TIES VM Quick Start GuideLearn how to install and use the TIES VM
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.|
If you are having trouble getting through the installation, you can get help from the TIES team through two main avenues.
- 5GB Disk Space
- 3GB RAM
- VM Player
- 1 Introduction
- 2 Getting Help
- 3 Requirements
- 4 Step 1: Download and install VMWare Player
- 5 Step 2: Download and unzip the VM
- 6 Step 3: Log into VM
- 7 Step 4: Launch the TIES Client
- 8 Step 5: Try a search
- 9 TIES Node
- 10 TIES Pipelines
- 11 TIES Data
- 12 TIES Directory Structure
- 13 TIES Virtual Slides
Step 1: Download and install VMWare Player
The TIES VM snapshot requires the VMWare Player to run. Download and install it before your proceed.
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
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
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.
|MySQL DB User||ties/ties|
|MySQL DB Admin||root/ties|
See Loading Your Data to learn more.
|TIP||Install VMWare Tools (see instructions) to enable shared folders and other helpful VMWare features.|
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 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 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
A sample HL7 file is located in
A sample structured data is located in
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:
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]