How to Propose a CSP Project

How do I submit my proposal?

Proposals for synthetic biology and small-scale microbial and metagenome projects may be submitted at any time as brief white papers and will be reviewed every six months. Deadline for submission is 60 days prior to the review.  See proposal schedule for specific dates. View submission instructions and submit a small-scale microbial/metagenome or synthetic biology proposal 

For the CSP15 annual call, a letter of intent is required to submit a proposal to JGI.  Submitters whose letters of intent/proposals are approved will receive further instructions via email.  View submission instructions and submit a CSP annual proposal

For the CSP15 JGI-EMSL joint call, a letter of intent is required to submit a proposal.  Submitters whose letters of intent/proposals are approved will receive further instructions via email.  View submission instructions and submit a JGI-EMSL joint proposal (through EMSL)

All proposals will be reviewed on the basis of scientific impact, technical demands on JGI resources, and pertinence to DOE missions in bioenergy, biogeochemistry, and carbon sequestration.  Human or animal disease-causing organisms will NOT be considered under this Program. Only plant pathogens of relevance to bioenergy-related crops or plants will be considered.

In the application, JGI requests that applicants focus primarily on describing the science that will be enabled by completion of the project rather than the technical details of how sequencing will be carried out, because the former is the primary criterion and the latter is subject to change.

Applicants with concerns about the suitability of their projects for this program are urged to contact the JGI prior to writing a proposal.

>> View the proposal schedule

What kind of proposals can be submitted?

For the CSP15 annual call

The DOE JGI’s Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry. While applications will be accepted that address any aspect of these mission areas, priority for this call will be given to projects that address the following areas of special emphasis and exploit the diversity of DOE JGI capabilities.

I. Functional Genomics and Microbiomes of DOE JGI Flagship Plants: The DOE JGI has produced several “flagship plant genomes” including Poplar, Sorghum, BrachypodiumChlamydomonas, Soybean, Foxtail millet, andPhyscomitrella. Additional emerging flagship plant species include Switchgrass, Miscanthus, and Hall’s panicgrass. These species are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. The 2015 call will focus on projects that directly relate to these genomes. For all plant proposals, multi-organism proposals will be given priority that 1) seek to compare among plants and/or analyze plant-microbiome interactions, and 2) large, collaborative, multi-investigator projects. Proposals for de novosequencing of new plant genomes will not be considered at this time.
Projects of interest may fall into the following three categories:

a) Gene Atlas and ENCODE-like projects - The DOE JGI is currently committed to sequencing flagship plant transcriptomes under a variety of experimental conditions for different plant tissues and developmental stages. New proposals are encouraged that expand the experimental conditions to be studied and extend functional studies beyond straightforward transcriptomics. Genome-wide methylation, RNA-Seq (including low-template RNA-seq), non-coding RNAs, small RNAs, histone binding assays, and other epigenomic assays are encouraged to address important mission-related phenotypes and other aspects of plant biology in flagship plant species. In addition, studies that make use of the DOE JGI’s DNA synthesis capacity to modify flagship organisms in order to understand gene function are encouraged.

b) Large-scale resequencing projects - Projects aimed at characterizing the genetic variation of species or populations by large-scale resequencing are encouraged. Preference will be given to species or populations that are relevant to flagship plant genomes. These can be natural populations or structured populations (mapping populations, recombinant inbred lines, etc.), suitable for linking genome variation to traits of interest.

c) Plant microbiomes - The DOE JGI encourages projects to study the microbiomes of flagship plants. Proposals aimed at studying microbial communities associated with various plant tissues are specifically encouraged, as are hypothesis-driven projects deciphering functional and phylogenetic community changes upon manipulation of the host and/or host environment.

II. Probing functional diversity of microbes: To complement its Genomic Encyclopedia of Bacteria & Archaea and 1000 Fungal Genomes initiatives, the DOE JGI has begun to explore microbial functional diversity. Proposals are now encouraged that extend this effort using high-throughput sequencing and the DOE JGI’s DNA synthesis capabilities to identify novel activities of relevance to DOE missions or to provide new annotations to genes whose functions are presently hypothetical or unknown. Proposals are expected to use one or a combination of the DOE JGI’s (meta-) genome, (meta-) transcriptome, single-cell and isolate sequencing and resequencing pipelines. ENCODE-like projects for functional genomics of bacteria, archaea and fungi that could serve as model organisms for DOE-relevant problems are encouraged and could include new JGI capabilities for genome-wide transcriptomics, including non-coding and small RNAs, and epigenomics, including methylation detection and ChIP-seq.

III. Microbial emission and capture of greenhouse gases in terrestrial systems: Bacteria, archaea and fungi are important consumers and producers of greenhouse gases in the environment. While a nascent understanding of carbon cycling in marine environments exists, our understanding of these processes in terrestrial systems ranging from deserts to wetlands has lagged behind. Proposals are encouraged that will provide insight into global carbon (including methane) and nitrogen cycles and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction through gene/genome engineering. Preference will be given to proposals focused on terrestrial environments.

IV. Discovery and expression of natural product pathways relevant to energy-related and environmental processes: Bacteria, archaea, fungi, and plants are important producers of natural products (NPs), many of which are relevant to energy and environmental processes of interest to DOE. The DOE JGI has developed a platform that enables the discovery of novel NPs based on technology combining computational genomics, pathway refactoring, host engineering, and high-throughput analytics. Proposals are encouraged to exploit this NP platform in order to identify and/or produce novel activities of relevance to DOE missions, e.g. NPs that contribute to plant-microbial interactions, microbial community structure, bioenergy development, carbon processing, or environmental contaminant cycling. Proposers should note that the DOE JGI’s intent is to support the identification and development of energy- or environment-relevant NPs, not the development of NPs for biomedical purposes.

Project Structure - CSP projects are expected to generate publicly available data that will answer important questions relevant to the organism or environment being sequenced, as well as providing the substrate for broader use by the DOE research community. CSP projects have historically provided a means for user communities to assemble and interact in collaborative ways. Proposals are encouraged that involve some or all of the following features: 1) a scale and complexity that exceeds the capacity of a single lab, 2) engaging a large group of collaborators, 3) involving more than a single species, and 4) requiring DOE JGI capabilities that reach beyond genome sequencing. Each proposal must carefully justify the amount of sequencing requested but no single proposal should expect more than 2 Tb of sequence allocation.

The DOE JGI provides extensive data analysis pipelines. Applicants should present a plan for all data analysis that may be required beyond these standard pipelines.

DOE JGI Capabilities
The DOE JGI employs primarily Illumina HiSeq and MiSeq sequencing platforms, with Pacific Biosciences long-read capabilities (3+kb and 10kb) for specific applications. The capabilities available for this call are listed below. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals but the scope is ultimately at the discretion of the DOE JGI. Successful projects frequently utilize a combination of capabilities:

Core Capabilities Include:

  • De novo sequencing of fungal, bacterial, and archaeal genomes
  • Resequencing for variation detection
  • Single-cell DNA sequencing
  • Microbial community DNA/RNA sequencing
  • Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
  • Target-enriched re-sequencing
  • Whole genome DNA methylation analysis
  • Chromatin analysis including mapping of histone modifications by ChIP-seq and formaldehyde-assisted isolation of regulatory elements (FAIRE)
  • DNA/gene synthesis linked to sequence data generation (note that there is a separate call for stand-alone DNA synthesis, gene and pathway synthesis available
  • Analysis pipelines for the datasets above

The DOE JGI also has limited capacity for the following developing capabilities:

  • 3rd generation single-molecule sequencing
  • Fluorescence-activated cell sorting, including single-cell sorting and amplification of genomic DNA
  • Transposon mutagenesis of bacteria
  • Custom genome analysis of generated datasets

Mechanism and Timing of Review
Letters of intent will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/between February 13 and April 10, 2014. The CSP Call is open to anyone with the understanding that CSP data is made publicly available immediately, without exception. Applicants will be advised by April 24, 2014, whether to prepare a full proposal. Full proposals will be due June 5. Guidance for submitting full proposals will be included in the email notification to invited applicants.

Proposals will be independently peer-reviewed and ranked following given review criteria. Final decisions will be made by DOE JGI senior management with final approval given by DOE program management. All projects will begin October 2014.

For questions about the appropriateness of projects, program specifics or application process, please contact Axel Visel.

For the JGI-EMSL Collaborative Science Initiative

The joint Call for Collaborative Science between EMSL and the Joint Genome Institute (JGI) is open from December 20, 2013 to April 7, 2014 for Letters of Intent. Both user facilities, which are stewarded by the Department of Energy Office of Biological and Environmental Research, play critical roles in supporting DOE’s energy, environment and basic research missions. This call represents a unique opportunity for researchers to combine the power of genomics and molecular characterization in one proposed research project.

Applications for this Collaborative Science program follow a proposal package, schedule, and review process that is tailored to meet both EMSL and JGI requirements. Details regarding this proposal process and schedule are available on the joint EMSL and JGI website, and returning users especially are advised to carefully review the unique elements of this joint program.

Highlights

Successful applications will focus on high risk/high payoff projects in the focused topic areas that can be completed in 18 months, utilize a broad range of the capabilities of each facility, and generate datasets unique to these two facilities and beyond what each could generate by itself. An individual application should not request more than 300 Gb of DOE-JGI sequencing, in addition to the EMSL resources necessary for the proposed work. Accepted projects must broadly address DOE/BER missions, but proof of concept for the demonstration of a technology that would be applicable to a DOE mission is appropriate.

Focused Topic Areas

  • Biogeochemistry - Projects that enhance our understanding of the relationship between microbial community structure-function and the biogeochemistry of metal contaminants, including radionuclides.
  • Carbon Cycling - Projects that elucidate the signaling and metabolic pathways in the rhizosphere and their potential impacts on carbon storage in terrestrial ecosystems.
  • Biofuels Production - Projects that link metabolism with microbial compartmentalization or organelle development in fungi to enable improved metabolic modeling for production of biofuel and chemical intermediates.

EMSL provides a wide range of unique and state-of-the-art resources that can be applied to proposals under this Call. Applications may request any combination of resources, but must provide adequate information to demonstrate the plan for integration and justify the amount requested. Applicants are strongly urged to discuss their resource needs with the respective Capability Leads or Instrument Scientists prior to responding to the Call. Contact information for these individuals is available on the resource description pages, or interested applicants may contact the EMSL User Support Office for assistance.

Researchers interested in learning more about EMSL and specific instruments can now view a dozen different instruments in four of EMSL’s laboratories through a panning 360-degree virtual tour. The tour includes lab and instrument overviews available through text, images, video and web pages. It features EMSL’s surface science instruments, nuclear magnetic resonance spectrometers, ion mobility mass spectrometers, and cell isolation and surface analysis tools. Recent sustainability projects, such as a solar array, also are highlighted.

DOE-JGI primarily employs next-generation short-read sequencing platforms, augmented by 3rd generation single-molecule/long-read capabilities (3kb up to 10kb). The capabilities available for this call are listed below. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals but if longer read sequencing is needed, the burden is on the submitter to justify the request. Successful projects frequently exploit a combination of capabilities:

DOE-JGI Core Capabilities Include:

  • De novo sequencing of plant, fungal, bacterial, and archaeal genomes
  • Resequencing for variation detection
  • Single-cell DNA sequencing
  • Microbial community DNA/RNA sequencing
  • Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
  • Target enriched re-sequencing
  • Whole genome DNA methylation analysis
  • Chromatin analysis including FAIRE, and histone modifications through ChIP-seq
  • DNA/gene synthesis
  • Analysis pipelines for the datasets above

DOE-JGI also has limited capacity for the following developing capabilities:

  • 3rd generation single-molecule sequencing
  • Fluorescence activated cell sorting, including single-cell sorting and amplification of genomic DNA
  • Transposon mutagenesis of bacteria
  • Custom genome analysis of generated datasets

For the CSP Microbial/Metagenome small-scale call, the JGI is targeting the following project types:

Bacterial and archaeal epigenomes
DNA base modifications (6mA, 5mC, 4mC and others) are known to be important in host defense (as part of restriction systems), but may have additional functional roles that have previously been difficult to detect. New technologies now allow direct sequencing of DNA base modifications, providing a first opportunity for genome-wide exploration of bacterial epigenomes. JGI is seeking proposals to examine the possible regulatory roles of DNA base modification in Bacteria and Archaea. Up to 12 isolates may be proposed. For projects with >12 genomes, please refer to the CSP 2015 annual call (to be released spring 2014)

Metagenomes 
Most microbes live in complex communities in oftentimes dynamic environments where the impact of changing environmental parameters on community structure and function are largely unknown. JGI is accepting proposals which include up to six metagenomes. Metatranscriptome samples should not be included. Up to 92 iTag samples may also be proposed, although iTag-only proposals will not be considered. Proposals must show clear DOE mission relevance in areas such as bioenergy-related plant-microbe interactions, carbon/nitrogen cycling and/or carbon sequestration processes in soils and sediments, and biogeochemical processes contributing to contaminant biotransformation and/or immobilization. For projects that fall outside these criteria, please refer to the CSP 2015 annual call (to be released spring 2014)

Proposal requests for bacterial and archaeal isolate and single-cell sequencing projects, as well as RNA sequencing and resequencing projects are expected to resume in the fall of 2015

For the CSP Synthetic Biology call:

DNA Synthesis
Sequence data from genomes, metagenomes and single cells allow the prediction of millions of novel genes as well as higher-level functions such as carbon-source utilization, secondary metabolite production, stress response, photosynthesis, and nitrogen fixation. DNA synthesis proposals are encouraged that address the re-factoring, screening and functional characterization of multi-gene pathways involved in DOE mission-relevant areas, both in microbes and eukaryotes.  Particular focus areas within this topic area are projects that involve functional prospecting of diverse species/metagenomes, require the construction of large DNA molecules (>10 kb), and exploit coupling to high-throughput screening technologies. Small-scale DNA synthesis requests that could be easily performed by commercial providers are discouraged.  Each proposal may request up to 250 kb of synthesis.  Additional DOE JGI capabilities including data mining, vector engineering, and construct design can also be included within synthesis proposals.  Sequencing requests are not allowed.

What are JGI’s capabilities?

DOE JGI employs almost exclusively next-generation short read sequencing platforms, with limited 3rd generation long-read capabilities (3+kb and 10kb). The capabilities available for this call are listed below. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals but if longer read sequencing is needed, the burden is on the submitter to justify the request. Successful projects frequently exploit a combination of capabilities:

Core Capabilities Include:

  • De novo sequencing of plant, fungal, bacterial, and archaeal genomes
  • Resequencing for variation detection
  • Single-cell DNA sequencing
  • Microbial community DNA/RNA sequencing
  • Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
  • Laser capture micro-dissection (LCM) coupled RNA-Seq
  • Target enriched re-sequencing
  • Whole genome DNA methylation analysis
  • Chromatin analysis including FAIRE, histone modifications through ChIP-seq
  • DNA/gene synthesis
  • Analysis pipelines for the datasets above

DOE JGI also has limited capacity for the following developing capabilities:

  • 3rd generation single-molecule sequencing
  • Fluorescence activated cell sorting, including single-cell sorting and amplification
  • Micromanipulation for isolation of single cells
  • Multiplex emulsion PCR amplicon sequencing
  • Transposon mutagenesis of bacteria
  • Custom genome analysis of generated datasets

Synthetic Biology Internal Review Process – Investigator Guidelines

Click here to submit a proposal

Additional information about proposals

Projects Contingent on Additional Funding
In some cases, a project that involves a large sequencing effort might not be approved without additional funding to accomplish other necessary studies. At the applicant’s request, projects can be selected provisionally, contingent on acquiring additional funds from other sources. With no additional funding, these projects will expire two years after being approved for sequencing.

Important note about DNA preparation
The preparation of high quality DNA/RNA for sequencing is frequently a bottleneck for large projects.  The success of large-scale projects depends on the community’s ability to deliver appropriate amounts of high quality material on a negotiated schedule that will allow timely turnaround of sequence data (view specific material requirements). Applicants should address the community’s strategy for preparing and delivering DNA to JGI in a timely fashion.   Inability to deliver DNA when expected will result in projects receiving a lower priority for sequencing that may result in substantial delay.

Proposal template for the CSP 2015 call