HR001118S0023 FREQUENTLY ASKED QUESTIONS

Transcription

1 HR001118S0023 FREQUENTLY ASKED QUESTIONS Last Updated: 4/24/18 NOTE: An amendment to the BAA was posted to the Federal Business Opportunities website on Thursday, April 19 and can be found at the URL below: Guidelines for samples: For human samples, the proposer should provide a table describing the required sample type (blood, buccal swab, etc.), exposure type, numbers, volumes, required formats of samples (PAX tubes, etc.). Performers should provide justification for sample types, numbers, and volumes/amounts. GENERAL INFORMATION 1. My research is not geared specifically to meet the ECHO program goals. Is there an alternate solicitation that I can respond to? A: Yes. DARPA/BTO has an office wide solicitation (HR001117S0030) for this purpose. Responses are being collected through April 28, Is Dr. Van Gieson available for a call to discuss our proposed approach? A: The best way to receive feedback on an approach is through the submission of a proposal abstract prior to the deadline specified in the BAA. The BAA describes the program, including metrics, in detail. If you have specific questions, please submit them by to ECHO@darpa.mil. Please be aware that your question and its answer may be published on this FAQ page, after the question has been revised to remove proprietary information. 3. Will the Proposers Day slides be posted online? A: Yes, information relayed during the Proposers Day will be made available on the BTO section of the DARPA Opportunities page: with us/opportunities. 4. Do I need to submit an abstract? What is the advantage of submitting an abstract? When do you anticipate providing feedback? A: Abstracts are strongly encouraged, but not required, to submit a full proposal. DARPA will provide feedback for each abstract submitted. We anticipate providing feedback by April 6 th, though this is dependent on the number of abstracts/white papers we receive. If DARPA does not recommend the proposer submit a full proposal, DARPA will provide feedback to the proposer regarding the rationale for this decision. Regardless of DARPA s response to an abstract, proposers may submit a full proposal. DARPA will review all full proposals submitted using the published evaluation criteria and without regard to any comments resulting from the review of an abstract. 5. Is there a minimum number of investigators required for each team? A: No. However, it is expected that successful teams will require deep expertise in fields that span the three Technical Areas, for example, in bacterial pathogenesis, high throughput phenotypic screening, and single cell genomics.

2 6. Can a performer or individual participate on more than one team? A: Yes. Proposers may join any number of teams as a subcontractor and still submit a separate proposal as the Principal Investigator (PI) (with or without subcontractors). The proposer should be very clear as to how hours will be charged in each proposed effort and describe what safeguards are in place to ensure that time is not double billed. 7. Can Federally Funded Research and Development Centers (FFRDCs) or other Government Entities submit proposals or apply as prime organizations? A: Yes, FFRDCs and government entities can submit proposals if they meet certain criteria specified in BAA Section Note that to avoid potential conflicts of interest, FFRDCs and other government entities, if selected for proposer work, will not be eligible for IV&V work. 8. Do proposed personnel have to be U.S. citizens? A: No. We welcome the best ideas and research from any source. Principal Investigators (PIs), coinvestigators, students, postdocs, employees, subcontractors, and institutions do not have to be U.S. citizens or based in the U.S. All proposed and awarded work must comply with U.S. laws and regulations. See BAA Section Non U.S. Organizations for details. Green card holders are authorized to participate in work including Controlled Unclassified Information (CUI). CONTRACTING/COST Per the BAA, In all cases, the Government contracting officer shall have sole discretion to select award instrument type, regardless of instrument type proposed, and to negotiate all instrument terms and conditions with selectees. Although proposers may request a Grant as the desired award instrument, DARPA (as stated on page 3 of the BAA) does NOT intent to award grants. 9. How much funding is available? What is the expected size of an award? A: We are not publishing the program s budget. DARPA has not predetermined award amounts. Proposers are required to provide a well justified budget appropriate for the scope of the proposed work. Cost should be based upon how much money is required to perform the tasks you feel are necessary to meet the program objectives. Proposals will be scrutinized for unnecessary or inflated expenses. 10. Do we need to adhere to the NIH salary cap? A: No. 11. Are you expecting to fund multiple, comprehensive teams? A: Yes, multiple integrated teams are expected. Teams must address both TAs with one prime contract. 12. When does DARPA expect to make awards? A: Fall What is Cost Realism? A: One of the review criteria described in Section is cost realism. Reviewers will evaluate staffing, equipment, supplies, travel, etc. in your proposed cost estimate, to determine whether the estimated costs are realistic for the work to be performed, reflect a clear understanding of contract requirements, and are consistent with the methods of performances and materials described in the technical proposal. During contract negotiation the contracting officer will question the cost reasonableness of every item in the budget. Provide detailed quotes and justifications for your proposed expenses. 14. Our institute has a high rate of indirect costs (67%) which contributes to the cost of the proposed budget. Does DARPA enforce a certain cap for indirect costs associated with the awards? A: No. Per Section 4.3 of the BAA, the only funding restriction is on direct costs of equipment purchases.

3 Please note, however, that proposals will be scrutinized for unnecessary or inflated expenses. PROGRAM STRUCTURE 15. Who do you want to lead a team from TA1 or a team from TA2? A: This decision is left up to the proposer. DARPA has no preference whether the lead is from TA1 or TA2. A system integrator is encouraged, i.e. an organization that can integrate TA1 and TA2 together. We are looking for good leadership, organization, and teams who can be responsive to the BAA. 16. How many teams are expected? A: Multiple awards are anticipated. 17. Can you identify some transition targets? A: Special Operations Command (SOCOM), Intelligence Community, Biomedical Advanced Research and Development Authority (BARDA), U.S. Army Medical Research and Materiel Command (USAMRMC), Joint Program Executive Office for Chemical Biological Defense (JPEO CBD). 18. What help will be provided to get the ECHO system to the higher TRL? A: We will have transition partners (identified above) participating throughout the program, attending the reviews and demonstrations. We encourage the teams to reach out to these partners throughout. Please keep in mind the end user in your design. 19. What is the expected TRL of the system at the end of the 48 month PoP (Period of Performance)? A: DARPA is not assigning a specific TRL to the system; please see the BAA metrics for the final system. 20. Is any of ECHO considered dual use? A: Dual use is not an aspect of the ECHO program. 21. Will there be publication restrictions or any access to classified data? A: Please see pg 13, Section 1.4 for a list of anticipated unclassified controlled information. This may change by time of contract award. There are no classified elements of the program. 22. The 12 month milestone requires 5 non biological signatures. Can we do 5 non biological in Phase II rather than at 12 Months? A: 5 non biological signatures are required at the (as a) 12 month milestone. At 12 months, a total of 7 signatures should be developed by each team. We do understand that teams will want to bias all of these signatures towards biological exposures in advance of the 18 month challenge. However, in the 18 month test, teams are only expected to distinguish an unknown sample provided to the teams as either viral or bacterial. This discrimination does not require species identification, and the unknown sample provided to the teams will represent one of the exposure pathogens from the 6 month molecular data sets that are shared by all teams on the database. 23. Can you clarify what was meant by leads? Does it mean that there are resources that we have identified and we will pursue them with stronger emphasis after the award has been granted? Can we list the potential resources in the proposal? A: Ideally, we'd like for you to have some sort of teaming or materials transfer agreement in place to allow for access post award. Absent of an agreement, we'd expect firm plans, NDAs, and ROMs/Costs for obtaining these samples from your partners. We are not interested in a list of potential resources unless you have a plan in place for developing data sets and/or signatures from the sample associated with the resource.

4 24. Before the pressure tests, can we get the samples to learn the signatures? A: Yes, the samples for pressure tests will be new but will derive from exposures that the team has analyzed before. 25. Based on the IRB presentation provided at Proposers Day, do we need two levels of IRB? A: Yes, at minimum, you will need your organization s IRB and DoD level IRB. With the samples provided by our Government partners, there are three levels due to the international site. 26. At Proposers Day, it was stated that the animal model would have to have equivalency to human. What is the equivalency, how are you assessing this? A: The team should propose criteria for equivalency, and the U.S. Government will review those criteria. This is an evolving target. You should provide a plan for this in the proposal abstract and full proposal. 27. We understand that teams may be funded for Phase I only or both Phases. This is clear for TA1 but how does this apply for TA2 which requires development of a portable device? A: TA2 Phase I is slightly dependent on TA1 Phase I as the epigenetic analysis tools selected and verified for signature creation will likely be the ones used in your team's portable device. Phase II is not guaranteed for either TA1 or TA2. If a team is successful on one TA and not the other, DARPA may consider only funding that TA. However, given the necessary integration between TA1 and TA2, if a team does not get funded for Phase II of TA1, it is most likely that their TA2 work will not be funded either. 28. Please provide clarification on "minimally trained operator"/"military staff" for the final demo. A: Minimally trained operators are defined as operators that do not possess any background in epigenetics, genetics or molecular biology. PROPOSALS 29. How will proposals be evaluated? A: A team of government reviewers will evaluate applications based on the evaluation criteria described in BAA Section 5.1 Evaluation Criteria. The review criteria are rank ordered, with the most important criterion listed first. The reviewers will have scientific or technical expertise relevant to the goals of the ECHO Program and may represent multiple government agencies. 30. Do page limits include table of contents, resumes, and bibliographies? A: Please see BAA Section 4.2 Content and Form of Application Submission for a description of the content encompassed by the page limits. 31. Should I submit via DARPA s BAA Portal ( or Grants.gov? A: Proposal abstracts MUST be submitted via DARPA s BAA Portal or hardcopy/cd ROM, and cannot be submitted via Grants.gov. Full proposals requesting cooperative agreements must be submitted via Grants.gov or hardcopy/cd ROM, and cannot be submitted via DARPA s BAA Portal. We encourage you to submit your proposal a few days ahead of the deadline. Again, regardless of the submission mechanism, expect that DARPA will not award grants. IV & V 32. When samples are supplied, under what conditions are they sampled? A: They are sampled in clinical environments as part of clinical studies or trials. Metadata will be specified and provided to the teams. All samples and metadata will be screened and analyzed by IV&V before distribution to teams. 33. Are the provided samples limited? A: Yes, samples are limited. See slides provided by Government partners on Proposers Day. Please plan accordingly and engage with Government partners who spoke at Proposers Day.

5 34. Both VA and DoD have extensive biorepositories, which are not easy to get access to. Would DARPA help the awardees with accessing the samples? A: We are pursuing partnerships with the VA and DoD, however, we do not have these partnerships finalized. We will continue to pursue additional sample access throughout the program. 35. Will all teams be provided access to de identified human samples from infectious disease surveillance sites, as described on p5 and if so, the available datasets as well? A: DARPA will provide de identified human samples for certain exposures, but these will not be sufficient for teams to complete their necessary exposure specific signature development for all 21 exposure types. Therefore, teams will have to work to build their own sample repositories. DARPA will focus it's effort on providing human samples for the biological exposure types listed as required exposures in Table 1 of the BAA. However, all teams will have access to the molecular datasets (and associated metadata with human samples used to build those datasets) generated by all teams on ECHO. They can use these datasets to build their own unique exposure specific signatures. 36. Will DARPA send biological samples which have been exposed to Lassa virus to performers? If so, in what form will this material arrive? A: Government partners will send biological samples exposed to LASV in the best possible condition taking into account the nature of the experiment and the safety regulations as LASV is a BSL4 pathogen. 37. Is the database a database schema or system? A: DARPA will provide that information (data formats/standards) at the kickoff meeting. We are not competing the database as part of this program. 38. Is the data generated de identified or HIPAA compliant? A: Depends on the (human) samples that you use. Both the Walter Reed Army Institute of Research (WRAIR) and the Naval Medical Research Center (NMRC) have clinical data and require human subjects research/irb compliance. Please review human subjects research requirements of the BAA. 39. Do you have a primary programming language that DARPA requires the teams to use? A: No, please specify the primary programming language you plan to use for the ECHO program in your response to the BAA. Please note any proprietary (e.g. a license is required) programming languages, software packages, or software tools that you will need to use and provide details. 40. Will the IV&V computing and software environment allow for use of pipelining tools? (e.g. Galaxy) A: Yes, please specify the pipelines that will be used and if there are any unique implementation requirements. 41. Will the IV&V computing and software environment allow for any tools for versioning, provenance, and collaboration? A: Yes, DARPA will work to accommodate and please provide details on these tools. 42. What will the final specifications for the system be (cloud or physical, memory, processors, storage, operating system and other frameworks if applicable) and will these resources be shared amongst all performers simultaneously? If shared, how will prioritization occur? A: DARPA requests that proposers provide the data requirements for storage of molecularepigenetic datasets in the DARPA database including: storage amount per year (GB/TB), total node hours for a given computing type (CPU/HPU/CPG), software stack description and any other computing infrastructure needs. 43. How will performers be required to access the system (secure login, from a Government facility, from the performer's facility, VPN, etc.) A: The system will be run on a private computing and storage infrastructure, operated in a non

6 government environment. Each team will have secure login guidance and will have the ability to decide who will have access to their data and algorithms, with the exception of molecular datasets that will be a common resource for all performers. 44. How will data sharing be handled and what types of data will be shared (full sequencing data sets, epigenetic feature sets, metadata, model information)? A: Data sharing will be handled by the IV&V team, which will decide at what level of data each team should share with the other performers. This generally will be any information that has not been analyzed for signature development and will, for example, consist of raw sequencing reads or immune labeling data that each team has generated but not yet analyzed. 45. Does the Government expect performers to provide or purchase a separate NIPSOM compliant system for this program at the performers facility in addition to the Government provided infrastructure? A: Performers will not be required to have a NISPOM system and the computing resource is operated by a private entity with its own access controls. DARPA intends to fund the computing and storage resource but does not control the security protocols the system is designed to enable all non government entities to use the resource remotely with no special hardware requirements. 46. What kind of IT support, if any, will be given for use of these systems? A: DARPA will provide IT support at no cost to the teams for using the government supplied computing and storage resources. TECHNICAL 47. What is your attitude towards (fill in the blank) technology? A: We will not comment on specific technologies. Proposed technologies and approaches must fit within the boundaries and spirit of the ECHO Program. 48. Are toxins, non traditional agents within scope of this effort? A: Yes. 49. Are samples derived from vaccination studies in the scope of ECHO? A: Yes. 50. Are small molecule and single cell approaches in scope of ECHO? A: Yes, but only if the approach is relevant to identify epigenetic signatures. 51. Can we use model systems like invertebrates? A: Yes, you can use any model system but will be required to show equivalency to human epigenetic responses. 52. Will the system be used for acute diagnostic purposes, post exposure determination(short term), detection of a historical event (greater than 90 days to 30 years post event), or all 3 things? A: All three things. Device should be used to solve all three. Temporal resolution requirement in the BAA is +/ 1 year. 53. It is very likely that the victims of a WMD will have different markers than the person that developed it. Do you expect the performers to account for this difference in obtaining/preparing the samples? A: Yes, we expect teams to distinguish precursors from agent but we don t expect teams to distinguish WMD exposure due to the manufacturing process from other (i.e. post production) exposures. Please consider how duration and dose of exposure could affect specific epigenetic signatures. Please consider discussing dose and duration response curves in your proposal.

7 54. Of the 17 additional samples each performer is supposed to work on (referenced on Table 1 of the BAA), how many of these samples do you expect each team to bring? Will all 17 be required or just a subset? A: All 17 are required for a total of Epigenetic reagents need cold storage in many cases. What device requirements pertain to reagent preservation on the field (PCR)? A: We do not have requirements on reagent stability but that should be a consideration in the final system. According to the BAA, the system will be required to run in an austere environment. 56. Due to circadian effects, have all provided samples been collected at a known time of the day and with/without fasting? A: Proposers should select epigenetic cues that are independent of circadian effects. Samples will provide all necessary metadata at the time of collection. Please consider all factors of epigenetic variability in your proposal. 57. Is the 20W power requirement firm, and can it be higher at peak performance? A: 20W is a maximum total power requirement, with the expectation that the system could operate at 20W continuously. 58. What Mil Spec ruggedization requirements will be required? A: This is a prototype (6.2 funding) while that is a question for an Acquisition project TRL of 6.4 or higher. 59. Does the sensor store raw data or just results? A: We don t have storage requirements. Presumably some storage is required for all the informatics requirements to operate without access to the cloud/or in low Quality of Service (QoS) environments. 60. Will the data captured in field in the ECHO device be able to be uploaded to a network/other devices to be included in a data sharing system? A: See the BAA metrics in TA2 for device requirements. 61. Can we use COTS in the ECHO device? A: Yes, but only if the components are essential and will meet the device requirements set forth in the BAA. 62. With your requirements for computation on the device; do you plan to use the collected data and feedback data to enhance the algorithm? A: Yes, we envision the platform to continue to evolve from a signature perspective. Keeping the operational requirements of the end user in mind, the system could use new data to inform the algorithm to calculate identification results. 63. Can we add samples/data from non human organisms that have been exposed to ECHO agents of interest in real world scenarios vice laboratory settings? A: Yes, but with any animal models you would need to show equivalency to human epigenetic responses. 64. Does it make sense to have each team work on only a subset of epigenetic features and then compare notes when we get access to the raw data rather than everyone try to do everything (HiC, histone modifications, DNA modifications, ATAC seq etc.?) A: Every team is expected to generate epigenetic molecular data sets that address TA1 requirements. The data access throughout teams is meant to increase the power in the creation of the exposure specific signature.

8 65. Does the program require that the TA1 ESPs be generated from all tissues listed or is it responsive to focus on the sample type that we believe will be the most informative and compatible with the assay device? A: The ESP should reflect the proposer's best judgment of which molecular analysis methods and tissue types will create the best exposure specific signature. 66. If the ESP needs to include all sample types, do we need to source all sample types for the 17 additional required ESPs or is it responsive to source only one of the sample types? A: The ESP doesn t need to include all sample types. 67. Does the device need to be able to handle all types of samples, or is it responsive to focus on one sample type? A: The device should only have to handle the sample types necessary to correlate an unknown exposure signature to a known exposure specific signature. 68. Are which cell types to focus on entirely up to the applicant, or do we need to include all the cell types listed in the application (T cell, keratinocytes, etc.) to be considered responsive? A: Cell type focus is entirely up to the applicant. 69. Can you clarify whether proposers can choose biological agents that are not part of the select agents and toxins list listed on A: Proposers are welcome to pursue as many biological agents as they desire as long say they still characterize the epigenetic signatures of the minimum set of four specified in the BAA. Please note that teams are strongly encouraged to address agents from each of the 10 subcategories and will be evaluated on the diversity of the additional 17 compound or agents selected.