Update README.md URLs

README.md

@@ -6,19 +6,19 @@ MIRA is a framework for representing systems using ontology-grounded **meta-mode
 
 ## Resources
 
-* Template JSON schema: [schema.json](https://github.com/indralab/mira/blob/main/mira/metamodel/schema.json)
+* Template JSON schema: [schema.json](https://github.com/gyorilab/mira/blob/main/mira/metamodel/schema.json)
 * Epidemiology Domain Knowledge Graph (DKG) service: [DKG service](http://34.230.33.149:8771/)
 * MIRA Metaregistry service: [Metaregistry service](http://34.230.33.149:8772/) 
 
 ## Example notebooks
 
-* Defining multiple model variants using MIRA Templates: [Notebook 1](https://github.com/indralab/mira/blob/main/notebooks/metamodel_intro.ipynb)
-* Generating an executable model from MIRA Templates and running simulation: [Notebook 2](https://github.com/indralab/mira/blob/main/notebooks/simulation.ipynb)
-* Stratifying and visualizing MIRA models, and exporting as Petri nets: [Notebook 3](https://github.com/indralab/mira/blob/main/notebooks/viz_strat_petri.ipynb)
-* Processing an SBML model from BioModels, visualizing and exporting into Petri nets: [Notebook 4](https://github.com/indralab/mira/blob/main/notebooks/biomodels.ipynb)
-* Using the MIRA Domain Knowledge Graph REST API: [Notebook 5](https://github.com/indralab/mira/blob/main/notebooks/dkg_api.ipynb)
-* Using the Model REST API to perform various model operations: [Notebook 6](https://github.com/indralab/mira/blob/main/notebooks/model_api.ipynb)
-* Using the web client in python that connects to the REST API: [Notebook 7](https://github.com/indralab/mira/blob/main/notebooks/web_client.ipynb)
+* Defining multiple model variants using MIRA Templates: [Notebook 1](https://github.com/gyorilab/mira/blob/main/notebooks/metamodel_intro.ipynb)
+* Generating an executable model from MIRA Templates and running simulation: [Notebook 2](https://github.com/gyorilab/mira/blob/main/notebooks/simulation.ipynb)
+* Stratifying and visualizing MIRA models, and exporting as Petri nets: [Notebook 3](https://github.com/gyorilab/mira/blob/main/notebooks/viz_strat_petri.ipynb)
+* Processing an SBML model from BioModels, visualizing and exporting into Petri nets: [Notebook 4](https://github.com/gyorilab/mira/blob/main/notebooks/biomodels.ipynb)
+* Using the MIRA Domain Knowledge Graph REST API: [Notebook 5](https://github.com/gyorilab/mira/blob/main/notebooks/dkg_api.ipynb)
+* Using the Model REST API to perform various model operations: [Notebook 6](https://github.com/gyorilab/mira/blob/main/notebooks/model_api.ipynb)
+* Using the web client in python that connects to the REST API: [Notebook 7](https://github.com/gyorilab/mira/blob/main/notebooks/web_client.ipynb)
 * Demonstrating MIRA TemplateModel capabilities [Notebook 8](https://github.com/gyorilab/mira/blob/main/notebooks/Hackathon%20Scenario%201.ipynb)
 * Rapid construction of DKGs in ASKEM: [Notebook 9](https://github.com/gyorilab/mira/blob/main/notebooks/Rapid%20construction%20of%20new%20DKGs.ipynb)
 * Implement a masking intervention in a compartmental model to simulate 
@@ -37,20 +37,20 @@ MIRA builds on and generalizes prior work including:
 * [EMMAA](https://emmaa.indra.bio): A framework for automatically maintaining a set of models surrounding the biology of viral pandemics, cancer, and other disease areas based on new findings as soon as they appear in the literature. Models are automatically analyzed against observations.
 * [INDRA](https://indra.bio): An automated model building system from literature mining, structured databases, and natural language input for molecular biology. INDRA Statements serve as domain-specific instances of MIRA Templates.
 * [INDRA CoGEx](https://discovery.indra.bio): A 3*10^7-relation scale domain-specific knowledge graph of biomedicine combining causal mechanisms with ontologies and relations derived from data.
-* [INDRA World](https://github.com/indralab/indra_world): A generalization of INDRA to modeling socio-economic systems, using a templated approach representing causal influence, events, and concepts.
+* [INDRA World](https://github.com/gyorilab/indra_world): A generalization of INDRA to modeling socio-economic systems, using a templated approach representing causal influence, events, and concepts.
 
 ## Installation
 
 The most recent code and data can be installed directly from GitHub with:
 
 ```shell
-python -m pip install git+https://github.com/indralab/mira.git
+python -m pip install git+https://github.com/gyorilab/mira.git
 ```
 
 To install in development mode, use the following:
 
 ```shell
-git clone git+https://github.com/indralab/mira.git
+git clone git+https://github.com/gyorilab/mira.git
 cd mira
 python -m pip install -e .
 ```