From 97b017f496f8045bf03165add347c55e5a3e7e4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A1ts=C3=A1gi?= Date: Tue, 26 Nov 2024 16:00:22 +0100 Subject: [PATCH] update designer --- .quarto/idx/guide.qmd.json | 2 +- .quarto/xref/0142f1c3 | 2 +- .quarto/xref/63bc2c9a | 2 +- _quarto.yml | 3 +++ designer.qmd | 3 --- docs/designer.html | 7 +------ docs/guide.html | 15 ++++++++++----- docs/images/datapackage.png | Bin 0 -> 30993 bytes docs/search.json | 4 ++-- guide.qmd | 10 +++++++--- images/datapackage.png | Bin 0 -> 30993 bytes 11 files changed, 26 insertions(+), 22 deletions(-) create mode 100644 docs/images/datapackage.png create mode 100644 images/datapackage.png diff --git a/.quarto/idx/guide.qmd.json b/.quarto/idx/guide.qmd.json index ab173ea..f90df10 100644 --- a/.quarto/idx/guide.qmd.json +++ b/.quarto/idx/guide.qmd.json @@ -1 +1 @@ -{"title":"Step-by-step guide","markdown":{"yaml":{"title":"Step-by-step guide","lightbox":true},"headingText":"YODA","containsRefs":false,"markdown":"\n\n\n**YODA** is used as a secure data solution, where data generators can upload the filled templates. \n\n::: {.callout-tip icon=\"false\" appearence=\"simple\"}\nMore information and a detailed ‘manual’ about YODA can be found on their [website](https://www.uu.nl/en/research/yoda/guide-to-yoda).\n:::\n\n::: {.callout-tip icon=\"false\" appearence=\"simple\"}\nGood to know: It is also possible to publish data straight from YODA.\n:::\n\nData generators receive an email to register, after which they can access the dedicated [website](https://dgk.yoda.uu.nl/) for data upload.\n\nThe main folder is called **‘research-enanomapper’** with an **‘enm_filesharing’** and an optional **‘for_publication’** folder within. There is also a README.txt file giving extra information on file naming. This information is also available under the [**naming convention**](/naming.qmd) tab.\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\nOnly MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.\n:::\n\n#### Explanation of folder stucture\n\n- The **enm_filesharing** is a dump folder that provides a collection place for Excel-based MOMENTUM data that will subsequently be transferred into the online database of eNanomapper. It has sub-folders corresponding to separate experiments. Templates should be uploaded into the fitting folder. If there is no fitting folder, one can simply create one (using lowercase letters and hyphens, if needed).\n- Furthermore, the provision of descriptive metadata in Excel format about other types of data (e.g. microscopy, DNA sequencing etc.) is required. The metadata should contain a link to where these other data types are stored/will be made available (e.g. in YODA or another well-established repository). \n- Data in other formats that is described by a template can be directly placed in this filesharing folder, according to experiment type, to make referencing easier. However, the data owner can choose to make these other files available in another repository as long as clear referencing in templates to linked files is achieved. \n- The **for_publication** folder is intended for the minimum 'data packages'. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these 'data bundles' however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom. This folder is rather empty still. Data generators are free to create sub-folders for their *intended publications* to keep data packages there.\n\n![](/images/dataflow_website_v5.png \"General flow of MOMENTUM data\")\n\n### eNanomapper\n\n\"The eNanoMapper database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project.\"[^1]\n\n[^1]: https://enanomapper.adma.ai/about/\n\n#### How to use eNanomapper for Momemtum data\n\n- Navigate to the [**template wizard**](https://enanomapper.adma.ai/projects/momentum/datatemplates/) of MOMENTUM.\n- Find template corresponding to experiment and adjust variables in the wizard. After downloading, fill in Excel sheet. In case the layout does not fit the experimental output (/you wish to adjust template layout to fit your data), please create a template in the [**template designer**](https://enanomapper.adma.ai/templates) instead. Same applies to the metadata templates. Templates obtained from the wizard and changed after download are not suitable for the data transfer into eNanomapper.\n- After downloading and filling in suitable templates according to your respective research, upload Excel files to the corresponding sub-folders (name as the template/experiment name). Naming convention is described under the [**corresponding tab**](/naming.qmd).\n- If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.\n- There are no sub-folders in the publication folder yet so create one for your paper if you decide to place data packages in YODA. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability.\n\n\n::: {.callout-important icon=\"false\" appearence=\"simple\"}\n## Template wizard\n\nFor a more elaborate walk-through, please consult the [user guide](https://enanomapper.adma.ai/assets/img/guide/guide.pdf) for the Template wizard.\n:::\n\n#### How to use the Template Designer\n- You can see the different steps of designing your own template on the [**Template designer tab**](/designer.qmd).\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\n## Next step\n\nWhen the folders are populated with data, the partner from eNanomapper can fetch this data and parse it into the eNanomapper database.\n:::","srcMarkdownNoYaml":"\n\n### YODA\n\n**YODA** is used as a secure data solution, where data generators can upload the filled templates. \n\n::: {.callout-tip icon=\"false\" appearence=\"simple\"}\nMore information and a detailed ‘manual’ about YODA can be found on their [website](https://www.uu.nl/en/research/yoda/guide-to-yoda).\n:::\n\n::: {.callout-tip icon=\"false\" appearence=\"simple\"}\nGood to know: It is also possible to publish data straight from YODA.\n:::\n\nData generators receive an email to register, after which they can access the dedicated [website](https://dgk.yoda.uu.nl/) for data upload.\n\nThe main folder is called **‘research-enanomapper’** with an **‘enm_filesharing’** and an optional **‘for_publication’** folder within. There is also a README.txt file giving extra information on file naming. This information is also available under the [**naming convention**](/naming.qmd) tab.\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\nOnly MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.\n:::\n\n#### Explanation of folder stucture\n\n- The **enm_filesharing** is a dump folder that provides a collection place for Excel-based MOMENTUM data that will subsequently be transferred into the online database of eNanomapper. It has sub-folders corresponding to separate experiments. Templates should be uploaded into the fitting folder. If there is no fitting folder, one can simply create one (using lowercase letters and hyphens, if needed).\n- Furthermore, the provision of descriptive metadata in Excel format about other types of data (e.g. microscopy, DNA sequencing etc.) is required. The metadata should contain a link to where these other data types are stored/will be made available (e.g. in YODA or another well-established repository). \n- Data in other formats that is described by a template can be directly placed in this filesharing folder, according to experiment type, to make referencing easier. However, the data owner can choose to make these other files available in another repository as long as clear referencing in templates to linked files is achieved. \n- The **for_publication** folder is intended for the minimum 'data packages'. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these 'data bundles' however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom. This folder is rather empty still. Data generators are free to create sub-folders for their *intended publications* to keep data packages there.\n\n![](/images/dataflow_website_v5.png \"General flow of MOMENTUM data\")\n\n### eNanomapper\n\n\"The eNanoMapper database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project.\"[^1]\n\n[^1]: https://enanomapper.adma.ai/about/\n\n#### How to use eNanomapper for Momemtum data\n\n- Navigate to the [**template wizard**](https://enanomapper.adma.ai/projects/momentum/datatemplates/) of MOMENTUM.\n- Find template corresponding to experiment and adjust variables in the wizard. After downloading, fill in Excel sheet. In case the layout does not fit the experimental output (/you wish to adjust template layout to fit your data), please create a template in the [**template designer**](https://enanomapper.adma.ai/templates) instead. Same applies to the metadata templates. Templates obtained from the wizard and changed after download are not suitable for the data transfer into eNanomapper.\n- After downloading and filling in suitable templates according to your respective research, upload Excel files to the corresponding sub-folders (name as the template/experiment name). Naming convention is described under the [**corresponding tab**](/naming.qmd).\n- If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.\n- There are no sub-folders in the publication folder yet so create one for your paper if you decide to place data packages in YODA. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability.\n\n\n::: {.callout-important icon=\"false\" appearence=\"simple\"}\n## Template wizard\n\nFor a more elaborate walk-through, please consult the [user guide](https://enanomapper.adma.ai/assets/img/guide/guide.pdf) for the Template wizard.\n:::\n\n#### How to use the Template Designer\n- You can see the different steps of designing your own template on the [**Template designer tab**](/designer.qmd).\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\n## Next step\n\nWhen the folders are populated with data, the partner from eNanomapper can fetch this data and parse it into the eNanomapper database.\n:::"},"formats":{"html":{"identifier":{"display-name":"HTML","target-format":"html","base-format":"html"},"execute":{"fig-width":7,"fig-height":5,"fig-format":"retina","fig-dpi":96,"df-print":"default","error":false,"eval":true,"cache":null,"freeze":false,"echo":true,"output":true,"warning":true,"include":true,"keep-md":false,"keep-ipynb":false,"ipynb":null,"enabled":null,"daemon":null,"daemon-restart":false,"debug":false,"ipynb-filters":[],"ipynb-shell-interactivity":null,"plotly-connected":true,"engine":"markdown"},"render":{"keep-tex":false,"keep-typ":false,"keep-source":false,"keep-hidden":false,"prefer-html":false,"output-divs":true,"output-ext":"html","fig-align":"default","fig-pos":null,"fig-env":null,"code-fold":"none","code-overflow":"scroll","code-link":false,"code-line-numbers":false,"code-tools":false,"tbl-colwidths":"auto","merge-includes":true,"inline-includes":false,"preserve-yaml":false,"latex-auto-mk":true,"latex-auto-install":true,"latex-clean":true,"latex-min-runs":1,"latex-max-runs":10,"latex-makeindex":"makeindex","latex-makeindex-opts":[],"latex-tlmgr-opts":[],"latex-input-paths":[],"latex-output-dir":null,"link-external-icon":false,"link-external-newwindow":false,"self-contained-math":false,"format-resources":[],"notebook-links":true},"pandoc":{"standalone":true,"wrap":"none","default-image-extension":"png","to":"html","embed-resources":true,"css":["styles.css"],"toc":true,"toc-depth":4,"output-file":"guide.html"},"language":{"toc-title-document":"Table 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navigation","crossref-fig-title":"Figure","crossref-tbl-title":"Table","crossref-lst-title":"Listing","crossref-thm-title":"Theorem","crossref-lem-title":"Lemma","crossref-cor-title":"Corollary","crossref-prp-title":"Proposition","crossref-cnj-title":"Conjecture","crossref-def-title":"Definition","crossref-exm-title":"Example","crossref-exr-title":"Exercise","crossref-ch-prefix":"Chapter","crossref-apx-prefix":"Appendix","crossref-sec-prefix":"Section","crossref-eq-prefix":"Equation","crossref-lof-title":"List of Figures","crossref-lot-title":"List of Tables","crossref-lol-title":"List of Listings","environment-proof-title":"Proof","environment-remark-title":"Remark","environment-solution-title":"Solution","listing-page-order-by":"Order By","listing-page-order-by-default":"Default","listing-page-order-by-date-asc":"Oldest","listing-page-order-by-date-desc":"Newest","listing-page-order-by-number-desc":"High to Low","listing-page-order-by-number-asc":"Low to High","listing-page-field-date":"Date","listing-page-field-title":"Title","listing-page-field-description":"Description","listing-page-field-author":"Author","listing-page-field-filename":"File Name","listing-page-field-filemodified":"Modified","listing-page-field-subtitle":"Subtitle","listing-page-field-readingtime":"Reading Time","listing-page-field-wordcount":"Word Count","listing-page-field-categories":"Categories","listing-page-minutes-compact":"{0} min","listing-page-category-all":"All","listing-page-no-matches":"No matching items","listing-page-words":"{0} words","listing-page-filter":"Filter","draft":"Draft"},"metadata":{"lang":"en","fig-responsive":true,"quarto-version":"1.5.57","theme":{"light":"flatly","dark":"darkly"},"toc-title":"Content","toc-location":"left","title":"Step-by-step guide","lightbox":true},"extensions":{"book":{"multiFile":true}}}},"projectFormats":["html"]} \ No newline at end of file +{"title":"Step-by-step guide","markdown":{"yaml":{"title":"Step-by-step guide","lightbox":true},"headingText":"YODA","containsRefs":false,"markdown":"\n\n\n**YODA** is used as a secure data solution, where data generators can upload the filled templates. \n\n::: {.callout-tip icon=\"false\" appearence=\"simple\"}\nMore information and a detailed ‘manual’ about YODA can be found on their [website](https://www.uu.nl/en/research/yoda/guide-to-yoda).\n:::\n\n::: {.callout-tip icon=\"false\" appearence=\"simple\" collapse=\"true\"}\n## Good to know\nIt is also possible to publish data straight from YODA.\n:::\n\nData generators receive an email to register, after which they can access the dedicated [website](https://dgk.yoda.uu.nl/) for data upload.\n\nThe main folder is called **‘research-enanomapper’** with an **‘enm_filesharing’** and an optional **‘for_publication’** folder within. There is also a README.txt file giving extra information on file naming. This information is also available under the [**naming convention**](/naming.qmd) tab.\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\nOnly MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.\n:::\n\n#### Explanation of folder stucture\n\n- The **enm_filesharing** is a dump folder that provides a collection place for Excel-based MOMENTUM data that will subsequently be transferred into the online database of eNanomapper. It has sub-folders corresponding to separate experiments. Templates should be uploaded into the fitting folder. If there is no fitting folder, one can simply create one (using lowercase letters and hyphens, if needed).\n- Furthermore, the provision of descriptive metadata in Excel format about other types of data (e.g. microscopy, DNA sequencing etc.) is required. The metadata should contain a link to where these other data types are stored/will be made available (e.g. in YODA or another well-established repository). \n- Data in other formats that is described by a template can be directly placed in this filesharing folder, according to experiment type, to make referencing easier. However, the data owner can choose to make these other files available in another repository as long as clear referencing in templates to linked files is achieved. \n- The **for_publication** folder is intended for the minimum 'data packages'. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these 'data bundles' however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom. \n- This folder is rather empty still. Data generators are free to create sub-folders for their *intended publications* to keep data packages there.\n\n![](/images/dataflow_website_v5.png \"General flow of MOMENTUM data\")\n\n![](/images/datapackage.png \"Simple folder organisation for MOMENTUM data\")\n\n### eNanomapper\n\n\"The eNanoMapper database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project.\"[^1]\n\n[^1]: https://enanomapper.adma.ai/about/\n\n#### How to use eNanomapper for Momemtum data\n\n- Navigate to the [**template wizard**](https://enanomapper.adma.ai/projects/momentum/datatemplates/) of MOMENTUM.\n- Find template corresponding to experiment and adjust variables in the wizard. After downloading, fill in Excel sheet. In case the layout does not fit the experimental output (/you wish to adjust template layout to fit your data), please create a template in the [**template designer**](https://enanomapper.adma.ai/templates) instead. Same applies to the metadata templates. Templates obtained from the wizard and changed after download are not suitable for the data transfer into eNanomapper.\n- After downloading and filling in suitable templates according to your respective research, upload Excel files to the corresponding sub-folders (name as the template/experiment name). Naming convention is described under the [**corresponding tab**](/naming.qmd).\n- If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.\n- There are no sub-folders in the publication folder yet so create one for your paper if you decide to place data packages in YODA. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability.\n\n\n::: {.callout-important icon=\"false\" appearence=\"simple\"}\n## Template wizard\n\nFor a more elaborate walk-through, please consult the [user guide](https://enanomapper.adma.ai/assets/img/guide/guide.pdf) for the Template wizard.\n:::\n\n#### How to use the Template Designer\n- You can see the different steps of designing your own template on the [**Template designer tab**](/designer.qmd).\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\n## Next step\n\nWhen the folders are populated with data, the partner from eNanomapper can fetch this data and parse it into the eNanomapper database.\n:::","srcMarkdownNoYaml":"\n\n### YODA\n\n**YODA** is used as a secure data solution, where data generators can upload the filled templates. \n\n::: {.callout-tip icon=\"false\" appearence=\"simple\"}\nMore information and a detailed ‘manual’ about YODA can be found on their [website](https://www.uu.nl/en/research/yoda/guide-to-yoda).\n:::\n\n::: {.callout-tip icon=\"false\" appearence=\"simple\" collapse=\"true\"}\n## Good to know\nIt is also possible to publish data straight from YODA.\n:::\n\nData generators receive an email to register, after which they can access the dedicated [website](https://dgk.yoda.uu.nl/) for data upload.\n\nThe main folder is called **‘research-enanomapper’** with an **‘enm_filesharing’** and an optional **‘for_publication’** folder within. There is also a README.txt file giving extra information on file naming. This information is also available under the [**naming convention**](/naming.qmd) tab.\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\nOnly MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.\n:::\n\n#### Explanation of folder stucture\n\n- The **enm_filesharing** is a dump folder that provides a collection place for Excel-based MOMENTUM data that will subsequently be transferred into the online database of eNanomapper. It has sub-folders corresponding to separate experiments. Templates should be uploaded into the fitting folder. If there is no fitting folder, one can simply create one (using lowercase letters and hyphens, if needed).\n- Furthermore, the provision of descriptive metadata in Excel format about other types of data (e.g. microscopy, DNA sequencing etc.) is required. The metadata should contain a link to where these other data types are stored/will be made available (e.g. in YODA or another well-established repository). \n- Data in other formats that is described by a template can be directly placed in this filesharing folder, according to experiment type, to make referencing easier. However, the data owner can choose to make these other files available in another repository as long as clear referencing in templates to linked files is achieved. \n- The **for_publication** folder is intended for the minimum 'data packages'. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these 'data bundles' however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom. \n- This folder is rather empty still. Data generators are free to create sub-folders for their *intended publications* to keep data packages there.\n\n![](/images/dataflow_website_v5.png \"General flow of MOMENTUM data\")\n\n![](/images/datapackage.png \"Simple folder organisation for MOMENTUM data\")\n\n### eNanomapper\n\n\"The eNanoMapper database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project.\"[^1]\n\n[^1]: https://enanomapper.adma.ai/about/\n\n#### How to use eNanomapper for Momemtum data\n\n- Navigate to the [**template wizard**](https://enanomapper.adma.ai/projects/momentum/datatemplates/) of MOMENTUM.\n- Find template corresponding to experiment and adjust variables in the wizard. After downloading, fill in Excel sheet. In case the layout does not fit the experimental output (/you wish to adjust template layout to fit your data), please create a template in the [**template designer**](https://enanomapper.adma.ai/templates) instead. Same applies to the metadata templates. Templates obtained from the wizard and changed after download are not suitable for the data transfer into eNanomapper.\n- After downloading and filling in suitable templates according to your respective research, upload Excel files to the corresponding sub-folders (name as the template/experiment name). Naming convention is described under the [**corresponding tab**](/naming.qmd).\n- If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.\n- There are no sub-folders in the publication folder yet so create one for your paper if you decide to place data packages in YODA. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability.\n\n\n::: {.callout-important icon=\"false\" appearence=\"simple\"}\n## Template wizard\n\nFor a more elaborate walk-through, please consult the [user guide](https://enanomapper.adma.ai/assets/img/guide/guide.pdf) for the Template wizard.\n:::\n\n#### How to use the Template Designer\n- You can see the different steps of designing your own template on the [**Template designer tab**](/designer.qmd).\n\n::: {.callout-note icon=\"false\" appearence=\"simple\" collapse=\"true\"}\n## Next step\n\nWhen the folders are populated with data, the partner from eNanomapper can fetch this data and parse it into the eNanomapper database.\n:::"},"formats":{"html":{"identifier":{"display-name":"HTML","target-format":"html","base-format":"html"},"execute":{"fig-width":7,"fig-height":5,"fig-format":"retina","fig-dpi":96,"df-print":"default","error":false,"eval":true,"cache":null,"freeze":false,"echo":true,"output":true,"warning":true,"include":true,"keep-md":false,"keep-ipynb":false,"ipynb":null,"enabled":null,"daemon":null,"daemon-restart":false,"debug":false,"ipynb-filters":[],"ipynb-shell-interactivity":null,"plotly-connected":true,"engine":"markdown"},"render":{"keep-tex":false,"keep-typ":false,"keep-source":false,"keep-hidden":false,"prefer-html":false,"output-divs":true,"output-ext":"html","fig-align":"default","fig-pos":null,"fig-env":null,"code-fold":"none","code-overflow":"scroll","code-link":false,"code-line-numbers":false,"code-tools":false,"tbl-colwidths":"auto","merge-includes":true,"inline-includes":false,"preserve-yaml":false,"latex-auto-mk":true,"latex-auto-install":true,"latex-clean":true,"latex-min-runs":1,"latex-max-runs":10,"latex-makeindex":"makeindex","latex-makeindex-opts":[],"latex-tlmgr-opts":[],"latex-input-paths":[],"latex-output-dir":null,"link-external-icon":false,"link-external-newwindow":false,"self-contained-math":false,"format-resources":[],"notebook-links":true},"pandoc":{"standalone":true,"wrap":"none","default-image-extension":"png","to":"html","embed-resources":true,"css":["styles.css"],"toc":true,"toc-depth":4,"output-file":"guide.html"},"language":{"toc-title-document":"Table 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208374b..7df77d5 100644 --- a/.quarto/xref/0142f1c3 +++ b/.quarto/xref/0142f1c3 @@ -1 +1 @@ -{"entries":[],"headings":[]} \ No newline at end of file +{"headings":[],"entries":[]} \ No newline at end of file diff --git a/.quarto/xref/63bc2c9a b/.quarto/xref/63bc2c9a index 866e85a..2725e7f 100644 --- a/.quarto/xref/63bc2c9a +++ b/.quarto/xref/63bc2c9a @@ -1 +1 @@ -{"entries":[],"headings":["further-references"]} \ No newline at end of file +{"headings":["further-references"],"entries":[]} \ No newline at end of file diff --git a/_quarto.yml b/_quarto.yml index 7ce00ca..b3654f5 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -17,6 +17,9 @@ website: - designer.qmd - naming.qmd - glossary.qmd + drafts: + - designer.qmd + draft-mode: visible search: true page-navigation: true back-to-top-navigation: true diff --git a/designer.qmd b/designer.qmd index 8ff5ede..091d2a8 100644 --- a/designer.qmd +++ b/designer.qmd @@ -45,6 +45,3 @@ You can link to your SOP, please provide a DOI in case it is published already. Here can write some additional tips ::: -- After downloading and filling in suitable templates according to your respective research, upload Excel files to the corresponding sub-folders (name as the template/experiment name). Naming convention is described under the [**corresponding tab**](/naming.qmd). -- If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder. -- There are no sub-folders in the non-tabular data folder yet so create one for your publication. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability. \ No newline at end of file diff --git a/docs/designer.html b/docs/designer.html index ba54327..ec90b46 100644 --- a/docs/designer.html +++ b/docs/designer.html @@ -4857,11 +4857,6 @@

corresponding tab. -
  • If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.
    • -
  • There are no sub-folders in the non-tabular data folder yet so create one for your publication. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability.
    • - @@ -5432,7 +5427,7 @@

    var lightboxQuarto = GLightbox({"descPosition":"bottom","loop":false,"openEffect":"zoom","closeEffect":"zoom","selector":".lightbox"}); (function() { let previousOnload = window.onload; window.onload = () => { diff --git a/docs/guide.html b/docs/guide.html index 45e7c77..7995baa 100644 --- a/docs/guide.html +++ b/docs/guide.html @@ -4848,16 +4848,19 @@

    YODA

    -
    + +
    -

    Good to know: It is also possible to publish data straight from YODA.

    +

    It is also possible to publish data straight from YODA.

    +

    Data generators receive an email to register, after which they can access the dedicated website for data upload.

    @@ -4884,9 +4887,11 @@

    Explanation
  • The enm_filesharing is a dump folder that provides a collection place for Excel-based MOMENTUM data that will subsequently be transferred into the online database of eNanomapper. It has sub-folders corresponding to separate experiments. Templates should be uploaded into the fitting folder. If there is no fitting folder, one can simply create one (using lowercase letters and hyphens, if needed).
  • Furthermore, the provision of descriptive metadata in Excel format about other types of data (e.g. microscopy, DNA sequencing etc.) is required. The metadata should contain a link to where these other data types are stored/will be made available (e.g. in YODA or another well-established repository).
  • Data in other formats that is described by a template can be directly placed in this filesharing folder, according to experiment type, to make referencing easier. However, the data owner can choose to make these other files available in another repository as long as clear referencing in templates to linked files is achieved.
    • -
  • The for_publication folder is intended for the minimum ‘data packages’. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these ‘data bundles’ however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom. This folder is rather empty still. Data generators are free to create sub-folders for their intended publications to keep data packages there.
    • +
  • The for_publication folder is intended for the minimum ‘data packages’. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these ‘data bundles’ however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom.
    • +
  • This folder is rather empty still. Data generators are free to create sub-folders for their intended publications to keep data packages there.

    • +

    @@ -5513,7 +5518,7 @@

    How to us });

    -