Getting Started With Server Analysis

From Array Suite Wiki

OmicSoft Studio Server-based analysis

OmicSoft Server allows users with OmicSoft Studio to use a centralized server to manage and share projects, and perform computation-intensive analysis. With OmicSoftServer, users can take advantage of powerful server resources, including High-Performance Computing Clusters and computing on the Cloud. The following video will help get you started in server-based OmicSoft Studio analysis.

If you have trouble viewing the videos on this page, you can find them here.

Server-Based project basics

Creating a Server-based project

This video will walk through creating your first server project, including connecting to a server, adding data to the server, creating a server-based OmicSoft Studio project, adding data to that project, and sharing your project data.

  • Connect to an OmicSoft Server [00:33]
  • Add data to the server [01:32]
  • Create a server-based project [02:38]
  • Add server data to a project [03:38]
  • Publish a project [04:56]

Browse Published Projects

Projects that have been published to OmicSoft Server can be viewed and explored. These projects can then be copied, viewed, filtered, and shared with colleagues.

  • Browse all projects on server [00:20]
  • Filter projects by metadata [00:38]
  • View Metadata for selected project [01:03]
  • Display project data structure [01:39]
  • Open or share project for analysis [02:15]

Search Projects

You can search projects on OmicSoft Server by metadata, and even subset the analyses within those projects by genes of interest.

  • View projects matching search and filter terms [00:22]
  • Subset projects by gene name [00:47]
  • Modify and share project Views [01:35]

Sample Management Basics

OmicSoft Suite includes a set of tools for managing data sets associated with samples, grouping samples into SampleSets, and running pipeline scripts on SampleSets.

Register Samples and SampleSets on OmicSoft Server

OmicSoft Suite includes a Sample Management system that allows you to track and group samples, and include those samples in OmicSoft Studio Analysis. Samples are added to OmicSoft Server by Registration Files, which can also include SampleSet and Pipeline script sections.

  • Check expected Sample/SampleSet columns for your Array Server [01:05]
  • Sample Registration File structure [01:42]
  • Associate multiple files with a sample [03:00]
  • Group samples in a SampleSet within a registration file [03:21]
  • Submit sample registration file to OmicSoft Server [03:40]
  • Identify missing metadata in sample registration file [04:05]
  • Group registered samples as a separate SampleSet [05:17]

Browse and Search Registered Samples

Samples and SampleSets that are registered on your OmicSoft Server can be browsed and searched by metadata, allowing you to quickly find the data you are looking for.

  • Browse and view samples within a SampleSet [00:24]
  • Group samples into SampleSets in the Sample Browser [00:57]
  • Search samples by SampleID and metadata [01:13]

Run Samples through Pipeline Script

Pipeline Scripts allow flexible execution of bioinformatics workflows on your data. Samples and SampleSets that have been registered on your OmicSoft Server can be processed by Pipeline Scripts during sample registration, through OmicSoft Server and OmicSoft Studio.

  • Run SampleSet through pipeline from Sample Browser [00:12]
  • Run SampleSet through pipeline to local analysis project [00:35]
  • Run pipeline from Sample Registration file [01:40]
  • Add sample data to Genome Browser [02:54]
  • Group sample tracks by Sample Registration file metadata [03:28]

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