# An Introduction to the CLEX Research Workflow

Below we describe 2 standard workflows that researchers might follow:

1. Typical for users of NCI's High Performance Computing (HPC) resources
2. Typical for non-NCI users

For NCI Users
-------------
<details><summary>Generic knowledge</summary>

  * [Shell](Shell.md)
  * [SSH](SSH.md)
  * [Introduction to NCI](Introduction_to_NCI.md)
  * [Storage management at NCI](Storage_management_at_NCI.md)
  * [Git Version control](Git.md)
  * [Cloud](Cloud.md)
  * [Data formats](FileFormats.md)
</details>

<details><summary>Planning resource needs - Aidan rev. Paola</summary>
 
  * [Compute and Storage Resources](Resources.md)
</details>

<details><summary>Finding data to run the model on (or to analyse) - Paola rev. Holger</summary>

  * [Data resources at NCI](NCI_data.md)
  * [Other data resources](remote_data.md)
  * [Accessing data remotely with THREDDS and OPenDAP](opendap.md)
</details>

<details><summary>Running a model - Holger rev. Scott</summary>

  * Pre-requisites: [Introduction to NCI](Introduction_to_NCI.md)
  * Pre-requisites: [Shell](Shell.md)
  * Pre-requisites: [SSH](SSH.md)
  * Configuring the model
    * [UM](Configuring_UM.md)
    * [payu / MOM](payu.md)
    * ACCESS
  * Running the model
    * UM
    * MOM
    * ACCESS
  * Postprocessing
  (Shouldn't this be part of Analysing?)

</details>

<details><summary>Analysing model results (or any data) - Scott rev. Danny</summary>

  * [Analysis Basics](AnalysisBasics.md)
  * [Plotting](Plotting.md)
  * [Big datasets](BigDatasets.md)
</details>

<details><summary>Code development and management - Danny rev. Claire</summary>

  * Pre-requisite: Version control
      * [SVN](SVN.md)
      * [Git](Git.md)
  * [Fortran development](Fortran.md)
  * [Python development](Python.md)
  * Debugging (See specific language for details)
  * [Code publishing](Code-publishing.md)
</details>

<details><summary>Publishing data - Claire rev. Aidan</summary>

  * [Open Access Requirements](Open_Access_details.md)
  * [Publication process](Publication_process_details.md)
  * [Complete a Data Management plan](DMP_details.md)
  * [Format your data](Data_formatting.md)
</details>

For Non-NCI Users
-----------------
<details><summary>Finding data to run the model on (or to analyse)</summary>
  * [Other data resources](remote_data.md)
  * [Accessing data remotely with THREDDS and OPenDAP](opendap.md)
</details>

<details><summary>Running a model locally</summary>
  * ???

</details>

<details><summary>Code development and management</summary>

  * Fortran basics
  * Python basics
  * Debugging
  * Version control
    * Svn
    * Git
  * Publishing
</details>

<details><summary>Local anaylsis</summary>
  * ???

</details>

<details><summary>Publishing data</summary>

  * ???
</details>