Getting Started with Partek Flow at NIH

Presented by Joe Wu, PhD (BTEP)
July 24, 2024
ncibtep@nih.gov

What is Partek Flow?

• Point-and-click software that enables analysis of multi-omics sequencing data including:

  • DNA (variant calling)
  • RNA
  • single cell RNA
  • ATAC/ChIP (bulk and single cell)
  • Spatial transcriptomics
  • VDJ profiling

• Users interact with this software through a web browser.

Build Work Flows are Partek Flow

Partek Flow Access for NCI Scientists

NCI holds an institutional license for Partek Flow. Complete the steps below to access this software.

1. Acquire a Biowulf (The High Performance Computing cluster) account — see here for information about how to obtain a HPC account.
2. Make sure that the user's /data directory on Biowulf has enough disk space to hold their Partek Flow files — please fill out this online form if you require more disk space.
3. Request a Partek Flow account — please contact staff@hpc.nih.gov.

Once these steps have been accomplished, copy https://partekflow.cit.nih.gov/flow to a web browser, sign onto the NIH Partek Flow server and start analyzing data.

Partek Flow is Hosted on Biowulf

• Even though Partek Flow is hosted on Biowulf, researchers will not need Unix command line expertise to use this software. However researchers should

  • Know that the analysis data are stored on Biowulf, the NIH high performance computing system.
  • Be able to sign onto the Biowulf cluster and navigate through its directories to find Partek Flow files.

• Investigators will be able to use the immense compute power of Biowulf to analyze large genomic data sets!!!!

Partek Flow Access for non-NCI Scientists

• NHGRI researchers should refer to https://research.nhgri.nih.gov/bi-training.shtml information on accessing Partek Flow. To BTEP's knowledge, NHGRI's Partek Flow instance is not hosted on Biowulf. Contact bioinformatics@nhgri.nih.gov with questions.
• Others at NIH should reach out the NIH Library (see https://www.nihlibrary.nih.gov/resources/tools/partek-flow). Contact Doug Joubert with questions (douglas.joubert@nih.gov).

Learning Objectives

• After this class, participants will

  • Understand the basics of Biowulf needed for using Partek Flow.
  • Know how to sign onto the NIH Partek Flow server and become familiar with the software's user interface.
  • Become familiar with transferring data the NCI CCR Sequencing Facility's Data Management Environment to the NIH Partek Flow server using Globus.
  • Import data into Partek Flow projects.

• Participants will not become Partek Flow experts after this class, but material presented form the basis for continual learning.

Disclaimer

Instructions for data transfer to the NIH Partek Flow server via command line and through the Partek Flow web GUI are also available in the class documentation. However, these will not be discussed during class and will be left for the participants to review at their leisure.