Update README.md

README.md

@@ -6,10 +6,10 @@
 | (2/5) license                      | [![github license badge](https://img.shields.io/github/license/NPLinker/nplinker)](https://github.com/NPLinker/nplinker) |
 | (3/5) community registry           | [![pypi badge](https://img.shields.io/pypi/v/nplinker.svg?color=blue)](https://pypi.python.org/project/nplinker/) ![Docker Image Version (latest by date)](https://img.shields.io/docker/v/nlesc/nplinker?arch=amd64&label=docker&sort=date)|
 | (4/5) citation                     | [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.4680218.svg)](https://doi.org/10.5281/zenodo.4680218) |
-| (5/5) checklist                    | Coming soon |
+| (5/5) checklist                    | ![Static Badge](https://img.shields.io/badge/Coming_Soon-lightgrey) |
 | how FAIR is                          | [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) |
 | **Other best practices**           |  |
-| Documentation                      | [![Documentation Status](https://readthedocs.org/projects/nplinker/badge/?version=latest)](https://nplinker.readthedocs.io/en/latest/?badge=latest) |
+| Documentation                      | [![Static Badge](https://img.shields.io/badge/Docs_Available-lightgreen)](https://nplinker.github.io/nplinker) [🔗](https://nplinker.github.io/nplinker)|
 | Build & Test                       | [![build](https://github.com/NPLinker/nplinker/actions/workflows/build.yml/badge.svg)](https://github.com/NPLinker/nplinker/actions/workflows/build.yml) |
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 | Coverage                           | [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=NPLinker_nplinker&metric=coverage)](https://sonarcloud.io/dashboard?id=NPLinker_nplinker) |
@@ -18,21 +18,21 @@
 
 
 # Natural Products Linker (NPLinker)
+NPLinker is a python framework for data mining microbial natural products by integrating genomics and metabolomics data.
 
-NPLinker aims to address the significant bottleneck that exists in the realization of the potential of genome-led metabolite discovery, namely the slow manual matching of predicted biosynthetic gene clusters (BGCs) with metabolites produced during bacterial culture; linking phenotype to genotype.
-
-NPLinker implements a new data-centric approach to alleviate this linking problem by searching for patterns of strain presence and absence between groups of similar spectra (molecular families; MF) and groups of similar BGCs (gene cluster families; GCF). Searches can be performed using a number of available analysis methods employed in isolation or together.
+Original paper: [Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions](https://doi.org/10.1371/journal.pcbi.1008920).
 
+## Setup and usage
 
-Currently available analysis methods (scoring methods):
-- **Metcalf** (standardised): see [Hjörleifsson Eldjárn G, et al. (2021)](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008920), [Doroghazi JR, et al. (2014)](https://www.nature.com/articles/nchembio.1659), and the [demo](notebooks/nplinker_demo1.ipynb).
-- **Rosetta**: see [Hjörleifsson Eldjárn G, et al. (2021)](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008920) and [Soldatou S, et al. (2021)](https://www.mdpi.com/1660-3397/19/2/103).
-- **NPClassScore**: see the preprint [Louwen JJR, et al. (2022)](https://www.researchsquare.com/article/rs-1391827/v2), and the [demo](notebooks/npclassscore_linking/NPClassScore_demo.ipynb).
+### Requirement
+- Linux, MacOS, or Windows with WSL ([Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/about)) enabled
+  - For Windows without WSL, please use the [docker image](https://hub.docker.com/r/nlesc/nplinker)
+- Python version ≥3.9
 
-## Setup and usage
 
+### Installation
 NPLinker is a Python package, you can install it as following:
-```
+```shell
 # create a new virtual environment
 python -m venv env
 source env/bin/activate
@@ -44,15 +44,12 @@ pip install nplinker
 install-nplinker-deps
 ```
 
-Due to hardware requirements of some non-pypi dependecies:
-- NPLinker can only be installed on `Linux` and `MacOS (Intel chip)`
-- `MacOS(Apple Silicon, M1/M2 chip)` user should execute the install commands in a [Rosseta-enabled terminal](https://support.apple.com/en-us/HT211861).
-- For `Windows` users, please use our [docker image](https://hub.docker.com/r/nlesc/nplinker).
-
+A virtual environment is *required* to install the the non-pypi dependencies. You can also use `conda`
+to manage python environments.
 
-See the example in [Jupyter notebook](notebooks/nplinker_demo1.ipynb) for a guided introduction to the NPLinker API which shows how to load and examine a dataset. Other notebooks are present showcasing other scoring methods, like for [NPClassScore](notebooks/npclassscore_linking/NPClassScore_demo.ipynb).
+### Usage
 
-If you want to visualize and manipulate NPLinker predictions, check [NPLinker Webapp](https://github.com/NPLinker/nplinker-webapp) for more info.
+See the [documentation](https://nplinker.github.io/nplinker) for more information about how to use NPLinker.
 
 ## Contributing