diff --git a/.gitignore b/.gitignore index f40fbd8..3183494 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,45 @@ _site .sass-cache .jekyll-cache .jekyll-metadata -vendor +ivendo + +# macOS system files +.DS_Store + +# Jekyll build output +_site/ +.sass-cache/ +.jekyll-cache/ +.jekyll-metadata + +# Logs and temp files +*.log +*.tmp + +# Bundler dependencies +/vendor/ +.bundle/ + +# Ruby gems +Gemfile.lock + +# Node dependencies (if used) +/node_modules/ + +# VS Code settings +.vscode/ + +# Other IDE files +.idea/ +*.swp + +# Ignore PDFs if generated (keep if source) +/pdfs/*.pdf + +# Ignore compiled CSS/JS if generated by build tool +/css/*.css.map +/js/*.js.map + + + + diff --git a/Events/AHM/ahm.html b/Events/AHM/ahm.html index 1214a28..798121d 100644 --- a/Events/AHM/ahm.html +++ b/Events/AHM/ahm.html @@ -1,77 +1,41 @@ - - - - - - - ELIXIR All Hands Meeting 2023 - - - - - - -
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Ireland hosts ELIXIR All Hands Meeting 2023

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Irish Head of Node, Prof. Denis Shields, welcomes meeting attendees during the opening presentation.
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From 5th-8th June 2023, ELIXIR Ireland had the pleasure of welcoming ELIXIR members from all over Europe to the 9th ELIXIR All Hands Meeting (AHM) hosted at Dublin's Convention Centre. The event brought together approximately 400 in-person guests, with a further 114 remote guests joining online. The annual event offered members from each of the 23 nodes - the opportunity to discuss the successes of the previous year and plan for the future.

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Prof. Des Higgins presenting the keynote talk "35 years since Clustal1".
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The keynote talk was given by Des Higgins, Professor Emeritus of Bioinformatics at University College Dublin, who reflected on the last 35 years of working on the revolutionary bioinformatics tool CLUSTAL for multiple sequence alignment. Prof. Higgins highlighted the challenges faced by early bioinformaticians and emphasized the benefits of using FAIR (Findable, Accessible, Interoperable, and Reusable) and Open Research principles in research. Unsurprisingly, Prof. Higgins received a roaring applause from the audience and his presentation was a highlight of the week.

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Prof. Gianpiero Cavalleri presenting an overview of ELIXIR, Ireland and Human Genomics.
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ELIXIR Ireland node members were well-represented throughout the event. Prof. Gianpiero Cavalleri (RCSI) gave an update on "ELIXIR, Ireland, and Human Genomics" during the Human Genomics and Translational Data 2024-28 mini-symposium. Prof. Cavalleri highlighted the genomics challenges Ireland has been experiencing and the changes that are currently taking place. These changes were recently announced in the HSE National Genetics and Genomics Strategy for Ireland as well as through Ireland’s participation in GDI co-led by Prof. Cavalleri with ELIXIR Ireland Head of Node, Prof. Denis Shields. This gives hope to a brighter future for genomics healthcare in Ireland through continued coordination between Genomic Data Infrastructure (GDI) Ireland and the emerging national strategy. Prof. Aedin Culhane (UL) and Dr. Maria Doyle (UL) alongside Prof. Leo Lahti (ELIXIR-FI) led a successful workshop titled "Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure" on 9th June. The workshop fostered an engaging discussion on connecting ELIXIR and Bioconductor to encourage collaboration in terms of training, data development, and infrastructure.

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Group photo of all ELIXIR members attending the meeting in Dublin.
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The meeting provided plenty of opportunities to socialize and network, with the main social event of the week taking place at the EPIC museum. Attendees had the chance to learn about the Irish diaspora and its global impact on science, politics, literature, and more. Entertainment was provided in the form of a traditional music session with Irish dancers showcasing Irish culture and it didn’t take much encouragement for all to join in, with ELIXIR Ireland members proudly stepping forward to lead everyone in their own rendition of the ”Siege of Ennis” céilí dance.

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Photo Credits: ELIXIR-EUR

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For more information about this event see the ELIXIR All Hands Meeting Report . We look forward to next year's ELIXIR All Hands Meeting in Uppsala, Sweden!

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- - - - - + + \ No newline at end of file diff --git a/_config.yml b/_config.yml index f203e53..8a86f8d 100644 --- a/_config.yml +++ b/_config.yml @@ -1,4 +1,4 @@ -# Welcome to Jekyll! +n# Welcome to Jekyll! # # This config file is meant for settings that affect your whole blog, values # which you are expected to set up once and rarely edit after that. If you find @@ -19,20 +19,17 @@ # in the templates via {{ site.myvariable }}. title: ELIXIR Ireland Node webpage -email: denis.shields2@gmail.com -description: >- # this means to ignore newlines until "baseurl:" - Write an awesome description for your new site here. You can edit this - line in _config.yml. It will appear in your document head meta (for - Google search results) and in your feed.xml site description. +email: elixir@ul.ie +description: ELIXIR-Ireland node. baseurl: elixir-ireland.github.io # the subpath of your site, e.g. /blog url: - https://elixir-ireland.github.io + https://aedin.github.io # the base hostname & protocol for your site, e.g. http://example.com twitter_username: elixir-ireland github_username: elixir-ireland # Build settings -theme: minima +theme: plugins: - jekyll-feed # Exclude from processing. diff --git a/_includes/footer.html b/_includes/footer.html new file mode 100644 index 0000000..36d9729 --- /dev/null +++ b/_includes/footer.html @@ -0,0 +1,14 @@ + diff --git a/_includes/header.html b/_includes/header.html new file mode 100644 index 0000000..a2b5b46 --- /dev/null +++ b/_includes/header.html @@ -0,0 +1,24 @@ + diff --git a/_includes/nav.html b/_includes/nav.html new file mode 100644 index 0000000..ab3514f --- /dev/null +++ b/_includes/nav.html @@ -0,0 +1,2 @@ + + diff --git a/_layouts/default.html b/_layouts/default.html new file mode 100644 index 0000000..2f2b144 --- /dev/null +++ b/_layouts/default.html @@ -0,0 +1,32 @@ + + + + + {% if page.title %}{{ page.title }} | {% endif %}{{ site.title }} + + + + + + + + {% if site.seo %} + {% seo %} + {% endif %} + + + + {% include header.html %} +
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+ + + {% include footer.html %} +
+ + \ No newline at end of file diff --git a/about.markdown b/about.md similarity index 100% rename from about.markdown rename to about.md diff --git a/headings.html b/archive/headings.html similarity index 100% rename from headings.html rename to archive/headings.html diff --git a/icon-fonts.html b/archive/icon-fonts.html similarity index 100% rename from icon-fonts.html rename to archive/icon-fonts.html diff --git a/archive/index.html b/archive/index.html new file mode 100644 index 0000000..778258d --- /dev/null +++ b/archive/index.html @@ -0,0 +1,224 @@ + + + + + Home page | ELIXIR Ireland + + + + + + + + + +
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About

+

+ ELIXIR Ireland is the Irish node of the international + organisation ELIXIR, centred in Europe, which promotes the + sharing of resources and expertise in computational biology. +

+

+ ELIXIR develops training, compute, data and tools platforms + (see ELIXIR-Europe) to make + them interoperable and sustainable. +

+

+ ELIXIR Ireland offers training, data and software. Our + vision is to bring Ireland to the forefront of computational + biology research in Europe. To do this we will leverage the + extensive networks across Europe in ELIXIR (including the + UK) to drive the local development and local use of + computational data, tools, platforms and training resources, + drawing on both local and EU funding support. +

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ELIXIR Ireland Institutions

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Team

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  • + Aedin Culhane, Head of Node, UL + +
    • +
  • + Colm Ryan, Deputy Head of Node, UCD + +
    • + Gavin Farrell, Node Coordinator, UL + +
  • + Lars Jermiin, Data Stewardship Manager, UG + +
    • +
  • + Pavel Baranov, Technical Coordinator, UCC + +
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  • + Maria Doyle, Training Coordinator, UL + +
    • +
  • + Anmol Kiran, Deputy Technical Coordinator, UCC + +
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News

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+ + + diff --git a/databases.html b/databases.html index aa3a612..66bb5ad 100644 --- a/databases.html +++ b/databases.html @@ -1,445 +1,122 @@ - - - - - Databases | ELIXIR Ireland - - - - - - - - - - -
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Databases

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- The following data resources are hosted by ELIXIR Ireland - associated researchers: -

- - - - - - - - - - - - - - - - - - - - +--- +layout: default +title: Databases +--- - - - - - - - - - - - - - -
DatabaseDescription
- DARNED - - A database of human RNA editing. It has not been - updated for a while, but is still surprisingly - popular. PMID: - 20547637, - 23074185; DOI: - 10.1093/bioinformatics/btq285, - 10.1093/nar/gks961. -
- Maintainer: Pavel Baranov -
- RiboSeq Data Portal - - A metadata repository of publicly available available - ribosome profiling datasets and facilitating - data-driven discoveries in the field of translation - regulation. A component of - - https://riboseq.org. PMID: - 39540432 - ; DOI: - 10.1093/nar/gkae1020. -
- Maintainer: Pavel Baranov -
- GWIPS-viz - - A genome browser for the visualisation of public - ribosome profiling data aligned to genomes. A - component of - - https://riboseq.org. PMID: - 28977460, - 24185699, - 29927076; DOI: - 10.1093/nar/gkx790 , - 10.1093/nar/gkt1035, - 10.1093/nar/gkx790, - 10.1002/cpbi.50. -
- Maintainer: Pavel Baranov -
- Trips-viz - - A computational environment for the analysis and - visualisation of public and user-generated ribosome - profiling data mapped to transcriptomes. A component - of - - https://riboseq.org. PMID: - - 30239879 , - 33950201 - ; DOI: - 10.1093/nar/gky842, - 10.1093/nar/gkab323. -
- Maintainer: Pavel Baranov -
- - CancerGD - - - Database of cancer genetic dependencies identified in - CRISPR/RNAi screens. PMID: - 28711281; DOI: - 10.1016/j.cels.2017.06.002. -
- Maintainer: Colm Ryan -
- ParalogSL - - Database of predicted synthetic lethal interactions - between paralogs in cancer. PMID: - 34529928; DOI: - 10.1016/j.cels.2021.08.006 - . -
- Maintainer: Colm Ryan -
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- - - + +

+ The following data resources are hosted by ELIXIR Ireland associated researchers: +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DatabaseDescription
+ DARNED + + A database of human RNA editing. It has not been updated for a while, but is still surprisingly popular. + PMID: + 20547637, + 23074185; + DOI: + 10.1093/bioinformatics/btq285, + 10.1093/nar/gks961. +
+ Maintainer: Pavel Baranov + +
+ RiboSeq Data Portal + + A metadata repository of publicly available ribosome profiling datasets and facilitating data-driven discoveries in the field of translation regulation. A component of + https://riboseq.org. + PMID: + 39540432; + DOI: + 10.1093/nar/gkae1020. +
+ Maintainer: Pavel Baranov + +
+ GWIPS-viz + + A genome browser for the visualisation of public ribosome profiling data aligned to genomes. A component of + https://riboseq.org. + PMID: + 28977460, + 24185699, + 29927076; + DOI: + 10.1093/nar/gkx790, + 10.1093/nar/gkt1035, + 10.1093/nar/gkx790, + 10.1002/cpbi.50. +
+ Maintainer: Pavel Baranov + +
+ Trips-viz + + A computational environment for the analysis and visualisation of public and user-generated ribosome profiling data mapped to transcriptomes. A component of + https://riboseq.org. + PMID: + 30239879, + 33950201; + DOI: + 10.1093/nar/gky842, + 10.1093/nar/gkab323. +
+ Maintainer: Pavel Baranov + +
+ CancerGD + + Database of cancer genetic dependencies identified in CRISPR/RNAi screens. + PMID: + 28711281; + DOI: + 10.1016/j.cels.2017.06.002. +
+ Maintainer: Colm Ryan + +
+ ParalogSL + + Database of predicted synthetic lethal interactions between paralogs in cancer. + PMID: + 34529928; + DOI: + 10.1016/j.cels.2021.08.006. +
+ Maintainer: Colm Ryan + +
+ diff --git a/elix_ire_funded.html b/elix_ire_funded.html index 4496896..1d6f06a 100644 --- a/elix_ire_funded.html +++ b/elix_ire_funded.html @@ -1,176 +1,37 @@ - - - - - ELIXIR Ireland Funded Projects | ELIXIR Ireland - - - - - - - - - -
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ELIXIR Ireland Funded Projects

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- EU Converge funding (ELIXIR-CONVERGE | ELIXIR - (elixir-europe.org) is allowing us to develop -

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  • Training programmes in data management
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  • - Support FAIR submission of COVID viral data to EGA archive -
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- The Genome Data Infrastructure programme (EU/HRB joint - funding; 2022-2026; European Genomic Data Infrastructure - (GDI) project (onemilliongenomes.eu) -

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  • - develop very robust systems and protocols for hosting and - exchanging sensitive human genetic research data -
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  • - Is allied with the European 1 Million+ genomes initiative. -
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- Commissioned services from ELIXIR Europe to Ireland include - in the area of machine learning (funding to Gianluca - Pollastri) and Single Cell Transcriptomics (funding to Aedin - Culhane). -

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- - - +--- +layout: default +title: ELIXIR Ireland Funded Projects +--- + + +

ELIXIR Ireland Funded Projects

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+ EU Converge funding ( + ELIXIR-CONVERGE + ) is allowing us to develop: +

+ +

+ The Genome Data Infrastructure programme (EU/HRB joint funding; 2022-2026; + European Genomic Data Infrastructure (GDI) project) + is enabling Ireland to: +

+ +

+ Commissioned services from ELIXIR Europe to Ireland include work in the area of: +

+

+ CANDLE is a three-year EU-funded project (2025 – 2028) supporting Member States and Associated Countries in setting up National Cancer Data Nodes. + Lead: University of Limerick (to Aedin Culhane. See The CANDLE mission begins in EU countries + +

+ diff --git a/events.html b/events.html index bd89755..862d8a5 100644 --- a/events.html +++ b/events.html @@ -1,191 +1,67 @@ - - - - - Events | ELIXIR Ireland - - - - - - - - - -
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Events

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  • - Ireland hosts ELIXIR All Hands Meeting 2023, June 5 - June - 8, 2023, Dublin. Image credit: - ELIXIR Europe. -
    - -
    - Head of Node, Prof. Denis Shields, welcomes meeting - attendees during the opening presentation. -
    +--- +layout: default +title: Events +--- - -
    - Prof. Des Higgins presenting the keynote talk "35 - years since Clustal1". -
    - -
    - Prof. Gianpiero Cavalleri presenting an overview of - ELIXIR, Ireland and Human Genomics. -
    - -
    - Group photo of all ELIXIR members attending the - meeting in Dublin. -
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  • - ELIXIR Ireland hosted a meeting of the ELIXIR - Intrinsically Disordered Protein (IDP) Community 30 August - - 31 August 2022, at UCD, Dublin IDPcentral. -
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Events

+ + +
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  • Annual Irish Society of Human Genetics (IGHG) meeting. Maynooth 2025
    • +
+ + +
    +
  • + ELIXIR hosts an annual All Hands Meeting This was hosted by Dublin in 2023, June 5 - June 8, 2023, Dublin. + + Image credit: ELIXIR Europe + + +
  • +
    + +
    + Head of Node, Prof. Denis Shields, welcomes meeting attendees during the opening presentation.
    + +
    + Prof. Des Higgins presenting the keynote talk "35 years since Clustal1". +
    + +
    + Prof. Gianpiero Cavalleri presenting an overview of ELIXIR, Ireland and Human Genomics. +
    + +
    + Group photo of all ELIXIR members attending the meeting in Dublin. +
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- ELIXIR Ireland -
- Head of Node: Denis Shields -
- UCD Conway Institute of Biomolecular and Biomedical Research -
- University College Dublin, Dublin 4 -
- ☏: +353 7166735 -
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- - - - + + + + + diff --git a/images/.DS_Store b/images/.DS_Store new file mode 100644 index 0000000..b122fff Binary files /dev/null and b/images/.DS_Store differ diff --git a/index.html b/index.html index 040ff06..b7de27a 100644 --- a/index.html +++ b/index.html @@ -1,225 +1,79 @@ - - - - - Home page | ELIXIR Ireland - - - - - - - - - -
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About

-

- ELIXIR Ireland is the Irish node of the international - organisation ELIXIR, centred in Europe, which promotes the - sharing of resources and expertise in computational biology. -

-

- ELIXIR develops training, compute, data and tools platforms - (see ELIXIR-Europe) to make - them interoperable and sustainable. -

-

- ELIXIR Ireland offers training, data and software. Our - vision is to bring Ireland to the forefront of computational - biology research in Europe. To do this we will leverage the - extensive networks across Europe in ELIXIR (including the - UK) to drive the local development and local use of - computational data, tools, platforms and training resources, - drawing on both local and EU funding support. -

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- - -
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ELIXIR Ireland Institutions

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Team

-
    -
  • - Denis Shields, Head of Node, UCD - -
    • -
  • - Colm Ryan, Deputy Head of Node, UCD - -
    • -
  • - Lars Jermiin, Data Stewardship Manager, UG - -
    • -
  • - Pavel Baranov, Technical Coordinator, UCC - -
    • -
  • - Siobhán Cleary, Research Data Management Coordinator, UCD - -
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  • - Maria Doyle, Training Coordinator, UL - -
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  • - Anmol Kiran, Deputy Technical Coordinator, UCC - -
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News

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- ELIXIR Ireland -
- Head of Node: Denis Shields -
- UCD Conway Institute of Biomolecular and Biomedical Research -
- University College Dublin, Dublin 4 -
- ☏: +353 7166735 -
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-
-
- - - +--- +layout: default +title: Home +--- + +

About

+

+ ELIXIR Ireland is the Irish node of the international + organisation ELIXIR, centred in Europe, which promotes the + sharing of resources and expertise in computational biology. +

+

+ ELIXIR develops training, compute, data and tools platforms + (see ELIXIR-Europe) to make + them interoperable and sustainable. +

+

+ ELIXIR Ireland offers training, data and software. Our + vision is to bring Ireland to the forefront of computational + biology research in Europe. To do this we will leverage the + extensive networks across Europe in ELIXIR (including the + UK) to drive the local development and local use of + computational data, tools, platforms and training resources, + drawing on both local and EU funding support. +

+ + + +
+

ELIXIR Ireland Institutions

+ +
+ + +
+

Team

+ + + + + + + diff --git a/index.markdown b/index.markdown deleted file mode 100644 index 0671507..0000000 --- a/index.markdown +++ /dev/null @@ -1,6 +0,0 @@ ---- -# Feel free to add content and custom Front Matter to this file. -# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - -layout: home ---- diff --git a/news.html b/news.html index 97ef9fb..24eda57 100644 --- a/news.html +++ b/news.html @@ -1,189 +1,23 @@ - - - - - News | ELIXIR Ireland - - - - - - - - - -
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News

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- Genomic Data Infrastructure Ireland project to - support discovery of genetic causes of disease -
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- University College Dublin are co-leading, with RCSI - University of Medicine and Health Sciences and - FutureNeuro, the Irish element of a new EU project to - support the integration of genomics into healthcare - and advance new treatments ... - Read more -
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- ☏: +353 7166735 -
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- - - +--- +layout: default +title: News +--- + + + + + diff --git a/platforms.html b/platforms.html index 9ac2444..86dc770 100644 --- a/platforms.html +++ b/platforms.html @@ -1,157 +1,31 @@ - - - - - Platforms | ELIXIR Ireland - - - - - - - - - -
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Platforms

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- Irish biologists and clinical researchers need to access - local resources for computation and data storage of genomic - and related data. We are working with colleagues in the - universities, in ICHEC (Irish centre for high end computing - www.ichec.ie) and HEANET (Higher Education Authority based) - to explore new solutions that meet the emerging needs of - biological data analysis, which involves large and sensitive - (human) datasets of DNAs, RNAs, proteins, and other data - features, and in some cases needs heavy CPU usage. -

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- ELIXIR Ireland -
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- University College Dublin, Dublin 4 -
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+ Ireland contributes to these platforms through national projects and collaborations, supporting discovery, analysis, and training for life science data. +

+ + + diff --git a/software.html b/software.html index 546fe7d..ac6eb15 100644 --- a/software.html +++ b/software.html @@ -1,963 +1,326 @@ - - - - - Home page | ELIXIR Ireland - - - - - - - - - -
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Software

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- The following bioinformatics software tools are developed, - maintained, or hosted by ELIXIR Ireland associated - researchers: -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +--- +layout: default +title: Software +--- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ToolDescription
- RiboGalaxy - - An instant of Galaxy tailored for ribosome profiling - data analysis. PMID: - 26821742,37356899; DOI: - 10.1080/15476286.2016.1141862,10.1016/j.jmb.2023.168043. -
- Maintainer: Pavel Baranov -
- Trips-viz - - A computational environment for the analysis and - visualisation of public and user-generated ribosome - profiling data mapped to transcriptomes. A component - of - - https://riboseq.org. PMID: - 30239879, - 33950201 - ; DOI: - 10.1093/nar/gky842, - 10.1093/nar/gkab323. -
- Maintainer: Pavel Baranov -
- BRCA-Core - - Source code (Python) to identify protein complexes - co-regulated in tumour proteomic samples. - PMID:29032073 - ???; DOI:10.1016/j.cels.2017.09.011. -
- Maintainer: Colm Ryan - -
- Homo (v2.1) - - Source code (C++). A program for analysing - compositional heterogeneity across aligned sequences - of nucleotides, genotypes, di-nucleotides, codons or - amino acids (controls the family-wise error rate and - the false discovery rate). The software also computes - three compositional distances and the - p distance (pending publication). -
- Maintainer: Lars Jermiin - -
- SatuRation (v1.0) - - Source code (C++). A program designed to estimate the - degree of saturation observed between two sequences of - nucleotides, genotypes, di-nucleotides, codons or - amino acids (pending publication). -
- Maintainer: Lars Jermiin - -
- AliStat (1.14) - - Source code (C++). Software for quantifying the - completeness of multiple sequence alignments used in - phylogenetic and phylogenomic research. PMID:33575581 - ; DOI:10.1093/nargab/lqaa024. -
- Maintainers: Thomas Wong , Lars Jermiin - -
- HAL-HAS (v2.6.4) - - Source code (C++). Software for identifying optimal - models of sequences evolution, which uses mixture - models nucleotide sequence evolution that account for - rate heterogeneity across sites and across lineages. - PMID:24927722 - ; DOI:10.1093/sysbio/syu036 - . -
- Maintainer: Thomas Wong - , Lars Jermiin - -
- Hetero2 (v2.4) - - Source code (C++). Software to simulate the evolution - of nucleotide sequences on phylogenetic trees under - heterogeneous Markovian conditions. PMID:24927722 - ; DOI:10.1093/sysbio/syu036 - . -
- Maintainers: Thomas Wong - , Lars Jermiin - -
- AliJack (v1.0) - - Source code (C++). Software to randomly sample subsets - of sequences from a multiple sequence alignment. The - jackknife procedure is used. PMID:28350004 - ; DOI:10.1038/srep45302. -
- Maintainer: Thomas Wong - , Lars Jermiin - -
- CheckJack (v1.0) - - Source code (C++). Software to compute jackknife - scores from trees generated from alignments generated - using AliJack. PMID:28350004 - ; DOI:10.1038/srep45302. -
- Maintainer: Thomas Wong - - , Lars Jermiin - -
- ModelFinder (v1.0) - - Source code (C++). Software for model selection during - phylogenetic analysis of nucleotide and amino acid - sequences. ModelFinder is embedded in IQ-TREE and - IQ-TREE2 and can only be access by downloading these - programs. PMID:28481363 - ; DOI:10.1038/nmeth.4285. -
- Maintainers: Minh Bui - - , Thomas Wong - , Lars Jermiin - -
- - NMF - - An R package for non-negative matrix factorization - -
- Maintainer:Renaud Gaujoux - - - - - , Cathal Seoighe - -
- - MREMA - - An R package implementing a mixture of random-effect - meta-analysis. PMID:36197939 - ; DOI:10.1371/journal.pcbi.1010278. -
- Maintainer:Dónal O’Shea - - - - - , Cathal Seoighe - -
- PGS-LMM - - Scripts intended to facilitate the calculation of the - LOCO PGS and its inclusion as a fixed effect in a - Linear Mixed Model (LMM) implemented with fastGWA. - PMID:34599249 - ; DOI:10.1038/s41598-021-99031-3. -
- Maintainer:Declan Bennett - - - - - , Cathal Seoighe - -
- SLiMs - - Prediction of function and 2D structures for proteins, - protein motifs and peptides (see - BioWare - or - DistillDeep). - - -
- Maintainer:Gianluca Pollastri - - - - - , Denis Shields - -
- autopeptideML - - AutoPeptideML is a tool that automates the development - of ML models for predicting peptide bioactivity, - facilitating robust evaluation and reproducibility. - PMID: - 39292535; DOI: - 10.1093/bioinformatics/btae555. -
- Maintainer: Raul Fernandez-Diaz - - - - -
- Clustal Omega - - Multiple Sequence Alignment package via on-line - server, in collaboration with groups in Germany, the - UK and France. PMID:21988835 - ; DOI:10.1038/msb.2011.75. - -
- Maintainer: -
- demuxSNP - - R/Bioconductor package that assists in demultiplexing - scRNAseq data using both cell hashing and SNPs data. - -
- Maintainer: Michael Lynch - - , Aedin Culhane -
- corral - - R/Bioconductor package for correspondence analysis for - single-cell data. - -
- Maintainer: Lauren Hsu - - - , Aedin Culhane - - - - -
- SingleCellMultiModal - - R/Bioconductor package providing multimodal - single-cell RNA-seq datasets for benchmarking and - method development. - -
- Maintainer: Marcel Ramos - - - , Aedin Culhane - - - - -
- mogsa - - R/Bioconductor package for multi-omics gene set - analysis. - -
- Maintainer: Chen Meng - - - , Aedin Culhane - - - - -
- iBBiG - - R/Bioconductor package for iterative binary - bi-clustering that extracts groups of phenotypes from - multiple studies that are associated with similar gene - sets. - -
- Maintainer: Aedin Culhane - - - - -
- made4 - - R/Bioconductor package for multivariate analysis of - microarray data. - -
- Maintainer: Aedin Culhane - - - - -
- - - - - - - - - - - - - - -
-
-
-
- -
-
- -
- -
-
-
-
-
- ELIXIR Ireland -
- Head of Node: Denis Shields -
- UCD Conway Institute of Biomolecular and Biomedical Research -
- University College Dublin, Dublin 4 -
- ☏: +353 7166735 -
-
-
-
-
-
- - - +

Software

+

+ The following bioinformatics software tools are developed, maintained, or hosted by ELIXIR Ireland associated researchers: +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ToolDescription
+ RiboGalaxy + + An instance of Galaxy tailored for ribosome profiling data analysis. + PMID: + 26821742, + 37356899; + DOI: + 10.1080/15476286.2016.1141862, + 10.1016/j.jmb.2023.168043. +
+ Maintainer: Pavel Baranov + +
+ Trips-viz + + A computational environment for the analysis and visualisation of public and user-generated ribosome profiling data mapped to transcriptomes. A component of + https://riboseq.org. + PMID: + 30239879, + 33950201; + DOI: + 10.1093/nar/gky842, + 10.1093/nar/gkab323. +
+ Maintainer: Pavel Baranov + +
+ BRCA-Core + + Source code (Python) to identify protein complexes co-regulated in tumour proteomic samples. + PMID:29032073; + DOI:10.1016/j.cels.2017.09.011. +
+ Maintainer: Colm Ryan + +
+ Homo (v2.1) + + Source code (C++). A program for analysing compositional heterogeneity across aligned sequences of nucleotides, genotypes, di-nucleotides, codons or amino acids (controls the family-wise error rate and the false discovery rate). The software also computes three compositional distances and the p distance (pending publication). +
+ Maintainer: Lars Jermiin + +
+ SatuRation (v1.0) + + Source code (C++). A program designed to estimate the degree of saturation observed between two sequences of nucleotides, genotypes, di-nucleotides, codons or amino acids (pending publication). +
+ Maintainer: Lars Jermiin + +
+ AliStat (1.14) + + Source code (C++). Software for quantifying the completeness of multiple sequence alignments used in phylogenetic and phylogenomic research. + PMID:33575581; + DOI:10.1093/nargab/lqaa024. +
+ Maintainers: Thomas Wong + , + Lars Jermiin + +
+ HAL-HAS (v2.6.4) + + Source code (C++). Software for identifying optimal models of sequence evolution, which uses mixture models nucleotide sequence evolution that account for rate heterogeneity across sites and across lineages. + PMID:24927722; + DOI:10.1093/sysbio/syu036. +
+ Maintainers: Thomas Wong + , Lars Jermiin + +
+ Hetero2 (v2.4) + + Source code (C++). Software to simulate the evolution of nucleotide sequences on phylogenetic trees under heterogeneous Markovian conditions. + PMID:24927722; + DOI:10.1093/sysbio/syu036. +
+ Maintainers: Thomas Wong + , Lars Jermiin + +
+ AliJack (v1.0) + + Source code (C++). Software to randomly sample subsets of sequences from a multiple sequence alignment. The jackknife procedure is used. + PMID:28350004; + DOI:10.1038/srep45302. +
+ Maintainers: Thomas Wong + , Lars Jermiin + +
+ CheckJack (v1.0) + + Source code (C++). Software to compute jackknife scores from trees generated from alignments generated using AliJack. + PMID:28350004; + DOI:10.1038/srep45302. +
+ Maintainers: Thomas Wong + , Lars Jermiin + +
+ ModelFinder (v1.0) + + Source code (C++). Software for model selection during phylogenetic analysis of nucleotide and amino acid sequences. ModelFinder is embedded in IQ-TREE and IQ-TREE2 and can only be accessed by downloading these programs. + PMID:28481363; + DOI:10.1038/nmeth.4285. +
+ Maintainers: Minh Bui + , Thomas Wong + , Lars Jermiin + +
+ NMF + + An R package for non-negative matrix factorization +
+ Maintainer: Renaud Gaujoux + , + Cathal Seoighe + +
+ MREMA + + An R package implementing a mixture of random-effect meta-analysis. + PMID:36197939; + DOI:10.1371/journal.pcbi.1010278. +
+ Maintainer: Dónal O’Shea + , Cathal Seoighe + +
+ PGS-LMM + + Scripts intended to facilitate the calculation of the LOCO PGS and its inclusion as a fixed effect in a Linear Mixed Model (LMM) implemented with fastGWA. + PMID:34599249; + DOI:10.1038/s41598-021-99031-3. +
+ Maintainer: Declan Bennett + , Cathal Seoighe + +
+ SLiMs + + Prediction of function and 2D structures for proteins, protein motifs and peptides (see + BioWare or + DistillDeep). +
+ Maintainer: Gianluca Pollastri + , Denis Shields + +
+ autopeptideML + + AutoPeptideML is a tool that automates the development of ML models for predicting peptide bioactivity, facilitating robust evaluation and reproducibility. + PMID: 39292535; + DOI: 10.1093/bioinformatics/btae555. +
+ Maintainer: Raul Fernandez-Diaz + +
+ Clustal Omega + + Multiple Sequence Alignment package via on-line server, in collaboration with groups in Germany, the UK and France. + PMID:21988835; + DOI:10.1038/msb.2011.75. +
+ Maintainer: +
+ demuxSNP + + R/Bioconductor package that assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. +
+ Maintainer: Michael Lynch + , Aedin Culhane + +
+ corral + + R/Bioconductor package for correspondence analysis for single-cell data. +
+ Maintainer: Lauren Hsu + , Aedin Culhane + +
+ SingleCellMultiModal + + R/Bioconductor package providing multimodal single-cell RNA-seq datasets for benchmarking and method development. +
+ Maintainer: Marcel Ramos + , Aedin Culhane + +
+ mogsa + + R/Bioconductor package for multi-omics gene set analysis. +
+ Maintainer: Chen Meng + , Aedin Culhane + +
+ iBBiG + + R/Bioconductor package for iterative binary bi-clustering that extracts groups of phenotypes from multiple studies that are associated with similar gene sets. +
+ Maintainer: Aedin Culhane + +
+ made4 + + R/Bioconductor package for multivariate analysis of microarray data. +
+ Maintainer: Aedin Culhane + +
+ diff --git a/training.html b/training.html index e2fdbda..96d2113 100644 --- a/training.html +++ b/training.html @@ -1,416 +1,203 @@ - - - - - - - - - - -
- - +--- +layout: default +title: Training +--- -
- - -
-
- -
-
-

What we provide

-

- ELIXIR Ireland offers training in fundamental data science - skills for life scientists, such as R analysis and data - management planning. -

-

- Our training primarily focuses on offering courses to over 100 - PhD students within the - Science Foundation Ireland (SFI) Centre for Research - Training in Genomics Data Science - program. -

-
-
-
-
-
-

Training Team

-
-
-
- Trainer -
-
- Maria Doyle - -
-

- Training Coordinator -
- University of Limerick -

-
-
-
-
-
- Trainer -
-
- Lars Jermiin - - - - -
-

- Data Stewardship Manager -
- University College Dublin -

-
-
-
-
-
- Trainer -
-
- Siobhán Cleary - - - - -
-

- Research Data Management -
- University College Dublin -

-
-
-
+

What we provide

+

+ ELIXIR Ireland offers training in fundamental data science + skills for life scientists, such as R analysis and data + management planning. +

+

+ Our training primarily focuses on offering courses to over 100 + PhD students within the + + Science Foundation Ireland (SFI) Centre for Research Training in Genomics Data Science + + program. +

+
+
+

Training Team

+
+
+
+ Trainer +
+
+ Maria Doyle + +
+

+ Training Coordinator
+ University of Limerick +

- -
- -
-
-
-
-
-

- Data Management Planning Resources and Training Material -

- - - - - - - - - - - - - -
TitleTrainerDateDownload
- Research Data Management and Data Management Planning - Lars JermiinFeb 2023 - -
-

ELIXIR Tools for Data Management

- - -
- - ... - -
-

- The Research Data Management kit (RDMkit) is a set of - guidelines for implementing good data management - practices amd making your data FAIR (Findable, - Accessible, Interoperable and Reusable). These best - practice guidelines have been compiled by a network of - data managers and data stewards from the ELIXIR nodes - acrooss Europe. Please view - this pdf for - our tips on using the RDMkit. -

-
-
-
- - ... - -
-

- The Data Stewardship Wizard (DSW) is an online web - tool designed by ELIXIR-CH to streamline the process - of creating a comprehensive data management plan - (DMP). By employing a user-friendly question-based - format, the DSW guides you through a series of - carefully crafted inquiries, ensuring that every - aspect of your data management plan is addressed while - tailoring it to your specific needs. Once you provide - your answers, the DSW incorporates the information - into a downloadable DMP document using a specified - template format. It allows multiple users to - collaborate on a single document. The DSW proves - particularly advantageous to individuals new to the - realm of DMP writing, as it alleviates uncertainties - regarding the detail required for each section. The - DSW provides metrics which allow you to assess how - FAIR your DMP is. Click - here - to be redirected to the online tool for writing DMPs. -

-
-
-
- - ... - -
-

- The FAIRCookbook provides step-by-step instructions, - best practices, and expert insights on implementing - FAIR data principles throughout the data lifecycle. It - covers a wide range of topics, including data - organization, metadata creation, data documentation, - data repository selection, data citation, and data - sharing protocols. -

-
-
-

- *Click on the images to be redirected to the - tool's website. -

-
-
+
+
+
+ Trainer +
+
+ Lars Jermiin + +
+

+ Data Stewardship Manager
+ University College Dublin +

-
-
-
-
-
-
-

Upcoming Events

-

Currently no events scheduled.

-

- Please get in contact with our - training coordinator - if you would like to participate in future training events - with ELIXIR Ireland. -

-

Past Events

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Bioconductor R analyses, Online, Global, 22-26 May 2023. -
- Data Management Planning, Vienna, Austria, 25 Jan - 2023. -
- Data Management Planning, Online, Ireland, 20 Jan 2023. -
- Applications of data science to cutting-edge - genomics technologies- Strand Sequencing - - Galway, Ireland, 06 Dec 2022. -
- Applications of data science to cutting-edge - genomics technologies- Single Cell Sequencing - Galway, Ireland, 05 Dec 2022. -
- Applications of data science to cutting-edge - genomics technologies- Synthetic Biology - Galway, Ireland, 01-02 Dec 2022. -
- Multiple Sequence Alignment and Molecular - Phylogenetics, Galway, Ireland Oct 2022. -
- IDPfun All Hands Meeting "Machine Learning and - Protein Structural Disorder" - , Dublin, Ireland, 30 Aug - 02 Sep 2022. -
-
-
+
+
+
+ Trainer +
+
+ Siobhán Cleary + +
+

+ Research Data Management
+ University College Dublin +

-
+
- -
-
-
-
-
- ELIXIR Ireland -
- Head of Node: Denis Shields -
- UCD Conway Institute of Biomolecular and Biomedical Research -
- University College Dublin, Dublin 4 -
- ☏: +353 7166735 -
-
+
+

Data Management Planning Resources and Training Material

+ + + + + + + + + + + + + +
TitleTrainerDateDownload
Research Data Management and Data Management PlanningLars JermiinFeb 2023 + PDF +
+

ELIXIR Tools for Data Management

+
+ + RDMkit + +
+

+ The Research Data Management kit (RDMkit) is a set of + guidelines for implementing good data management practices and making your data FAIR (Findable, + Accessible, Interoperable and Reusable). These best practice guidelines have been compiled by a network of + data managers and data stewards from the ELIXIR nodes across Europe. Please view + this pdf for our tips on using the RDMkit. +

-
-
- -
- - + +
+ + Data Stewardship Wizard + +
+

+ The Data Stewardship Wizard (DSW) is an online web tool designed by ELIXIR-CH to streamline the process + of creating a comprehensive data management plan (DMP). By employing a user-friendly question-based + format, the DSW guides you through a series of carefully crafted inquiries, ensuring that every + aspect of your data management plan is addressed while tailoring it to your specific needs. Once you provide + your answers, the DSW incorporates the information into a downloadable DMP document using a specified + template format. It allows multiple users to collaborate on a single document. The DSW proves + particularly advantageous to individuals new to the realm of DMP writing, as it alleviates uncertainties + regarding the detail required for each section. The DSW provides metrics which allow you to assess how + FAIR your DMP is. Click here + to be redirected to the online tool for writing DMPs. +

+
+
+
+ + Faircookbook + +
+

+ The FAIRCookbook provides step-by-step instructions, + best practices, and expert insights on implementing + FAIR data principles throughout the data lifecycle. It + covers a wide range of topics, including data + organization, metadata creation, data documentation, + data repository selection, data citation, and data + sharing protocols. +

+
+
+

+ *Click on the images to be redirected to the + tool's website. +

+ +
+

Upcoming Events

+

Currently no events scheduled.

+

+ Please get in contact with our + training coordinator + if you would like to participate in future training events + with ELIXIR Ireland. +

+

Past Events

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Bioconductor R analyses, Online, Global, 22-26 May 2023. +
+ Data Management Planning, Vienna, Austria, 25 Jan 2023. +
+ Data Management Planning, Online, Ireland, 20 Jan 2023. +
+ Applications of data science to cutting-edge genomics technologies- Strand Sequencing + Galway, Ireland, 06 Dec 2022. +
+ Applications of data science to cutting-edge genomics technologies- Single Cell Sequencing + Galway, Ireland, 05 Dec 2022. +
+ Applications of data science to cutting-edge genomics technologies- Synthetic Biology + Galway, Ireland, 01-02 Dec 2022. +
+ Multiple Sequence Alignment and Molecular Phylogenetics, Galway, Ireland Oct 2022. +
+ IDPfun All Hands Meeting "Machine Learning and Protein Structural Disorder" + , Dublin, Ireland, 30 Aug - 02 Sep 2022. +
+