TIES VM Quick Start Guide

Learn how to install and use the TIES VM

Introduction

The TIES VM snapshot is a Ubuntu Linux VM that has all the TIES software installed and configured. You will be able to add your own documents to TIES and have them processed and searchable through the TIES client installed in the VM. However, you will not be able to participate in or  search other TIES nodes in the TCRN(TIES Cancer Research Network) with this VM.

TIP If you want to allow others to access TIES, enable networking features of the VM or deploy it in a virtualized IT infrastructure.

Getting Help

If you are having trouble getting through the installation, you can get help from the TIES team through two main avenues.


Requirements

  • 5GB Disk Space
  • 3GB RAM
  • VM Player

Step 1: Download and install VMWare Player

DOWNLOAD VMWARE PLAYER

The TIES VM snapshot requires the VMWare Player to run. Download and install it before your proceed.

Step 2: Download and unzip the VM

DOWNLOAD HERE

The TIES VM is distributed as a zipped directory. Download and unzip it to a location on your hard disk. The unzipped directory takes 13GB of space.

TIP If you have issues unzipping, please try using the free zip utility 7Zip.

 

Step 3: Log into VM

You can run the VM by opening the TIES.vmx file in VMWare Player. VMWare may ask you if you moved or copied this VM snapshot. You should answer “copied”.

Ubuntu Login Details

Username ties
Password ties

Step 4: Launch the TIES Client

To launch TIES client, click on TIES icon in the dock on the left hand side. You can also invoke it from the command line by typing “ties”. TIES Client gives you a choice to login into Production or Test Networks. To start off we will use the Test Network as it is loaded with some test data for you to try TIES out with. Use the Test Researcher credentials below to login to the Test Network.

TIES Login Details

Network Role Username/Password
Both Administrator admin/Admin20!3
Production Researcher ties/Password20!3
Test Researcher test/Password20!3

Production Network – is the location where your real data should be loaded. Test Network – is preloaded sample data that you can browse to test the client.

 

Step 5: Try a search

Since the Test Network is loaded with test data, only certain search terms will be found. You can search for “core biopsy” to start things out. That should get you about 44 hits.

 

Loading your own documents in TIES

TIES has an HL7 importer that can import reports in a specific HL7 format.

Place your HL7 files into /opt/ties/HL7  and start the HL7 Pipe Controller if it is not already started. Monitor the logs for any errors.

TIP A sample HL7 file is located in /opt/ties/data/HL7

HL7Importer Configuration Options

The configuration file is found in /opt/ties/pipelines/HL7ImportPipeController/classes/caTIES.properties

 

TIES data is stored in MySQL database. You are welcome to use MySQL Workbench to explore the data in the database.

Username/Password
MySQL DB User ties/ties
MySQL DB Admin root/ties

See Loading Your Data to learn more.

 

Node Administration

TIP Install VMWare Tools (see instructions) to enable shared folders and other helpful VMWare features.

TIES Node

TIES Node is the back-end system that handles all major aspects of the TIES system. To start/stop TIES Node type:

sudo ties-node <start|stop|status>

enter ‘ties’ when prompted for a password


TIES Pipelines

TIES pipelines are stand alone processes that run in the background and process data. To start/stop TIES Pipelines type:

sudo ties-pipelines <start|stop|status>

enter ‘ties’ when prompted for a password You can also start/stop individual pipelines by typing:

ties-HL7-pipe, ties-DeID-pipe, ties-coder-pipe or ties-indexer-pipe


TIES Data

TIES support data in HL7 format. For more details please read this: http://ties.dbmi.pitt.edu/documentation/for-installers/loading-your-data To get started with processing your own data, place HL7 files into

/opt/ties/HL7

A sample HL7 file is located in

/opt/ties/sampledata/HL7

A sample structured data is located in

/opt/ties/sampledata/STRUCTURED_DATA

TIES data is stored in MySQL database. You are welcome to use MySQL Workbench to explore the data in the database MySQL DB User:     ties/ties MySQL DB Admin:    root/ties To completely delete all data from production database type:

clear_ties_data


TIES Directory Structure

/opt/ties/configuration ties node startup script location
/opt/ties/data mysql data location, sql data backup, sample HL7 file
/opt/ties/HL7 location for HL7 files to be imported
/opt/ties/indices Lucene indexes for searching TIES system
/opt/ties/nobletools NLP support tools, s.a. gate and medical dictionaries
/opt/ties/sampledata sample data to test the VM
/opt/ties/slideimages directory for hosting virtual slides
/opt/ties/tomcatHub TIES Hub web services
/opt/ties/tomcatPub TIES Public web services
/opt/ties/tomcatPvt TIES Private web services
/opt/ties/pipelines/HL7ImportPipeController pipeline for importing HL7 data
/opt/ties/pipelines/DeidPipeController pipeline for de-identifying input data
/opt/ties/pipelines/TiesPipeController pipeline to concept coding reports
/opt/ties/pipelines/IndexPipeController pipeline for placing coded reports into Lucene index for searching

TIES Virtual Slides

TIES VM comes bundled with OpenSlide Image server that can serve Whole Slide Images (WSI) also known as virtual slide. OpenSlide Image Server is a vendor neutral image server that supports multiple WSI vendors:

  • Aperio (.svs, .tif)
  • Hamamatsu (.vms, .vmu, .ndpi)
  • Leica (.scn)
  • MIRAX (.mrxs)
  • Philips (.tiff)
  • Sakura (.svslide)
  • Trestle (.tif)
  • Ventana (.bif, .tif)
  • Generic tiled TIFF (.tif)

OpenSlide Image Server is hosted on http://ties-vm/openslide. It can serve WSI files located in /opt/ties/slideimages. You can use bundled OpenSlide viewer to open virtual slides directly. To do so, simply type:

openslide-view [image location]