Tools assembly -> tool assembly

CODEOWNERS

@@ -10,10 +10,10 @@
 /pages/contribute/style_guide.md       @martin-nc
 CONTRIBUTING.md       @floradanna @pinarpink
 /pages/your_problem       @DanFaria @floradanna
-/pages/your_role       @MijkeJetten @pinarpink 
+/pages/your_role       @MijkeJetten @pinarpink
 /pages/rdm_cycle       @wittigue @floradanna @smza
-/pages/tools_assembly       @korbinib
-/pages/your_domain       @DanFaria @pinarpink 
+/pages/tool_assembly       @korbinib
+/pages/your_domain       @DanFaria @pinarpink
 /pages/about/about.md       @frederikcoppens @CaroleGoble
 CODE_OF_CONDUCT.md       @frederikcoppens @CaroleGoble
 /assets       @martin-nc @bedroesb

_data/sidebars/main.yml

@@ -65,7 +65,7 @@ subitems:
     description: Browse the RDMkit's catalogue of tools and resources for research data management.
     url: /all_tools_and_resources.html
     hr: True
-  - title: Tools assembly
+  - title: Tool assembly
     description: Find concrete combinations of tools and resources assembled into a workflow for research data management.
     hr: True
     subitems:

pages/about/about.md

@@ -4,7 +4,7 @@ sidebar: about
 ---
 
 ## Who is the RDMkit for?
-The ELIXIR Research Data Management Kit (RDMkit) has been designed to guide life scientists in their efforts to better manage their research data following the FAIR Principles. It is based on the various steps of the data lifecycle, although not all the steps will be relevant to everyone. RDMkit can be navigated via ‘data life cycle’, ‘role’, ‘domain’, ‘problem’, ‘tools and resources’ and ‘tools assembly’. The contents are generated and maintained by the ELIXIR community coming together as part of the [ELIXIR-CONVERGE](https://elixir-europe.org/about-us/how-funded/eu-projects/converge) project.
+The ELIXIR Research Data Management Kit (RDMkit) has been designed to guide life scientists in their efforts to better manage their research data following the FAIR Principles. It is based on the various steps of the data lifecycle, although not all the steps will be relevant to everyone. RDMkit can be navigated via ‘data life cycle’, ‘role’, ‘domain’, ‘problem’, ‘tools and resources’ and ‘tool assembly’. The contents are generated and maintained by the ELIXIR community coming together as part of the [ELIXIR-CONVERGE](https://elixir-europe.org/about-us/how-funded/eu-projects/converge) project.
 
 ## Why are the FAIR principles needed?
 At the heart of FAIR Science lies good data management practice. This is increasingly important as life science research becomes data-intensive and traditional ‘wet labs’ make space for ‘dry (computer) labs’. Having that in mind, the [FAIR Principles](https://www.nature.com/articles/sdata201618) were designed to improve the infrastructure supporting the reuse of research data. The intention of these principles is to act as a guide to improve the **F**indability, **A**ccessibility, **I**nteroperability and **R**euse of digital assets.

pages/contribute/style_guide.md

@@ -39,7 +39,7 @@ In general, we follow the European Commission's [Web Writing Style Guide](https:
     * "The cat that was on the table suddenly got up" is telling us which cat it was. It is important to the meaning of the sentence because you are not talking about any cat, just the cat on the table.
     * "The cat, which was sitting on the table, suddenly got up" is giving us extra information about the cat. The information is not necessary to understand the sentence. You can remove the clause and the sentence will still be clear. Clauses starting with "which" usually begin with a comma.
   * **Titles:** Only the first word and acronyms are capitalised.
-  * **Tools Assembly:** There are multiple tools in one assembly.
+  * **Tool Assembly:** There are multiple tools in **one** assembly.
   * **Training:** training is an uncountable noun and cannot have a plural. You can write "training courses" and "training materials" but not "trainings".
 
 ## Graphic design

pages/rdm_cycle/collecting.md

@@ -18,7 +18,7 @@ Apart from being the source of information to build your findings on, the collec
 
 ## What should be considered for data collection?
 
-Appropriate tools or integration of multiple tools (also called tools assembly or ecosystem) can help you with data management and documentation during data collection. Suitable tools for data management and documentation during data collection are Electronic Lab Notebooks (ELNs), Electronic Data Capture (EDC) systems, Laboratory Information Management Systems (LIMS). Moreover, online platforms for collaborative research and file sharing services could also be used as ELN or data management systems.
+Appropriate tools or integration of multiple tools (also called tool assembly or ecosystem) can help you with data management and documentation during data collection. Suitable tools for data management and documentation during data collection are Electronic Lab Notebooks (ELNs), Electronic Data Capture (EDC) systems, Laboratory Information Management Systems (LIMS). Moreover, online platforms for collaborative research and file sharing services could also be used as ELN or data management systems.
 
 Independently of the tools you will use, consider the following, while collecting data
 

pages/tool_assembly/NO_tsd_assembly.md

@@ -0,0 +1,33 @@
+---
+title: Assembly page title
+search_exclude: true
+contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
+tags: [<!---REPLACE THIS with comma separated list of (outgoing) tags to other pages related to this page--->]
+---
+
+<!--- Tool Assembly pages should detail a particular data management tool assembly which covers one more life cycle stages from an infrastructural or domain perspective. For an example for an infrastructural example, please see: https://github.com/elixir-europe/rdmkit/blob/master/pages/tools_assembly/nels_assembly.md 
+In the event that you describe a domain specific tool assembly and no adequate Domain page exists, consider first contributing to create one or raising a GitHub issue.  --->
+
+## Introduction 
+
+<!--- In this section you should provide a brief overview of the tool assembly, mentioning and putting into context the challenges that are particularly solved by the tool assembly and define potential users  --->
+
+
+## section 1 title
+
+### What can you use the TOOL ASSEMBLY for?
+<!--- Sections within Tool Assembly pages (aside from "Introduction" at the start and "Relevant tools and resources " at the end) should be used to describe the potential usage of the tools and the tool assembly --->
+
+
+<!--- ## Section 2 Title --->
+<!--- Add more sections as needed. --->
+...
+
+## Training for the tool assembly? <!--- (optional) --->
+
+{% include tess.html search="<!---TAG--->" %}
+
+## Tools used within the tool assembly?
+<!--- Automatically generated table; edit the TAG below to the tag for this page, so that tools that have this page's tag are listed here. You can get the tag for this page from the [list of tags](https://github.com/elixir-europe/rdmkit/blob/master/_data/tags.yml). If it isn't listed there, please raise an issue.--->
+
+{% include toollist.html tag="<!---TAG--->" %}

pages/tool_assembly/TEMPLATE_tool_assembly.md

@@ -0,0 +1,33 @@
+---
+title: Assembly page title
+search_exclude: true
+contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
+tags: [<!---REPLACE THIS with comma separated list of (outgoing) tags to other pages related to this page--->]
+---
+
+<!--- Tool Assembly pages should detail a particular data management tool assembly which covers one more life cycle stages from an infrastructural or domain perspective. For an example for an infrastructural example, please see: https://github.com/elixir-europe/rdmkit/blob/master/pages/tool_assembly/nels_assembly.md 
+In the event that you describe a domain specific tool assembly and no adequate Domain page exists, consider first contributing to create one or raising a GitHub issue.  --->
+
+## Introduction 
+
+<!--- In this section you should provide a brief overview of the tool assembly, mentioning and putting into context the challenges that are particularly solved by the tool assembly and define potential users  --->
+
+
+## section 1 title
+
+### What can you use the TOOL ASSEMBLY for?
+<!--- Sections within Tool Assembly pages (aside from "Introduction" at the start and "Relevant tools and resources " at the end) should be used to describe the potential usage of the tool and the tool assembly --->
+
+
+<!--- ## Section 2 Title --->
+<!--- Add more sections as needed. --->
+...
+
+## Training for the tool assembly? <!--- (optional) --->
+
+{% include tess.html search="<!---TAG--->" %}
+
+## Tools used within the tool assembly?
+<!--- Automatically generated table; edit the TAG below to the tag for this page, so that tools that have this page's tag are listed here. You can get the tag for this page from the [list of tags](https://github.com/elixir-europe/rdmkit/blob/master/_data/tags.yml). If it isn't listed there, please raise an issue.--->
+
+{% include toollist.html tag="<!---TAG--->" %}

pages/tools_assembly/nels_assembly.md → pages/tool_assembly/nels_assembly.md

@@ -1,43 +1,43 @@
 ---
 title: NeLS assembly 
 contributors: [Korbinian Bösl, Federico Bianchini, Erik Hjerde]
-summary: This is an example of a Data Management tools assembly, NeLS as an infrastructure is funded and aimed for researchers in Norway and their collaborators.
+summary: This is an example of a Data Management tool assembly, NeLS as an infrastructure is funded and aimed for researchers in Norway and their collaborators.
 ---
 
-## What is the NeLS data management tools assembly?
+## What is the NeLS data management tool assembly?
 
 The [Norwegian e-Infrastructure for Life Sciences (NeLS)](https://nels.bioinfo.no/) is an infrastructure provided by [ELIXIR Norway](https://elixir.no/). [NeLS](https://doi.org/10.12688/f1000research.15119.1) provides necessary tools for Data Management and covers [Planning](planning), [Processing](processing), [Analysing](analysing) and [Sharing](sharing) Data Life Cycle stages and offers [Data Storage](storage) capacities.
 
-## Who can use the NeLS data management tools assembly?
+## Who can use the NeLS data management tool assembly?
 
 NeLS and the underlying infrastructure are accessible for researchers in Norway and their collaborators. Eligible researchers can apply for storage quotas and get support through the National (Norwegian) bioinformatics support desk [[email protected]](mailto:[email protected]). Most of the tools in NeLS are open source and can be reused.
 
 
 
-## For what can you use the NeLS data management tools assembly?
+## For what can you use the NeLS data management tool assembly?
 
-{% include image.html file="NeLS_toolkit.svg" caption="Figure 1. The Norwegian e-Infrastructure for Life Sciences (NeLS) Data Management tools assembly." alt="NeLS RDMkit" %}
+{% include image.html file="NeLS_toolkit.svg" caption="Figure 1. The Norwegian e-Infrastructure for Life Sciences (NeLS) Data Management tool assembly." alt="NeLS RDMkit" %}
 
 You can access all tools in NeLS using the the national solution for secure login and data sharing in the educational and research sector [FEIDE](https://www.feide.no/), when coupled with [ELIXIR AAI](https://elixir-europe.org/services/compute/aai).
-The NeLS Data Management tools assembly provides support with [Data Management Planning](planning) through an [instance of the Data Steward Wizard](https://elixir-no.ds-wizard.org) following the guidelines of the major national and European funding bodys. Dedicated references guide you through national infrastructure, resources, laws and regulations and also include the [Tryggve ELSI Checklist](https://neic.no/tryggve/links/) for Ethical, Legal and Social Implications. Soon you will be able to submit storage request forms for [Data Storage](storage) in NeLS with defined access permissions through the Data Stewardship Wizard.
+The NeLS Data Management tool assembly provides support with [Data Management Planning](planning) through an [instance of the Data Steward Wizard](https://elixir-no.ds-wizard.org) following the guidelines of the major national and European funding bodys. Dedicated references guide you through national infrastructure, resources, laws and regulations and also include the [Tryggve ELSI Checklist](https://neic.no/tryggve/links/) for Ethical, Legal and Social Implications. Soon you will be able to submit storage request forms for [Data Storage](storage) in NeLS with defined access permissions through the Data Stewardship Wizard.
 
 [Data Storage](storage) is the core functionality of NeLS and builds upon a 3 layer tiered system: the first layer is intended for short-term storage when computing, processing and analysing data; the second layer of medium capacity (NeLS) is intended for sharing and storing active research data, while the third layer (StoreBioinfo) of high capacity is intended for longer storage until end of a project.
 Data in the second (NeLS) layer is protected against hardware failure on disk or server level and snapshots of the data are kept for 4 weeks. The third layer is implemented on top of the national research data storage solutions operated by Sigma2 Uninett A/S and is protected against data loss by snapshots and geo-replication.
 National Norwegian research infrastructures, such as the Norwegian sequencing infrastructure [NorSeq](https://www.norseq.org/) can directly upload data to your NeLS project for you.
 
-For [Processing](processing) and [Analysing](analysing) your data, the NeLS Data Management tools assembly provides access to a national [instance of Galaxy](https://usegalaxy.no) with ~2000 tools.
+For [Processing](processing) and [Analysing](analysing) your data, the NeLS Data Management tool assembly provides access to a national [instance of Galaxy](https://usegalaxy.no) with ~2000 tools.
 Data stored in NeLS is directly available within this Galaxy instance, hence you do not need to keep local copies of your data.
 
 In order to help you keeping track of metadata, NeLS is integrated with the [SEEK](https://seek4science.org/) web-based cataloguing and sharing platform. You can use any instance of SEEK such as the public [FAIRDOMHub](https://fairdomhub.org/) to [manage metadata](metadata_management) associated with your data stored in NeLS and access the data through SEEK. SEEK uses the ISA (Investigation, Study, Assay) structure to organise your data and recommended minimal information such as sample characteristics, technologies, measurements and relationships between samples, data and models. Public SEEK instances like the [FAIRDOMHub](https://fairdomhub.org/) can also be used to collaborate on data and to [share](sharing) them publicly. If you are doing modelling, you can also use the inbuilt [JWS Online](https://jjj.mib.ac.uk/) simulator for your SBML models.
 
-One recommended way to share your data is to deposit them in the [ELIXIR Deposition Databases for Biomolecular Data](https://elixir-europe.org/platforms/data/elixir-deposition-databases). The NeLS Data Management tools assembly will soon offer tools to help you with the deposition step for data stored in NeLS.
+One recommended way to share your data is to deposit them in the [ELIXIR Deposition Databases for Biomolecular Data](https://elixir-europe.org/platforms/data/elixir-deposition-databases). The NeLS Data Management tool assembly will soon offer tools to help you with the deposition step for data stored in NeLS.
 
 
-## Where can I find training materials and events about the NeLS data management tools assembly?
+## Where can I find training materials and events about the NeLS data management tool assembly?
 
 {% include tess.html search="Norway" %}
 
 
-## What tools are used within the NeLS data management tools assembly?
+## What tools are used within the NeLS data management tool assembly?
 
 {% include toollist.html tag="nels" %}

pages/your_problem/metadata_management.md

@@ -15,7 +15,7 @@ Due to the large variety of experiments, techniques and collaborative studies th
 ### Considerations
 * Write the documentation in such a way that someone else who is known to the field can not mis-interpret any of the data, even if they tried.
 
-* It is best practice to use one appropriate tool or an integration of multiple tools (also called tools assembly or ecosystem) for data documentation during a project. Suitable tools for data documentation are Electronic Lab Notebooks (ELNs), Electronic Data Capture (EDC) systems, Laboratory Information Management Systems (LIMS). Moreover, online platforms for collaborative research and file sharing services (such as OSF) could also be used as ELN or data management systems. Check with your institute to know what is offered.
+* It is best practice to use one appropriate tool or an integration of multiple tools (also called tool assembly or ecosystem) for data documentation during a project. Suitable tools for data documentation are Electronic Lab Notebooks (ELNs), Electronic Data Capture (EDC) systems, Laboratory Information Management Systems (LIMS). Moreover, online platforms for collaborative research and file sharing services (such as OSF) could also be used as ELN or data management systems. Check with your institute to know what is offered.
 
 * Independently of the tools you will use, data documentation is needed at two levels: documentation about the entire study or project and documentation about individual records, observations or data points.
   * Study-level documentation describes the project title and summary, study aims, authors, institutions involved, funds, methods, licence and identifier for each dataset, folders structure, file naming conventions, versioning system, relation between files or tables and other general information.