Merge branch 'mkda' of github.com:neurostuff/compose-docs into mkda

docs/guide/Explore/index.mdx

@@ -0,0 +1,26 @@
+---
+title: Explore
+sidebar_position: 1
+---
+
+# Explore
+
+Here, you can browse and search existing public `Studies`, `StudySets` and `Meta-Analyses` created on the platform. 
+
+## Studies
+
+The `Studies` page lets you browse and search all studies that exist on the NeuroStore server. This interface is similar to what you'll see when importing studies into your `Project`. However, here it's simply provided for your browsing pleasure. 
+
+For more information on how advanced search functionally, see [Searching Studies](./Explore/Searching)
+
+## StudySets and Meta-Analyses
+
+For `StudySets` and `Meta-Analyses`, you can browse and search any user-contributed items, including those from other users. 
+
+Note that although you see all publically available items, you cannot edit somebody else's content. 
+
+:::note
+We are currently working on a way to allow users to fork other users' `StudySets` and `Meta-Analyses` to create their own versions.
+Stay tuned!
+::::
+

docs/guide/walkthrough/Project/index.mdx → docs/guide/Project/index.mdx

@@ -11,9 +11,8 @@ Within a project you will be able to:
  1. **[Curate](./Project/Curation)** studies of interest and select the ones to be included in the meta-analysis 
  2. **[Extract](./Project/Extraction)** the relevant data such as activation coordinates and other meta-data
  3. **[Specify](./Project/Specification)** the algorithm and corrector you would like to use
- 4. **Run** the meta-analysis and **View** the results
 
-In each project, you can define a define a single StudySe (i.e. a collection of related studies), and one or more MetaAnalysis specifications.
+In each project, you can define a define a single StudySet (i.e. a collection of related studies), and one or more MetaAnalysis specifications.
 
 
 You can open a specific project by logging in, navigating to the 

docs/guide/Running/index.mdx

@@ -0,0 +1,85 @@
+---
+title: Running Analyses
+sidebar_position: 2
+---
+
+# Running Analyses
+
+You have a several options for running the analysis. In all cases, you will need your unique `<meta-analysis-id>`, which you can access for each Meta-Analysis within your Project.
+
+![Meta-analysis run](/tutorial/ma_run.png)
+
+Under the hood, analyses are managed by the [nsc-runner](https://github.com/neurostuff/nsc-runner) Python package, and executed by the [NiMARE](https://nimare.readthedocs.io/en/stable/) (Neuroimaging Meta-Analysis Research Environment) Python package. 
+
+## Google Colab
+
+[![text](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neurostuff/neurosynth-compose-notebook/blob/main/run_and_explore.ipynb)
+
+The easiest way to run an analysis is to use the [Google Colab](https://colab.research.google.com/) notebook linked above.
+
+The provided notebook runs entirely in the cloud, and does not require any local installation of software.
+To use simply paste your analysis ID into the first cell (`META_ID`), and using the Toolbar selet (Runtime -> Run All) 
+or the keyboard shortcut (Ctrl or ⌘ + F9) to run the notebook.
+
+![Colab notebook](/guide/nsc_colab_notebook.png)
+
+The notebook will install all required software, run the analysis, and upload the results to Neurosynth Compose.
+Once the analysis is complete, you can use the notebook to explore the results using the interative report, download an archive 
+of the results, or browse the results in the Neurosynth Compose web interface, in the Meta-Analysis section of your Project.
+
+:::tip
+The Colab notebook has limited and varying freely available resources, and may not be able to run large analyses.
+If your analysis fails, try running it again, or using one of the other methods below.
+:::
+
+## Docker 
+
+The easiest way to run analyses locally is to use the `nsc-runner` [Docker](https://www.docker.com/) image provided by Neurosynth Compose.
+
+Docker is a containerization technology that allows you to run software in a consistent environment, regardless of the underlying operating system.
+
+To run the Docker image, you will need to install Docker on your local machine.
+Instructions for installing Docker can be found [here](https://docs.docker.com/get-docker/).
+
+Once Docker is installed, you can run your analysis using the using the following command:
+
+```
+docker run -it -v -v /local/dir:/results ghcr.io/neurostuff/nsc-runner:latest <meta-analysis-id>
+```
+
+where `/local/dir` is the path to a local directory where you would like to save the results of your analysis, and `<meta-analysis-id>` is the ID of the meta-analysis you would like to run.
+
+The Docker image will download all required software, run the analysis, and upload the results to Neurovault & Neurosynth Compose.
+An HTML report will be saved in the results directory, and the results will be available in the Meta-Analysis section of your Project on Neurosynth Compose.
+
+### Updating the Docker image
+
+For every release of `nsc-runner`, we publish a corresponding Docker image.
+
+You can manually download a specific neuroscout-cli release as follows:
+
+```
+docker pull ghcr.io/neurostuff/nsc-runner:<version>
+```
+
+where `<version>` is the version of `nsc-runner` that you want to download. If you omit version, the latest stable version will be downloaded.
+
+You can see the tags available for download on [GitHub](https://github.com/neurostuff/compose-runner/pkgs/container/nsc-runner)
+
+## Manually prepared environment using pip 
+
+:::warning
+Manually installing `nsc-runner` may be difficult due to complex dependencies in the SciPy stack, or fMRI-specific tooling. Proceed only if you know what you’re doing.
+:::
+
+Use pip to install `nsc-runner` from PyPI:
+
+```
+pip install nsc-runner
+```
+
+and then run the analysis using the following command:
+
+```
+nsc-runner <meta-analysis-id>
+```

docs/guide/glossary.md

@@ -1,6 +1,6 @@
 ---
 title: Glossary
-sidebar_position: 1
+sidebar_position: 3
 ---
 
 # Glossary