BD2K-LINCS-Perturbation Data
Coordination & Integration
Center
Applicant Information Webinar for
RFA-HG-14-001
Ajay Pillai and Jennie Larkin
January 13, 2013
1:00 - 2:30 PM EDT
RFA-HG-14-001 Applicant Information
Webinar
BD2K-LINCS-Perturbation Data Coordination and
Integration Center (DCIC) (U54)
Today’s Webinar:
• BD2K and LINCS program introduction
• Overview of new FOA
• Questions
Big Data To Knowledge (BD2K): Overview
A trans-NIH initiative
BD2K Mission
enable biomedical scientists to capitalize more fully the
Big Data being generated by the research community
http://bd2k.nih.gov/
BD2K: Background
• Major challenges in using biomedical Big Data
include:
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Locating data and software tools.
Getting access to the data and software tools.
Standardizing data and metadata.
Extending policies and practices for data and software
sharing.
– Organizing, managing, and processing biomedical Big Data.
– Developing new methods for analyzing & integrating
biomedical data.
– Training researchers who can use biomedical Big Data
effectively.
BD2K Centers
• There was a separate call for Investigator-initiated Centers
(RFA-HG-13-009)
• This will be the first NIH-specified BD2K center.
• This center will focus on perturbation – response data,
including that generated by the LINCS consortium.
• This Center will include the BD2K focus areas:
– Collaborative environments and technologies
– Data Integration
LINCS aims to inform a network-based
understanding of biological systems in health
and disease that can facilitate drug and
biomarker development.
LINCS is:
 Developing a library of molecular and cellular
signatures that describe how different cell
types respond to a variety of perturbations.
 Addressing challenges in high-throughput
data generation, data integration,
annotation, and analysis.
 Actively exploring collaborations with new
biomedical research communities.
Human cell types
LINCS: Library of Integrated Network-based
Cellular Signatures
Perturbations
• RNAi
• small molecules
http://lincsproject.org
LINCS Program (2014 – 2020)
• LINCS goals
– inform a network-based understanding of cellular functions and
response
– expand the scope and richness of cellular responses to be measured.
– support the addition of a broader and more informative range of
human cell types, perturbations, and measurements.
• LINCS Program Structure
– 3-5 Data and Signature Generating Centers (RFA-RM13-013) to be
funded in FY14
– One BD2K-LINCS Perturbagen Data Coordination and Integration
Center (RFA-HG14-001) to be funded in FY15
– 6 year program with Mid-Course Review (~July 2017)
Background:
LINCS Data and Signature Generating Centers
• Data and Signature production at scale, within first year of
award (tens of thousands of data points per year)
• Cell Types: human cells (cell lines, primary tissue, iPS cells and
their differentiated derivatives)
• Perturbagens:
– Pilot: small molecules, growth factors, and genetic (knockdown or upregulation by gene overexpression)
– These will continue but applicants may propose other perturbations
• Assays:
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Should be medium to high throughput
Provide measures of wide interest to biomedical researchers
Should be flexible and amenable to multiple cell types
Should be replicable with high level of QC/QA under SOPs
BD2K-LINCS Perturbagen DCIC
HG-14-001
• Aims in both section I and IV of RFA: read both
carefully
• 1 award, $5M in 2015. Future year amounts will
depend on annual appropriations.
• Application budget may be up to $3 million direct
costs per year, not including the F&A costs of
subcontracts.
• 5-yr duration, it is a cooperative agreement
• Familiarize yourself well with RFA-RM-13-013
• Data science is described in RFA-HG-13-009.
BD2K-LINCS Perturbagen DCIC
Goals
• address significant data science challenges
associated with perturbagen-response
datasets
• establish a community resource for
perturbagen-response data
• coordinate LINCS consortium activities
• Goal: enable advances in understanding of
cellular function and its relationship with
disease and normal biology
BD2K-LINCS Perturbagen DCIC
• Integrated Knowledge Environment
– Data Integration:
• integrating LINCS data with other perturbation data and
other non-perturbation datasets
– Collaborative Environments and Technologies:
• utilize novel methods to provide access while
supporting data attribution and provenance
– Support Unified Access to LINCS DSGC Resources:
• Support single-point of access for community to DSGC
and DCIC tools & data
• For bench & computational scientists
LINCS Data/Signature Access
• Each DSGC will build an appropriate database and an
underlying infrastructure to support queries and
other analytical requirements on their datasets
• Metadata annotation by DSGCs for both data and
software resources is crucial.
• LINCS will have a distributed data resource and
infrastructure to support queries
• LINCS aims to create a single user interface via the
separate DCIC for all of the LINCS resources for all
biomedical researchers, including computational
biologists
BD2K-LINCS Perturbagen DCIC
• Data Science Research Collaborations
– Internal innovative DSR projects related to
perturbation data; short-term; adaptable/flexible;
– External Data Science Collaborations:
• bring in novel expertise and analytical capabilities, to
engage in high-risk high-reward approaches
• set aside $700,000 in direct costs each year
• identify 3 collaborative projects (lasting 12 months)
with groups that are not part of the application
• Propose a plan to identify three such innovative
projects each year of the funded grant
BD2K-LINCS Perturbagen DCIC
• Consortium Coordination and Administration
– May request up to $100,000/yr for BD2K
coordination efforts
– Support Incorporation of LINCS-related Data Types
from External Resources
• You do not expected to replicate other databases, but
can retain relevant indexes/summaries for efficiency in
retrieval
– Coordinate Annotation of Data, Tools, and
Resources
• Enable coordination activities for the LINCS consortium
(DSGCs and the DCIC)
BD2K-LINCS Perturbagen DCIC
• Community Training and Outreach
– Data science
• address questions of access and use of perturbationtype by community
– Access to LINCS Resources
• Work with LINCS DSGC to establishing the LINCS
resource & approach within multiple biomedical
communities.
• Propose how your training/outreach will enable
subsets of the biomedical community to leverage the
whole LINCS resource.
DCIC: program administration
• Cooperative agreement, with substantial
collaboration between LINCS grantees and
involvement of program staff.
– Integral part of LINCS Steering Committee with relevant
and appropriate leadership role to enable overall LINCS
goals.
– Participate in BD2K Working Groups and other suitable
activities including annual BD2K meetings.
• Questions: lincsproject@mail.nih.gov
DCIC: Review
• Reviewers will provide an impact score for each
component of the Center; Impact score of the
Overall Component is the impact score of the entire
application.
• Some significant questions:
– data integration challenges within and across LINCS &
other existing public resources
– single user-interface for all LINCS data & signature
– community access & scalability
– coordination & metadata for LINCS
– integration of components of the center
APPENDIX
NIH Common Fund
• Supports cross-cutting programs that are expected to have
exceptionally high impact.
• Develops bold, innovative, and often risky approaches to
address problems that may seem intractable or to seize new
opportunities that offer the potential for rapid progress.
• NIH LINCS Program Co-Chairs:
– Alan Michelson, PhD (NHLBI)
– Mark Guyer, PhD (NHGRI)
• NIH LINCS Coordinators
– Ajay Pillai, PhD (NHGRI)
– Jennie Larkin, PhD (NHLBI)
LINCS Pilot Phase (2010 – 2013)
• Pilot goals:
– Develop a limited yet coherent data, and signature
resource that could be used by the general research
community.
– Identify key issues in data annotation, integration, and
analysis.
• Pilot activities:
– Two data and signature generating U54 awards
– Development of new high-throughput assays to detect
perturbation-induced cellular responses
– Novel computational methods for integrative data analysis
– Active collaborations and working groups
http://lincsproject.org
Background:
LINCS Data and Signature Generating Centers
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RFA-RM13-013 (going to May 2014 Council)
Will fund 3-5 DSGC awards
Part of a collaborative LINCS program
DSGC structure:
1.
2.
3.
4.
Data Generation (40% effort)
Data Analysis and Signature Identification (40% effort)
Community Interactions Outreach
(20% effort)
Administrative
BD2K Centers
• A combination of Investigator-Initiated and NIHspecified Centers
• Centers to conduct research & provide resources
• Centers will form an interactive consortium
• Investigator Initiated Centers FOA : Centers of
Excellence for Big Data Computing in the Biomedical
Sciences (U54) RFA-HG-13-009
– 6-8 will be funded Summer 2014.
• Potential Centers focus areas:
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Collaborative environments and technologies
Data Integration
Analysis and modeling methods
Computer science and statistical approaches
NIH Big Data to Knowledge (BD2K)
Programmatic Areas
I.
Facilitating Broad Use of Biomedical Big Data: Mike
Huerta NLM & Jennie Larkin NHLBI
II.
Developing and Disseminating Analysis Methods
and Software for Biomedical Big Data: Vivien Bonazzi
NHGRI & Jennifer Couch NCI
III.
Enhancing Training for Biomedical Big Data:
Michelle Dunn NCI
IV.
Establishing Centers of Excellence for Biomedical
Big Data: Lisa Brooks NHGRI, Mike Huerta NLM, Peter
Lyster NIGMS & Belinda Seto NIBIB)
Perturbation DCIC:
linking two programs (BD2K and LINCS)
• BD2K: supports necessary advances in data science,
other quantitative sciences, policy, and training to
support the effective use of Big Data in biomedical
research.
• LINCS: promote a new understanding of health and
disease through an integrative approach that
identifies common patterns (signatures) in molecular
and cellular responses to a wide range of
perturbations, including small molecules, other
environmental stimuli, genetic variation, and disease