Major docs restructure (#229)

* fix broken links * fix broken links * relink developer quickstart guide * update TOPPView intensity mode description * update tutorials * remove duplicated tutorial * reordered sections * download fix * major restructure * fixed installation cross ref * updated knime tutorial references * fixed warnings * fixed download link * fixed links * fixed links --------- Co-authored-by: Samuel Wein <[email protected]>
OpenMS · Apr 15, 2024 · 99c9232 · 99c9232
1 parent 8f1c156
commit 99c9232
Show file tree

Hide file tree

Showing 268 changed files with 4,048 additions and 2,133 deletions.
diff --git a/...mages/additional-resources/click-fork.png → ...mages/additional-resources/click-fork.png b/...mages/additional-resources/click-fork.png → ...mages/additional-resources/click-fork.png
diff --git a/...rces/Existing-Projects-into-Workspace.png → ...rces/Existing-Projects-into-Workspace.png b/...rces/Existing-Projects-into-Workspace.png → ...rces/Existing-Projects-into-Workspace.png
diff --git a/...advanced-resources/KNIME-Build-System.png → ...advanced-resources/KNIME-Build-System.png b/...advanced-resources/KNIME-Build-System.png → ...advanced-resources/KNIME-Build-System.png
diff --git a/...d-resources/KNIME-Desktop-Update-Site.png → ...d-resources/KNIME-Desktop-Update-Site.png b/...d-resources/KNIME-Desktop-Update-Site.png → ...d-resources/KNIME-Desktop-Update-Site.png
diff --git a/...d-resources/KNIME-File-Handling-Nodes.png → ...d-resources/KNIME-File-Handling-Nodes.png b/...d-resources/KNIME-File-Handling-Nodes.png → ...d-resources/KNIME-File-Handling-Nodes.png
diff --git a/...dvanced-resources/eclipse-application.png → ...dvanced-resources/eclipse-application.png b/...dvanced-resources/eclipse-application.png → ...dvanced-resources/eclipse-application.png
diff --git a/.../advanced-resources/new-configuration.png → .../advanced-resources/new-configuration.png b/.../advanced-resources/new-configuration.png → .../advanced-resources/new-configuration.png
diff --git a/...anced-resources/select-root-directory.png → ...anced-resources/select-root-directory.png b/...anced-resources/select-root-directory.png → ...anced-resources/select-root-directory.png
diff --git a/docs/images/installations/Windows_logo.svg → docs/_images/installations/Windows_logo.svg b/docs/images/installations/Windows_logo.svg → docs/_images/installations/Windows_logo.svg
diff --git a/docs/images/installations/linux_logo.svg → docs/_images/installations/linux_logo.svg b/docs/images/installations/linux_logo.svg → docs/_images/installations/linux_logo.svg
diff --git a/...lations/macos/copying-to-applications.png → ...lations/macos/copying-to-applications.png b/...lations/macos/copying-to-applications.png → ...lations/macos/copying-to-applications.png
diff --git a/...nstallations/macos/license-agreements.png → ...nstallations/macos/license-agreements.png b/...nstallations/macos/license-agreements.png → ...nstallations/macos/license-agreements.png
diff --git a/...ons/macos/move-openms-to-applications.png → ...ons/macos/move-openms-to-applications.png b/...ons/macos/move-openms-to-applications.png → ...ons/macos/move-openms-to-applications.png
diff --git a/...lations/macos/opening-openms2-8-macos.png → ...lations/macos/opening-openms2-8-macos.png b/...lations/macos/opening-openms2-8-macos.png → ...lations/macos/opening-openms2-8-macos.png
diff --git a/...cos/preparing-to-copy-to-applications.png → ...cos/preparing-to-copy-to-applications.png b/...cos/preparing-to-copy-to-applications.png → ...cos/preparing-to-copy-to-applications.png
diff --git a/...tions/macos/verifying-openms2-8-macos.png → ...tions/macos/verifying-openms2-8-macos.png b/...tions/macos/verifying-openms2-8-macos.png → ...tions/macos/verifying-openms2-8-macos.png
diff --git a/docs/images/installations/macos_logo.svg → docs/_images/installations/macos_logo.svg b/docs/images/installations/macos_logo.svg → docs/_images/installations/macos_logo.svg
diff --git a/.../images/installations/win/smartscreen.gif → ..._images/installations/win/smartscreen.gif b/.../images/installations/win/smartscreen.gif → ..._images/installations/win/smartscreen.gif
diff --git a/...es/introduction/250px-KNIMELogoTM.svg.png → ...es/introduction/250px-KNIMELogoTM.svg.png b/...es/introduction/250px-KNIMELogoTM.svg.png → ...es/introduction/250px-KNIMELogoTM.svg.png
diff --git a/docs/images/introduction/KNIMELogoTM.svg → docs/_images/introduction/KNIMELogoTM.svg b/docs/images/introduction/KNIMELogoTM.svg → docs/_images/introduction/KNIMELogoTM.svg
diff --git a/...images/introduction/KNIMELogoTM_white.svg → ...images/introduction/KNIMELogoTM_white.svg b/...images/introduction/KNIMELogoTM_white.svg → ...images/introduction/KNIMELogoTM_white.svg
diff --git a/docs/images/introduction/MALDI.png → docs/_images/introduction/MALDI.png b/docs/images/introduction/MALDI.png → docs/_images/introduction/MALDI.png
diff --git a/docs/images/introduction/TOF.png → docs/_images/introduction/TOF.png b/docs/images/introduction/TOF.png → docs/_images/introduction/TOF.png
diff --git a/.../images/introduction/TOPPAS_logo_dark.png → ..._images/introduction/TOPPAS_logo_dark.png b/.../images/introduction/TOPPAS_logo_dark.png → ..._images/introduction/TOPPAS_logo_dark.png
diff --git a/...images/introduction/TOPPAS_logo_white.png → ...images/introduction/TOPPAS_logo_white.png b/...images/introduction/TOPPAS_logo_white.png → ...images/introduction/TOPPAS_logo_white.png
diff --git a/.../introduction/electrospray-ionization.png → .../introduction/electrospray-ionization.png b/.../introduction/electrospray-ionization.png → .../introduction/electrospray-ionization.png
diff --git a/...ion/galaxy_logo_25percent_transparent.png → ...ion/galaxy_logo_25percent_transparent.png b/...ion/galaxy_logo_25percent_transparent.png → ...ion/galaxy_logo_25percent_transparent.png
diff --git a/...ages/introduction/galaxy_project_logo.png → ...ages/introduction/galaxy_project_logo.png b/...ages/introduction/galaxy_project_logo.png → ...ages/introduction/galaxy_project_logo.png
diff --git a/...troduction/galaxy_project_logo_square.png → ...troduction/galaxy_project_logo_square.png b/...troduction/galaxy_project_logo_square.png → ...troduction/galaxy_project_logo_square.png
diff --git a/...ntroduction/galaxy_project_logo_white.png → ...ntroduction/galaxy_project_logo_white.png b/...ntroduction/galaxy_project_logo_white.png → ...ntroduction/galaxy_project_logo_white.png
diff --git a/...oduction/hplc-mass-spectrometry-setup.png → ...oduction/hplc-mass-spectrometry-setup.png b/...oduction/hplc-mass-spectrometry-setup.png → ...oduction/hplc-mass-spectrometry-setup.png
diff --git a/docs/images/introduction/introduction_LC.png → .../_images/introduction/introduction_LC.png b/docs/images/introduction/introduction_LC.png → .../_images/introduction/introduction_LC.png
diff --git a/docs/images/introduction/introduction_MS.png → .../_images/introduction/introduction_MS.png b/docs/images/introduction/introduction_MS.png → .../_images/introduction/introduction_MS.png
diff --git a/docs/images/introduction/knime.png → docs/_images/introduction/knime.png b/docs/images/introduction/knime.png → docs/_images/introduction/knime.png
diff --git a/docs/images/introduction/knime_dark.png → docs/_images/introduction/knime_dark.png b/docs/images/introduction/knime_dark.png → docs/_images/introduction/knime_dark.png
diff --git a/docs/images/introduction/lc-components.png → docs/_images/introduction/lc-components.png b/docs/images/introduction/lc-components.png → docs/_images/introduction/lc-components.png
diff --git a/docs/images/introduction/lc-ms-setup.png → docs/_images/introduction/lc-ms-setup.png b/docs/images/introduction/lc-ms-setup.png → docs/_images/introduction/lc-ms-setup.png
diff --git a/...oduction/mass-spectrometry-components.png → ...oduction/mass-spectrometry-components.png b/...oduction/mass-spectrometry-components.png → ...oduction/mass-spectrometry-components.png
diff --git a/...ntroduction/nextflow2014_no-bg-bright.png → ...ntroduction/nextflow2014_no-bg-bright.png b/...ntroduction/nextflow2014_no-bg-bright.png → ...ntroduction/nextflow2014_no-bg-bright.png
diff --git a/...mages/introduction/nextflow2014_no-bg.png → ...mages/introduction/nextflow2014_no-bg.png b/...mages/introduction/nextflow2014_no-bg.png → ...mages/introduction/nextflow2014_no-bg.png
diff --git a/...ages/introduction/openms-architecture.png → ...ages/introduction/openms-architecture.png b/...ages/introduction/openms-architecture.png → ...ages/introduction/openms-architecture.png
diff --git a/docs/_images/introduction/openms-overview.jpg b/docs/_images/introduction/openms-overview.jpg
diff --git a/docs/images/introduction/orbitrap.png → docs/_images/introduction/orbitrap.png b/docs/images/introduction/orbitrap.png → docs/_images/introduction/orbitrap.png
diff --git a/...ages/introduction/quadrupole-analyzer.png → ...ages/introduction/quadrupole-analyzer.png b/...ages/introduction/quadrupole-analyzer.png → ...ages/introduction/quadrupole-analyzer.png
diff --git a/.../images/introduction/spectrum_peakmap.png → ..._images/introduction/spectrum_peakmap.png b/.../images/introduction/spectrum_peakmap.png → ..._images/introduction/spectrum_peakmap.png
diff --git a/...nms-user-tutorial/introduction/3dview.png → ...nms-user-tutorial/introduction/3dview.png b/...nms-user-tutorial/introduction/3dview.png → ...nms-user-tutorial/introduction/3dview.png
diff --git a/.../introduction/KNIME_switch_to_classic.png → .../introduction/KNIME_switch_to_classic.png b/.../introduction/KNIME_switch_to_classic.png → .../introduction/KNIME_switch_to_classic.png
diff --git a/...s-user-tutorial/introduction/TOPPView.png → ...s-user-tutorial/introduction/TOPPView.png b/...s-user-tutorial/introduction/TOPPView.png → ...s-user-tutorial/introduction/TOPPView.png
diff --git a/...utorial/introduction/ms2_introduction.png → ...utorial/introduction/ms2_introduction.png b/...utorial/introduction/ms2_introduction.png → ...utorial/introduction/ms2_introduction.png
diff --git a/...torial/introduction/profilecentroided.png → ...torial/introduction/profilecentroided.png b/...torial/introduction/profilecentroided.png → ...torial/introduction/profilecentroided.png
diff --git a/...er-tutorial/introduction/proteowizard.png → ...er-tutorial/introduction/proteowizard.png b/...er-tutorial/introduction/proteowizard.png → ...er-tutorial/introduction/proteowizard.png
diff --git a/...sobaric/isobaric_experimental_design.jpeg → ...sobaric/isobaric_experimental_design.jpeg b/...sobaric/isobaric_experimental_design.jpeg → ...sobaric/isobaric_experimental_design.jpeg
diff --git a/...al/isobaric/isobaric_img_output_knime.png → ...al/isobaric/isobaric_img_output_knime.png b/...al/isobaric/isobaric_img_output_knime.png → ...al/isobaric/isobaric_img_output_knime.png
diff --git a/...torial/isobaric/isobaric_inference_wf.png → ...torial/isobaric/isobaric_inference_wf.png b/...torial/isobaric/isobaric_inference_wf.png → ...torial/isobaric/isobaric_inference_wf.png
diff --git a/...orial/isobaric/isobaric_msstatstmt_wf.png → ...orial/isobaric/isobaric_msstatstmt_wf.png b/...orial/isobaric/isobaric_msstatstmt_wf.png → ...orial/isobaric/isobaric_msstatstmt_wf.png
diff --git a/...nime-setup/KNIME_annotated_FileFilter.png → ...nime-setup/KNIME_annotated_FileFilter.png b/...nime-setup/KNIME_annotated_FileFilter.png → ...nime-setup/KNIME_annotated_FileFilter.png
diff --git a/...e-setup/Minimal_RawFileConverter_Loop.png → ...e-setup/Minimal_RawFileConverter_Loop.png b/...e-setup/Minimal_RawFileConverter_Loop.png → ...e-setup/Minimal_RawFileConverter_Loop.png
diff --git a/...e-setup/Minimal_RawFileConverter_Loop.svg → ...e-setup/Minimal_RawFileConverter_Loop.svg b/...e-setup/Minimal_RawFileConverter_Loop.svg → ...e-setup/Minimal_RawFileConverter_Loop.svg
diff --git a/...al/knime-setup/knime_configure_dialog.png → ...al/knime-setup/knime_configure_dialog.png b/...al/knime-setup/knime_configure_dialog.png → ...al/knime-setup/knime_configure_dialog.png
diff --git a/...al/knime-setup/knime_workbench_marked.png → ...al/knime-setup/knime_workbench_marked.png b/...al/knime-setup/knime_workbench_marked.png → ...al/knime-setup/knime_workbench_marked.png
diff --git a/...tutorial/knime-setup/minimal_FileInfo.png → ...tutorial/knime-setup/minimal_FileInfo.png b/...tutorial/knime-setup/minimal_FileInfo.png → ...tutorial/knime-setup/minimal_FileInfo.png
diff --git a/...tutorial/knime-setup/minimal_FileInfo.svg → ...tutorial/knime-setup/minimal_FileInfo.svg b/...tutorial/knime-setup/minimal_FileInfo.svg → ...tutorial/knime-setup/minimal_FileInfo.svg
diff --git a/...penms-user-tutorial/labelfree/MSstats.png → ...penms-user-tutorial/labelfree/MSstats.png b/...penms-user-tutorial/labelfree/MSstats.png → ...penms-user-tutorial/labelfree/MSstats.png
diff --git a/...ser-tutorial/labelfree/PepConsensusId.png → ...ser-tutorial/labelfree/PepConsensusId.png b/...ser-tutorial/labelfree/PepConsensusId.png → ...ser-tutorial/labelfree/PepConsensusId.png
diff --git a/...enms-user-tutorial/labelfree/PepIdFDR.png → ...enms-user-tutorial/labelfree/PepIdFDR.png b/...enms-user-tutorial/labelfree/PepIdFDR.png → ...enms-user-tutorial/labelfree/PepIdFDR.png
diff --git a/...ms-user-tutorial/labelfree/PepQuantId.png → ...ms-user-tutorial/labelfree/PepQuantId.png b/...ms-user-tutorial/labelfree/PepQuantId.png → ...ms-user-tutorial/labelfree/PepQuantId.png
diff --git a/...-tutorial/labelfree/PepQuantIdNoAlign.png → ...-tutorial/labelfree/PepQuantIdNoAlign.png b/...-tutorial/labelfree/PepQuantIdNoAlign.png → ...-tutorial/labelfree/PepQuantIdNoAlign.png
diff --git a/...openms-user-tutorial/labelfree/c2_c1-.png → ...openms-user-tutorial/labelfree/c2_c1-.png b/...openms-user-tutorial/labelfree/c2_c1-.png → ...openms-user-tutorial/labelfree/c2_c1-.png
diff --git a/...openms-user-tutorial/labelfree/c3_c2-.png → ...openms-user-tutorial/labelfree/c3_c2-.png b/...openms-user-tutorial/labelfree/c3_c2-.png → ...openms-user-tutorial/labelfree/c3_c2-.png
diff --git a/...user-tutorial/labelfree/data_analysis.png → ...user-tutorial/labelfree/data_analysis.png b/...user-tutorial/labelfree/data_analysis.png → ...user-tutorial/labelfree/data_analysis.png
diff --git a/...ms-user-tutorial/labelfree/featureXML.png → ...ms-user-tutorial/labelfree/featureXML.png b/...ms-user-tutorial/labelfree/featureXML.png → ...ms-user-tutorial/labelfree/featureXML.png
diff --git a/...-tutorial/labelfree/handout-clean129x.svg → ...-tutorial/labelfree/handout-clean129x.svg b/...-tutorial/labelfree/handout-clean129x.svg → ...-tutorial/labelfree/handout-clean129x.svg
diff --git a/...enms-user-tutorial/labelfree/iPRG_lfq.png → ...enms-user-tutorial/labelfree/iPRG_lfq.png b/...enms-user-tutorial/labelfree/iPRG_lfq.png → ...enms-user-tutorial/labelfree/iPRG_lfq.png
diff --git a/...-user-tutorial/labelfree/iPRG_lfq_old.png → ...-user-tutorial/labelfree/iPRG_lfq_old.png b/...-user-tutorial/labelfree/iPRG_lfq_old.png → ...-user-tutorial/labelfree/iPRG_lfq_old.png
diff --git a/...ser-tutorial/metabo/KNIME_SMILES_type.png → ...ser-tutorial/metabo/KNIME_SMILES_type.png b/...ser-tutorial/metabo/KNIME_SMILES_type.png → ...ser-tutorial/metabo/KNIME_SMILES_type.png
diff --git a/...penms-user-tutorial/metabo/ToppView_1.png → ...penms-user-tutorial/metabo/ToppView_1.png b/...penms-user-tutorial/metabo/ToppView_1.png → ...penms-user-tutorial/metabo/ToppView_1.png
diff --git a/...penms-user-tutorial/metabo/ToppView_2.png → ...penms-user-tutorial/metabo/ToppView_2.png b/...penms-user-tutorial/metabo/ToppView_2.png → ...penms-user-tutorial/metabo/ToppView_2.png
diff --git a/...penms-user-tutorial/metabo/ToppView_3.png → ...penms-user-tutorial/metabo/ToppView_3.png b/...penms-user-tutorial/metabo/ToppView_3.png → ...penms-user-tutorial/metabo/ToppView_3.png
diff --git a/...penms-user-tutorial/metabo/ToppView_4.png → ...penms-user-tutorial/metabo/ToppView_4.png b/...penms-user-tutorial/metabo/ToppView_4.png → ...penms-user-tutorial/metabo/ToppView_4.png
diff --git a/...penms-user-tutorial/metabo/ToppView_5.png → ...penms-user-tutorial/metabo/ToppView_5.png b/...penms-user-tutorial/metabo/ToppView_5.png → ...penms-user-tutorial/metabo/ToppView_5.png
diff --git a/...ges/openms-user-tutorial/metabo/align.png → ...ges/openms-user-tutorial/metabo/align.png b/...ges/openms-user-tutorial/metabo/align.png → ...ges/openms-user-tutorial/metabo/align.png
diff --git a/.../openms-user-tutorial/metabo/denovoid.png → .../openms-user-tutorial/metabo/denovoid.png b/.../openms-user-tutorial/metabo/denovoid.png → .../openms-user-tutorial/metabo/denovoid.png
diff --git a/...ser-tutorial/metabo/glutathioneMetlin.png → ...ser-tutorial/metabo/glutathioneMetlin.png b/...ser-tutorial/metabo/glutathioneMetlin.png → ...ser-tutorial/metabo/glutathioneMetlin.png
diff --git a/...ms-user-tutorial/metabo/glutathioneTV.png → ...ms-user-tutorial/metabo/glutathioneTV.png b/...ms-user-tutorial/metabo/glutathioneTV.png → ...ms-user-tutorial/metabo/glutathioneTV.png
diff --git a/...ages/openms-user-tutorial/metabo/link.png → ...ages/openms-user-tutorial/metabo/link.png b/...ages/openms-user-tutorial/metabo/link.png → ...ages/openms-user-tutorial/metabo/link.png
diff --git a/...mages/openms-user-tutorial/metabo/mad.png → ...mages/openms-user-tutorial/metabo/mad.png b/...mages/openms-user-tutorial/metabo/mad.png → ...mages/openms-user-tutorial/metabo/mad.png
diff --git a/...orial/metabo/metabo_part1_with_labels.png → ...orial/metabo/metabo_part1_with_labels.png b/...orial/metabo/metabo_part1_with_labels.png → ...orial/metabo/metabo_part1_with_labels.png
diff --git a/...nms-user-tutorial/metabo/metabo_part2.png → ...nms-user-tutorial/metabo/metabo_part2.png b/...nms-user-tutorial/metabo/metabo_part2.png → ...nms-user-tutorial/metabo/metabo_part2.png
diff --git a/...nms-user-tutorial/metabo/metabo_part3.png → ...nms-user-tutorial/metabo/metabo_part3.png b/...nms-user-tutorial/metabo/metabo_part3.png → ...nms-user-tutorial/metabo/metabo_part3.png
diff --git a/...s-user-tutorial/metabo/minimal_FFM_wf.png → ...s-user-tutorial/metabo/minimal_FFM_wf.png b/...s-user-tutorial/metabo/minimal_FFM_wf.png → ...s-user-tutorial/metabo/minimal_FFM_wf.png
diff --git a/...openms-user-tutorial/metabo/reporting.png → ...openms-user-tutorial/metabo/reporting.png b/...openms-user-tutorial/metabo/reporting.png → ...openms-user-tutorial/metabo/reporting.png
diff --git a/...s/openms-user-tutorial/metabo/speclib.png → ...s/openms-user-tutorial/metabo/speclib.png b/...s/openms-user-tutorial/metabo/speclib.png → ...s/openms-user-tutorial/metabo/speclib.png
diff --git a/...rial/metabo/structures_filter_results.png → ...rial/metabo/structures_filter_results.png b/...rial/metabo/structures_filter_results.png → ...rial/metabo/structures_filter_results.png
diff --git a/...ial/metabo/structures_filter_workflow.png → ...ial/metabo/structures_filter_workflow.png b/...ial/metabo/structures_filter_workflow.png → ...ial/metabo/structures_filter_workflow.png
diff --git a/...s-user-tutorial/openswath/OpenSWATHWF.png → ...s-user-tutorial/openswath/OpenSWATHWF.png b/...s-user-tutorial/openswath/OpenSWATHWF.png → ...s-user-tutorial/openswath/OpenSWATHWF.png
diff --git a/...al/openswath/assay_library_generation.png → ...al/openswath/assay_library_generation.png b/...al/openswath/assay_library_generation.png → ...al/openswath/assay_library_generation.png
diff --git a/...r-tutorial/openswath/decoy_generation.png → ...r-tutorial/openswath/decoy_generation.png b/...r-tutorial/openswath/decoy_generation.png → ...r-tutorial/openswath/decoy_generation.png
diff --git a/...er-tutorial/openswath/oswm_example_wf.png → ...er-tutorial/openswath/oswm_example_wf.png b/...er-tutorial/openswath/oswm_example_wf.png → ...er-tutorial/openswath/oswm_example_wf.png
diff --git a/...-tutorial/openswath/pipeline_overview.png → ...-tutorial/openswath/pipeline_overview.png b/...-tutorial/openswath/pipeline_overview.png → ...-tutorial/openswath/pipeline_overview.png
diff --git a/.../protein-inference/inference_metanode.png → .../protein-inference/inference_metanode.png b/.../protein-inference/inference_metanode.png → .../protein-inference/inference_metanode.png
diff --git a/...tutorial/protein-inference/proteinFDR.png → ...tutorial/protein-inference/proteinFDR.png b/...tutorial/protein-inference/proteinFDR.png → ...tutorial/protein-inference/proteinFDR.png
diff --git a/...ser-tutorial/quality-control/qc_basic.png → ...ser-tutorial/quality-control/qc_basic.png b/...ser-tutorial/quality-control/qc_basic.png → ...ser-tutorial/quality-control/qc_basic.png
diff --git a/...ser-tutorial/quality-control/qc_extra.png → ...ser-tutorial/quality-control/qc_extra.png b/...ser-tutorial/quality-control/qc_extra.png → ...ser-tutorial/quality-control/qc_extra.png
diff --git a/...-user-tutorial/quality-control/qc_set.png → ...-user-tutorial/quality-control/qc_set.png b/...-user-tutorial/quality-control/qc_set.png → ...-user-tutorial/quality-control/qc_set.png
diff --git a/...s/research/whitepapers/design-summary.png → ...s/research/whitepapers/design-summary.png b/...s/research/whitepapers/design-summary.png → ...s/research/whitepapers/design-summary.png
diff --git a/docs/images/research/whitepapers/summary.png → .../_images/research/whitepapers/summary.png b/docs/images/research/whitepapers/summary.png → .../_images/research/whitepapers/summary.png
diff --git a/...th-openms-tools/galaxy/topp-tool-list.png → ...th-openms-tools/galaxy/topp-tool-list.png b/...th-openms-tools/galaxy/topp-tool-list.png → ...th-openms-tools/galaxy/topp-tool-list.png
diff --git a/...th-openms-tools/knime/node-repository.png → ...th-openms-tools/knime/node-repository.png b/...th-openms-tools/knime/node-repository.png → ...th-openms-tools/knime/node-repository.png
diff --git a/docs/images/topp/INIFileEditor.png → docs/_images/topp/INIFileEditor.png b/docs/images/topp/INIFileEditor.png → docs/_images/topp/INIFileEditor.png
diff --git a/docs/images/topp/SwathWizard.png → docs/_images/topp/SwathWizard.png b/docs/images/topp/SwathWizard.png → docs/_images/topp/SwathWizard.png
diff --git a/docs/images/topp/TOPPAS_simple_example.png → docs/_images/topp/TOPPAS_simple_example.png b/docs/images/topp/TOPPAS_simple_example.png → docs/_images/topp/TOPPAS_simple_example.png
diff --git a/docs/images/topp/TOPPView.png → docs/_images/topp/TOPPView.png b/docs/images/topp/TOPPView.png → docs/_images/topp/TOPPView.png
diff --git a/docs/images/topp/command-line-call.png → docs/_images/topp/command-line-call.png b/docs/images/topp/command-line-call.png → docs/_images/topp/command-line-call.png
diff --git a/.../images/tutorials/knime/KNIME_Install.png → ..._images/tutorials/knime/KNIME_Install.png b/.../images/tutorials/knime/KNIME_Install.png → ..._images/tutorials/knime/KNIME_Install.png
diff --git a/...ages/tutorials/knime/KNIME_screenshot.png → ...ages/tutorials/knime/KNIME_screenshot.png b/...ages/tutorials/knime/KNIME_screenshot.png → ...ages/tutorials/knime/KNIME_screenshot.png
diff --git a/...es/tutorials/knime/KNIME_update_site.jpeg → ...es/tutorials/knime/KNIME_update_site.jpeg b/...es/tutorials/knime/KNIME_update_site.jpeg → ...es/tutorials/knime/KNIME_update_site.jpeg
diff --git a/...tutorials/knime/add-node-to-workspace.gif → ...tutorials/knime/add-node-to-workspace.gif b/...tutorials/knime/add-node-to-workspace.gif → ...tutorials/knime/add-node-to-workspace.gif
diff --git a/...ials/knime/connected-nodes-configured.png → ...ials/knime/connected-nodes-configured.png b/...ials/knime/connected-nodes-configured.png → ...ials/knime/connected-nodes-configured.png
diff --git a/.../knime/connected-nodes-not-configured.png → .../knime/connected-nodes-not-configured.png b/.../knime/connected-nodes-not-configured.png → .../knime/connected-nodes-not-configured.png
diff --git a/docs/images/tutorials/knime/output-file.png → docs/_images/tutorials/knime/output-file.png b/docs/images/tutorials/knime/output-file.png → docs/_images/tutorials/knime/output-file.png
diff --git a/docs/images/tutorials/knime/play-button.png → docs/_images/tutorials/knime/play-button.png b/docs/images/tutorials/knime/play-button.png → docs/_images/tutorials/knime/play-button.png
diff --git a/...bolomics-preprocessing-knime-workflow.png → ...bolomics-preprocessing-knime-workflow.png b/...bolomics-preprocessing-knime-workflow.png → ...bolomics-preprocessing-knime-workflow.png
diff --git a/.../tutorials/metabolomics-preprocessing.png → .../tutorials/metabolomics-preprocessing.png b/.../tutorials/metabolomics-preprocessing.png → .../tutorials/metabolomics-preprocessing.png
diff --git a/docs/images/tutorials/proteowizard.png → docs/_images/tutorials/proteowizard.png b/docs/images/tutorials/proteowizard.png → docs/_images/tutorials/proteowizard.png
diff --git a/docs/images/tutorials/topp/INIFileEditor.png → .../_images/tutorials/topp/INIFileEditor.png b/docs/images/tutorials/topp/INIFileEditor.png → .../_images/tutorials/topp/INIFileEditor.png
diff --git a/...images/tutorials/topp/MetaDataBrowser.png → ...images/tutorials/topp/MetaDataBrowser.png b/...images/tutorials/topp/MetaDataBrowser.png → ...images/tutorials/topp/MetaDataBrowser.png
diff --git a/docs/images/tutorials/topp/Plot2DWidget.png → docs/_images/tutorials/topp/Plot2DWidget.png b/docs/images/tutorials/topp/Plot2DWidget.png → docs/_images/tutorials/topp/Plot2DWidget.png
diff --git a/docs/images/tutorials/topp/Plot3DWidget.png → docs/_images/tutorials/topp/Plot3DWidget.png b/docs/images/tutorials/topp/Plot3DWidget.png → docs/_images/tutorials/topp/Plot3DWidget.png
diff --git a/docs/images/tutorials/topp/TOPPView_1D.png → docs/_images/tutorials/topp/TOPPView_1D.png b/docs/images/tutorials/topp/TOPPView_1D.png → docs/_images/tutorials/topp/TOPPView_1D.png
diff --git a/docs/images/tutorials/topp/TOPPView_help.png → .../_images/tutorials/topp/TOPPView_help.png b/docs/images/tutorials/topp/TOPPView_help.png → .../_images/tutorials/topp/TOPPView_help.png
diff --git a/.../images/tutorials/topp/TOPPView_icons.png → ..._images/tutorials/topp/TOPPView_icons.png b/.../images/tutorials/topp/TOPPView_icons.png → ..._images/tutorials/topp/TOPPView_icons.png
diff --git a/.../images/tutorials/topp/TOPPView_parts.png → ..._images/tutorials/topp/TOPPView_parts.png b/.../images/tutorials/topp/TOPPView_parts.png → ..._images/tutorials/topp/TOPPView_parts.png
diff --git a/...es/tutorials/topp/TOPPView_statistics.png → ...es/tutorials/topp/TOPPView_statistics.png b/...es/tutorials/topp/TOPPView_statistics.png → ...es/tutorials/topp/TOPPView_statistics.png
diff --git a/.../images/tutorials/topp/TOPPView_tools.png → ..._images/tutorials/topp/TOPPView_tools.png b/.../images/tutorials/topp/TOPPView_tools.png → ..._images/tutorials/topp/TOPPView_tools.png
diff --git a/...utorials/topp/TOPPView_tools_baseline.png → ...utorials/topp/TOPPView_tools_baseline.png b/...utorials/topp/TOPPView_tools_baseline.png → ...utorials/topp/TOPPView_tools_baseline.png
diff --git a/...topp/TOPPView_tools_baseline_filtered.png → ...topp/TOPPView_tools_baseline_filtered.png b/...topp/TOPPView_tools_baseline_filtered.png → ...topp/TOPPView_tools_baseline_filtered.png
diff --git a/...als/topp/TOPPView_tools_ff_centroided.png → ...als/topp/TOPPView_tools_ff_centroided.png b/...als/topp/TOPPView_tools_ff_centroided.png → ...als/topp/TOPPView_tools_ff_centroided.png
diff --git a/...es/tutorials/topp/TOPPView_tools_menu.png → ...es/tutorials/topp/TOPPView_tools_menu.png b/...es/tutorials/topp/TOPPView_tools_menu.png → ...es/tutorials/topp/TOPPView_tools_menu.png
diff --git a/...rials/topp/TOPPView_tools_noisefilter.png → ...rials/topp/TOPPView_tools_noisefilter.png b/...rials/topp/TOPPView_tools_noisefilter.png → ...rials/topp/TOPPView_tools_noisefilter.png
diff --git a/...p/TOPPView_tools_noisefilter_filtered.png → ...p/TOPPView_tools_noisefilter_filtered.png b/...p/TOPPView_tools_noisefilter_filtered.png → ...p/TOPPView_tools_noisefilter_filtered.png
diff --git a/...torials/topp/TOPPView_tools_pp_picked.png → ...torials/topp/TOPPView_tools_pp_picked.png b/...torials/topp/TOPPView_tools_pp_picked.png → ...torials/topp/TOPPView_tools_pp_picked.png
diff --git a/.../images/tutorials/topp/TOPP_alignment.png → ..._images/tutorials/topp/TOPP_alignment.png b/.../images/tutorials/topp/TOPP_alignment.png → ..._images/tutorials/topp/TOPP_alignment.png
diff --git a/...ages/tutorials/topp/TOPP_consensus_id.png → ...ages/tutorials/topp/TOPP_consensus_id.png b/...ages/tutorials/topp/TOPP_consensus_id.png → ...ages/tutorials/topp/TOPP_consensus_id.png
diff --git a/...ges/tutorials/topp/TOPP_labeled_quant.png → ...ges/tutorials/topp/TOPP_labeled_quant.png b/...ges/tutorials/topp/TOPP_labeled_quant.png → ...ges/tutorials/topp/TOPP_labeled_quant.png
diff --git a/...s/tutorials/topp/TOPP_labelfree_quant.png → ...s/tutorials/topp/TOPP_labelfree_quant.png b/...s/tutorials/topp/TOPP_labelfree_quant.png → ...s/tutorials/topp/TOPP_labelfree_quant.png
diff --git a/...es/tutorials/topp/TOPP_qualitycontrol.png → ...es/tutorials/topp/TOPP_qualitycontrol.png b/...es/tutorials/topp/TOPP_qualitycontrol.png → ...es/tutorials/topp/TOPP_qualitycontrol.png
diff --git a/docs/images/tutorials/topp/TOPP_raw_data.png → .../_images/tutorials/topp/TOPP_raw_data.png b/docs/images/tutorials/topp/TOPP_raw_data.png → .../_images/tutorials/topp/TOPP_raw_data.png
diff --git a/...orials/toppas/TOPPAS_BSA_Quantitation.png → ...orials/toppas/TOPPAS_BSA_Quantitation.png b/...orials/toppas/TOPPAS_BSA_Quantitation.png → ...orials/toppas/TOPPAS_BSA_Quantitation.png
diff --git a/...utorials/toppas/TOPPAS_BSA_results_2d.png → ...utorials/toppas/TOPPAS_BSA_results_2d.png b/...utorials/toppas/TOPPAS_BSA_results_2d.png → ...utorials/toppas/TOPPAS_BSA_results_2d.png
diff --git a/...utorials/toppas/TOPPAS_BSA_results_3d.png → ...utorials/toppas/TOPPAS_BSA_results_3d.png b/...utorials/toppas/TOPPAS_BSA_results_3d.png → ...utorials/toppas/TOPPAS_BSA_results_3d.png
diff --git a/.../images/tutorials/toppas/TOPPAS_edges.png → ..._images/tutorials/toppas/TOPPAS_edges.png b/.../images/tutorials/toppas/TOPPAS_edges.png → ..._images/tutorials/toppas/TOPPAS_edges.png
diff --git a/...utorials/toppas/TOPPAS_example_merger.png → ...utorials/toppas/TOPPAS_example_merger.png b/...utorials/toppas/TOPPAS_example_merger.png → ...utorials/toppas/TOPPAS_example_merger.png
diff --git a/...OPPAS_example_profile_data_processing.png → ...OPPAS_example_profile_data_processing.png b/...OPPAS_example_profile_data_processing.png → ...OPPAS_example_profile_data_processing.png
diff --git a/...es/tutorials/toppas/TOPPAS_parameters.png → ...es/tutorials/toppas/TOPPAS_parameters.png b/...es/tutorials/toppas/TOPPAS_parameters.png → ...es/tutorials/toppas/TOPPAS_parameters.png
diff --git a/...s/tutorials/toppas/TOPPAS_run_options.png → ...s/tutorials/toppas/TOPPAS_run_options.png b/...s/tutorials/toppas/TOPPAS_run_options.png → ...s/tutorials/toppas/TOPPAS_run_options.png
diff --git a/...utorials/toppas/TOPPAS_simple_example.png → ...utorials/toppas/TOPPAS_simple_example.png b/...utorials/toppas/TOPPAS_simple_example.png → ...utorials/toppas/TOPPAS_simple_example.png
diff --git a/...als/toppview/apply-topp-tool-to-layer.png → ...als/toppview/apply-topp-tool-to-layer.png b/...als/toppview/apply-topp-tool-to-layer.png → ...als/toppview/apply-topp-tool-to-layer.png
diff --git a/...utorials/toppview/data-import-options.png → ...utorials/toppview/data-import-options.png b/...utorials/toppview/data-import-options.png → ...utorials/toppview/data-import-options.png
diff --git a/...utorials/toppview/file-import-options.png → ...utorials/toppview/file-import-options.png b/...utorials/toppview/file-import-options.png → ...utorials/toppview/file-import-options.png
diff --git a/.../tutorials/toppview/filtering-options.png → .../tutorials/toppview/filtering-options.png b/.../tutorials/toppview/filtering-options.png → .../tutorials/toppview/filtering-options.png
diff --git a/...rials/toppview/layer-loaded-in-viewer.png → ...rials/toppview/layer-loaded-in-viewer.png b/...rials/toppview/layer-loaded-in-viewer.png → ...rials/toppview/layer-loaded-in-viewer.png
diff --git a/...ages/tutorials/toppview/layers-window.png → ...ages/tutorials/toppview/layers-window.png b/...ages/tutorials/toppview/layers-window.png → ...ages/tutorials/toppview/layers-window.png
diff --git a/...s/toppview/select-data-filters-window.png → ...s/toppview/select-data-filters-window.png b/...s/toppview/select-data-filters-window.png → ...s/toppview/select-data-filters-window.png
diff --git a/...w/topp-tool-arguments-and-description.png → ...w/topp-tool-arguments-and-description.png b/...w/topp-tool-arguments-and-description.png → ...w/topp-tool-arguments-and-description.png
diff --git a/...torials/toppview/topp-tool-parameters.png → ...torials/toppview/topp-tool-parameters.png b/...torials/toppview/topp-tool-parameters.png → ...torials/toppview/topp-tool-parameters.png
diff --git a/...ges/tutorials/toppview/user-interface.png → ...ges/tutorials/toppview/user-interface.png b/...ges/tutorials/toppview/user-interface.png → ...ges/tutorials/toppview/user-interface.png
diff --git a/docs/_images/webapps/flashtaggerviewer.png b/docs/_images/webapps/flashtaggerviewer.png
diff --git a/docs/_images/webapps/nuxl.jpg b/docs/_images/webapps/nuxl.jpg
diff --git a/docs/_images/webapps/umetaflow.png b/docs/_images/webapps/umetaflow.png
diff --git a/docs/about/communication.md b/docs/about/communication.md
@@ -0,0 +1,83 @@
+Community
+=========
+
+Welcome to OpenMS!
+------------------
+
+OpenMS is a community-driven open source project developed by a diverse group of [contributors](https://openms.de/contributors/). The OpenMS leadership has made a strong commitment to creating an open, inclusive, and positive community. Please read the [OpenMS Code of Conduct](https://github.com/OpenMS/OpenMS/blob/develop/CODE_OF_CONDUCT.md) for guidance on how to interact with others in a way that makes the community thrive.
+
+Here's how to get started:
+
+- 📚 Browse through the main library code under [OpenMS/OpenMS](https://github.com/openms/openms/issues)
+- 👩‍💻 Check out the [documentation](https://openms.readthedocs.io/en/latest/index.html).
+- 🙋‍♀️ Come and say hi on our [![Discord Shield](https://img.shields.io/discord/832282841836159006?style=flat-square&message=Discord&color=5865F2&logo=Discord&logoColor=FFFFFF&label=Discord)](https://discord.gg/4TAGhqJ7s5) or [![Gitter](https://img.shields.io/static/v1?style=flat-square&message=on%20Gitter&color=ED1965&logo=Gitter&logoColor=FFFFFF&label=Chat)](https://gitter.im/OpenMS/OpenMS?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) channels.
+- 🍿 Tune in for news about developer/user meetings and events, [get involved](https://openms.de/news/)!
+- 🌈 Please abide by our [community code of conduct](https://github.com/OpenMS/OpenMS/blob/develop/CODE_OF_CONDUCT.md)
+
+We offer several communication channels to learn, share your knowledge and connect with others within the OpenMS community.
+
+***
+
+### <a class="button cta rounded primary-btn raised" href="https://discord.gg/aJyWqf6uCn">Discord</a>
+
+Discord allows the users to communicate in different channels, publicly as well as privately
+
+***
+
+### <a class="button cta rounded primary-btn raised" href="https://github.com/openms">GitHub</a>
+
+The following repositories can be used:
+- [OpenMS](https://github.com/OpenMS/OpenMS) (Bug Reports, Feature requests)
+- [OpenMS-docs](https://github.com/OpenMS/OpenMS-docs) (Documentation-related issues)
+- [OpenMS.de](https://github.com/OpenMS/openms.de) (Any issue related to website)
+- [pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) (Any issue related to pyopenms)
+
+In case if you are confused, please ask your query [here](https://openms.de/help-request/)
+
+***
+
+### <a class="button cta rounded primary-btn raised" href="https://github.com/openms/openms/issues">GitHub issue tracker</a>
+
+The issue tracker can be used for:
+
+OpenMS
+- [Bug reports](https://github.com/OpenMS/OpenMS/labels/bug) (e.g. "Filter doesn't work for 1D data")
+- [Feature requests](https://github.com/OpenMS/OpenMS/labels/enhancement)
+- [Tools](https://github.com/OpenMS/OpenMS/issues?q=is%3Aopen+is%3Aissue+label%3ATOPP) (**T**he **O**penMS **P**i**p**eline - TOPP)
+- [TOPPView](https://github.com/OpenMS/OpenMS/labels/TOPPView)
+
+Documentation
+- [Bug reports](https://github.com/OpenMS/OpenMS-docs/labels/bug)
+- [Feature requests](https://github.com/OpenMS/OpenMS-docs/labels/enhancement)
+
+***
+
+### <a class="button cta rounded primary-btn raised" href="https://gitter.im/OpenMS/OpenMS">Gitter</a>
+
+A real-time chat room to ask questions about OpenMS.
+
+***
+
+### <a class="button cta rounded primary-btn raised" href="https://sourceforge.net/p/open-ms/mailman/open-ms-announcements">OpenMS mailing list</a>
+
+
+These lists are the main form of receiving OpenMS-related updates, like new features, changes to the roadmap, and all kinds of project-wide decision making.
+
+There are two mailing list currently:
+- [open-ms-announcements](https://sourceforge.net/p/open-ms/mailman/open-ms-announcements/) - Announcements about OpenMS, such as for releases, developer meetings, sprints or conference talks are made on this list.
+- [open-ms-general](https://sourceforge.net/p/open-ms/mailman/open-ms-general/) - For addressing any queries or suggestion from the users.
+
+***
+
+### <a class="button cta rounded primary-btn raised" href="https://x.com/OpenMSTeam">Twitter</a>
+
+Contact us or just follow the latest OpenMS news on Twitter.
+
+***
+
+Join the OpenMS Community
+-------------------------
+
+To thrive, the OpenMS project needs your expertise and enthusiasm. Not a coder? Not a problem! There are many ways to contribute to OpenMS.
+
+If you are interested in becoming a OpenMS contributor (yay!) we recommend checking out our [Contribute](/manual/contribute.md) page.
diff --git a/docs/about/installation.rst b/docs/about/installation.rst
@@ -0,0 +1,92 @@
+Installation
+============
+
+.. toctree::
+    :hidden:
+
+    installation/installation-on-gnu-linux.md
+    installation/installation-on-macos.md
+    installation/installation-on-windows.md
+
+Workflow Editor
+---------------
+
+You can run OpenMS TOPP tools from the command line using your custom scripts, or use powerful
+workflow systems designed to make workflow creation and maintenance more fun, find out more in :ref:`workflows`.
+
+.. list-table::
+   :widths: 25 25 25 25
+   :class: borderless only-light
+   :align: center
+
+   * - .. image:: /_images/introduction/KNIMELogoTM.svg
+         :target: ../getting-started/knime-get-started.html
+         :width: 90%
+
+     - .. image:: /_images/introduction/nextflow2014_no-bg.png
+         :target: ../getting-started/nextflow-get-started.html
+         :width: 90%
+
+     - .. image:: /_images/introduction/galaxy_project_logo.png
+         :target: ../getting-started/galaxy-get-started.html
+         :width: 90%
+
+     - .. image:: /_images/introduction/TOPPAS_logo_white.png
+         :target: ../getting-started/toppas-get-started.html
+         :width: 90%
+
+
+.. list-table::
+   :widths: 25 25 25 25
+   :class: borderless only-dark
+   :align: center
+
+   * - .. image:: /_images/introduction/KNIMELogoTM_white.svg
+         :target: ../getting-started/knime-get-started.html
+         :width: 90%
+
+     - .. image:: /_images/introduction/nextflow2014_no-bg-bright.png
+         :target: ../getting-started/nextflow-get-started.html
+         :width: 90%
+
+     - .. image:: /_images/introduction/galaxy_project_logo_white.png
+         :target: ../getting-started/galaxy-get-started.html
+         :width: 90%
+
+     - .. image:: /_images/introduction/TOPPAS_logo_dark.png
+         :target: ../getting-started/toppas-get-started.html
+         :width: 90%
+
+
+Graphical and Command-Line Tools
+--------------------------------
+For instructions on how to install the OpenMS graphical and command-line tools, choose your operating system
+from the items below.
+
+
+.. grid::
+    :gutter: 4
+
+    .. grid-item-card:: GNU/Linux
+        :img-top: /_images/installations/linux_logo.svg
+        :link: installation/installation-on-gnu-linux
+        :link-type: doc
+        :columns: 4
+
+        Installation on Linux
+
+    .. grid-item-card:: macOS
+        :img-top: /_images/installations/macos_logo.svg
+        :link: installation/installation-on-macos
+        :link-type: doc
+        :columns: 4
+
+        Installation on macOS
+
+    .. grid-item-card:: Windows
+        :img-top: /_images/installations/Windows_logo.svg
+        :link: installation/installation-on-windows
+        :link-type: doc
+        :columns: 4
+
+        Installation on Windows
diff --git a/...installation/installation-on-gnu-linux.md → ...installation/installation-on-gnu-linux.md b/...installation/installation-on-gnu-linux.md → ...installation/installation-on-gnu-linux.md
@@ -1,7 +1,9 @@
 GNU/Linux
 =========================
 
+
 ```{include} installation-with-conda.md
+:start-after: "% start-after"
 ```
 
 ## Install via package managers
@@ -65,6 +67,7 @@ If you encounter errors with unavailable packages, troubleshoot using the follow
    Add the folders in your `PATH` for a convenient use of the adapters.
 
 ```{include} run-in-container.md
+:start-after: "% start-after"
 ```
 
 ## Build OpenMS from source

diff --git a/...ols/installation/installation-on-macos.md → ...out/installation/installation-on-macos.md b/...ols/installation/installation-on-macos.md → ...out/installation/installation-on-macos.md
@@ -2,6 +2,7 @@ macOS
 ====================
 
 ```{include} installation-with-conda.md
+:start-after: "% start-after"
 ```
 
 ## Install via macOS installer
@@ -11,40 +12,40 @@ To install OpenMS on macOS, run the following steps:
 1. Download and install the macOS drag-and-drop installer from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/).
 2. Double click on the downloaded file. It will start to open the `OpenMS-<version>-macOS.dmg` disk image file.
 
-```{image} /images/installations/macos/opening-openms2-8-macos.png
+```{image} /_images/installations/macos/opening-openms2-8-macos.png
 :alt: Opening OpenMS-<version>-macOS.dmg
 :width: 500px
 ```
 
 3. Verify the download.
 
-```{image} /images/installations/macos/verifying-openms2-8-macos.png
+```{image} /_images/installations/macos/verifying-openms2-8-macos.png
 :alt: Verifying OpenMS-<version>-macOS.dmg
 :width: 500px
 ```
 
 4. Agree to the license agreements.
 
-```{image} /images/installations/macos/license-agreements.png
+```{image} /_images/installations/macos/license-agreements.png
 :alt: License agreement
 :width: 500px
 ```
 
 5. Drag OpenMS to the Applications folder.
 
-```{image} /images/installations/macos/move-openms-to-applications.png
+```{image} /_images/installations/macos/move-openms-to-applications.png
 :alt: Move to Applications
 :width: 500px
 ```
 
 6. It will start copying to applications.
 
-```{image} /images/installations/macos/preparing-to-copy-to-applications.png
+```{image} /_images/installations/macos/preparing-to-copy-to-applications.png
 :alt: Preparing to copy to Applications
 :width: 500px
 ```
 
-```{image} /images/installations/macos/copying-to-applications.png
+```{image} /_images/installations/macos/copying-to-applications.png
 :alt: Copying to Applications
 :width: 500px
 ```
@@ -85,6 +86,7 @@ To use {term}`TOPP` as regular app in the shell, add the following lines to the
 :::
 
 ```{include} run-in-container.md
+:start-after: "% start-after"
 ```
 
 ## Build OpenMS from source

diff --git a/...s/installation/installation-on-windows.md → ...t/installation/installation-on-windows.md b/...s/installation/installation-on-windows.md → ...t/installation/installation-on-windows.md
@@ -12,7 +12,7 @@ To Install the binary package of OpenMS & {term}`TOPP`:
 
    Click on "More Info", and then "Run anyways".
 
-   ![](/images/installations/win/smartscreen.gif)
+   ![](/_images/installations/win/smartscreen.gif)
 
    When asked for an admin authentication, please enter the credentials (it is not advised to directly invoke the installer using an admin account).
 

diff --git a/...s/installation/installation-with-conda.md → ...t/installation/installation-with-conda.md b/...s/installation/installation-with-conda.md → ...t/installation/installation-with-conda.md
@@ -1,3 +1,6 @@
+# Conda
+
+% start-after
 ## Install via Conda
 
 ```{warning}

diff --git a/...nd-tools/installation/run-in-container.md → docs/about/installation/run-in-container.md b/...nd-tools/installation/run-in-container.md → docs/about/installation/run-in-container.md
@@ -1,3 +1,6 @@
+# Container
+
+% start-after
 ## Run OpenMS inside a (Bio)Container
 
 1. Install a containerization software (e.g., [Docker](https://docs.docker.com/engine/install/) or [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps))