diff --git a/content/resources/getting-started/_index.md b/content/resources/getting-started/_index.md index 5f3308b..0acf5df 100644 --- a/content/resources/getting-started/_index.md +++ b/content/resources/getting-started/_index.md @@ -8,18 +8,19 @@ weight: 2 ReproNim offers best practices, tools and training to implement reproducible neuroimaging in your lab. Here is a brief overview of our website: * **New to reproducible neuroimaging?** - * Why reproducible neuroimaging - * What is reproducible neuroimaging? + * [Why reproducible neuroimaging](https://repronim.netlify.app/about/why/) + * [What is reproducible neuroimaging?](/about/why/#what-is-reproducible-neuroimaging) + * [ReproNim's principles and supporting actions](/about/in-practice/) for reproducible neuroimaging * **Wondering what ReproNim can do for you?** - * Meet our exemplary user personas and the issues they face in running neuroimaging studies - * View our introduction to the ReproNim way, step-by-step guides on some steps you can take using ReproNim tools to improve your ability to perform robust and shareable neuroimaging studies + * Meet our [exemplary user personas and the issues they face in running neuroimaging studies](/resources/getting-started/#meet-our-user-personas) + * View our introduction to the [ReproNim approach](/about/repronim-approach/) and some step-by-step tutorials on how to use ReproNim tools to improve your ability to perform robust and shareable neuroimaging studies * **Tools and how-to guide:** - * Our ReproGuide provides descriptions of our tools and how to use them + * Our [Resource](https://repronim.netlify.app/resources/) section provides a listing of [tools](/resources/tools/) and [tutorials](/resources/tutorials/) on how to use them to support principles of reproducible neuroimaging * **Training:** * [On-line training course](https://www.repronim.org/teach.html) on a range of basic and more advanced topics related to reproducible neuroimaging - * ReproNim Fellows Program: Become a ReproNim fellow through our train the trainer program + * [ReproNim Fellows Program](/fellowship/): Become a ReproNim fellow through our train the trainer program -## Meet our users personas +## Meet our user personas To introduce you to ReproNim, we have created a set of exemplary user personas that represent some typical users and given them a face (through the magic of AI), a set of skills and interests. We then produced a set of basic use cases that showcased how adopting the principles of neuroimaging and ReproNim tools can help them in their goals. @@ -82,13 +83,13 @@ ReproNim can help Sarah learn more about data and software management and other * Principle \= planning * Implementing data management basics: Using ReproNim tools to [convert data to the BIDS standard](/resources/tutorials/dicom-to-bids/) and [create a data dictionary](/resources/tutorials/data-dictionary/) * Principle: Data and metadata management - * Foundations: Standards, Annotation + * Actions: Standards, Annotation * Implementing software management basics: [Using Git to manage workflow/pipeline versions](/resources/tutorials/git/) * Principle: Software management - * Foundations: Versioning + * Actions: Versioning * Publishing your work as a “Re-executable paper”( \= text, data, code): Standards-based data sharing through OpenNeuro * Principle: Publishing re-executable papers - * Foundations: Standards, Annotation + * Actions: Standards, Annotation ### Richard @@ -108,7 +109,7 @@ ReproNim can help Richard learn how standards such as BIDS and NIDM can help wit * Advanced data management: Putting your derived data into BIDS derivatives and creating a semantically-enriched data dictionary using NIDM, a standard for annotating neuroimaging data * Principles: Data management - * Foundations: Standards, annotation + * Actions: Standards, annotation * Working with containers: Using Neurodocker to containerize computational * Principles: Re-executability * Advanced data and software management: [DataLad containers/run \+, YODA principles](/resources/tutorials/repronim-containers/) @@ -154,13 +155,13 @@ ReproNim is not an end to end platform, but has several tools that can take her * Planning and data management: Learn how a data collection and annotation framework for behavioral data to be collected can be set up using [ReproSchema and shared across multiple sites](https://repronim.netlify.app/resources/tutorials/reproschema/). * Principles: planning, data management - * Foundations: standards, annotations + * Actions: standards, annotations * Basic software management for distributed data: [Curating and processing a single study to generate standardized, analysis-ready data to participate in distributed projects using Nipoppy](/resources/tutorials/nipoppy/) * Principles: Software management - * Standards: Standards, annotation + * Actions: Standards, annotation * Advanced data management: Adding standards and semantics to data dictionaries to promote data harmonization and findability * Principles: data management, FAIR - * Foundations: Standards, Annotation + * Actions: Standards, Annotation * Advanced metadata management: [Searching and sharing metadata through ReproPond and ReproLake](/resources/tutorials/pond-lake/) * Principles: Metadata management - * Foundations: Standards, Annotation + * Actions: Standards, Annotation diff --git a/content/resources/tools/reproschema/_index.md b/content/resources/tools/reproschema/_index.md index 2435c8f..dc0ba1f 100644 --- a/content/resources/tools/reproschema/_index.md +++ b/content/resources/tools/reproschema/_index.md @@ -38,6 +38,7 @@ ReproSchema applies reproducible neuroimaging principles to assessments, allowin - Tutorials: - https://www.repronim.org/reproschema/user-guide/create-new-protocol/ - https://www.repronim.org/reproschema/tutorials/using-reproschema/ + - [Set up a data collection and annotation framework for multi-site behavioral studies using ReproSchema](/resources/tutorials/reproschema/) - Installation: https://pypi.org/project/reproschema/ - Full documentation: https://www.repronim.org/reproschema/ - How to get help: https://github.com/ReproNim/reproschema/issues diff --git a/content/resources/tutorials/_index.md b/content/resources/tutorials/_index.md index 2b8d413..dc9a3b3 100644 --- a/content/resources/tutorials/_index.md +++ b/content/resources/tutorials/_index.md @@ -8,4 +8,33 @@ TODO: [GH 124](https://github.com/ReproNim/repronim.org/issues/124) To get started with ReproNim, we have created a set of tutorials to show how ReproNim’s tools and services support best practices laid out in [ReproNim’s principles of Reproducible Neuroimaging](/about/in-practice/) and [ReproNim’s 4 Core Actions](/about/in-practice/). We have organized these tutorials based on our [user personas](/resources/getting-started/) to illustrate how ReproNim’s tools can meet the needs of different types of users with different skill sets and objectives. These tutorials are designed in a modular fashion, showing how individual steps to improve reproducibility can be fit together into an [overall reproducible workflow](/about/repronim-approach/). -Tutorials are organized into basic and more advanced approaches. Each tutorial is organized in a similar fashion, providing a list of tools, necessary skills and system requirements, along with step by step instructions to implement and use the tools. +Tutorials are organized into basic and more advanced approaches. Each tutorial is organized in a similar fashion, providing a list of tools, necessary skills and system requirements, along with step by step instructions to implement and use the tools. Below we provide a list of available tutorials, organized according to [ReproNim’s principles of Reproducible Neuroimaging](/about/in-practice/): + +**Principle 1: Study Planning** + +* Creating a [neuroimaging data management and sharing plan](/resources/tutorials/data-management-and-sharing/) +* Set up a data collection and annotation framework for a multisite study using [ReproSchema](https://repronim.netlify.app/resources/tutorials/reproschema/). + +**Principle 2: Data and metadata management** + + * Actions: Standards, Annotation and Provenance, Version control + +* *Basic:* Using ReproNim tools to [convert data to the BIDS standard](/resources/tutorials/dicom-to-bids/) and [create a data dictionary](/resources/tutorials/data-dictionary/) +* *Basic+:* Adding standards and semantics to data dictionaries to promote data harmonization and findability +* *Advanced:* Putting your derived data into BIDS derivatives and creating a semantically-enriched data dictionary using NIDM, a standard for annotating neuroimaging data +* *Advanced:* [DataLad containers/run \+, YODA principles](/resources/tutorials/repronim-containers/) +* *Advanced:* [Searching and sharing metadata through ReproPond and ReproLake](/resources/tutorials/pond-lake/) + +**Principle 3: Software management** + + * Actions: Version control, Annotation, Use containers + +* *Basic:* [Using Git to manage workflow/pipeline versions](/resources/tutorials/git/) +* *Basic+:* [Curating and processing a single study to generate standardized, analysis-ready data to participate in distributed projects using * + Nipoppy](/resources/tutorials/nipoppy/) +* *Basic+:* Working with containers: Using Neurodocker to containerize computational +* *Advanced:* [DataLad containers/run \+, YODA principles](/resources/tutorials/repronim-containers/) + +**Principle 4: Publish everything** + +* Publishing your work as a “Re-executable paper”( \= text, data, code): Standards-based data sharing through OpenNeuro diff --git a/content/resources/tutorials/data-dictionary.md b/content/resources/tutorials/data-dictionary.md index 8fb3f0e..cde4c84 100644 --- a/content/resources/tutorials/data-dictionary.md +++ b/content/resources/tutorials/data-dictionary.md @@ -1,6 +1,6 @@ --- title: Creating a BIDS Data Dictionary and Adding Semantics to for FAIR -linkTitle: Data dictionary +linkTitle: Creating a data dictionary type: docs weight: 5 --- diff --git a/content/resources/tutorials/dicom-to-bids.md b/content/resources/tutorials/dicom-to-bids.md index ed5bec9..4c863d3 100644 --- a/content/resources/tutorials/dicom-to-bids.md +++ b/content/resources/tutorials/dicom-to-bids.md @@ -1,6 +1,6 @@ --- title: Converting DICOM data to BIDS -linkTitle: DICOM to BIDS +linkTitle: Converting DICOM to BIDS type: docs weight: 5 --- diff --git a/content/resources/tutorials/git.md b/content/resources/tutorials/git.md index 0054e1b..7e0128e 100644 --- a/content/resources/tutorials/git.md +++ b/content/resources/tutorials/git.md @@ -1,6 +1,6 @@ --- title: Using Git to manage workflow/pipeline versions -linkTitle: Git +linkTitle: Basic software versioning using Git type: docs weight: 5 --- diff --git a/content/resources/tutorials/nipoppy.md b/content/resources/tutorials/nipoppy.md index 6b689d6..1d476c1 100644 --- a/content/resources/tutorials/nipoppy.md +++ b/content/resources/tutorials/nipoppy.md @@ -1,6 +1,6 @@ --- title: Streamlining Neuroimaging Processing with Nipoppy -linkTitle: Nipoppy +linkTitle: Higher order process management type: docs weight: 5 --- diff --git a/content/resources/tutorials/pond-lake.md b/content/resources/tutorials/pond-lake.md index ba62c50..249bc78 100644 --- a/content/resources/tutorials/pond-lake.md +++ b/content/resources/tutorials/pond-lake.md @@ -1,6 +1,6 @@ --- title: Advanced metadata management - Sharing and searching metadata through a ReproPond and the ReproLake -linkTitle: ReproPond and ReproLake +linkTitle: Search across studies type: docs weight: 5 --- diff --git a/content/resources/tutorials/repronim-containers.md b/content/resources/tutorials/repronim-containers.md index 6711c8a..5973017 100644 --- a/content/resources/tutorials/repronim-containers.md +++ b/content/resources/tutorials/repronim-containers.md @@ -1,5 +1,5 @@ --- -title: ReproNim Containers and Yoda +title: Advanced containerization using DataLad type: docs weight: 5 --- diff --git a/content/resources/tutorials/reproschema.md b/content/resources/tutorials/reproschema.md index d803168..25aeb03 100644 --- a/content/resources/tutorials/reproschema.md +++ b/content/resources/tutorials/reproschema.md @@ -1,23 +1,21 @@ --- -title: Set Up a Data Collection and Annotation Framework Using ReproSchema for Multi-Site Behavioral Studies -linkTitle: ReproSchema +title: Set Up a Data Collection and Annotation Framework for Multi-Site Behavioral Studies Using ReproSchema +linkTitle: Planning a distributed project using ReproSchema type: docs weight: 5 --- **[Reproducible neuroimaging principles](/about/in-practice/#repronims-principles-of-reproducible-neuroimaging)** +- Principle 2c: Data and Metadata management: Annotate data using standard, reproducible procedures **[Actions](/about/in-practice/#repronims-4-core-actions)** - - Standards - Annotation **Standards** - - BIDS **Tools** - - ReproSchema ## Challenge