diff --git a/_data/CONTRIBUTORS.yaml b/_data/CONTRIBUTORS.yaml index a3096ae..eb9a469 100644 --- a/_data/CONTRIBUTORS.yaml +++ b/_data/CONTRIBUTORS.yaml @@ -5,4 +5,26 @@ Bert Droesbeke: git: bedroesb email: bedro@psb.ugent.be - orcid: 0000-0003-0522-5674 \ No newline at end of file + orcid: 0000-0003-0522-5674 + +Johan Gustafsson: + git: supernord + orcid: 0000-0002-2977-5032 + role: product owner + affiliation: Australian BioCommons / University of Melbourne + +Frederik Coppens: + git: frederikcoppens + role: product owner + affiliation: VIB + +Carole Goble: + git: CaroleGoble + orcid: 0000-0003-1219-2137 + role: product owner + affiliation: University of Manchester + +Finn Bacall: + git: fbacall + role: lead developer + affiliation: University of Manchester diff --git a/_data/footer.yml b/_data/footer.yml index c474c71..97c8174 100644 --- a/_data/footer.yml +++ b/_data/footer.yml @@ -1,7 +1,3 @@ -extra_line: | - ![Flag of the European Union](/assets/img/eu-flag-small.png) - [EOSC-Life](https://www.eosc-life.eu/) is funded by European Union’s Horizon 2020 programme under - grant agreement number [824087](https://doi.org/10.3030/824087) and [additional funding](/project/acknowledgements/#funding). copyright: | [about.workflowhub.eu](https://about.workflowhub.eu/) content is distributed under [BSD 3-Clause "New" or "Revised" License](https://github.com/workflowhub-eu/about/blob/master/LICENSE), @@ -10,8 +6,8 @@ columns: - type: image image_width: 120px width: 3 - src: '/assets/img/eosc-life.svg' - alt: EOSC-Life + src: '/assets/img/workflowhub-square.svg' + alt: workflowhub logo square - type: links width: 3 children: diff --git a/_data/tiles.yml b/_data/tiles.yml new file mode 100644 index 0000000..a3fbbae --- /dev/null +++ b/_data/tiles.yml @@ -0,0 +1,12 @@ +- title: "Production instance" + url: https://workflowhub.eu/ +- title: "Sandbox instance" + url: https://dev.workflowhub.eu/ +- title: "Source code" + url: https://github.com/seek4science/seek +- title: "Documentation" + url: docs/ +- title: "Outreach and Publications" + url: project/outreach +- title: "Roadmap" + url: project/roadmap diff --git a/_data/topnav.yml b/_data/topnav.yml index ded7827..d5605eb 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -1,9 +1,7 @@ ## Topnav single links ## if you want to list an external url, use external_url instead of url. the theme will apply a different link base. subitems: - - title: Home - url: / - title: About - url: /project/ + url: / - title: Documentation url: /docs/ diff --git a/_includes/citation.md b/_includes/citation.md index 84d6cac..c6d4bed 100644 --- a/_includes/citation.md +++ b/_includes/citation.md @@ -5,5 +5,3 @@ Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes _arXiv_:2410.06941 [cs.DL] - -See also [publication and outreach](/project/outreach) for more specific work. diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html new file mode 100644 index 0000000..d666386 --- /dev/null +++ b/_includes/tiles-simple.html @@ -0,0 +1,9 @@ +
+ {%- for item in site.data.tiles %} + {%- if item.title %} +
+ {{item.title}} +
+ {%- endif %} + {%- endfor %} +
\ No newline at end of file diff --git a/docs/index.md b/docs/index.md index f3d57f0..9f26c4f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,7 @@ --- -title: Quick start guide +title: Documentation toc: false +page_id: docs redirect_from: - /docs/before-you-start/ - /docs/onboarding/ @@ -8,16 +9,18 @@ redirect_from: --- +## Quick start guide + **WorkflowHub will help make your workflows findable and citable, and this guide will help you get started with that process.** {% include callout.html type="tip" content="if you want to test WorkflowHub and its features, there is a [development instance available here](https://dev.workflowhub.eu/)." %} -## 1. Register yourself on WorkflowHub +### 1. Register yourself on WorkflowHub Register yourself on the [sign up page](https://workflowhub.eu/signup) of WorkflowHub if you do not have an account. You can also log in using your [LS Login](https://lifescience-ri.eu/ls-login/) or [GitHub](https://github.com/) credentials. -## 2. Decide which `Space` you would like to create a `Team` in +### 2. Decide which `Space` you would like to create a `Team` in **Figure 1** below highlights the basic structure of WorkflowHub, and examples of the three types of `Spaces` where you could create a `Team`. Learn more about `Teams` and `Spaces` [here](/docs/space-team-organisation). @@ -36,7 +39,7 @@ You can request to create a `Team` in any or all of the following `Spaces`: {% include callout.html type="note" content="you can create multiple teams in multiple spaces, depending on your requirements." %} -## 3. Create a team or join an existing team +### 3. Create a team or join an existing team Go to the [create](https://workflowhub.eu/projects/guided_create) and [join](https://workflowhub.eu/projects/guided_join) a team page from WorkflowHub to do so. @@ -56,7 +59,7 @@ More information on how to join a team can be found on the [how to create and jo {% include image.html file="team.svg" caption="Fig 2. Screenshot of required minimum information (numbered) that needs to be entered into the *Create a New Team* wizard on WorkflowHub." alt="minimum information" %} -## 4. Register workflow(s) +### 4. Register workflow(s) Workflows can be registered using the [WorkflowHub wizard](https://workflowhub.eu/workflows/new) diff --git a/index.md b/index.md index 5c9cf94..c9dd05f 100644 --- a/index.md +++ b/index.md @@ -1,70 +1,122 @@ --- title: WorkflowHub project -toc: false +toc: true permalink: / # There are special sidebar rules for the index page in layouts/default.html hide_sidebar: true sidebar: true --- -[WorkflowHub](https://workflowhub.eu/) is a FAIR **workflow registry** sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR and [multiple EU-wide projects](/project/acknowledgements/#funding). It is workflow management system agnostic: workflows may remain in their native repositories in their native forms. +## About -This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). +This website describes the open source project for developing and running [**WorkflowHub**](https://workflowhub.eu/): a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). -For more details, see [About WorkflowHub](/project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](/project/outreach). +[WorkflowHub](https://workflowhub.eu): -For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](/project/community)! +* Is a **domain-agnostic** workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* Is **workflow management system agnostic**: workflows may remain in their native repositories in their native forms. +* Provides features such as community spaces, collections, versioning and snapshots, and contributor credit. +* Allows workflows to be FAIR, citable, have managed metadata profiles, and be openly available for review and analytics. -## Documentation +In addition: + +* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. +* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. +* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. +* In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. +* WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). +* The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. + +For more details, see [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](project/outreach). + +For any kind of questions, or suggestions on using WorkflowHub, feel free to join our [community](#community)! + + +## Did you know? + +* The first beta-release was in Sept 2020, +* Production-release was in September 2022, +* The WorkflowHub now holds over [700 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/), +* It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/), and is a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). + + +## Citation + +{% include citation.md %} + +{% include callout.html type="tip" content="See also [publication and outreach](/project/outreach) for more specific work." %} -* [Documentation & Quick Start guide](docs/) (See also _Detailed Documentation_) -* [Guide to using WorkflowHub](docs/guide-to-using-workflowhub/) -* [Developer docs](developer/) -* Tutorial vidoes: - - [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) - - [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session ## Project resources -* **Production instance**: -* **Sandbox instance**: (use for testing; occasionally wiped) -* **Source code**: [seek4science/seek](https://github.com/seek4science/seek) -* **API documentation**: -* **[Outreach and Publications](/project/outreach/)** -* **EOSC-Life Deliverable 2.3**: -* **Tasks**: - * [WorkflowHub roadmap](/project/roadmap) (deprecated -- now managed in Trello) - * WorkflowHub implementation (SEEK) - * General WorkflowHub +{% include tiles-simple.html col = "2" %} + +* **Tutorial videos:** + * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) + * [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session + + +## Get involved + + +### Community + +While WorkflowHub is largely developed as a collaboration between [several projects](/project/acknowledgements), any contributors are welcome to join our **open community**. + +Anyone can [join the WorkflowHub club](https://github.com/workflowhub-eu/about/issues/1)! Either sign up on GitHub [issue #1](https://github.com/workflowhub-eu/about/issues/1) or join the [next bi-weekly Zoom call](https://s.apache.org/workflowhub-minutes) and introduce yourself. + +* **When:** Alternate Wednesdays 10:00 current UK time zone / 11:00 current Central European time zone +* **Agenda, telcon details and minutes:** + +See the list of WorkflowHub Club members on the [acknowledgements page](/project/acknowledgements). + +For asynchronous communication, see also: + * **Mailing list**: [`workflowhub😊elixir-europe.org`](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org) ([subscribe](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org)/[archive](https://mail.elixir-europe.org/pipermail/workflowhub_elixir-europe.org/)) * **Slack chat**: [#workflows on seek4science.slack.com](https://seek4science.slack.com/archives/CPLLVV94L) ([join](https://join.slack.com/t/seek4science/shared_invite/zt-csqh94qb-kf~kFbZxuHl1Hpxhbc8avw)) -* [Google Drive](https://drive.google.com/drive/folders/1_bZ63W4oRtWL5OnWJNYvE4u3A27VyGGe) - (to request write-access, ask in Slack channel) -* **Slides/posters** (for complete list, see [Outreach](/project/outreach/)): - * [WorkflowHub: FAIR Workflow Registry](https://doi.org/10.5281/zenodo.7323471). Justin Clark-Casey et al, EOSC Symposium 2022, 2022-11-14 - * [WorkflowHub – a FAIR registry for workflows](https://doi.org/10.7490/f1000research.1118984.1). Carole Goble, ELIXIR All Hands 2022 - * [WorkflowHub - a registry for workflows](https://doi.org/10.5281/zenodo.4012124). Carole Goble, ECCB 2020, 2020-09-02 - * [Poster: The WorkflowHub, a registry for Life Science Workflows](https://workflowhub.eu/presentations/1). Ambarish Kumar, ISMB, 2020-07-13 - * [WorkflowHub Introduction slides](https://drive.google.com/open?id=1hfBAjjRnL9jGoxHEvq66Wo-wuKqouR3C). Carole Goble, 2020-03-25 +* [Google Drive](https://drive.google.com/drive/folders/1_bZ63W4oRtWL5OnWJNYvE4u3A27VyGGe): to request write-access, ask in Slack channel -## Community -Regular meeting: **WorkflowHub Club** - all welcome! +### Development -Anyone is welcome to join the bi-weekly [WorkflowHub Club](/project/community) calls using Zoom. +Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. See the [roadmap page](/project/roadmap) for a list of in-flight and future development activities. -* When: Alternate Wednesdays 10:00 current UK time zone / 11:00 current Central European time zone -* Agenda, telcon details and minutes: +You can also see a complete list of contributors on the [acknowledgements](/project/acknowledgements) page. + + + +### Contact Us + +The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). + +* [Provide feedback or ask questions](https://workflowhub.eu/home/feedback) +* [Contribute to WorkflowHub club](#community) +* [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: + - Contact `workflowhub.eu` system administrators: + - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: +* Academic collaborations: + + +## WfCommons and WorkflowHub + +Note that the US-based [WfCommons](https://wfcommons.org/), a Python-based framework for enabling scientific workflow research and development, was previously [called "WorkflowHub"](https://doi.org/10.1109/WORKS51914.2020.00012). While that framework is not related to our registry workflowhub.eu, this name collision could cause some confusion, so in common agreement with Rafael Ferreira da Silva, their former domain name `workflowhub.org` +now kindly redirect to our workflow registry , their framework was renamed to "WfCommons" and moved to and their Python package `workflowhub` was renamed [`wfcommons`](https://pypi.org/project/wfcommons/). -See the list of club members on the [acknowledgement](/project/acknowledgements) page. ## Code of conduct This project has a [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) to ensure interactions are friendly, respectful and inclusive. You can contact if you have any concerns or questions. -## Citation -{% include citation.md %} +## Retention and End-of-Life policy + +WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. + + +## Governance + +{% include contributor-tiles-all.html custom="Johan Gustafsson, Frederik Coppens, Carole Goble" %} + ## Acknowledgements @@ -73,3 +125,10 @@ We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu + + + + + + + diff --git a/project/acknowledgements.md b/project/acknowledgements.md index e5c21ee..c3322f1 100644 --- a/project/acknowledgements.md +++ b/project/acknowledgements.md @@ -1,9 +1,11 @@ --- title: Acknowledgements +sidebar: false --- Main development, hosting and maintenance of WorkflowHub is done by the [eScience Lab](https://esciencelab.org.uk/) at The University of Manchester led by [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). + ## Funding @@ -24,12 +26,14 @@ We are also grateful for contributions by: * [BIOINDUSTRY 4.0](https://www.ibisba.eu/EU-Projects/Horizon-Europe) ([HORIZON-INFRA-2022-TECH-01 101094287](https://doi.org/10.3030/101094287), [UKRI 10048146](https://gtr.ukri.org/projects?ref=10048146)) * ..in addition to contributions from [WorkflowHub Club](#workflowhub-club) participants + ### EOSC-Life {% include affiliation-tiles-selection.html type="EOSC-Life"%} workflowhub.eu was founded as part of [**EOSC-Life**](https://www.eosc-life.eu/) ([WP2 _Tools Collaboratory_](https://github.com/eosc-life/tools-collaboratory-roadmap)), funded by European Union’s [Horizon 2020](https://ec.europa.eu/programmes/horizon2020/) programme under grant agreement [H2020-INFRAEOSC-2018-2 824087](https://doi.org/10.3030/824087). + ### Previous funding {% include affiliation-tiles-selection.html type="previous"%} @@ -48,6 +52,7 @@ Previous contributions were funded by: The main [WorkflowHub codebase](https://github.com/seek4science/seek/tree/workflowhub) is based on [SEEK](https://seek4science.org/about_us.html) and builds on previous experience with developing [myExperiment](https://www.myexperiment.org/about). SEEK is implemented in [Ruby on Rails](https://rubyonrails.org/) using a wide range of open source [Ruby gems](https://github.com/seek4science/seek/blob/workflowhub/Gemfile.lock). + ## Related projects ### ELIXIR @@ -65,6 +70,7 @@ WorkflowHub activities are strongly coordinated with [ELIXIR Europe](https://eli * [ELIXIR Netherlands](https://www.elixir-europe.org/about-us/who-we-are/nodes/netherlands) * [ELIXIR Hub](https://elixir-europe.org/about-us/who-we-are/hub) + ### Collaborations The WorkflowHub community collaborates closely with (at least) these projects: @@ -78,9 +84,10 @@ The WorkflowHub community collaborates closely with (at least) these projects: * [FAIRDOM](https://fair-dom.org) * [FAIRDOM-SEEK](https://fairdomseek.org/) + ## WorkflowHub Club -The weekly [WorkflowHub Club](/project/community) is chaired by **Finn Bacall**. +The weekly [WorkflowHub Club](/project/community) is chaired by **Johan Gustafsson**. Participants include: diff --git a/project/citation.md b/project/citation.md index 5dd34ec..d16d00d 100644 --- a/project/citation.md +++ b/project/citation.md @@ -1,5 +1,8 @@ --- title: Citation +sidebar: false --- {% include citation.md %} + +{% include callout.html type="tip" content="See also [publication and outreach](/project/outreach) for more specific work." %} diff --git a/project/community.md b/project/community.md index 93d15ec..a761248 100644 --- a/project/community.md +++ b/project/community.md @@ -3,36 +3,3 @@ title: WorkflowHub community --- -While WorkflowHub is largely developed as a collaboration between [several projects](/project/acknowledgements), any contributors are welcome to join our **open community**. - - -## WorkflowHub Club - -[WorkflowHub Club](https://s.apache.org/workflowhub-minutes): - -* **Schedule**: Bi-weekly, Wednesday 10:00 BST / 11:00 CEST -* **Agenda / call details**: - -Anyone can [join the WorkflowHub club](https://github.com/workflowhub-eu/about/issues/1)! Either sign up on GitHub [issue #1](https://github.com/workflowhub-eu/about/issues/1) or join the [next call](https://s.apache.org/workflowhub-minutes) and introduce yourself. - -See [acknowledgements](/project/acknowledgements#workflowhub-club) for a complete list of participants in the WorkflowHub Club. - -For asynchronous communication, see also: - -* **Mailing list**: [`workflowhub😊elixir-europe.org`](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org) ([subscribe](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org)/[archive](https://mail.elixir-europe.org/pipermail/workflowhub_elixir-europe.org/)) -* **Slack chat**: [#workflows on seek4science.slack.com](https://seek4science.slack.com/archives/CPLLVV94L) ([join](https://join.slack.com/t/seek4science/shared_invite/zt-csqh94qb-kf~kFbZxuHl1Hpxhbc8avw)) -* [Google Drive](https://drive.google.com/drive/folders/1_bZ63W4oRtWL5OnWJNYvE4u3A27VyGGe) - (to request write-access, ask in Slack channel) - -### Governance - -Product Owners: - -* Johan Gustafsson, Australian Biocommons -* Carole Goble, The University of Manchester -* Frederik Coppens, VIB - - -## Code of conduct - -This project has a [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) to ensure interactions are friendly, respectful and inclusive. You can contact if you have any concerns or questions. diff --git a/project/events.md b/project/events.md index cb69efd..ac1d4c0 100644 --- a/project/events.md +++ b/project/events.md @@ -1,5 +1,6 @@ --- title: Events +page_id: events --- diff --git a/project/index.md b/project/index.md index 88ea7e1..213728e 100644 --- a/project/index.md +++ b/project/index.md @@ -2,50 +2,5 @@ title: About WorkflowHub --- -* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). -* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. -* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. -* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. -* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. -* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. -* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. -* In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. -* WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). -* The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. -* First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). -## Contact Us -The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). - -* [Provide feedback or ask question](https://workflowhub.eu/home/feedback) -* Contribute to [WorkflowHub club](https://about.workflowhub.eu/project/community/) (Regular telcons, Slack chat, public mailing list) -* [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: - - Contact `workflowhub.eu` system administrators: - - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: -* Academic collaborations: - - -## WfCommons and WorkflowHub - -Note that the US-based [WfCommons](https://wfcommons.org/), a Python-based framework for enabling scientific workflow research and development, was previously [called "WorkflowHub"](https://doi.org/10.1109/WORKS51914.2020.00012). While that framework is not related to our registry workflowhub.eu, this name collision could cause some confusion, so in common agreement with Rafael Ferreira da Silva, their former domain name `workflowhub.org` -now kindly redirect to our workflow registry , their framework was renamed to "WfCommons" and moved to and their Python package `workflowhub` was renamed [`wfcommons`](https://pypi.org/project/wfcommons/). - - - -## Development - -Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. - -See a complete list of contributors on the [acknowledgement](/project/acknowledgements) page. - -Aims of the project include: - -* Evolvement of [myExperiment](https://myexperiment.org/) that is workflow system agnostic, supports a repository of workflows in native and standardised form (e.g. [CWL](https://www.commonwl.org/) and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry would support a **common API** to simplify access for tool developers. -* Standardised workflow identifiers and metadata descriptions needed for workflow discovery, reuse, preservation, interoperability and monitoring and metadata harvesting using standard protocols. Workflows are usually multi-component (requiring links to test data, example runs, explanatory documentation, etc) and used in collections for scientific use cases. We plan to use the Research Object specification for packaging workflows, which has already been combined with [CWL](https://www.commonwl.org/) and is part of the [BioComputeObject](http://biocomputeobject.org/) specification. -* Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. -* The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. - -## Retention and End-of-Life policy - -WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. diff --git a/project/news.md b/project/news.md index ccc6de4..f9644e5 100644 --- a/project/news.md +++ b/project/news.md @@ -1,5 +1,6 @@ --- title: News +page_id: news --- {% include news.html truncate=true %} diff --git a/project/outreach.md b/project/outreach.md index 4338b1a..c95cd36 100644 --- a/project/outreach.md +++ b/project/outreach.md @@ -1,5 +1,7 @@ --- title: Outreach and Publications +page_id: outreach +sidebar: false --- @@ -175,6 +177,7 @@ Gareth Price, Johan Gustafsson (2022): _Australian BioCommons Webinar_ + ### 2021 Carole Goble (2021): @@ -319,6 +322,11 @@ The Global Alliance for Genomics And Health (GA4GH) 10th Plenary Meeting. _F1000Research_ **11**:1318 (poster) +Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodríguez Navas, José María Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Simone Leo, Luca Pireddu, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2022): +[**WorkflowHub – a FAIR registry for workflows**](https://doi.org/10.7490/f1000research.1118984.1). +_ELIXIR All Hands 2022_, Amsterdam, Netherlands, 7-10 June 2022. + + Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Simone Leo, Luca Pireddu, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2021): [**The WorkflowHub: A FAIR Registry for Workflows and Workflow Research Objects**](https://drive.google.com/file/d/1Ge5bcKQBH03t5VH9IDIT0F8pfenNrw9-/view?usp=sharing). _[BOSC 2021](https://www.open-bio.org/events/bosc-2021/)_, diff --git a/project/roadmap.md b/project/roadmap.md index 887a5c2..3e58d3a 100644 --- a/project/roadmap.md +++ b/project/roadmap.md @@ -1,18 +1,18 @@ --- title: Roadmap +page_id: roadmap +sidebar: false redirect_from: /roadmap/ --- -_Please feel free to help contribute to this roadmap through the [WorkflowHub Club](/community/) or as [feedback](https://workflowhub.eu/home/feedback)!_ +{% include callout.html type="note" content="_Please feel free to help contribute to this roadmap through the [WorkflowHub Club](/community/) or as [feedback](https://workflowhub.eu/home/feedback)!_" %} -Please note that the roadmap isn't a project plan or release schedule. + +Please note that the roadmap is not a project plan or release schedule. The WorkflowHub Club is a very dynamic and agile team, and the roadmap is reviewed and updated regularly. -It's purpose is to give a general indication of intent and direction of travel. +Its purpose is to give a general indication of intent and direction of travel. -See also: - * WorkflowHub implementation (SEEK) - * General WorkflowHub