Moderator:
Rudy Potenzone VP Marketing tranSMART Foundation
Clinical and Biomarker data loading 101
Trainer:
Natalia Boukharov Clarivate Analytics SILVER Member of tranSMART
Monday Feb 27th, 2017
2017 Training Program
• Our revised Training Program will consist of training classes held on the last Monday of every month. • The classes will start at 11AM Eastern. tranSMART for beginners – only twice in 2017 Loading data in to TranSMART Exploring tranSMART Advanced workflows Developers training
• Monthly topics will vary: – – – –
• Training is donated by tranSMART Members Rancho Biosciences, Clarivate Analytics (formerly Thomson Reuters), and the Hyve
Data loading for beginners
April
August
U Luxemborg
SmartR
May
September How to get started with modelling your data for tranSMART
March
Rancho Biosciences
To Be Announced
The hyve
February
2017 Training Program January Intro to tranSMART
July
Clarivate Anayltics
How to get started with tranSMART development The Hyve
Advanced training for tranSMART
November
December TranSMART training using complex clinical dataset
Clinical and Biomarker data loading 101 Clarivate Anayltics
Rancho Biosciences
To Be Announced
Rancho Biosciences
Rancho Biosciences
October TranSMART training using complex clinical dataset
Clarivate Anayltics
The Huyve
June Programmatic access to data in tranSMART 17.1
Rancho Biosciences
• In May, there will be special training classes at the eTriks Conference in Barcelona • And BioIT World in Boston
LOADING DATA with tMDataLoader Natalia Boukharov Translational Data Management Clarivate Analytics
[email protected] February 27, 2017
State of innovation
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Loading data on Mac
Data loading set up for Windows
Other HDD examples
GSE36700 data curation example
tranSMART Foundation wiki
tMDataLoader wiki
TRAINING OUTLINE
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tMDataLoader
• tMDataLoader is a tool developed by Clarivate Analytics (Formerly the IP & Science business of Thomson Reuters)
• Open-source software, written in Groovy and available for download for both Oracle and PostgreSQL versions of tranSMART
https://github.com/ThomsonReuters-LSPS/tMDataLoader/
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DATA LOADING HELP: TF WIKI • tranSMART Foundation wiki useful information • Curating and Loading data (ETL) • Data curation standards development • TranSMART ETL Guide (Kettle) • TranSMART ETL Guide (tMDataLoader) • TranSMART Guide for Manual Data Deleting • TranSMART Tree Library • Supported Data Types • Curated Data Repository • Data loading tutorials
https://wiki.transmartfoundation.org/
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WinSCP (Windows Secure Copy) is a free and open-source SFTP, FTP, WebDAV and SCP client for Microsoft Windows for secure file transfer between a local and a remote computer
MOVING DATA to the SERVER
tranSMART ETL Server
Set it up and connect
Your Computer
RUNNING tMDataLoader Set it up and connect
• PuTTY is a free and open-source terminal emulator which supports several network protocols, including SSH
• SSH allows remote command-line login and remote command execution
Run tMDataLoader
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CYBERDUCK
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Cyberduck is an open source client for FTP and SFTP, WebDAV, OpenStack Swift, and Amazon S3, available for macOS and Windows
Additional contact information:
Natalia Boukharov
[email protected]
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