Merge pull request #26 from chaselgrove/tools

Add initial tools content

content/resources/tools/_index.md

@@ -6,10 +6,14 @@ weight: 10
 
 ## ReproNim Core Tools
 
-- [Heudiconv/ReproIn](reproin/index.html)
-- [ReproSchema](reproschema/index.html)
+- [Heudiconv/ReproIn](reproin/index.html): Converter from DICOM into structured directory layouts (e.g. BIDS).
+- [ReproSchema](reproschema/index.html): A tool for defining, sharing, and reusing structured research protocols, enabling versioning and interoperability across studies.
 - [Neurodocker](neurodocker/index.html)
-- [Neurobagel + ReproPond + ReproLake](neurobagel/index.html)
-- [DataLad](datalad/index.html)
+- [Neurobagel](neurobagel/index.html): A set of tools to query and share data (clinical and brain imaging) in a fully distributed way, keeping the local governance.
+- [DataLad](datalad/index.html): Distribution and version control system for all digital objects of science.
+
+## ReproNim Core Standards
+
 - [NIDM](nidm/index.html)
 - [BIDS](bids/index.html)
+- Nipoppy: A protocol and a set of tools to help standardize the processing a study that has neuroimaging data.

content/resources/tools/bids/_index.md

@@ -3,12 +3,19 @@ title: "BIDS"
 date: 2024-10-28T15:17:52-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+### Citation information
+
+### Requisite knowledge to use
+
+### Requisite technical requirements
+
+### Conformance statement
+
+### Links
+
+- Home page
+- Tutorial
+- Installation
+- Full documentation
+- How to get help
+- Testimonials

content/resources/tools/datalad/_index.md

@@ -3,12 +3,33 @@ title: "DataLad"
 date: 2024-10-28T15:17:52-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+*The sine qua non of ReproNim.*
+
+DataLad is a command-line tool for data sharing.  DataLad can download DataLad-prepared data sets and can assist in sharing your own data.  DataLad supports data versioning.
+
+### Citation information
+
+RRID:SCR_003931
+
+### Requisite knowledge to use
+
+- Command-line familiarity
+- Git familiarity is helpful but not mandatory
+
+### Requisite technical requirements
+
+- Debian: apt proficiency.
+- Mac: conda proficiency or Homebrew installed
+
+### Conformance statement
+
+100% lives to its promise.
+
+### Links
+
+- [Home page](https://datalad.org)
+- [Tutorial](https://handbook.datalad.org/)
+- [Installation](https://handbook.datalad.org/en/latest/intro/installation.html)
+- [Full documentation](http://docs.datalad.org/en/stable/)
+- [How to get help](https://github.com/datalad/datalad/issues)
+- [Testimonials](https://github.com/datalad/datalad/wiki/Testimonials)

content/resources/tools/neurobagel/_index.md

@@ -3,12 +3,30 @@ title: "Neurobagel"
 date: 2024-10-28T15:17:51-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+*I got bored one day.  So I put everything on a bagel.*
+
+Neurobagel integrates a suite of tools to:
+- annotate with a standard model csv-like data and the corresponding BIDS data,
+- create a local node to query these data to recreate a cohort of subjects with specific characteristics, and 
+- enable to search across nodes and retrieve brain data (if these are datalad) or clinical data if the node enables this, letting the local researchers to set the level of accessibility of the data.
+
+### Citation information
+
+### Requisite knowledge to use
+
+Command-line familiarity.
+
+### Requisite technical requirements
+
+All required element should be installed when setting up a neurobagel node.
+
+### Conformance statement
+
+### Links
+
+- [Home page](https://neurobagel.org/)
+- Tutorial
+- Installation
+- Full documentation
+- How to get help
+- Testimonials

content/resources/tools/neurodocker/_index.md

@@ -1,14 +1,21 @@
 ---
-title: "Neurodocker"
+title: "NeuroDocker"
 date: 2024-10-28T15:17:51-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+### Citation information
+
+### Requisite knowledge to use
+
+### Requisite technical requirements
+
+### Conformance statement
+
+### Links
+
+- Home page
+- Tutorial
+- Installation
+- Full documentation
+- How to get help
+- Testimonials

content/resources/tools/nidm/_index.md

@@ -3,12 +3,19 @@ title: "NIDM"
 date: 2024-10-28T15:17:52-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+### Citation information
+
+### Requisite knowledge to use
+
+### Requisite technical requirements
+
+### Conformance statement
+
+### Links
+
+- Home page
+- Tutorial
+- Installation
+- Full documentation
+- How to get help
+- Testimonials

content/resources/tools/reproin/_index.md

@@ -3,12 +3,33 @@ title: "ReproIn"
 date: 2024-10-28T15:17:51-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+*Flexible DICOM conversion into structured directory layouts.*
+
+### Citation information
+
+RRID:SCR_017427
+
+### Requisite knowledge to use
+
+HeuDiConv (Heuristic DICOM Converter) enables flexible and efficient conversion of spatially reconstructed neuroimaging data from the DICOM format (quasi-ubiquitous in biomedical image acquisition systems, particularly in clinical settings) to BIDS, as well as other file layouts.
+
+### Requisite technical requirements
+
+- Command line
+- Desired project structure (BIDS)
+- Python
+
+### Conformance statement
+
+- Collecting DICOMs from MRI (not NIfTI, PAR/REC, etc)
+- Python OR Docker OR Singularity OR Debian
+- DataLad (optional)
+
+### Links
+
+- [Home page](https://heudiconv.readthedocs.io/)
+- [Tutorial](https://heudiconv.readthedocs.io/en/latest/tutorials.html)
+- [Installation](https://heudiconv.readthedocs.io/en/latest/installation.html)
+- [Full documentation](https://heudiconv.readthedocs.io/)
+- [How to get help 1](https://github.com/nipy/heudiconv/issues) [How to get help 2](https://neurostars.org/tag/heudiconv)
+- Testimonials

content/resources/tools/reproschema/_index.md

@@ -3,12 +3,33 @@ title: "ReproSchema"
 date: 2024-10-28T15:17:51-04:00
 ---
 
-- Name
-- Tagline (optional)
-- RRID
-- Citation information
-- Description
-- Requisite knowledge to use
-- Required installations
-- Links
-- Conformance statement
+Reproschema is a framework for survey data collection. It allows researchers to create reusable, version-controlled schemas for protocols. Reproschema supports structured data capture, ensuring consistency and reproducibility across studies.
+
+### Citation information
+
+### Requisite knowledge to use
+
+- Git familiarity (https://git-scm.com/doc)
+- Command-line familiarity is helpful (https://ubuntu.com/tutorials/command-line-for-beginners#1-overview)
+- Python familiarity is helpful but not mandatory (https://www.python.org/about/gettingstarted/)
+
+### Requisite technical requirements
+
+- Any platform with Python 3.9+ installed
+- Package management tools: pip or conda
+
+### Conformance statement
+
+Reproschema fully supports the creation, sharing, and reuse of structured research protocols as described. It reliably handles schema versioning and ensures interoperability between different tools, making it suitable for various research workflows. However, users should note that advanced features, such as full integration with some external tools or platforms, may require additional customization or familiarity with JSON-LD and Git.
+
+### Links
+
+- Home page
+https://github.com/ReproNim/reproschema
+- [Tutorial 1](https://www.repronim.org/reproschema/user-guide/create-new-protocol/) [Tutorial 2](https://www.repronim.org/reproschema/tutorials/using-reproschema/)
+- [Installation](https://pypi.org/project/reproschema/)
+- [Full documentation](https://www.repronim.org/reproschema/)
+- [How to get help](https://github.com/ReproNim/reproschema/issues)
+- Testimonials
+
+