{"repo":"szczurek-lab/seqme","free":true,"listed":false,"github":"https://github.com/szczurek-lab/seqme","clone":"git clone https://github.com/szczurek-lab/seqme.git","description":"Metrics for evaluating biological sequence design","language":"Python","stars":16,"topics":["metrics","dna","rna","benchmark","drug-design","peptides","proteins","biological-sequences","molecules"],"license":"BSD-3-Clause","category":"analytics","readme_excerpt":"seqme is a modular and extendable python library containing model-agnostic metrics for evaluating biological sequence designs. It enables benchmarking and comparison of generative models for small molecules, DNA, RNA, peptides, and proteins. Key features : - Metrics : A collection of sequence-, embedding-, and property-based metrics for evaluating generative models designs. - Models : Out-of-the-box, pre-trained property and embedding models for small molecules, DNA, RNA, peptides, and proteins. - Visualizations : Functionality to display metric results from single-shot and iterative optimization methods as tables and plots. Is a metric or model missing? seqme's modular metric and third-party model interfaces make adding your own easy. Installation You need to have Python 3.10 or newer installed on your system. To install the base package do: To install sequence-specific models as well, include the appropriate extras specifiers. Check the individual model docs for installation instructions. Quick start Install seqme and the protein language model, ESM-2. Run in a Jupyter notebook: Check out the docs for in-depth tutorials and examples. Citation If you use seqme in your research, consider citing our publication:","default_branch":null,"files":null,"tree":[],"storefront":"/r/szczurek-lab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/szczurek-lab/seqme/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}