Subsections of Howto TRR379

Subsections of Websites

www.trr379.de

This is the main website of the TRR379.

This website is not just a public-facing view on the consortium. It is specifically built to be the core component of the metadata concept of TRR379. It provides a collection of canonical definitions of entities essential for the function of TRR379. Such entities include

  • projects of the TRR
  • contributors to the TRR
  • publication from the TRR membership
  • site of the consortium
  • …

Semantics

Any such entity has a dedicated page on the website, with a stable URL that serves as a URI for that entity. As such, these URLs can be used in any TRR379-related metadata to declare relationships to TRR379 entities, for example, the authorship of a publication, the origin project of a data release, etc.

The website is built with the static site generator Hugo. It capitalized on its taxonomy feature. Any page on the site is built from a metadata record. For Hugo, this metadata is presented in the form of a page’s front matter. However, these metadata may themselves be generated from the result of a database query.

Here is an example record for TRR379 spokesperson Ute Habel:

title: Ute Habel
projects:
- a02
- a04
- q01
- q04
sites:
- Aachen
- Juelich
roles:
- pi
- spokesperson
layout: contributor
params:
  orcid:  0000-0003-0703-7722
  name-title: Prof. Dr. rer. soc.
  affiliation: Department of Psychiatry, Psychotherapy and Psychosomatics, Faculty of Medicine, RWTH Aachen University
  sortkey: "Habel, Ute"

<additional content on the page's subject>

From this information, the page that identifies and describes Ute Habel as a spokesperson is generated. It also links and references her record on the respective pages for projects, sites, and roles she is associated with. Consequently, the URL https://www.trr379.de/contributors/ute-habel/ can serve as a URI for Ute Habel within the TRR379 metadata. Moreover, ute-habel is a unique identifier for her as a contributor to TRR379.

While other special-purpose identification systems exist (e.g., https://orcid.org for academics), this approach is automatically applicable to any concept and entity relevant to TRR379. Including roles, data acquisition methods, instruments, etc. The domain root trr379.de represents a unique namespace to define and reference any required entities. This enables a timely and unencumbered development of a metadata concept for TRR379, without hindering alignment with and mapping to more global efforts and initiatives.

Look

Structured metadata is rendered to an HTML website with Hugo using a template. This approach separates the information from its presentation.

The look of the website can be altered by adjusting the template, or switching to a different template entirely. This requires familiarity with Hugo and its templating mechanism.

At present, the congo template is used.

docs.trr379.de

https://docs.trr379.de (this site) is the main documentation source for the TRR379. It offers information on facilities and procedures.

data.trr379.de

https://data.trr379.de hosts the data catalog of the TTR379. This site is currently work in progress, and will be published once the project has started.

Calendars

TRR379 uses a dedicated CalDAV server at https://cal.trr379.de. This service can be used to host any number of online calendars. Individual calendars can be configured to be publicly accessible, or only for internal (authenticated) consumption.

Internal calendars

Any number of non-public calendars can be created and shared with specific audiences. This can be useful to coordinate data acquisition sessions, organize room bookings, or schedule slots for internal meetings and events.

Contact the management team to request a dedicated calendar.

Public calendars

All public calenders are available via CalDAV URL and can be included in any calendar solution, such as Google calendar.

The URLs follow the pattern https://cal.trr379.de/public/<name>, where <name> is the calendar name, as stated in the list below. For the events calendar this is https://cal.trr379.de/public/events.

For use with Google calendar, replace https:// with webcal://. For example, the events calendar can be added to Google calender with the URL webcal://cal.trr379.de/public/events.

Available public calendars:

  • events: General TRR379 events [preview]

Plans

Subsections of Plans

RDM Infrastructure

[This is a draft under discussion]

The planned RDM infrastructure is a federation of interoperable site infrastructures. The key design principle is that no primary data are aggregated to a central infrastructure.

We aim to establish an infrastructure that is suitable for use within the TRR379, but not limited to this scope. Once deployed, the associated services are usable beyond the scope of TRR379.

The following schema sketches the planned infrastructure. Components that hold (primary) data are depicted in yellow. Components that hold (mostly or exclusively) metadata are shown in blue. The direction of information flow is indicated by arrows, exchange of data by solid arrows, and metadata-only exchange by dotted arrows. Infrastructures that are only accessible to authorized agents are labeled with a “lock” symbol. Further details on individual components are provided below.

graph TB;
    subgraph Central services
        C1[("Collaboration portal<br>hub.trr379.de<br> 🔐")]:::meta
        C2{{"Data search<br>query.trr379.de<br> 🔐"}}:::meta
        C3(Main website<br>www.trr379.de):::meta
        C4("Data catalog<br>data.trr379.de"):::meta
    end
    subgraph "Aachen 🔐"
        A1[(hub)]:::data
        A1a[(lab1)]:::data
        A1b[(lab2)]:::data
        A2{{query}}:::meta
    end
    subgraph "Frankfurt 🔐"
        F1[(hub)]:::data
        F2{{query}}:::meta
    end
    subgraph "Heidelberg 🔐"
        H1[(hub)]:::data
        H1a[(ZI-hub)]:::data
        H1b[(lab1)]:::data
        H2{{query}}:::meta
    end
    A1 -.-> C1
    A1a -.-> A1
    A1b <---> A1
    A1 -.-> A2
    A2 <-.-> C2
    F1 -.-> C1
    F2 <-.-> C2
    F1 -.-> F2
    C3 <-.-> C1
    C3 -.-> C2
    H1 -.-> C1
    H1a <-.-> C1
    H1a <-.-> H1
    H1b <---> H1
    H1 -.-> H2
    H2 <-.-> C2
    C1 -.-> C2
    C1 -.-> C4
    C3 -.-> C4
    H1b <---> A1a
    %% node links to actual services
    click C1 href "https://hub.trr379.de"
    click C3 href "https://www.trr379.de"
    %% classes to distinguish data and metadata nodes
    classDef data fill:#ffa200,color:#000
    classDef meta fill:#5C99C8,color:#000
    %% invisible link purely for manipulating the grouping
    C2 ~~~ A1b
    C4 ~~~ A1b
    C2 ~~~ F1
    C2 ~~~ H1b

Central services

All central services a metadata-focused. No primary data acquired at participating sites are aggregated into central databases/storage.

Collaboration portal (hub.trr379.de)

This is the main hub for collecting actionable links to all TRR379 resources and information. The software solution for this hub is Forgejo-ankesajo. It is a free and open-source software package, and the direct service counterpart of DataLad, the main tool proposed for implementing reproducible research workflows in TRR379 labs.

The hub will store DataLad datasets, referencing all TRR379 data resources without hosting any actual data. Instead the DataLad dataset point to the individual institutional data stores, or to community data repositories when and where data have been published.

The hub is also a place to deposit (shared) computational environments, and implementations of (shared) data processing pipelines, software publications, and source code repositories under a uniform TRR379 umbrella.

A test site is deployed at https://hub.trr379.de and is being evaluated.

Main website

See this page for a description of the main website. Importantly, the website renders essential metadata for the TRR379 (contributors, roles, publications, projects, research topics, etc.) It provides a unique URI for any such entity, to be used as identifiers in all TRR379 (meta)data resources.

The website is programmatically generated from a repository hosted on the TRR379 hub, to enable contributions by all TRR379 members.

Data catalog

The TRR379 data catalog is a website dedicated to providing a uniform (read-only) view on the TRR’s data resources. It is rendered programmatically by DataLad Catalog from metadata on TRR379 data resources hosts in the TRR379 hub.

This site is indexed by specialized search engines like Google’s dataset search and a key enabler for general findability of TRR379 resources.

This is a federated data discovery service that is tailored to the cohort dataset acquired by TRR379 as a whole. It will enable the discovery of individual data records matching a given set of criteria, regardless of the contributing TRR379 site.

The service is federated. Each sites runs their own instance, and has the sole authority on deciding what metadata are shared with other TRR379 sites. Only these metadata property will be accessible by TRR379 at large, while more detailed metadata records can be use for in-house queries.

The proposed solution for the query service is a version of NeuroBagel adapted to the data nature and needs of TRR379.

Site infrastructure

Sites are free to implement any RDM solutions, as long as that infrastructure provides

  • (programmatically) queriable metadata of a previously agreed upon nature
  • (programmatically) accessible data to any authorized members of TRR379

with the aim to enable reproducible research from primary data to published results within and across TRR379.

Q02 supports sites with software solution that facilitate interoperability within TRR379. This includes the local deployment of the software systems used to run the central services.

We aim at individual sites running their own data hubs (using the same software solution) as the central https://hub.trr379.de. In contrast to the central hub, these institutional sites can directly use the storage features of Forgejo-ankesajo, and host arbitrary amounts of data. TRR379 can communicate data availability using a federation protocol.