Hey DCoP Members!
There’s been some posts on AMP PD, accessing AMP PD data and the Terra platform. I wanted to combine these topics and point you to some AMP PD Terra Resources.
Once you have Tier 1 or Tier 2 access for AMP PD data, you will have access to all of these resources. There are getting started workspaces that are meant to help you get started with the data, show you where in GCS it is and how to access it.
I want to first point you to the AMP PD featured workspace, which has compiled all of the Terra resources available through AMP PD. If you do not have Tier 1 or Tier 2 access, you are still able to see this public facing featured workspace.
I want to draw your attention to the Simulated Proteomics Data Set workspace as well. This workspace uses a simulated proteomics data set and takes you through a few analyses with the data. This is meant to provide a preview of what types of analyses AMP PD has provided through Terra. Note that you do need a Terra account and a terra billing project. @psaffie had a great post on explaining the Terra Platform if you are interested in more info.
Now, getting into the AMP PD resources.
There are AMP PD generated “Getting Started” workspaces, meant to help you get started with the data. This workspace familiarizes you with the available data, locations and data formats.
There are also AMP PD analysis workspaces, which can help you dive deeper into the data and get more familiar with the data. Some notebooks within the workspace can merge -omics data with other data types, including demographics and other available clinical data. Several of the notebooks within this workspace do things like generate a PCA, boxplots or other visualizations. Note that these workspaces are meant to be an example of how the data can be used.
Lastly, there are the community provided workspaces, which have been provided by the AMP PD community. This include more complex analyses and pipelines that you can use for your own data analysis.
AMP PD has created a webinar series to familiarize users with some of these resources and Terra workspaces. In addition, AMP PD tries to put an emphasis on the community provided workspaces so that those in the community that generate these resources can showcase their work.