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Getting Started with Partek Flow at NIH

Learning Objectives

After this class, participants will

  • Know how to acquire access to Partek Flow
  • Become familiar with approaches for transferring data to the NIH Partek Flow server such as Globus
  • Be able to import data into a Partek Flow project

What is Partek Flow?

Partek Flow is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing sequencing data through command line and/or code. It enables the analysis of high dimensional multi-omics sequencing data including DNA, RNA, single cell RNA, ATAC/ChIP, and spatial transcriptomics. At NIH, Partek Flow is hosted on the Biowulf High Performance Computing (HPC) cluster. Researchers interact with Partek Flow through a web browser using a URL supplied by Biowulf after a Biowulf and Partek Flow account has been established. This enables investigators to take advantage of the compute power offered by HPC while using a graphical user interface to construct a sequencing data analysis workflow. Partek Flow also enables the creation of publication quality visualizations.

Note

NCI holds a license for Partek Flow.

Instructions for Obtaining Access to Partek Flow

NCI researchers can find instructions for accessing Partek Flow at https://bioinformatics.ccr.cancer.gov/btep/partek-flow-bulk-and-single-cell-rna-seq-data-analysis/. Here is what is needed:

Once these steps have been accomplished, use https://partekflow.cit.nih.gov/flow to sign onto the NIH Partek Flow server.

Overview of the Partek Flow User Interface

Once connected to the Partek Flow server, sign on to Partek Flow. Replace username with the user's own NIH user name. The password may not correspond to the user's Biowulf/NIH password as it will be set when Biowulf staff creates the Partek Flow account.

Upon logging in, users will be taken to Partek Flow's main page. In this page users can access

  • Help
  • View a list of existing projects
  • Create new project
  • Transfer files (this does not use Globus)
  • Access user profile

Users can access help documentation, how-to videos and information for contacting support under the "Help" menu. The email for Partek support is support@partek.com.

Where applicable, users can find links to how-to video and documentation for specific tasks, such as importing data.

The settings section is divided into five tabs, which are expandable to reveal more options.

Click on the user profile tab at the top right to reveal the option for changing settings.

User profiles can be viewed and edited under "My Profile" in the "Personal" settings section. Note the information regarding the user's Biowulf /data folder storage usage and quota.

Users can access an example bulk and single cell RNA sequencing dataset under the "System" setting tab.

An important feature in the settings is that users can manage genomic references and annotations by clicking on "Library files" under "Components".

Users can view "Systems resources" under the "Usage" settings. Here, users are informed of how many tasks are running and waiting in the queue. A visualization of Biowulf Partek Flow worker nodes is also provided.