Merge pull request #199 from chaselgrove/action-numbers

Update action numbers in code

content/about/in-practice.md

@@ -76,11 +76,11 @@ As indicated by the blue highlights in the figure below, four core actions are k
 
     Using standard data formats and extending them to meet specific research needs is important for data and metadata management (Principle 2) in reproducible neuroimaging.
 
-3. **Annotation and provenance**
+2. **Annotation and provenance**
 
    Annotating data using standard, reproducible procedures ensures clarity and transparency in data management (Principle 2). _Provenance_ refers to the origin and history of data and processes, enabling researchers to track how data was generated, modified, and analyzed (Principles 2, 3, and 4). This is essential for understanding the context of data and ensuring reproducibility.
 
-4. **Implementation of version control**
+3. **Implementation of version control**
 
    Version control is crucial for both data and software management. It allows researchers to track changes over time, revert to previous versions if necessary, and collaborate effectively.
 
@@ -90,7 +90,7 @@ As indicated by the blue highlights in the figure below, four core actions are k
 
    And even publications can be versioned (Principle 4).
 
-5. **Use of containers**
+4. **Use of containers**
 
    Containers provide a portable and self-contained environment for running software, ensuring that the analysis can be executed consistently across different computing environments (Principle 3). Containers encapsulate all of the software dependencies needed to run an analysis, making it easier to share software (Principle 4) and reproduce results.
 

content/resources/tools/_index.md

@@ -21,6 +21,10 @@ This section describes core tools and standards produced by ReproNim.  For a mor
 - [The Brain Imaging Data Structure (BIDS)](bids/index.html): A standard for organizing neuroimaging data and metadata on disk.
 - [The Neuroimaging Data Model (NIDM)](nidm/index.html): A Semantic Web extension for neuroimaging concepts.
 
+## Infrastructure
+
+- [ReproLake](reprolake/index.html): A public triplestore of neuroimaging metadata.
+
 ## Best Practices
 
 - [ReproIn](reproin/index.html): Scripts and configuration files for DICOM to BIDS conversion.

content/resources/tools/reprolake/_index.md

@@ -0,0 +1,24 @@
+---
+title: ReproLake
+weight: 100
+---
+
+The ReproLake is a publicly available triplestore that contains information on publicly available neuroimaging datasets. The data within the ReproLake conforms to the NIDM standard and can be queried by the Neurobagel user interface or via a SPARQL API. Researchers using PyNIDM can also generate a local triplestore (i.e. a ReproPond) from their data which can be queried through PyNIDM and can also be added to Neurobagel as a local private node.
+
+## Development status
+
+The ReproLake is a public production data store that is currently hosted via a Stardog cloud based endpoint.
+
+## Innovation
+
+The ReproLake uses the NIDM and BIDS standards to provide a formal data store for neuroimaging data.  Using the same standards and tools, researchers are also able to generate their own local data stores that they can query and interrogate.
+
+## How to use
+
+[Neurobagel](/resources/tools/neurobagel/) queries will access the ReproLake.
+
+The ReproLake can also be accessed directly using SPARQL queries.
+
+## Links
+
+- Tutorial: [Sharing and Searching Metadata Using a ReproPond and the ReproLake](/resources/tutorials/pond-lake/)

content/resources/tutorials/nipoppy.md

@@ -9,7 +9,7 @@ weight: 5
 
 **Standards**: [BIDS](/resources/tools/bids/index.html).
 
-**Tools**: [Nipoppy](/resources/tools/nipoppy/index.html).
+**Tools**: [Nipoppy](/resources/tools/nipoppy/index.html), [ReproLake](/resources/tools/reprolake/).
 
 ## Challenge
 

content/resources/tutorials/pond-lake.md

@@ -11,7 +11,7 @@ weight: 5
 
 **Standards**: [BIDS](/resources/tools/bids/index.html), [NIDM](/resources/tools/nidm/index.html).
 
-**Tools**: [Neurobagel](https://neurobagel.org/), [PyNIDM](/resources/tools/pynidm/index.html).
+**Tools**: [Neurobagel](https://neurobagel.org/), [PyNIDM](/resources/tools/pynidm/index.html), [ReproLake](/resources/tools/reprolake/).
 
 ## Challenge