update designer

.quarto/xref/0142f1c3

@@ -1 +1 @@
-{"entries":[],"headings":[]}
+{"headings":[],"entries":[]}

.quarto/xref/63bc2c9a

@@ -1 +1 @@
-{"entries":[],"headings":["further-references"]}
+{"headings":["further-references"],"entries":[]}

_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

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.

docs/designer.html

@@ -4857,11 +4857,6 @@ <h4 class="anchored" data-anchor-id="how-to-design-a-template-that-fits-your-dat
 <p>Here can write some additional tips</p>
 </div>
 </div>
-<ul>
-<li>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 <a href="./naming.html"><strong>corresponding tab</strong></a>.</li>
-<li>If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.</li>
-<li>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.</li>
-</ul>
 
 
 </section>
@@ -5432,7 +5427,7 @@ <h4 class="anchored" data-anchor-id="how-to-design-a-template-that-fits-your-dat
 });
 </script>
 </div> <!-- /content -->
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"openEffect":"zoom","closeEffect":"zoom","descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","loop":false,"openEffect":"zoom","closeEffect":"zoom","selector":".lightbox"});
 (function() {
   let previousOnload = window.onload;
   window.onload = () => {

docs/search.json

@@ -11,7 +11,7 @@
     "href": "guide.html",
     "title": "Step-by-step guide",
     "section": "",
-    "text": "YODA is used as a secure data solution, where data generators can upload the filled templates.\n\n\n\n\n\n\nTip\n\n\n\nMore information and a detailed ‘manual’ about YODA can be found on their website.\n\n\n\n\n\n\n\n\nTip\n\n\n\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 for data upload.\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 tab.\n\n\n\n\n\n\nNote\n\n\n\n\n\nOnly MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.\n\n\n\n\n\n\nThe 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).\nFurthermore, 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).\nData 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.\nThe 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."
+    "text": "YODA is used as a secure data solution, where data generators can upload the filled templates.\n\n\n\n\n\n\nTip\n\n\n\nMore information and a detailed ‘manual’ about YODA can be found on their website.\n\n\n\n\n\n\n\n\nGood to know\n\n\n\n\n\nIt is also possible to publish data straight from YODA.\n\n\n\nData generators receive an email to register, after which they can access the dedicated website for data upload.\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 tab.\n\n\n\n\n\n\nNote\n\n\n\n\n\nOnly MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.\n\n\n\n\n\n\nThe 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).\nFurthermore, 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).\nData 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.\nThe 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.\nThis folder is rather empty still. Data generators are free to create sub-folders for their intended publications to keep data packages there."
   },
   {
     "objectID": "guide.html#footnotes",
@@ -25,7 +25,7 @@
     "href": "designer.html",
     "title": "Template Designer",
     "section": "",
-    "text": "How to design a template that fits your data\n\nNavigate to the template designer of Momentum.\nClick on “Create new draft”\nCan also browse Finalized and Draft Blueprints to see templates designed by others\n\nWhen creating a new draft, a sequence of sheets pop up that need to be populated with information about your data.\n\nPlease provide a name for your template, your name as author and your affiliation or project for the acknowledgement.\n\nChoose your role. Drafts can only be finalized if “data manager” is chosen, however, templates are still functioning when they are not finalized. Please remember that you can always reach out to a data steward at your institute or the responsible person at UU.\n\nYou can link to your SOP, please provide a DOI in case it is published already.\n\n\n\n\n\n\n\n\n\n\n\n\n\nTip\n\n\n\nHere can write some additional tips\n\n\n\nAfter 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.\nIf there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.\nThere 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.\n\n\n\n\n\n Back to top"
+    "text": "How to design a template that fits your data\n\nNavigate to the template designer of Momentum.\nClick on “Create new draft”\nCan also browse Finalized and Draft Blueprints to see templates designed by others\n\nWhen creating a new draft, a sequence of sheets pop up that need to be populated with information about your data.\n\nPlease provide a name for your template, your name as author and your affiliation or project for the acknowledgement.\n\nChoose your role. Drafts can only be finalized if “data manager” is chosen, however, templates are still functioning when they are not finalized. Please remember that you can always reach out to a data steward at your institute or the responsible person at UU.\n\nYou can link to your SOP, please provide a DOI in case it is published already.\n\n\n\n\n\n\n\n\n\n\n\n\n\nTip\n\n\n\nHere can write some additional tips\n\n\n\n\n\n\n Back to top"
   },
   {
     "objectID": "about.html",

guide.qmd

@@ -11,8 +11,9 @@ lightbox: true
 More information and a detailed ‘manual’ about YODA can be found on their [website](https://www.uu.nl/en/research/yoda/guide-to-yoda).
 :::
 
-::: {.callout-tip icon="false" appearence="simple"}
-Good to know: It is also possible to publish data straight from YODA.
+::: {.callout-tip icon="false" appearence="simple" collapse="true"}
+## Good to know
+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](https://dgk.yoda.uu.nl/) for data upload.
@@ -28,10 +29,13 @@ Only MOMENTUM data generators, the responsible person from eNanomapper and data
 -   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.
 
 ![](/images/dataflow_website_v5.png "General flow of MOMENTUM data")
 
+![](/images/datapackage.png "Simple folder organisation for MOMENTUM data")
+
 ### eNanomapper
 
 "The eNanoMapper database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project."[^1]