A PDF version of the LINCS Agenda is: here.  The agenda is also pasted below.

LINCS Investigator Meeting


November 15-16, 2012

Lister Hill, NIH, Bethesda, Maryland 20852-1699




Day 1: Thursday, November 15, 2012

8:00 – 8:30 am              Registration

8:30 – 8:45 am              Welcome, Overview and Introductions

                                    Mark Guyer

Session 1: Data Production and Data Access

Moderators: Ajay Pillai

8:45 – 9:45 am              U54 Updates

20 minute presentations, 5 minutes for questions. Focus on data generation and accessibility, and new science.

·         Broad Institute: Large Scale Expression Analysis of Cellular States

·         Harvard Medical School

·         Joint Project (10 minutes):

9:45 – 10:45 am            U01 Technology Development

20 minute presentations.  Update on technology development, data generation capacity, and TCP data generation.

·         Arizona State University: Live-Cell Microarray For High-Throughput Observation Of Metabolic Signatures

·         Broad Institute: Accelerated Protein Signaling Signature (Ms-Based Approach)

·         Yale University: Integrated microchip for high-content, high-throughput analysis of single cell phosphoprotein signatures


10:45 – 11:05 am           BREAK


11:05 – 11:35 am           Panel with Technology Development U01 and U54 PIs: Generation and accessibility of LINCS data


11:35 – 11:55 am           LINCS Trans-Center Project: Data generation and analysis update. 

11:55 – 12:15 pm          Data Working Group: Update & Future

Stephan Schurer

12:15 pm – 1:15 pm      LUNCH



Session 2: Data Access and Tools for Biomedical Researchers

Moderator:  Jennie Larkin

1:15 – 3:00 pm              Updates (U54s, Comp U01s, Collaborative Supplements)

                                    15 minute presentations

                                    Miami: LINCS Information FramEwork (LIFE)

                                    Cincinnati: Integrated LINCS (iLINCS) Data Portal

Broad U54: Broad WebApps: Interrogate L1000 profiles with biologist-friendly user interfaces

Broad U54: lincscloud: Cloud-based data access and compute

HMS (Josh Stuart): Linking genomic perturbations to transcriptional signatures reveals cancer cell circuitry.

Methodist: itNETZ Tool Package

Columbia (Mukesh Bansal): Network dysregulation following drug perturbation reveals drug mode of action


3:00 –  3:30 pm             BREAK

3:30 – 4:15pm               5 Minute Demonstration for each tool

                                    Miami: LINCS Information FramEwork (LIFE)

                                    Cincinnati: Integrated LINCS (iLINCS) Data Portal

HMS (Avi Ma’ayan): Interactive Web and Mobile App for Visualization and Analysis of L1000 Data.

HMS (Jeremy Muhlich): Pathway Browsing LINCS data via a New User Interface

                                    Methodist: itNETZ Tool Package

                                    Methodist: pLINDAW Data Warehouse

Broad U01 (Mike MacCoss): Skyline and Panorama: Tools for the development and dissemination of quantitative proteomics methods and results.


4:15 –  6:15 pm             Poster Session & Hands-on “Try the Tools”

5:45 –  6:15 pm             Steering Committee Meeting NIH–PI

                                    In Lister Hill Auditorium

7:15 pm                        Dinner @ Lebanese Taverna

(PIs and Co-PIs, ESP, NIH)

Day 2: Friday, November 16, 2012

8:00 – 8:15 am              Evan Snyder: A springboard for delineating the intracellular signaling pathways in neuropsychiatric disorders: using hiPSCs from bipolar patients to study lithium targets & its mechanism of action

8:15 – 8:45 am              U01 Computational & Technology Development: Columbia


Session 3: Outreach & Tools

Moderator:  Stephan Schurer & Aravind Subramanian


8:45 – 9:15 am              Outreach Discussion/Report (30 minutes): DREAM and LINCS data access; data normalization consensus and LINCS best practices; other outreach to MLP, ENCODE, CTD2, others, March workshop, Nov/Dec 2013 LINCS Public Meeting etc. (Aravind)

9:15 – 10:10 am            Hands-on “Try the Tools”

10:10 – 10:30 am           BREAK

10:30 – 11:00 am           Discussion: Missing Tools and Visualization Challenges



Session 4: Round Table Discussions

Moderator:  Peter Sorger

 11:00 – 11:30 am           Evaluating community response and needs

                                    Panel: Caroline Shamu, Aravind Subramanian, Deirdre Meldrum, Jennie Larkin

·         What can we do in the next 4 months?


11:30 – 12:00 pm          Easing the burden of navigation/access of LINCS tools & data for community: Reflections from and on the presentations and hands-on demos on Day 1

                                    Panel: Stephan Schurer, Mario Medvedovic, Xiaobo Zhou, Avi Ma’ayan, Ajay Pillai

·         What can we do in the next 4 months?

 12:00 pm                      Meeting Adjourns



12:00 – 12:30 pm          NIH-ESP meeting to discuss scientific scope of Bridge Yr &  Phase 2

                                    Break-out room


12:30 – 1:00 pm            NIH-ESP-PI meeting to discuss scientific scope of Bridge Yr &  Phase 2

                                    Break-out room 

 2:00 – 3:00 pm              LINCS NIH Project Team Meeting

The PT meeting will be in conference room 7N-710 in Building 38A (the same building as Lister Hill Auditorium).