Merge branch 'main' into 13-measurements

docs/how_to/install_this_plugin.md

@@ -1,4 +1,8 @@
 # Install This Plugin
 
-!!! note "Attention"
-    TODO
+To install this plugin follow (part 4 of the FAIRmat tutorial 13)[https://github.com/FAIRmat-NFDI/AreaA-Examples/tree/main/tutorial13/part4] or read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/plugins/plugins.html#add-a-plugin-to-your-nomad) for all details on how to deploy the plugin on your NOMAD instance.
+
+
+If you already have an Oasis, you just need to add the line
+`git+https://github.com/FAIRmat-NFDI/nomad-unisyscat-plugin.git@main` to the plugin.txt in your Oasis repositorium.
+

docs/how_to/use_this_plugin.md

@@ -1,10 +1,32 @@
 # How to Use This Plugin
 
-This plugin can be used in a NOMAD Oasis installation.
+This plugin can be used in a NOMAD Oasis installation. Check the tips in [Install this plugin](install_this_plugin.md) for details.
 
-## Add This Plugin to Your NOMAD installation
+Once the Oasis is deployed, you can generate different entries as shown below.
 
-Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/plugins/plugins.html#add-a-plugin-to-your-nomad) for all details on how to deploy the plugin on your NOMAD instance.
+## Add new sample entries
+<iframe src="https://scribehow.com/embed/Upload_custom_data_entry_with_specific_schema_in_NOMAD_Oasis__mRg47mlZSpOSQ5G_HFlq7A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
 
-!!! note "Attention"
-    TODO
+## Add instrument entry
+<iframe src="https://scribehow.com/embed/Create_a_Custom_Instrument_Schema_in_Nomad_Oasis__-RkLffMjT22hj9BAipE1KQ" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## Add measurement entry
+
+<iframe src="https://scribehow.com/embed/Create_a_Measurement_Upload_in_NOMAD_Oasis__xqwktvKPQUSPK8aT0E-58A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## Upload gaussian DFT
+
+<iframe src="https://scribehow.com/embed/Upload_DFT_Files_Using_Nomad_Oasis_Interface__qdOffE1DSnSuvKsjP8dwZw" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## run a jupyter notebook to visualize the pdb file
+
+<iframe src="https://scribehow.com/embed/Visualizing_pdb_files_through_NOMAD_Remote_Tools_Hub__IdryIk1lRpaDI8TQm6ajbg" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## User management
+
+<iframe src="https://scribehow.com/embed/Add_Users_to_a_Nomad_Oasis_Upload__hGhkAMCATXWdHGjeleDB0A" width="100%" height="640" allowfullscreen frameborder="0"></iframe>
+
+## Use the dedicated UniSysCat Explore App to get an overview and find entries
+
+!!! Attention:
+TODO add introduction of App

docs/index.md

@@ -1,22 +1,54 @@
 # Welcome to the `nomad-unisyscat` documentation
 
-A example plugin for a demonstration for UniSysCat.
+![Combined logos for NOMAD Oasis and UniSysCat](images/Logos.png)
+
+Welcome to the NOMAD Oasis demonstration! This documentation provides an overview of the example dataset, supported entry types, and details about the data and publications used in this demonstration. Our goal is to help UniSysCat users effectively manage and explore research data using NOMAD.
+
+This demonstration highlights [NOMAD Oasis](https://nomad-lab.eu/nomad-lab/nomad-oasis.html), a data management and sharing platform developed as part of the [FAIRmat](https://www.fairmat-nfdi.eu/fairmat/) project within the National Research Data Infrastructure ([NFDI](https://www.nfdi.de/)). NOMAD facilitates the collection, storage, analysis, and dissemination of research data, adhering to the principles of FAIR (Findable, Accessible, Interoperable, and Reusable) data management.
+
 
 ## Introduction
 
-!!! note "Attention"
-    TODO
+This example demonstrates how NOMAD effectively manages diverse research data, particularly in computational and experimental research. It encompasses various entry types, showcasing NOMAD's flexibility and robust data integration features.
 
-<div markdown="block" class="home-grid">
-<div markdown="block">
+The dataset used in this demonstration originates from a paper by C. Lorent *et al.*
+[(Angew. Chem. Int. Ed. 2021, 60, 15854–15862)](doi.org/10.1002/anie.202100451).
 
-### Tutorial
+The paper introduces an innovative experimental setup for spectroscopic analyses of gas-converting metalloenzymes. It allows for adjustments in gas composition and temperature, enabling the preparation of specific redox states for characterization using complementary spectroscopic tools such as IR, EPR, or NRVS.
 
-TODO
+![Alt text](images/TOC%20figure%20from%20paper.png)
 
-- [Tutorial](tutorial/tutorial.md)
 
-</div>
+This NOMAD Oasis demonstration illustrates the Research Data Management (RDM) of experiments focusing on the regulatory [NiFe]-hydrogenase from Ralstonia eutropha (ReRH). The experiments involve preparing the catalytic intermediate (Ni<sub>a</sub>-C) using highly concentrated lyophilized samples of ReRH treated either in H<sub>2</sub> or D<sub>2</sub>, followed by characterizing the sample via IR, Raman spectroscopy (RR), and Nuclear Resonance Vibrational Spectroscopy (NRVS). Additionally, it includes the calculation of vibrational frequencies.
+
+The demonstration covers creating entries for different parts of the experiment, uploading raw data files from measurements and calculations, visualizing them in NOMAD, and demonstrating how different project members can collaborate.
+
+
+### **Supported Entry Types**
+In this demonstration, NOMAD supports multiple entry types, including:
+
+1. **Experimental Data:**
+- Tabular data files with the .dat file format.
+- Binary data files with the .DSC file format.
+- Electronic Lab Notebook (ELN) entries for samples, instruments, and processing, based on the NOMAD schema.
+
+
+2. **Computational data:**
+- Output files from Density Functional Theory (DFT) calculations based on the Gaussian 09 package.
+
+### **Research Data:**
+
+The data used in this NOMAD Oasis demonstration come from various sources, ensuring a comprehensive representation of the types of entries NOMAD can manage. The primary sources include:
+
+- In-situ Infrared (IR) spectroscopy for ReRH_Ni<sub>a</sub>-C_H.
+- <sup>57</sup>Fe nuclear resonance vibrational spectroscopy (NRVS), both measured and simulated, for ReRH_Ni<sub>a</sub>-C_H and ReRH_Ni<sub>a</sub>-C_D.
+- Electron paramagnetic spectroscopy (EPR) for ReRH_Ni<sub>a</sub>-C_H.
+- Density functional theory (DFT) calculations using the Gaussian package for ReRH_Ni<sub>a</sub>-C_H and ReRH_Ni<sub>a</sub>-C_D.
+
+By exploring this demonstration, users will gain a clearer understanding of how NOMAD can streamline research data management processes, enhance data quality, and foster collaboration across UniSysCat.
+
+
+<div markdown="block" class="home-grid">
 <div markdown="block">
 
 ### How-to guides
@@ -25,19 +57,11 @@ How-to guides provide step-by-step instructions for a wide range of tasks, with
 
 - [Install this plugin](how_to/install_this_plugin.md)
 - [Use this plugin](how_to/use_this_plugin.md)
-- [Contribute to this plugin](how_to/contribute_to_this_plugin.md)
-- [Contribute to the documentation](how_to/contribute_to_the_documentation.md)
 
 </div>
 
 <div markdown="block">
 
-### Explanation
-
-The explanation [section](explanation/explanation.md) provides background knowledge on this plugin.
-
-</div>
-<div markdown="block">
 
 ### Reference
 

docs/reference/references.md

@@ -2,3 +2,9 @@
 
 !!! note "Attention"
     TODO
+
+!!! note "List of (Entry Data type) Schemas from the Plugin"
+    EPR
+    IRSpectroscopy
+    NRVSpectroscopy
+