From 449cc9e405246c500555f71765a685a0596a7670 Mon Sep 17 00:00:00 2001
From: "spaceBearAmadeus (Alex)" <alexanderpatrie@gmail.com>
Date: Fri, 30 Aug 2024 15:28:38 -0400
Subject: [PATCH] updates to readme

---
 README.md | 33 +++++++--------------------------
 1 file changed, 7 insertions(+), 26 deletions(-)

diff --git a/README.md b/README.md
index 832eabacc..778f50b45 100644
--- a/README.md
+++ b/README.md
@@ -1,27 +1,12 @@
 ![GitHub CI](https://github.com/biosimulators/bio-check/actions/workflows/ci.yaml/badge.svg)
 ![GitHub CD](https://github.com/biosimulators/bio-check/actions/workflows/cd.yaml/badge.svg)
-# BioCheck: A Biological Simulation Verification Service
+# BioCheck (bio-compose-server): A Biological Simulation Verification Service
 #### __This service utilizes separate containers for REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance.__
 
 ## Getting Started:
 
-### **HIGH-LEVEL `bio_check` API:**
+#### **The REST API can be accessed via Swagger UI here: [https://biochecknet.biosimulations.org/docs](https://biochecknet.biosimulations.org/docs)
 
-The primary method of user-facing interaction for this service is done through the use of a high-level "notebook" api called `bio_check`. 
-A convenient notebook demonstrating the functionality of this service is hosted on Google Colab and can be accessed by clicking the above "Open In Colab" badge.
-
-[View the template notebook as markdown](docs/verification_api_demo.md)
-
-
-Installation of this tooling can be performed using PyPI as such:
-
-```bash
-pip install bio-check
-```
-
-**PLEASE NOTE: You must have `>=python3.9` in order to use the high-level api.**
-
-#### Alternatively, **the REST API can be accessed via Swagger UI here: [https://biochecknet.biosimulations.org/docs](https://biochecknet.biosimulations.org/docs)
 ### **FOR DEVELOPERS:**
 
 This application (`bio_check`) uses a microservices architecture which presents the following libraries:
@@ -33,22 +18,18 @@ This application (`bio_check`) uses a microservices architecture which presents
 The installation process is outlined as follows:
 
 1. `git clone https://github.com/biosimulators/bio-check.git`
-2. `cd bio-check/bio_check`
-3. `touch .env`
-4. Enter the following fields into the `.env` file: 
+2. `cd assets`
+3. `touch .env_dev`
+4. Enter the following fields into the `.env_dev` file: 
         
         MONGO_URI=<uri of your mongo instance. In this case we use the standard mongodb image with the app name bio-check>
         GOOGLE_APPLICATION_CREDENTIALS=<path to your gcloud credentials .json file. Contact us for access>
         BUCKET_NAME=bio-check-requests-1  # name of the bucket used in this app
 
-5. **Ensure that your IP address has been authorized in the `bio-check` cluster within Mongo Atlas.**
+5. Pull the and run the latest version of Mongo from the Docker Hub. (`docker run -d -it mongo:latest` or similar.)
 
 
 ### Notes:
-- This application currently uses MongoDB as the database store in which jobs are read/written. Database access is given to both the `api` and `worker` libraries. Such database access is 
+- This application currently uses MongoDB as the database store in which jobs are read/written. Database access is given to both the `compose_api` and `compose_worker` libraries. Such database access is 
 executed/implemented with the use of a `Supervisor` singleton.
 
-
-### **Note (05/22/2024):**
-The only package source that is currently supported by this tooling is `PyPI`. The support of other potential 
-package sources such as `conda`, `brew`, `apt`, and more is currently under development.