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











Loading data on Mac

Data loading set up for Windows

Other HDD examples

GSE36700 data curation example

tranSMART Foundation wiki

tMDataLoader wiki

TRAINING OUTLINE



2

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/

3

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/

4

5

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

6

CYBERDUCK

7

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]

8

Copy of tMDataLoader Training 27 Feb 2017.pdf

Moderator: tranSMART Foundation. VP Marketing. Rudy Potenzone. Trainer: Natalia Boukharov. Clarivate Analytics. SILVER Member of tranSMART. Monday.

2MB Sizes 1 Downloads 172 Views

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