and comments about METL, the best way to reach out is through opening a github issue in the [METL repository](https://github.com/gitter-lab/metl/issues) issues page.
+For questions and comments about METL, the best way to reach out is through opening a GitHub issue in the [METL repository](https://github.com/gitter-lab/metl/issues).