diff --git a/.env b/.env new file mode 100644 index 00000000..5d9ddbd7 --- /dev/null +++ b/.env @@ -0,0 +1,3 @@ +LC_ALL: "C.UTF-8" +LANG: "en_US.UTF-8" +LANGUAGE: "en_US.UTF-8" diff --git a/.github/workflows/htmlproofer.yml b/.github/workflows/htmlproofer.yml new file mode 100644 index 00000000..d2b9ee5d --- /dev/null +++ b/.github/workflows/htmlproofer.yml @@ -0,0 +1,43 @@ +name: htmlproofer + +on: + push: + branches: + - htmlproofer + + workflow_dispatch: + inputs: + branchname: + description: 'Run htmlproofer on branch' + default: 'htmlproofer' + required: true + + +jobs: + htmlproofer1: + runs-on: ubuntu-latest + strategy: + fail-fast: false + steps: + - name: Checkout ${{ github.event.inputs.branchname }} + uses: actions/checkout@v2 + with: + ref: ${{ github.event.inputs.branchname }} + - name: Setup Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: '2.7' + - name: Build jekyll site + run: | + bundle install + bundle update github-pages + bundle exec jekyll build + + - name: Run HTMLProofer action + run: | + bundle exec htmlproofer --empty_alt_ignore --checks-to-ignore ImageCheck --only_4xx --url-ignore "https://fonts.gstatic.com,https://fonts.gstatic.com/,https://www.linkedin.com,https://github.com/jku-vds-lab/rubiks-cube-demonstrator,https://www.amd.com/en/support,https://support.amd.com/us/gpudownload/Pages/index.aspx,dx.doi.org/10.33313/380/218" --assume-extension ./_site + + #branding: + #icon: "check" + #color: "green" + diff --git a/.gitignore b/.gitignore index 6b51989f..d6db5823 100644 --- a/.gitignore +++ b/.gitignore @@ -10,6 +10,8 @@ css/site.css .jekyll-metadata _data/repos-expected.yml *.swp +workflow/ +workflow/* /Gemfile.lock # Ignoring Gemfile.lock is generally a mistake, but here the deployment that matters diff --git a/README.md b/README.md index ef397340..723b6c44 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ # JKU Visual Data Science Lab Website +[![htmlproofer](https://github.com/jku-vds-lab/jku-vds-lab.github.io/actions/workflows/htmlproofer.yml/badge.svg?branch=htmlproofer&event=push)](https://github.com/jku-vds-lab/jku-vds-lab.github.io/actions/workflows/htmlproofer.yml) The new Visual Data Science Lab Website built with [Jekyll](https://jekyllrb.com), [SASS](https://www.sass-lang.com), diff --git a/_layouts/release_caleydo.html b/_layouts/release_caleydo.html index 3319d7b3..f3bd86ba 100644 --- a/_layouts/release_caleydo.html +++ b/_layouts/release_caleydo.html @@ -206,7 +206,7 @@

Graphics Cards

graphics card better of the NVidia Geforce 8 series or better should be fine). Also make sure that you have the latest drivers installed. Download NVidia - or AMD + or AMD drivers.


@@ -230,4 +230,4 @@

Source Code

- \ No newline at end of file + diff --git a/_layouts/release_domino.html b/_layouts/release_domino.html index 50e93813..d785ba6e 100644 --- a/_layouts/release_domino.html +++ b/_layouts/release_domino.html @@ -203,7 +203,7 @@

Graphics Cards

graphics card better of the NVidia Geforce 8 series or better should be fine). Also make sure that you have the latest drivers installed. Download NVidia - or AMD + or AMD drivers.


@@ -227,4 +227,4 @@

Source Code

- \ No newline at end of file + diff --git a/_persons/kawan.md b/_persons/kawan.md index 98dfceeb..f9a2e38a 100644 --- a/_persons/kawan.md +++ b/_persons/kawan.md @@ -7,7 +7,6 @@ key: kawan permalink: /persons/kawan/ role: alumni # email: bikram.kawan@jku.at -# image: /assets/images/team_colored/placeholder.png organization: Johannes Kepler University Linz position: PhD Student website: diff --git a/_persons/schoefl.md b/_persons/schoefl.md index ef0e84aa..61cb4789 100644 --- a/_persons/schoefl.md +++ b/_persons/schoefl.md @@ -3,7 +3,6 @@ layout: team-member first_name: Moritz last_name: Heckmann title: "Moritz Heckmann" -# cg_website: "https://www.jku.at/en/institute-of-computer-graphics/about-us/team/moritz-schoefl/" #remove to show person directly on data-vis page key: heckmann permalink: /persons/heckmann/ role: undergrad @@ -13,4 +12,4 @@ organization: Johannes Kepler University Linz position: Technical Support website: --- -o \ No newline at end of file +o diff --git a/_publications/2013_infovis_lineup.md b/_publications/2013_infovis_lineup.md index 68578355..fc28fc4c 100644 --- a/_publications/2013_infovis_lineup.md +++ b/_publications/2013_infovis_lineup.md @@ -57,7 +57,7 @@ abstract: " In the examples and demos we have used three datasets: * [Times Higher Education 100 Under 50 University Ranking](https://www.timeshighereducation.co.uk/world-university-rankings/2012/one-hundred-under-fifty) -* [QS World University Ranking](https://www.iu.qs.com/university-rankings/world-university-rankings/) +* [QS World University Ranking](https://www.topuniversities.com/university-rankings) * [USDA National Nutrient Database](https://www.ars.usda.gov/ba/bhnrc/ndl) # Related Work diff --git a/_publications/2014_bmc_furby.md b/_publications/2014_bmc_furby.md index c7f6d8b1..47312bda 100644 --- a/_publications/2014_bmc_furby.md +++ b/_publications/2014_bmc_furby.md @@ -76,7 +76,7 @@ Datasets The following projects contain public demo data, which can be used to test Furby. But everyone is welcome to load his/her own data, via the `Load BiCluster Results` tab within the Caleydo Startup-Wizard. -*  [Caleydo-Project (CAL)]({{site.paper_content_url}}2014_bmc_furby_multi_tissue_fabia20.cal) containing Microarray data from Broad Institute "Cancer Program Data Sets" which was produced by [Su et al. 2002](https://www.broadinstitute.org/cgi-bin/cancer/datasets.cgi). It consists of 102 samples and 5565 genes as was clustered using the FABIA algorithm. +*  [Caleydo-Project (CAL)]({{site.paper_content_url}}2014_bmc_furby_multi_tissue_fabia20.cal) containing Microarray data from Broad Institute "Cancer Program Data Sets" which was produced by [Su et al. 2002](https://www.broadinstitute.org/cancer/cancer-program-scientific-tools-and-resources). It consists of 102 samples and 5565 genes as was clustered using the FABIA algorithm. *  [Zip package (ZIP)]({{site.paper_content_url}}2014_bmc_furby_multi_tissue_fabia20.zip) containing the exported CSV-files using to create the previous Caleydo-Project Utilities @@ -84,4 +84,4 @@ Utilities We provide two helper R-Scripts, which simplify exporting R bicluster results in the correct format. *  [R-Script]({{site.paper_content_url}}2014_bmc_furby_export_fabia.R) for exporting FABIA results, generated via the [fabia](https://www.bioconductor.org/packages/2.12/bioc/html/fabia.html) bioconductor package. -*  [R-Script]({{site.paper_content_url}}2014_bmc_furby_export_biclust.R) for exporting result from the [biclust](https://cran.r-project.org/web/packages/biclust/index.html) CRAN package. \ No newline at end of file +*  [R-Script]({{site.paper_content_url}}2014_bmc_furby_export_biclust.R) for exporting result from the [biclust](https://cran.r-project.org/web/packages/biclust/index.html) CRAN package. diff --git a/_publications/2019_eurova_rubik.md b/_publications/2019_eurova_rubik.md index ba06e752..5c655901 100644 --- a/_publications/2019_eurova_rubik.md +++ b/_publications/2019_eurova_rubik.md @@ -81,7 +81,7 @@ supplements: # linksym: true # Link to the repository where the code is hosted -code: https://github.com/JKU-ICG/rubiks-cube-demonstrator +code: https://github.com/jku-vds-lab/rubiks-cube-demonstrator abstract: " diff --git a/_publications/2020_imimic_projective-latent-space-deculttering.md b/_publications/2020_imimic_projective-latent-space-deculttering.md index 41e865b9..bf4022e6 100644 --- a/_publications/2020_imimic_projective-latent-space-deculttering.md +++ b/_publications/2020_imimic_projective-latent-space-deculttering.md @@ -33,7 +33,7 @@ bib: editor: Cardoso, Jaime and others series: Lecture Notes in Computer Science doi: 10.1007/978-3-030-61166-8_2 - url: + url: https://link.springer.com/chapter/10.1007%2F978-3-030-61166-8_2 volume: 12446 number: pages: 13--22 diff --git a/_publications/2021_forecasting_model_sinter.md b/_publications/2021_forecasting_model_sinter.md index fe7308e2..0df72128 100644 --- a/_publications/2021_forecasting_model_sinter.md +++ b/_publications/2021_forecasting_model_sinter.md @@ -15,7 +15,7 @@ abstract: "Sintering is a complex production process where the process stability # set this url, if your paper is on another server; defaults to data.jku-vds-lab.at -paper_content_url: https://www.scopus.com/record/display.uri?eid=2-s2.0-85092267170&origin=inward&txGid=5f94bfde7a78639aa60327d0e70e1a23 +paper_content_url: https://dx.doi.org/10.33313/380/218 # uncomment the "hide" property, if you do not want the publication to be displayed on the website (usually you don't need this) # hide: True # uncomment the "hide" property, if you only want the publication to be displayed on your personal page (i.e. publications where you contributed, but does not have anything to do with the Vis Group e.g. Master Thesis,...) @@ -67,7 +67,7 @@ bib: pages: month: -preprint: https://www.scopus.com/record/display.uri?eid=2-s2.0-85092267170&origin=inward&txGid=5f94bfde7a78639aa60327d0e70e1a23 # here you can put the preprint link (arxiv.org, osf.io,...) e.g. https://arxiv.org/abs/1910.00969 +preprint: http://digital.library.aist.org/pages/PR-380-218.htm # here you can put the preprint link (arxiv.org, osf.io,...) e.g. https://arxiv.org/abs/1910.00969 # Add things like "Best Paper Award at InfoVis 2099, selected out of 4000 submissions" @@ -104,4 +104,4 @@ code: --- # Acknowledgements -This work has partially been supported by the FFG, Contract No. 854184: “Pro2Future is funded within the Austrian COMET Program Competence Centers for Excellent Technologies under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry for Digital and Economic Affairs and of the Provinces of Upper Austria and Styria. COMET is managed by the Austrian Research Promotion Agency FFG.” \ No newline at end of file +This work has partially been supported by the FFG, Contract No. 854184: “Pro2Future is funded within the Austrian COMET Program Competence Centers for Excellent Technologies under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry for Digital and Economic Affairs and of the Provinces of Upper Austria and Styria. COMET is managed by the Austrian Research Promotion Agency FFG.” diff --git a/_publications/2021_preprint_dashboard_onboarding.md b/_publications/2021_preprint_dashboard_onboarding.md index 7ab34194..e71b8137 100644 --- a/_publications/2021_preprint_dashboard_onboarding.md +++ b/_publications/2021_preprint_dashboard_onboarding.md @@ -52,7 +52,7 @@ non_group_project: False project: # Use this if you have an external project website -external-project: +external-project: https://osf.io/zsb5a/ # The reference to the video entry video: @@ -62,7 +62,7 @@ video: # the prerint pdf: 2021_preprint_dashboard-onboarding.pdf # A supplement PDF -supplement: https://osf.io/zsb5a/ +supplement: # Extra supplements, such as talk slides, data sets, etc. supplements: diff --git a/_publications/2021_tvcg_fuzzy-spreadsheets.md b/_publications/2021_tvcg_fuzzy-spreadsheets.md index 447ce498..b4f3d0c5 100644 --- a/_publications/2021_tvcg_fuzzy-spreadsheets.md +++ b/_publications/2021_tvcg_fuzzy-spreadsheets.md @@ -60,15 +60,15 @@ video: 2021_fuzzy-spreadsheets_video # the prerint pdf: 2020_preprint_fuzzy-spreadsheets.pdf # A supplement PDF -supplement: https://osf.io/8ypux/ +supplement: # Extra supplements, such as talk slides, data sets, etc. supplements: -#- name: General UpSet +- name: Fuzzy Spreadsheet # # use link instead of abslink if you want to link to the master directory -# abslink: http://vials.io/talk/ + abslink: https://osf.io/8ypux/ # # defaults to a download icon, use this if you want a link-out icon -# linksym: true + linksym: true # Link to the repository where the code is hostet code: https://github.com/jku-vds-lab/fuzzy-spreadsheet diff --git a/acknowledgements.md b/acknowledgements.md index da9e664f..d0de9cb9 100644 --- a/acknowledgements.md +++ b/acknowledgements.md @@ -18,7 +18,7 @@ Visual Data Science Lab makes use of a range of open source tools, bioinformatic # Bioinformatics Resources -* [David Bioinformatics Resources](http://david.abcc.ncifcrf.gov/) - Gene ID mapping. +* [David Bioinformatics Resources](https://david.ncifcrf.gov/) - Gene ID mapping. * [KEGG](http://www.genome.jp/kegg/pathway.html) - Pathways. * [WikiPathways](https://www.wikipathways.org/index.php/WikiPathways) - Pathways. diff --git a/apps/embedding-structure-explorer/index.html b/apps/embedding-structure-explorer/index.html index de9f07d2..5e9dbbc1 100644 --- a/apps/embedding-structure-explorer/index.html +++ b/apps/embedding-structure-explorer/index.html @@ -7,7 +7,7 @@ - + @@ -64,4 +64,4 @@ - \ No newline at end of file + diff --git a/assets/papers/2021_preprint_dashboard-onboarding.pdf b/assets/papers/2021_preprint_dashboard-onboarding.pdf new file mode 100644 index 00000000..b3dcc147 Binary files /dev/null and b/assets/papers/2021_preprint_dashboard-onboarding.pdf differ diff --git a/former-caleydo/_posts/2014-07-26-vis-papers.md b/former-caleydo/_posts/2014-07-26-vis-papers.md index 9b1bcdc3..03c55538 100644 --- a/former-caleydo/_posts/2014-07-26-vis-papers.md +++ b/former-caleydo/_posts/2014-07-26-vis-papers.md @@ -4,4 +4,4 @@ title: Two new Caleydo papers at IEEE VIS 2014 date: 2014-07-26 20:00:00 categories: event --- -Two papers about new Caleydo projects have ben accepted at the premier conference for visualization, IEEE VIS. Domino is a new technique to visualize dataset slices and create advanced, customized visualization techniques. Contour allows analysts to explore multi-relational datasets to understand, for example, the interdependencies between drug candidates, phenotypic effects and pathways. Both papers will be presented by Caleydo team members in November in Paris. \ No newline at end of file +Two papers about new Caleydo projects have ben accepted at the premier conference for visualization, IEEE VIS. Domino is a new technique to visualize dataset slices and create advanced, customized visualization techniques. Contour allows analysts to explore multi-relational datasets to understand, for example, the interdependencies between drug candidates, phenotypic effects and pathways. Both papers will be presented by Caleydo team members in November in Paris. diff --git a/former-caleydo/_posts/2015-04-22-open_phd_position_JKU.markdown b/former-caleydo/_posts/2015-04-22-open_phd_position_JKU.markdown deleted file mode 100644 index d03e253f..00000000 --- a/former-caleydo/_posts/2015-04-22-open_phd_position_JKU.markdown +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Open Research Assistant Position @ JKU Linz -date: 2015-04-22 20:00:00 -categories: event ---- -Interested in doing a PhD in the Caleydo project? We have an open Research Assistant position in the field of Information Visualization / Visual Analytics at the Johannes Kepler University Linz, Austria. Find more information in the detailed job announcement. diff --git a/former-caleydo/_posts/2015-06-19-open_positions_utah.md b/former-caleydo/_posts/2015-06-19-open_positions_utah.md deleted file mode 100644 index 69a7d44d..00000000 --- a/former-caleydo/_posts/2015-06-19-open_positions_utah.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Open PostDoc and PhD Student Position @ University of Utah -date: 2015-06-19 20:00:00 -categories: event ---- -We are seeking a **postdoctoral fellow** and **multiple PhD students** to join the Caleydo team at the University of Utah. For the postdoctoral position, please refer to [this announcement](http://www.sci.utah.edu/75-sci-opportunities/post-doc/536-post-doc-lex.html). If you are interested in the University of Utah PhD program, please get in touch with Alexander Lex at [alex@sci.utah.edu](mailto:alex@sci.utah.edu). \ No newline at end of file diff --git a/former-caleydo/_posts/2016-03-01-open_positions_harvard.md b/former-caleydo/_posts/2016-03-01-open_positions_harvard.md deleted file mode 100644 index 72cde978..00000000 --- a/former-caleydo/_posts/2016-03-01-open_positions_harvard.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -layout: post -title: Postdoc and software developer postions at Harvard Medical School -date: 2016-03-01 10:00:00 -categories: event ---- -The [Gehlenborg Lab](http://gehlenborglab.org) in the [Department of Biomedical Informatics at Harvard Medical School](https://dbmi.hms.harvard.edu) is seeking [postdoctoral fellows](https://dbmi.hms.harvard.edu/careers/postdoctoral-fellows/gehlenborg-lab) and [software developers](https://dbmi.hms.harvard.edu/careers/software-engineers/visualization-software-developer) to work on exciting problems in data science, visualization of biomedical data, and reproducible research. Please apply directly or get in touch with [Nils Gehlenborg](mailto:nils@hms.harvard.edu) if you are interested. \ No newline at end of file diff --git a/htmlproofer.event b/htmlproofer.event new file mode 100644 index 00000000..7b3ee86f --- /dev/null +++ b/htmlproofer.event @@ -0,0 +1,6 @@ +{ + "action": "push", + "inputs": { + "branchname": "htmlproofer" + } +} diff --git a/templates/person-template.md b/templates/person-template.md index 818ea6d1..71057ecd 100644 --- a/templates/person-template.md +++ b/templates/person-template.md @@ -16,7 +16,7 @@ key: doe # this should be your lastname in lower case; the key is important for role: raPhD email: john.doe@jku.at # this is your work e-mail address -image: /assets/images/team_colored/doe.jpg # insert the relative link to your profile image +# image: /assets/images/team_colored/doe.jpg # insert the relative link to your profile image organization: Johannes Kepler University Linz # usually you leave this unchanged, but if your have a different organization, feel free to change the property position: Project Assistant # This is the position that you have within your organization. e.g. "Project Assistant", "University Assistant", "Technical Support", "Student Research" (or whatever Marc tells you^^) #### @@ -66,4 +66,4 @@ website: #### --- -Write some Text about yourself \ No newline at end of file +Write some Text about yourself