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HTS Bioinf - NIPT Hardware and IT Infrastructure

Scope

This document describes the hardware and IT infrastructure of the NIPT project.

Responsibility

HTS bioinformaticians are responsible for setting up NIPT hardware and IT infrastructure (with help from NSC bioinformaticians).

Hardware and IT components

  • 1 Hamilton ML STAR robot - dedicated (used only for NIPT)
  • 1 VeriSeq Onsite Server (VOS) - dedicated
  • 2 NextSeq's - dedicated
  • 1 PCR machine - dedicated
  • 1 SpectraMax - dedicated
  • 1 SwissLab (SWL) - shared (also used for other projects)
  • 1 Clarity LIMS (LIMS server) - shared
  • 1 Windows server("Endpoint") - shared
  • 1 File Server ("Boston") - shared
  • 1 Linux Server ("gdx-login") - shared

Networks

Except for SWL which is in the Oslo Universitetet Sykehus (OUS) network, all other servers and machines are connected in the local NSC network.

The OUS network and the NSC network are isolated. To transfer files between these two networks, Ironkeys are used.

IT Infrastructure

The core of the NIPT IT infrastructure consists of:

  • Hamilton ML STAR (for lab prep)
  • NextSeq (for sequencing)
  • VOS (for sequence data analysis and NIPT report generation).

Software on the Hamilton robot's instrument control computer can communicates with the VeriSeq server using a proprietary Internet Protocol (IP) based protocol. NextSeq is configured to use a share named "diagRuns" (\\boston.nscamg.local\diagRuns; local path: /ifs/data/diag/runs) on the Linux File Server named boston to store sequence data files. This "diagRuns" share is mounted on the VOS and is monitored by VeriSeq NIPT Solution software for new sequencing runs. Once a run is finished, data analysis starts.

An auxiliary storage area "NIPT-Lab"(D:\Felles\NIPT-Lab) is established on the Windows server named "Endpoint", for exchanging files between the Clarity LIMS and the Hamilton robot's instrument control computer. This storage area (\\endpoint.nscamg.local\NIPT\Lab) is mounted on the LIMS server, SpectraMax and the Hamilton robot's computer using the SMB protocol.

The VOS exposes an SMB share "output" (\\veriseq.ous.nsc.local\output). A series of reports generated along with the whole NIPT workflow, i.e., lab-prep, sequencing and Veriseq NIPT data analysis, are stored in this share. The "output" share is mounted on the Clarity LIMS server. The Clarity integration and automation system monitors this share.

The VOS sends notifications over email (SMTP). A local mail server receives these notifications and makes them available to clients via the IMAP protocol.

The VOS's "output" shares, and the share from boston, are mounted on a Linux server gdx-login, which is used to orchestrate the data backup to TSD.