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minor changes #1

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7 changes: 4 additions & 3 deletions FlowDataManagementRecommendations.md
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Expand Up @@ -8,9 +8,9 @@ Currently flow cytometry data is exported on to the local computer attached to t
> **_NOTE:_** It is recommended that researchers use [Handover](https://wehieduau.sharepoint.com/sites/rc2/SitePages/HandOver-Data-Sharing.aspx) to transfer their data. As it provides additional data security by ensuring that only the named researchers are able to access the folder.

## NAS Storage and FlowJo: _What is a NAS and why does the storage location matter so much for Flowjo?_
A NAS is a Network Attached Storage. Similar to a hard drive, a NAS provides additional storage which can be viewed through finder/file explorer. However, as implied in the name, a NAS uses a network connection (such as WEHI_staff WiFi) to connect your computer to the storage drive. Due to the use of a network connection, any disruptions to the network will break your connection to the storage and lead to file corruption.
A NAS is a **Network Attached Storage**. Similar to a hard drive, a NAS provides additional storage which can be viewed through finder/file explorer. However, as implied in the name, a NAS uses a network connection (such as WEHI_staff WiFi) to connect your computer to the storage drive. Due to the use of a network connection, any disruptions to the network will break your connection to the storage and lead to file corruption.

Hence, analysis via Flowjo which is a local laptop/desktop only software, should _never_
Hence, analysis via Flowjo which is a local laptop/desktop only software, should **_never_**
be performed directly on files stored on a NAS file system. These files should be downloaded on to the computer on which analysis is occurring. Upon completion of analysis, the Flowjo workspace file and exported output tables should be uploaded to the appropriate VAST project folder and backed-up onto Stornext, if appropriate.

> **Note**: Milton, the WEHI HPC, does _not_ use a network based connection to VAST/Stornext and as such analysis run on the HPC may occur directly on files in those locations
Expand All @@ -21,13 +21,14 @@ Hence, analysis via Flowjo which is a local laptop/desktop only software, should
Researchers may be familiar with the window pop-up in Flowjo, where Flowjo indicates that it can't find the FCS files associated with the workspace. Typically, this warning occurs after moving either the workspace file (`.wsp`/`.flowjo`) or the FCS files into other folders or locations. This is because Flowjo doesn't retain a copy of your data in it's workspace, instead Flowjo records a "relative path" from the location of the workspace file and the data.

Taking the example folder structure below:

![folder](exampleFolders.png)

Flowjo will use the workspace (`.wsp` ) file as the anchor for describing where the data is. In this case, the data could be described as "from the location of the workspace file, we go back one folder level and locate the 'data' folder". As such, retaining and mirroring this folder structure as you move around the workspace/data files, will ensure that Flowjo is able to find the associated data .

## Cloud-based analysis software (OMIQ/Cytobank): _Where can my data be stored long-term?_

> **Policy Note**: If you are using any cloud platforms, you must fill in the [WEHI Cloud Usage Form](PLACEHOLDER) to ensure that ITS & RCP are aware of the platforms in use.
> **Policy Note**: If you are using any cloud platforms, you must fill in the [WEHI Cloud Usage Form](https://forms.monday.com/forms/29cbac9efec6ff0e9b3cc2e6437ac5fa?r=apse2) to ensure that ITS & RCP are aware of the platforms in use.

Cloud based analysis software has rapidly become popular for flow cytometry analysis, with OMIQ and Cytobank as the primary contenders. Due to the cloud based nature of these softwares, data must be uploaded to the appropriate cloud servers to be analysed with their analysis software. For data that is located on a NAS storage device, the data should be downloaded to your local computer and from the local copy to the cloud service. This intermediate storage of data on your local computer minimises the risk of data corruption, due to the network disruptions.

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5 changes: 4 additions & 1 deletion README.md
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# FlowCytometryDataManagement
# FlowCytometryDataManagement


* [RCP Recommendations](FlowDataManagementRecommendations.md)