diff --git a/README.md b/README.md index 435dcba..2099edb 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,12 @@ # Integartive Network Modeling -The broad goal of inm is to contribute to the characterization of biological networks by integrating data from diverse sources. -inm is under development and will be distributed as an Integrative Modeling Platform ([IMP](https://github.com/salilab/imp/)) module. +Integrative network modeling (INM) is a method and framework (library) for modeling biological interaction networks. The INM library supports the modeling of protein interactions networks based on AP-MS data. +INM can: +- Predict direct protein-protein interaction (PPI) networks for all pairs of protein types (matrix model) on the order of hundreds or perhaps thousands of nodes +- Predict condition specific PPI networks (e.g., gene deletion, chemical perturbation, cell-type) +- Predict a distribution over networks to estimate both the average network and ascociated uncertainty +- Has a scoring funciton that may be extended to other types of information that may inform PPI networks (e.g, deep learning based PPI prediction, proximity labeling) + Modeling proceeds in 5 stages: (i) gathering AP-MS protein spectral counts under multiple conditions, (ii) representing a model where nodes represent protein types and edges represent a protein interaction between at least one pair of molecules of the corresponding types, (iii) a scoring function @@ -9,3 +14,24 @@ that scores the agreement between AP-MS spectral counts and a network model, (iv (v) analysis of the output sample of network models. inm includes an example system and benchmarks against Protein Data Bank and Humap 2.0 derived interactions. + +## Installation + +To clone the repository use the following command +```bash +git clone https://github.com/ajipalar/inm.git +``` + +Create and activate the conda environment +```bash +cd inm +conda env create -f environment.yml +conda activate py39 +``` + +## Run tests +```bash +python3 -m unittest discover -s tests +``` + + INM is a part of the Integrative Modeling Platform ([IMP](https://github.com/salilab/imp/)) module.