Discovery Frontiers Call for Proposals:
Advancing Big Data Science in Genomics Research

Important Information

• Researchers Invited to Apply
• Frequently Asked Questions

Description

Discovery Frontiers (DF) grants support a limited number of large international activities, opportunities or projects that are of high priority in the context of advanced research in Canada. These will be led by teams of world-class Canadian researchers and will generate substantial benefits for Canada.

This initiative aims to bring together groups of researchers in new ways to address a major research challenge. The teams will incorporate new and emerging ideas and will combine their complementary expertise to conduct transformative, paradigm-changing research.

Massive amounts of data are being generated by genomics¹ research across all life science sectors. The lack of efficient tools and methodologies available to effectively mine, rapidly access and efficiently analyse vast quantities of genomic information and integrate it with other data sets is a major challenge for the research community. 

To address this global research challenge, the Natural Sciences and Engineering Research Council of Canada (NSERC), Genome Canada, the Canadian Institutes of Health Research (CIHR) and the Canada Foundation for Innovation (CFI) will partner on this 2013 DF call for proposals, which will focus on advancing big data science in genomics research. This initiative will support the development of tools and methodologies to integrate currently available complex data sets in the fields of ‘omics sciences with each other, as well as with phenotypic data and data from other related fields of biological sciences. This DF call for proposals will build on past and ongoing investments in this area, the most recent being the  Bioinformatics and Computational Biology Request for Applications launched in June 2012 by Genome Canada and CIHR.

Objective

The objective of this 2013 DF call is to support the establishment of a major initiative with strong international linkages. The initiative will develop tools and methodologies for integrating various types of ‘omics data (e.g., genomics, proteomics, metabolomics) with: 1) each other; 2) phenotypic data collected from different organisms of study; or 3) data sets originating from diverse scientific disciplines/fields, including but not limited to imaging, ontology/semantics, biophysics, environmental science and evolution.

As appropriate for the proposed research, this initiative will bring together experts from a wide range of disciplines, including computer science, engineering, mathematics, machine learning, statistics, genomics and the relevant scientific disciplines being studied. 

Together, they will focus on exploring and developing diverse computational and mathematical approaches and techniques, including, but not limited to, creating new algorithms, information systems, Web technologies, artificial intelligence, software engineering, data mining, image processing, modeling and simulation. Clear linkages to the international community must be demonstrated through, for example, the participation of international scientists in the initiative, in international collaborations or in relevant international initiatives. 

Approaches used will emphasize bold initiatives and interdisciplinary thinking, with potential for major breakthroughs and impact across a range of scientific disciplines.

Benefits

It is expected that the end product of this DF grant will further strengthen Canada’s leadership role and capacity in the area of genomics research and produce valuable knowledge that will be disseminated in the appropriate fashion to maximize its impact. This initiative will provide a training opportunity for highly qualified personnel in a focused, multidisciplinary national and international environment. Most importantly, this initiative is intended to build synergies with, but not duplicate, existing large-scale genomic research funding initiatives. The outcome and impacts of DF grants should be transformative, not merely incremental.

All applications must describe, with supporting evidence, the deliverable(s) that will be realized by the end of the project and include a plan that describes how the deliverables from the research will be transferred, disseminated, used, and/or applied to realize the benefits to the research community. Although the open source/open access model currently informs the development of methodologies within the area of biological science research data analysis, applicants may articulate alternative options for community availability and downstream development as long as the dissemination plan ensures maximum community uptake. Preference will be given to applications with a high potential for community impact and/or uptake regardless of the type of dissemination plan proposed.

Projects must have a strategy for knowledge and technology transfer to all stakeholders and the general public, as appropriate, that conforms to NSERC’s Policy on Intellectual Property (IP). The details of this strategy do not need to be outlined in the application documents, but may be requested at the time of award.  

Funds Available

NSERC, Genome Canada, CIHR and the CFI plan to award one DF grant through this call, at a total funding level of $1.5 million per year for four years for the direct research costs, plus an additional $1 million for costs related to infrastructure, if required. Applicants invited to submit a full application will be eligible to receive a development grant (up to $25,000 per approved LOI), up to a maximum of $200,000 for the competition. The contribution from each partner is as follows:

• NSERC – up to $800,000 per year,
• Genome Canada – up to $500,000 per year,
• CIHR – up to $250,000 per year,
• CFI – one-time award of up to $1,000,000 for infrastructure costs, with an additional 30% towards eligible operating and maintenance costs of the infrastructure.

Use of Funds

Funds from each agency will be used for eligible expenses as defined in the relevant guidelines. For NSERC and CIHR, refer to the Use of Grant Funds section of the Tri-Agency Financial Administration Guide. For Genome Canada, refer to the  Genome Canada Guidelines for Funding Research Projects. For CFI, refer to the  CFI Policy and Program Guide.

Additional Guidelines

The following are ineligible costs:

• costs associated with generating new data, and
• salaries, benefits and associated costs for the performance of wet lab work.

High-Performance Computing (HPC) infrastructure

Although funding for high-performance computing (HPC) infrastructure may be requested from the CFI, the CFI requires that, if possible, the HPC infrastructure be housed and managed by Compute Canada. Consultation with Compute Canada is therefore required prior to application. A determination of whether Compute Canada services can or cannot be used for the proposed initiative will be required at the time of full application. This determination can take the form of a formal letter of support from Compute Canada.

Although this determination is not required at the Letter of Intent stage, applicants considering a request for HPC infrastructure are strongly encouraged to contact and begin discussions with Compute Canada as early as possible.

For the purposes of these guidelines, high-performance computing (HPC) infrastructure encompasses any computing system with capabilities larger or more powerful than typically available in a standard desktop system. Such HPC infrastructure normally includes systems or resources such as the following:

• capacity or throughput computing,
• capability computing supporting tightly coupled, fine grained applications,
• shared memory systems,
• systems supporting very large memory requirements,
• high-performance storage,
• long-term storage,
• cloud computing,
• computing using specialized accelerators including GP-CPU and others,
• high-performance visualization systems, and
• systems suitable for computational steering and interactive use.

Typically, such systems cost more than $50,000.

In each case, the term HPC encompasses the software and environment needed for a given discipline to effectively utilize these types of infrastructure and encompasses needs such as high levels of data security and integrity as may be required by specific disciplines or researchers.

Eligibility

For your application to be eligible, the applicant and co-applicants must meet NSERC, Genome Canada and CIHR eligibility criteria and be at an institution eligible to receive NSERC, Genome Canada, and CIHR funds. Applicants applying for infrastructure funding must be affiliated with an institution that is eligible to receive CFI funds. Applicants are reminded that the CFI provides research infrastructure funds to institutions, not individual researchers or teams of researchers. Applicants applying for infrastructure funding must therefore contact the CFI liaison officer at their institution prior to drafting Letters of Intent.

In addition to meeting the funders’ general eligibility criteria, proposals must demonstrate that the project responds to the objectives of the Discovery Frontiers initiative.

Application Procedures

NSERC will work with Genome Canada, CIHR and CFI throughout the competition process. Applicants are required to apply for funding through NSERC. The application process has two steps: Letter of Intent (LOI) and Full Application.

Applicants may also request up to $1 million in infrastructure funding from the CFI. Note that a request for infrastructure support from the CFI is not a requirement for the application to NSERC, but that infrastructure funding will not be provided separately from the Discovery Frontiers program application.

Letters of Intent

Content

Applicants begin by submitting a Letter of Intent. The Letter of Intent must include a cover page (one page), a research proposal (maximum five pages) and biographical information on the team (maximum two pages). All documents should follow the NSERC presentation standards.

The cover page must include:

• the project title,
• a list of up to 10 keywords,
• an approximate budget request, by project year, for direct costs of research,
• an approximate budget request for infrastructure, for teams applying for infrastructure,
• the applicant’s name, affiliation, telephone number and email address, and
• a list of all co-applicants, with affiliation and email address.

The research proposal should include:

• a description of the main research challenges and activities,
• a discussion of anticipated participation by collaborators, such as international researchers and government scientists, and their roles,
• a discussion of anticipated outcomes and benefits,
• a description of the plans for training of highly qualified personnel, and
• a high level summary of the major budget items with justification, including any infrastructure.

The biographical information should contain short biographies of the applicant and co-applicants and their areas of expertise.

The Letter of Intent should be saved as a single PDF document, and uploaded to NSERC’s secure portalbefore the deadline.

Note that details concerning proposals that are successful at the LOI stage will be published on NSERC’s Web site.

Review Procedures and Selection Criteria

A multidisciplinary international committee will review the Letters of Intent. The review process at the LOI stage is intended to select those proposals that best fit the program objectives and best address the LOI review criteria with an emphasis on the merit of the proposal. The review criteria are as follows:

• merit of the research proposal;
  • novelty of the proposed approach
  • potential to be transformative and have high international impact
  • potential to create new fields of research
  • potential to extend and/or complement national and international work in the area
  • appropriateness of the methods and approaches (including handling of data and resources) in terms of the research objectives
  • feasibility of the research given the projected resources and time-lines
  • degree of integration across disciplines and with international collaborators
  • relevance to the end users identified, including potential application beyond the field of genomics
  • anticipated outcomes and benefits to the wider community
• excellence of the applicants and complementarity of expertise;
• potential for value-added training of highly qualified personnel.

Full Proposals

Content

Applicants who are invited to submit a full proposal will be given further instructions on submission details at the time of invitation.

Review Procedures and Selection Criteria

Full proposals will be reviewed through a rigorous independent peer review process, undertaken by a multidisciplinary international committee, to assess their eligibility, research merit and potential for benefits to the research community as well as to ensure that sound management and financial practices are implemented. Excellence in terms of the review criteria at the very highest of international standards must be demonstrated for funding to be awarded to the most meritorious proposal.

The applications will be reviewed using the following criteria. Please note that the descriptive phrases that follow the criteria below are not all-inclusive.

Research Proposal

• Research Context and Originality
  • To what extent does the proposed research lead, extend and/or complement national and international work in the area?
  • To what extent does the proposed research reflect creative, original thinking?
  • To what extent is the research relevant to the end users identified?
  • To what extent will the proposed tools or methodologies increase the productivity of genomics research?
  • To what extent could the proposed research have an impact beyond the field of genomics research?

• Research Plans
  • How appropriate are the methods and approaches (including handling of data and resources) in terms of the research objectives?
  • How feasible is the research given the projected resources and timelines?

• Research Expertise
  • How appropriate is the expertise of the research team in terms of realizing the research goals?
  • How effectively will the project bring together expertise from complementary disciplines?

• Research Environment
  • How suitable are the available facilities and equipment?

Benefits

• Deliverables
  • To what extent have the applicants identified appropriate deliverables in terms of their potential to have practical applicability to the research community?
  • What is the probability that the deliverables will be realized by the end of the funding period?

• Expected Benefits
  • How significant are the anticipated benefits described in the proposal to the genomics community?
  • What is the probability that the benefits will be realized by the research community within a short time-frame after the end of the project?
  • What is the potential for the initiative to achieve excellence in the training of highly qualified personnel?

• Strategy for Realizing Benefits
  • How appropriate is the plan for access to, and dissemination of, the tools and methodologies developed?
  • Quality of the plan describing how the deliverables from the research will be transferred, disseminated, used, and/or applied to realize the benefits.
  • How high is the potential for community impact and/or uptake, regardless of the type of dissemination plan proposed?

• Expertise for Realizing Benefits
  • To what extent are likely end-users involved in the project and the strategy to realize benefits?

Management and Finance

• Management Plans and Expertise
  • How well does the management plan cover project governance, accountabilities of personnel, and processes for decision-making on research direction and strategy for realizing benefits?
  • How convincing is the management plan in terms of coordination of current and future partnerships?
  • How realistic is the project schedule?
  • To what extent do the project leaders have experience in managing projects with multi-disciplinary teams involving research and the application of results?
  • How good are the plans to ensure that an adequate number of highly qualified personnel—both support personnel (e .g., technicians) and trainees (e.g., post-doctoral fellows)—are available to meet the needs of the proposed research through recruitment and/or training?

• Budget and Expenditure Controls
  • How reasonable is the proposed budget in terms of the anticipated level of effort and deliverables?
  • To what extent does the proposal provide assurance that expenditures from a funded project would be closely and critically monitored?

For proposals that contain infrastructure requests from the CFI, the following criteria will also be considered:

• To what extent is the infrastructure necessary and appropriate to conduct the research or technology development programs? 
• To what extent will the use of the infrastructure be maximized within and among institutions and sectors (private, public and non-profit)?
• To what extent will the proposed infrastructure be effectively managed, operated and maintained for its useful life?

Reporting

Regular reporting will be required for this award. A scientific review committee will assess scientific progress annually. The review will provide information regarding the progress of the project according to the proposed timelines. The scientific review committee can also provide advice to the project team if it feels that changes to project milestones or direction are necessary. NSERC, Genome Canada and CIHR will use the scientific review committee’s report to determine whether funding for the project will be continued, reduced or terminated.

Financial reports will also be reviewed annually by all funding partners.

Specific details on the format and schedule and other required information will be available at the time of award.

Contact

Dave Bowen
Discovery Frontiers
350 Albert St.
Ottawa, Ontario
K1A 1H5

E-mail: dave.bowen@nserc-crsng.gc.ca
Tel.: 613-992-1482

¹ The term genomics is defined here as the comprehensive study, using high throughput technologies, of the genetic information of a cell or organism, including the function of specific genes, their interactions with each other and the activation and suppression of genes. For purposes of describing Genome Canada’s mandate, it also includes related disciplines, such as bioinformatics, epigenomics, metabolomics, metagenomics, nutrigenomics, pharmacogenomics, proteomics and transcriptomics.