Our 2017 Program this year included training classes from our Silver Partners who are once again volunteering their staff to conduct our training program:
- Rancho BioSciences
- Clarivate Analytics (formerly Thomson Reuters)
- the Hyve
The Program consisted of training classes held on the last Monday of every month. This year, these classes will include different topics on a quarterly schedule with classes starting at 11AM Eastern.
Classes were 60 to 90 minutes of training plus up to 30 minutes for Q&A.
| Training Class | Date | Instructor | Company | Slides | Recording |
|---|---|---|---|---|---|
| 2019 Training Sessions |
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| Install and Upgrade | July 29 2019 | Michael Mendis | Partners HealthCare, Inc. | Coming Soon |  |
| Preview of v16.4 of the tranSMART Platform | June 24 2019 | Peter Rice | i2b2 tranSMART Foundation, Axiomedix Inc. | SLIDE DECK |  |
| Glowing Bear | April 30 2019 | Ward Weistra & Elisa Cirillo | The Hyve |  |  |
| TranSMART: Complex Clinical Datasets | March 25 2019 | Maren Lowrance | U Kansas Medical Center |  |  |
| Loading Data into tranSMART | February 25, 2019 | Yulia Stovpen | Rancho BioSciences |  |  |
| 2018 Training Sessions |
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| TranSMART v16.2 training using complex clinical datasets | December 17 2018 | Alena Fedarovich | Rancho BioSciences |  |  |
| i2b2 Training Ontology for beginners | July 30 2018 | Michael Mendis | Partners HealthCare, Inc. | COMING SOON |  |
| Installing and Upgrading i2b2 | May 29 2018 | Michael Mendis | Partners HealthCare, Inc. |  |  |
| DATA CURATION & LOADING (using tMDataLoader) | April 30 2018 | Monica Coelho | Rancho BioSciences |  |  |
| i2b2 (HERON) Overview | March 26, 2018 | Maren Wennberg | University of Kansas Medical Center Kansas City, Kansas |  |  |
| 2017 Training Sessions | |||||
| Basic training | December 18, 2017 | Oksana Tyurina | Rancho BioSciences |  |  |
| Data Representation | November 27 2017 | Stephen Wicks | Clarivate Analytics |  |  |
| TranSMART v16.2 training using complex clinical datasets | October 30 2017 | Alena Fedarovich | Rancho BioSciences |  |  |
| tranSMART data loading with tmtk, the Arborist and transmart-batch | September 25, 2017 | Ward Weistra & Jochem Bijlard | The Hyve |  |  |
| Advanced Training | July 31, 2017 | Yulia Skovpen | Rancho BioSciences | SLIDE DECK | RECORDING |
| SmartR: Use of the SmartT workflows will be described and examples presented. There will also be a short section on how to create a new SmartR Workflow | May 31st, 2017 | Sascha Herzinger | U Luxemburg |  |  |
| Introduction to Data Loading for Beginners | April 24, 2017 | Mónica Coelho | Rancho BioSciences |  |  |
| LOADING DATA with tMDataLoader | February 27, 2017 | Natalia Boukharov | Thomson Reuters |  |  |
| Introduction to the tranSMART Platform | January 30, 2017 | Alena Fedarovich | Rancho Biosciences |  |  |
| 2016 Training Sessions |
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| tranSMART Basics | December 20, 2016 | Alena Fedarovich | Rancho Biosciences |  |  |
| tranSMART for beginners | September 26, 2016 | Natalia Boukharov | Thomson Reuters |  |  |
| Data science with tranSMART REST API in Python and R. | August 29, 2016 | Ruslan Forostianov, Piotr Zakrzewski | The Hyve |  |  |
| tranSMART for Beginners | July 25, 2016 | Alena Fedarovich | Rancho Biosciences |  |  |
| ETL using tMDataLoader | July 5, 2016 | Ioannis Pandis, | Thomson Reuters |  |  |
| Exploring Advanced Workflows | May 23, 2016 | Yulia Skovpen | Rancho Biosciences |  |  |
| tranSMART for Beginners | Apr 25, 2016 | Shruthi S Bharadwaj | Thomson Reuters |  |  |
| Loading Data into tranSMART | Mar 30, 2016 | Janneke Schoots Wibo Pipping | The Hyve |  | |
| tranSMART Basics | Feb 29, 2016 | Viktoria Andreeva | Rancho Biosciences |  | |
| tranSMART for Beginners | Jan 25, 2016 | Natalia Boukharov | Thomson Reuters |  |  |
| 2015 Training Sessions |
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| Intro to tranSMART | Dec 21, 2015 | John Obenauer | Rancho Biosciences |  |  |
Recording and slides of the 2017 Training Webinars
| Date | Title | Abstract | Trainer | Company | REGISTRATION REQUIRED |
|---|---|---|---|---|---|
| January 30th, 11AM Eastern | Intro to tranSMART | This class offers an overview of tranSMART platform and its features. We will walk through the Search and Browse interface, and the Analyze interface. The analytic capabilities will be demonstrated using use cases from publicly available datasets. | Alena Fedarovich | Rancho Biosciences | Recordings & Slides |
| February 27th, 11AM Eastern | Clinical and Biomarker data loading 101 | The first part of this training will cover basic data curation and preparing data files for loading into tranSMART. The second part will focus on installing and configuring necessary tools to transfer data files to the server and loading into the database using tMDataLoader. | Natalia Boukharov | Clarivate Analytics | Recordings & Slides |
| March 27th, 11AM Eastern | How to get started with tranSMART development | We'll show you how to set up your tranSMART development environment, give an overview of what repository does what and the basics of the the Core API, REST API and the i2b2/tranSMART database model. | Ewelina Grudzién and Ruslan Forostianov | The Hyve | Postponed |
| April 24th, 11AM Eastern | Data loading for beginners | Data Loading for Beginners" training session will start by a brief introduction of tM user interface and functionalities such as browse and search datasets loaded, variable types and patient cohort selection, saving queries, summary statistics, grid view and advanced workflow. tranSMART 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 Coelho | Rancho Biosciences | Recordings & Slides |
| May 31st, 11AM Eastern (due to US Memorial Day) | SmartR | Use of the SmartT workflows will be described and examples presented. There will also be a short section on how to create a new SmartR Workflow | Sascha Herzinger | U Luxemburg | Recordings & Slides |
| June 26th, 11AM Eastern | Programmatic access to data in tranSMART 17.1: The tranSMART REST API V2 | Learn all the new REST API calls that have become available with the 17.1 version of tranSMART. Access your time series and sample data, low and high dimensional via a programmatic interface. See what is possible and how you can use this to build a REST client on top. | The Hyve | Postponed | |
| July 31st, 11AM Eastern | Advanced training for tranSMART | This webinar will cover major functionalities of tranSMART v.16.1 with focusing on Advanced workflows, preparation of VCF data for Genome Browser, analysis of RNA seq in tranSMART. | Yulia Skovpen | Rancho Biosciences | Recordings & Slides |
| Aug 28th, 11AM Eastern | How to load your data to make the most of it | This 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 Wicks | Clarivate Analytics | Re-scheduled for November 2017 (see below) |
| Sep 25th, 11AM Eastern | How 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 Soon | The Hyve | Recordings & Slides |
| Oct 30th, 11AM Eastern | TranSMART training using complex clinical dataset | An overview of tranSMART using Parkinson’s 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 tools. | Alena Fedarovich | Rancho Biosciences | Recordings & Slides |
| Nov 27th, 11AM Eastern | Cross-study analysis using R Interface | This training will show participants how to analyzing data with R Interface. Examples of cross-study data analysis will be discussed. | Eugene Myshkin | Clarivate Analytics | POSPONED. Replaced by the Aug class by Stephen Wicks. See next row. |
| Nov 27th, 11AM Eastern | How to load your data to make the most of it | This 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 Wicks | Clarivate Analytics | Recordings & Slides |
| Dec 18th, 11AM Eastern | TranSMART Platform basic training | The training will cover overview of basic main features of tranSMART 16.1. We will cover the principles of creating cohorts and working with different workflows. We will explore different functional analyses available in tranSMART in order to evaluate robustness of several putative biomarkers identified in two example studies of uveal melanoma. We will learn how to use correlation analyses, box plot with Anova and clustering techniques to verify reported findings and also to generate novel hypotheses in the form of new gene lists (biomarkers). We will learn how to test new hypotheses on the fly in different studies. | Oksana Tyurina | Rancho Biosciences | Register HERE |
Recordings and Slides from the previous Training Classes: slide deck and recordings