The i2b2 tranSMART Foundation 2019 Training Program offers entry level and advanced webinars on i2b2 and tranSMART by our training partners.  We will add more sessions soon.

Recordings of previous Training Webinars can be found HERE.

Please use the Registration links below to sign up for a class or two.

DateTitleAbstractTrainerCompanyREGISTRATION REQUIRED
January 28th
No training webinar this month.
February 25th, 11AM EasternHow to get your data into tranSMARTDuring this session we will guide you on the process required to get your data into tranSMART. TranSMART curation and loading workflow will be discussed and we will demonstrate this process by using sample public data. Learn how to transform and map your dataset into tM navigation tree. Demonstration of the data manipulation process required to load different data types supported by tM will include clinical data, for which we will highlight the importance of data cleaning and standardization using defined ontologies, and how to prepare high dimensional data files such as gene expression data. Following data files preparation, we will guide you on the data loading process using tM ETL tool: how to organize your source data the folder and files and how to run the ETL tool, demonstrating the main commands and sharing some tips on how to troubleshoot data loading issues.Yulia SkovpenRancho BiosciencesRecordings & Slides
March 25th, 11AM EasternBasics of i2b2This training will cover basic tips on using the i2b2 interface for the new user. We will review how to find data points of interest using the i2b2 hierarchy as well as the search by names and search by code features. Additionally, we will look at creating a cohort of patients, using the same financial encounter, and using the timeline and demographic plugins.Maren WennbergU Kansas Med CtrRecordings & Slides
April 29th, 11AM EasternIntroduction to Glowing Bear, the modern tranSMART interface, and Fractalis visual analyticsGlowing Bear (https://glowingbear.app) is the modern interface for the tranSMART data warehouse. Leverage new tranSMART 17.1 functionality and build cohorts you were not able to build before.

Its use cases include:
Feasibility queries, with a powerful cohort selection interface supporting longitudinal research questions such as: “How many patients had treatment A from the year 2016 until now?”
Hypothesis forming and testing with the cross table and Fractalis visual analytics, in which a range of interacting visualisations from box plot to survival plot can be used to explore a dataset.
Data distribution portal, with powerful access controls and export functionality.

Since Glowing Bear was developed as a stand alone tool, it is not limited to querying just tranSMART. In principle, Glowing Bear can be used to explore any database backend via the API, as long as the data models are compatible.

In this training we will help you getting started with the most advanced tranSMART interface to date, with your own account on the The Hyve’s public demonstration server!
Elisa Cirillo - Product owner Glowing Bear
Ward Weistra - Data warehousing expert
The HyveRecordings & Slides
May 28th, 11AM Eastern (due to US Memorial Day)i2b2 Training Ontology for beginnersThis webinar will introduce users to the i2b2 ontology and how it is setupMike MendisPartnersRecordings & Slides
June 24th, 11AM Eastern
This webinar will introduce the newest features of the tranSMART Platform in version 16.4
Peter RiceAxiomedixRecordings & Slides
July 29th, 11AM Easterni2b2 Training Install and UpgradeThis training will talk about the install process of i2b2 using both the source code and docker on a Linux machine and also go over the upgrade from a earlier version to the latestMike MendisPartnersRecordings & Slides
Aug 26th, 11AM Eastern
Summer break.
No webinar scheduled.
Sep 30th, 11AM Eastern
No Session Scheduled.
No webinar scheduled.
Oct 28thAn overview of the 16.4 tranSMART PlatformThis webinar will demonstrate the newest features and updates of the tranSMART Platform in version 16.4Peter RiceAxiomedixCANCELLED. We will reschedule this shortly.
Nov 25th, 11AM EasternHow to load your data into tranSMART make the most of itThis webinar will focus on practical solutions to data mapping into tranSMART tree. Examples of different ways to map variables to get the most of your data analysis using tranSMART analytics will be discussed.Stephen WicksClarivate AnalyticsREGISTER
Dec 23rd
Holiday Break
No webinar scheduled.

The i2b2 tranSMART Foundation 2018 Training Program consisted of training classes that covered tranSMART and i2b2.


Our 2018 Program

DateTitleAbstractTrainerCompanyREGISTRATION REQUIRED
March 26th, 11AM EasternIntroduction to i2b2This training will cover basic tips on using the i2b2 interface for the new user. We will review how to find data points of interest using the i2b2 hierarchy as well as the search by names and search by code features. Additionally, we will look at creating a cohort of patients, using the same financial encounter, and using the timeline and demographic plugins.Maren WennbergU Kansas Med CtrRecording & Slides
April 30th, 11AM EasterntranSMART Data loading for beginnerstranSMART curation workflow will be discussed and we will use sample data (GEO data) to demonstrate how to transform and map dataset into tM navigation tree. Demonstration of the curation process required to load data types supported by tM will include clinical data curation, for which we will highlight the importance of data cleaning and mapping clinical variables using defined ontologies, and how to prepare high dimensional data files using gene expression as an example. After preparing the data files we will show the folder/file structure required to load data using tM ETL tool, and how to use the ETL tool (main commands) and how to troubleshoot data loading issues.Monica Beato CoelhoRancho BiosciencesRecording & Slides
May 29th, 11AM Eastern (due to US Memorial Day)i2b2 Training Install and UpgradeThis training will talk about the install process of i2b2 using both the source code and docker on a Linux machine and also go over the upgrade from a earlier version to the latestMike MendisPartnersRecording & Slides
July 9th, 11AM EasternAn overview of the new 16.3 tranSMART PlatformThis webinar will provide a walk-through of the basic capabilities of the latest 16.3 versopm of the tranSMART Platform.Peter RiceAxiomedixRecording & Slides
July 30th, 11AM Easterni2b2 Training Ontology for beginnersThis webinar will introduce users to the i2b2 ontology and how it is setupMike MendisPartnersRecording & Slides
Aug 27th, 11AM EasternHow to load your data into tranSMART make the most of itThis webinar will focus on practical solutions to data mapping into tranSMART tree. Examples of different ways to map variables to get the most of your data analysis using tranSMART analytics will be discussed.Stephen WicksClarivate AnalyticsRecording & Slides
Sep 24th, 11AM Easterni2b2 training using geonomicsThis training will talk about loading 133 genomics data from the 1000 geonome project and querying it using the i2b2 interfaceMike MendisPartnersPOSTPONED
Oct 29th, 11AM EasternHow to get started with modelling your data for tranSMART: Modelling and loading with the Arborist and tranSMART-batch.The training will show you the basis of how to set up the Python package for tranSMART Arborist and work in Jupyter Notebook to transform your data and shape the tree for loading in tranSMART.
Next we'll cover the basics of loading the data with transmart-batch to your tranSMART database.
Coming SoonThe HyveComing soon
Nov 27th, 11AM Easterni2b2/tranSMART PlatformThe combined version of the latest verion of i2b2 witht the latest version of tranSMART will be demonstrated and the key features explored in this training webinar. This version merges key capabilities of each platform allowing them to be used in combination as well as with the new extended version of SmartR, now called Fractalis.Paul AvillachHarvardPostponed until early 2019
Dec 17th, 11AM EasternTranSMART training using complex clinical datasetAn overview of tranSMART using Parkinson Data. The webinar will demonstrate clinical and biological data analysis using two curated Parkinson's datasets from the Michael J Fox Foundation. Clinical and biological data from more than 1,500 people with and without Parkinson's in the Parkinson's Progression Markers Initiative (PPMI), and 220 moderate to advanced Parkinson's patients and control volunteers in the Fox Investigation for New Discovery of Biomarkers (BioFIND) studies will be used to demonstrate the visualization and analysis toolsAlena FedarovichRancho BiosciencesREGISTER

NOTE:  classes for MAY and DECEMBER are changed to avoid US holiday conflicts.

Class instructor time is being provided at no cost to the Foundation by Sponsors Rancho Biosciences, Clarivate Analytics, the Hyve and the University of Kansas and Axiomedix.  We expect to be adding more classes and more contributors as the year unfolds.

Classes generally will be 60 minutes of training plus up to 30 minutes for Q&A.

Virtually unlimited attendance:  up to 100 per session!!  But you must register for each class you would like to attend

 Every class will be recorded and the recording and slide deck will be made available here within one day of the class.

 


Recordings and Slides from the Training Classes:   slide deck and recordings will be posted shortly after each webinar!  


This TRAINING Program is brought to you by the TRAINING Working Group – HOME PAGE.