New Resource: L1000 Characteristic Direction Signature Search Engine (L1000CDS2)

Posted on: August 17th, 2015 by Sherry Jenkins No Comments

L1000CDS2, developed by Ma’ayan Laboratory for the BD2K-LINCS DCIC, queries gene expression signatures against the LINCS L1000 to identify and prioritize small molecules that can reverse or mimic the observed input expression pattern.

BD2K-LINCS DCIC Resources

Data Standards Update

Posted on: August 17th, 2015 by Sherry Jenkins No Comments

The Data Standards page has been updated to reflect the most recent standards releases in LINCS Production Phase 2.

Data Releases: DToxS, HMS LINCS, LINCS Center for Transcriptomics, LINCS PCCSE, and NeuroLINCS

Posted on: August 13th, 2015 by Sherry Jenkins No Comments

LINCS centers recently released the first wave of data which includes RNA-seq, L1000, P100, SWATH, Cell Viability and Growth, KinomeScan, and RPPA profiling human cell lines treated with many drugs and small molecules.

The data releases and milestones page describes the collections of data released and planned to be released to the public by the LINCS consortia.

Workshop: Interdisciplinary Approaches to Biomedical Data Science Challenges: SAMSI Innovations Lab | July 20-24, 2015

Posted on: August 6th, 2015 by Sherry Jenkins No Comments

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.  The workshop took place from July 20 to 24, 2015 at the Hamner Conference Center at the NC Biotechnology Center, 15 TW Alexander Drive in Research Triangle Park, North Carolina.

Workshop Summary | Detailed Description

Workshop: Genomic and Computational Approaches for Biomarker and Drug Discovery | June 19, 2015

Posted on: April 13th, 2015 by Sherry Jenkins No Comments

Purpose of this workshop is 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.

Date | Time | Location

  • Friday, June 19, 2015 from 2-5 PM
  • Grand Hyatt (Room: Travis C/D), San Antonio, TX

Register

  • Please RSVP by May 1, 2015 to Matthew Reilly at reillymt@mail.nih.gov
  • Space is limited to 50 participants

Agenda

Welcome and Opening Remarks
Matthew Reilly PhD and Ajay Pillai PhD, NIH

Hands-on Session: Web Apps and Tools
Session Leaders: Avi Ma’ayan PhD, BD2K-LINCS Data Coordination and Integration Center and Aravind Subramanian PhD, LINCS Center for Transcriptomics

This session will consist of a hands on demonstration of currently available web apps and tools from the LINCS Common Fund program. Participants will learn how to apply these tools to their own research programs. Please bring your laptop computer and gene expression or other genomic data to analyze.

Additional Information

  • Please register and create a lincscloud.org account before the workshop.
  • Your genomics datasets you bring to analyze should be formatted either as (1) official gene symbols or (2) Affymetrix U133A probe IDs. Some of the web tools require a list of both up-regulated and down-regulated gene lists and some of the tools only accept gene symbols.
  • Because the majority of the LINCS datasets use human cell lines, gene sets should be annotated for mammalian species.
  • When you RSVP for the workshop, please indicate your area of expertise: genomics, computational or other.
  • Also, if you already have experience with working with any of the LINCS tools, you are welcome to submit questions/concerns, suggestions or other feedback in advance of the workshop. You can submit your questions etc., to the workshop organizer: Matthew Reilly at reillymt@mail.nih.gov.

Administrative Supplements to Extend the Scope and Reach of LINCS Datasets

Posted on: February 28th, 2015 by Sherry Jenkins No Comments

This notice (NOT-RM-15-102) announces an opportunity to request administrative supplements to existing NIH research grants, to support generation of new data that will also advance the goals of the LINCS program. Please view the funding opportunities page for more details.

Call for External Collaborations with the BD2K-LINCS Data Coordination and Integration Center

Posted on: February 24th, 2015 by Avi Maayan No Comments

The BD2K-LINCS DCIC announces a call for applications for the next round of external data science research projects. The call is for two year projects that would leverage LINCS generated data through application of novel computational methods. For more information, please visit: http://www.lincs-dcic.org/#/edsr. Please visit the funding opportunities page for more details.

LINCS Cell Line Data Integrated into ChEMBL

Posted on: February 20th, 2015 by Sherry Jenkins No Comments

CHEMBL now provides CHEMBL IDs for all cell lines stored in their database and also cross references to the LINCS project.

chembl_screenshot

LINCS Investigators Present at the AACR Special Conference on Computational and Systems Biology of Cancer

Posted on: February 8th, 2015 by Sherry Jenkins No Comments

February 8-11, 2015
The Fairmont San Francisco
San Francisco, California

Conference Co-Chairpersons
Andrea Califano, Columbia University, New York, New York
Brenda J. Andrews, University of Toronto, Toronto, Ontario, Canada
Peter K. Jackson, Stanford University, Stanford, California

View Program

Spatial Systems Biology and Cancer
Joe W. Gray, MEP LINCS Center

Using Single-cell Pharmacology to Improve Drug Design
Peter K. Sorger, HMS LINCS Center

Lean Data Integration Strategy in Cancer Systems Biology and Systems Pharmacology
Avi Ma’ayan, BD2K-LINCS Data Coordination and Integration Center

Transcriptional Landscape of Drug Response Guides the Design of Specific and Potent Drug Combinations
Marc Hafner, HMS LINCS Center

Spotlight on LINCS Information FramEwork (LIFE)

Posted on: January 28th, 2015 by Sherry Jenkins No Comments

BioGPS Spotlight on the LINCS Information FramEwork (LIFE) which is a novel knowledge-based, extensible information system of interconnected components that leverages semantic-web technologies and domain level ontologies.

The full article is posted here.

NIH Launches a United Ecosystem for Big Data

Posted on: January 8th, 2015 by Sherry Jenkins No Comments

12 Big Data to Knowledge Centers of Excellence Funded

Article about the recently funded Big Data to Knowledge Centers of Excellence was published in Biomedical Computation Review. The Data Integration and Cellular Signaling section of the article describes the BD2K-LINCS Data Coordination and Integration Center’s efforts.

The full article is posted here.

NIH invests almost $32 million to increase utility of biomedical research data

Posted on: October 9th, 2014 by Sherry Jenkins No Comments

News release published by the National Institutes of Health about the Big Data to Knowledge (BD2K) initiative. The BD2K-LINCS Data Coordination and Integration Center is one of the components of the new BD2K awards.

The BD2K-LINCS Data Coordination and Integration Center will be a data coordination center for the NIH Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program, which aims to characterize how a variety of types of cells, tissues and networks respond to disruption by drugs and other factors. The center will support data science research focusing on interpreting and integrating LINCS-generated data from different data types and databases in the LINCS-funded projects. This center is co-funded by BD2K and the NIH Common Fund.

http://www.nih.gov/news/health/oct2014/od-09.htm

NIH awards aim to improve understanding of cell pathways, development of new therapies

Posted on: September 11th, 2014 by Sherry Jenkins No Comments

News release published by the National Institutes of Health about the funding of six Data and Signature Generating Centers for the Library of Integrated Network-based Cellular Signatures (LINCS) program.

The LINCS program aims to catalog and analyze cellular function and molecular activity in response to perturbing agents — such as drugs and genetic factors — that are potentially disruptive to cells. LINCS researchers then will measure the cells’ tiniest molecular and biochemical responses, and use computer analyses to uncover common patterns in these responses — called “signatures.” LINCS data will be freely available to any scientist.

http://www.nih.gov/news/health/sep2014/nhgri-11.htm