Workshops

Members of the Consortium conduct LINCS-related workshops

MCF10A Common Project

April 16, 2019

Portland, OR

Members of the LINCS consortium participated in this workshop hosted by the MEP LINCS Center in Portland, Oregon. This workshop was organized into the following sessions: 1) MCF10A Deep Dive, 2) Integrative Analysis, 3) Data Management, and 4) Publication Strategy

Links

Connectivity Map and L1000 Data: Applications and New Developments

April 10, 2019 to April 11, 2019

Wellcome Trust Genome Campus, Hinxton, Cambridge UK

A workshop hosted by EMBL-EBI with presentations from the BD2K-LINCS DCIC (Avi Ma'ayan PhD) and the LINCS Center for Transcriptomics (Aravind Subramanian PhD).

Links

LINCS Connectivity Map Workshop Series 2018

December 4, 2018 to December 6, 2018

Cambridge, MA

The NIH LINCS Program and the Connectivity Map at the Broad Institute created a series of training workshops on the analysis of large-scale perturbational datasets for biological applications.

Links

MCF10A Common Project - Organization and Integrative Analysis

September 12, 2018 to September 13, 2018

Portland, OR

Members of the LINCS consortium participated in this workshop hosted by the MEP LINCS Center in Portland, Oregon. This two-day workshop was organized into the following sessions: 1) Project Overview and Motivation, 2) Overview of Datasets, 3) Integrative Analysis and Modeling, and 4) Data Sharing.

Links

Building RNA-seq Analysis Pipelines with Jupyter

July 3, 2018

New York, NY

Members of the BD2K-LINCS DCIC delivered this workshop to fellows of the BD2K-LINCS DCIC Summer Research Training Program and other members of the biomedical research community at the Icahn School of Medicine at Mount Sinai. During the workshop, participants were guided through the process of RNA-sequencing data analysis and generated interactive Jupyter Notebooks from published datasets using the BioJupies web application (http://biojupies.cloud). Participants then downloaded the generated notebooks onto their laptops, and performed a variety of programming exercises to explore the data and the results of the analyses using Python. Covered topics include interactive data exploration approaches, such as principal component analysis and clustered heatmap analysis, differential gene expression, enrichment analysis. The analysis also included the querying of the RNA-seq signatures against LINCS signatures.

Links

ICSB 2017 Workshop on Drug Response Measurement and Analysis

August 7, 2017

Blacksburg, VA

HMS LINCS researchers delivered an outreach workshop on Drug Response Measurement and Analysis at the International Conference on Systems Biology 2017. They presented the experimental and computational methods they developed to generate reproducible dose-response measurements across cell lines, as well as theoretical approaches to quantify the sensitivity of cells to single drugs and drug combinations.

Links

Computational Biophysics to Systems Biology (CBSB2017)

May 18, 2017 to May 20, 2017

Cincinnati, OH

The BD2K-LINCS Data Science Symposium (DSS 2017) was co-localized with the Computational Biophysics and Systems Biology (CBSB2017) Workshop where Avi Ma'ayan PhD presented "Global Analysis and Visualization of Thousands of Expression Signatures for Drug and Target Discovery" and Stephan Schurer PhD presented "Novel Therapeutic Combinations and Targeted Poly-pharmacology in Glioblastoma".

Links

Clustergrammer: Interactive Heatmap Visualizations Built using D3.js

July 22, 2016

United Nations, New York, NY

Postdoctoral fellow from the BD2K-LINCS DCIC, Nicolas Fernandez PhD (Ma’ayan Lab) held this workshop session at the Data Visualization Camp.

Links

Transcriptomic Signatures of Cardiotoxicity for Protein Kinase Inhibitor Cancer Drugs from Cell Based Assays

June 15, 2016

Broad Institute, Cambridge, MA

Members of the DToxS Center (Marc Birtwistle PhD, Jens Hansen MD and Coen Van Hasselt PhD) held a workshop session at the Systems Biology of Human Disease 2016 meeting at the Broad Institute. This was a hands-on workshop that focused on different aspects of collection, analysis, and quality control of transcriptomics-based cellular signatures of cardiotoxicity.

Links

Clustergrammer: A Web-based Visualization Tool for Making and Sharing Interactive Clustered Heatmaps

February 22, 2016

Pivotal Labs, New York, NY

Postdoctoral fellow from the BD2K-LINCS DCIC, Nicolas Fernandez PhD (Ma’ayan Lab) hosted a workshop on Clustergrammer, which is a web-based matrix visualization tool, built using D3, that enables users to easily generate highly-interactive (zooming, reordering, searching, and filtering) and shareable clustergram-heatmap visualizations. Clustergrammer is an open source project available on GitHub.

Links

UHack

February 20, 2016 to February 21, 2016

University of Miami, Miami, FL

The BD2K-LINCS DCIC was one of the sponsors for the UHack hackathon at the University of Miami. Members of the DCIC participated in this 24-hour hackathon for app development.

Links

Targeted Proteomics Workshop

December 10, 2015 to December 14, 2015

Indian Institute of Technology (IIT) Bombay, India

Jake Jaffe PhD and the members of the LINCS Proteomic Characterization Center for Signaling and Epigenetics held hands-on Skyline workshops/tutorials at the Targeted Proteomics Workshop & International Symposium.

Links

SAMSI Innovation Workshop: Interdisciplinary Approaches to Biomedical Data Science Challenges

July 20, 2015 to July 24, 2015

Research Triangle Park, NC

Stephan Schurer PhD, BD2K-LINCS Data Coordination and Integration Center, served as a mentor in this workshop to guide scientists in the formation of interdisciplinary projects aimed at developing models, methods, and approaches to overcome biomedical data science challenges. During the course of the workshop, participants were exposed to LINCS resources.

Links

NIAAA Workshop: Genomic and Computational Approaches for Biomarker and Drug Discovery

June 19, 2015

San Antonio, TX

The session leaders were Avi Ma’ayan PhD, BD2K-LINCS Data Coordination and Integration Center and Aravind Subramanian PhD, LINCS Center for Transcriptomics. The purpose of this workshop was to bring together (Library of Integrated Network-based Cellular Signatures) LINCS scientists and scientists from the alcohol research community to explore how LINCS resources can facilitate identification of druggable targets and novel and/or repurposed compounds for the treatment of alcohol dependence.

Links

Connectivity Map and LINCS Workshop at the EMBL-EBI

March 18, 2015 to March 19, 2015

Cambridge, UK

Workshop presented by the LINCS Center for Transcriptomics and the LINCS Proteomic Characterization Center for Signaling and Epigenetics.

Links