From 6fa63fcd572a05d39d50ee2d0f344cb594b9aefc Mon Sep 17 00:00:00 2001 From: Phil Reed Date: Thu, 19 Sep 2024 15:31:05 +0100 Subject: [PATCH 1/6] Engagement with other communities --- pages/communities/communities.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pages/communities/communities.md b/pages/communities/communities.md index d9fb5be..04bfe81 100644 --- a/pages/communities/communities.md +++ b/pages/communities/communities.md @@ -11,7 +11,11 @@ FAIRDOM organizes user meetings twice a year. The purpose of the [FAIRDOM user m ## Engagement with other communities -[BioHackathon](https://biohackathon-europe.org) is the hackathon run by ELIXIR, the European ESFRI Infrastructure for Bioinformatics. [de.NBI](https://www.denbi.de), the organisation behind the German node of ELIXIR runs a [similar set of hackathons](https://www.denbi.de/de-nbi-events). FAIRDOM is typically involved in several projects of these hackathons each year. +FAIRDOM is typically involved in several **hackathon projects** each year, including [ELIXIR BioHackathon Europe](https://biohackathon-europe.org) (the European ESFRI Infrastructure for bioinformatics) and [de.NBI BioHackathon Germany](https://www.denbi.de/de-nbi-events) (the organisation behind the German node of ELIXIR). For example: + +- At [ELIXIR BioHackathon 2023 and 2024 (project 23)](https://github.com/elixir-europe/biohackathon-projects-2024/blob/main/23.md) MARS: Multi-omics Adapter for Repository Submissions made great strides in producing a proof of concept for dispatching metadata to multiple repositories using the ISA-JSON format, a standard supported in and popularised by FAIRDOM-SEEK. +- At [ELIXIR BioHackathon 2022 (project 27)](https://github.com/elixir-europe/biohackathon-projects-2022/blob/main/27/paper.md), a comprehensive strategy for an ISA-JSON-to-ELIXIR Repository brokering system was devised, in order to efficiently share heterogenous, multi-omics metadata to public repositories such as [DataHub](/fairdom-in-use/Datahub). +- At [1st BioHackathon Germany](https://www.denbi.de/de-nbi-events/1479-miappe-wizard-enabling-easy-creation-of-miappe-compliant-isa-metadata-for-plant-phenotyping-experiments), a tool was produced to make it easier to generate [MIAPPE](/fairdom-in-use/plant-is-and-miappe)-compliant ISA-JSON metadata, supported in FAIRDOM-SEEK. The [Systems Biology Community of ELIXIR](https://elixir-europe.org/communities/systems-biology) is the community of systems biology experts within the infrastructure ELIXIR. It coordinates work done within ELIXIR to interlink and harmonize infrastructure for models, software and data. The overarching long-term goal of the ELIXIR Systems Biology Community is to make systems biology modelling a central pillar of research in biology. From 177b1728e80226604356607cabad3214aa2a1fad Mon Sep 17 00:00:00 2001 From: Phil Reed Date: Thu, 19 Sep 2024 15:33:47 +0100 Subject: [PATCH 2/6] User meetings --- pages/communities/communities.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/communities/communities.md b/pages/communities/communities.md index 04bfe81..c80d452 100644 --- a/pages/communities/communities.md +++ b/pages/communities/communities.md @@ -7,7 +7,7 @@ images: ["images/communities/ERASysAPP-PALS-Berlin-2015-3.jpg", "images/communit ## FAIRDOM user meetings -FAIRDOM organizes user meetings twice a year. The purpose of the [FAIRDOM user meetings](https://fair-dom.org/events) is to establish an active FAIRDOM user community to allow networking between various FAIRDOM-SEEK users and to learn from data management experiences in different research projects. +FAIRDOM organises [user meetings](https://fair-dom.org/events) twice a year. The purpose of these events is to maintain an active FAIRDOM user community, providing networking between various FAIRDOM-SEEK users and to learn from data management experiences in different research projects. ## Engagement with other communities From b46c77837948fa7065b9fc209017c68e154b837d Mon Sep 17 00:00:00 2001 From: Munazah Date: Tue, 29 Oct 2024 11:58:25 +0000 Subject: [PATCH 3/6] Update communities.md --- pages/communities/communities.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/communities/communities.md b/pages/communities/communities.md index c80d452..e64721f 100644 --- a/pages/communities/communities.md +++ b/pages/communities/communities.md @@ -23,6 +23,6 @@ The [Systems Biology Community of ELIXIR](https://elixir-europe.org/communities/ {% include pic-carousel.html %} -From 2012 to 2018 we ran four “foundry” meetings with practitioners in support delivery for systems biology all over Europe, to exchange ideas and practices, to share software and to interoperate systems where useful to do so. We did not continue these meetings as we found the grounds of the foundry meetings is covered by two sets of activities, the Systems Biology Community in ELIXIR that covers the conceptual aspects of systems biology infrastructure, and the Biohackathons that help increasing interaction of systems biology infrastructure around concrete projects. +From 2012 to 2018 we ran four “foundry” meetings with practitioners in support delivery for systems biology all over Europe, to exchange ideas and practices, to share software and to interoperate systems where useful to do so. We discontunues these meetings as the activities of foundry meetings were covered by the Systems Biology Community in ELIXIR, covering conceptual aspects of systems biology infrastructure, and the Biohackathons promoting exchange of ideas and information of systems biology infrastructure. -From 2011 to 2022, FAIRDOM PALs were “front line” experimentalists, modellers and bioinformaticians from each of the projects we work with. They acted as our advocates and communicate our progress back to their projects. Today, we encourage advocacy through our dedicated [community channels and regular meetings](/get_involved). For more about PALs, see the [PALs presentations](https://fairdomhub.org/presentations?filter%5Bquery%5D=pals&order=created_at_desc). +From 2011 to 2022, FAIRDOM PALs were the “front line” experimentalists, modellers and bioinformaticians from each of the projects we worked with. They acted as our advocates and communicated our progress back to their projects. We have now created dedicated [community channels and regular meetings](/get_involved) and encourage advocacy through these channels. For more about PALs, see the [PALs presentations](https://fairdomhub.org/presentations?filter%5Bquery%5D=pals&order=created_at_desc). From b352f6a525ba62e3e977ecf0cd64f4debb8e6140 Mon Sep 17 00:00:00 2001 From: Munazah Date: Tue, 29 Oct 2024 12:01:13 +0000 Subject: [PATCH 4/6] Update communities.md --- pages/communities/communities.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/communities/communities.md b/pages/communities/communities.md index c80d452..0edf04e 100644 --- a/pages/communities/communities.md +++ b/pages/communities/communities.md @@ -11,7 +11,7 @@ FAIRDOM organises [user meetings](https://fair-dom.org/events) twice a year. The ## Engagement with other communities -FAIRDOM is typically involved in several **hackathon projects** each year, including [ELIXIR BioHackathon Europe](https://biohackathon-europe.org) (the European ESFRI Infrastructure for bioinformatics) and [de.NBI BioHackathon Germany](https://www.denbi.de/de-nbi-events) (the organisation behind the German node of ELIXIR). For example: +FAIRDOM is typically involved in several **hackathon projects** each year, including [ELIXIR BioHackathon Europe](https://biohackathon-europe.org) (the European ESFRI life sciences Infrastructure) and [de.NBI BioHackathon Germany](https://www.denbi.de/de-nbi-events) (the organisation behind the German node of ELIXIR). For example: - At [ELIXIR BioHackathon 2023 and 2024 (project 23)](https://github.com/elixir-europe/biohackathon-projects-2024/blob/main/23.md) MARS: Multi-omics Adapter for Repository Submissions made great strides in producing a proof of concept for dispatching metadata to multiple repositories using the ISA-JSON format, a standard supported in and popularised by FAIRDOM-SEEK. - At [ELIXIR BioHackathon 2022 (project 27)](https://github.com/elixir-europe/biohackathon-projects-2022/blob/main/27/paper.md), a comprehensive strategy for an ISA-JSON-to-ELIXIR Repository brokering system was devised, in order to efficiently share heterogenous, multi-omics metadata to public repositories such as [DataHub](/fairdom-in-use/Datahub). From 266dc66dce6e8f6fe85204d231019d9b484e0486 Mon Sep 17 00:00:00 2001 From: Phil Reed Date: Tue, 29 Oct 2024 14:35:09 +0000 Subject: [PATCH 5/6] Typo in communities history --- pages/communities/communities.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/communities/communities.md b/pages/communities/communities.md index a033017..8f53c9a 100644 --- a/pages/communities/communities.md +++ b/pages/communities/communities.md @@ -23,6 +23,6 @@ The [Systems Biology Community of ELIXIR](https://elixir-europe.org/communities/ {% include pic-carousel.html %} -From 2012 to 2018 we ran four “foundry” meetings with practitioners in support delivery for systems biology all over Europe, to exchange ideas and practices, to share software and to interoperate systems where useful to do so. We discontunues these meetings as the activities of foundry meetings were covered by the Systems Biology Community in ELIXIR, covering conceptual aspects of systems biology infrastructure, and the Biohackathons promoting exchange of ideas and information of systems biology infrastructure. +From 2012 to 2018 we ran four “foundry” meetings with practitioners in support delivery for systems biology all over Europe, to exchange ideas and practices, to share software and to interoperate systems where useful to do so. We discontinued these meetings as the activities of foundry meetings were covered by the Systems Biology Community in ELIXIR, covering conceptual aspects of systems biology infrastructure, and the Biohackathons promoting exchange of ideas and information of systems biology infrastructure. From 2011 to 2022, FAIRDOM PALs were the “front line” experimentalists, modellers and bioinformaticians from each of the projects we worked with. They acted as our advocates and communicated our progress back to their projects. We have now created dedicated [community channels and regular meetings](/get_involved) and encourage advocacy through these channels. For more about PALs, see the [PALs presentations](https://fairdomhub.org/presentations?filter%5Bquery%5D=pals&order=created_at_desc). From 4284d2c982ac8ac123c98fb29d4539174f1bb963 Mon Sep 17 00:00:00 2001 From: Phil Reed Date: Tue, 29 Oct 2024 14:51:29 +0000 Subject: [PATCH 6/6] Added example of FAIRDOM supporting systems biology explicitly --- pages/communities/communities.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pages/communities/communities.md b/pages/communities/communities.md index 8f53c9a..4ccf504 100644 --- a/pages/communities/communities.md +++ b/pages/communities/communities.md @@ -17,7 +17,11 @@ FAIRDOM is typically involved in several **hackathon projects** each year, inclu - At [ELIXIR BioHackathon 2022 (project 27)](https://github.com/elixir-europe/biohackathon-projects-2022/blob/main/27/paper.md), a comprehensive strategy for an ISA-JSON-to-ELIXIR Repository brokering system was devised, in order to efficiently share heterogenous, multi-omics metadata to public repositories such as [DataHub](/fairdom-in-use/Datahub). - At [1st BioHackathon Germany](https://www.denbi.de/de-nbi-events/1479-miappe-wizard-enabling-easy-creation-of-miappe-compliant-isa-metadata-for-plant-phenotyping-experiments), a tool was produced to make it easier to generate [MIAPPE](/fairdom-in-use/plant-is-and-miappe)-compliant ISA-JSON metadata, supported in FAIRDOM-SEEK. -The [Systems Biology Community of ELIXIR](https://elixir-europe.org/communities/systems-biology) is the community of systems biology experts within the infrastructure ELIXIR. It coordinates work done within ELIXIR to interlink and harmonize infrastructure for models, software and data. The overarching long-term goal of the ELIXIR Systems Biology Community is to make systems biology modelling a central pillar of research in biology. +The [Systems Biology Community of ELIXIR](https://elixir-europe.org/communities/systems-biology) is the community of systems biology experts within the infrastructure ELIXIR. It coordinates work done within ELIXIR to interlink and harmonise infrastructure for models, software and data. The overarching long-term goal of the ELIXIR Systems Biology Community is to make systems biology modelling a central pillar of research in biology. +One way that FAIRDOM facilitates this goal is by providing a public joint repository for both models and data, [FAIRDOMHub](/fairdom-in-use/fairdomhub), +which allows interlinking of experimental data, computational models and simulation results in a project-centred approach +([Martins dos Santos et al. 2022](https://f1000research.com/articles/11-1265/v1), [Wolstencroft et al. 2017](https://doi.org/10.1093/nar/gkw1032)). + ## History