Attachment No. 9 Sample TORFPs Task Areas 2 - 7.pdf
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- Attached to
- BRAIN Initiative Cell Atlas Network (BICAN) Sequencing Core Federal contract opportunity
- Solicitation number
- NIH-NIMH-75N95022R00031
About this file
This document contains seven sample task order requests for proposal related to the BRAIN Initiative Cell Atlas Network Sequencing Core multiple award indefinite delivery/indefinite quantity contracts. The task order RFPs seek proposals for large-scale single-cell and bulk tissue genomics, epigenomics, transcriptomics, and multi-omics sequencing services to support several National Institutes of Health laboratories. Services include high-throughput DNA and RNA sequencing, data analysis, storage and transfer to NIH archives. Task areas include single-cell and bulk tissue sequencing and profiling, with performance periods of six to twelve months. Offerors must propose separate technical and cost approaches for each task order. The National Institute of Mental Health will evaluate proposals and make multiple awards to create an integrated sequencing network to serve the BRAIN Initiative Cell Atlas Network program.
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ATTACHMENT 9
NOTE TO OFFERORS: This sample task order is for evaluation purposes only and may or may not be issued at time of award.
SAMPLE TASK ORDER (TO)
REQUEST FOR PROPOSAL
Task Area Two (2)
Contractor:
Contract No: TBD Task Order No. TBD Modification No: N/A TO Title: TBD Project Officer: TBD Date Prepared:
Contract Task Area: Two (2): Large-Scale Single-cell Transcriptome Sequencing
REQUEST FOR TO PROPOSAL RELEVANT INFORMATION
A. Period of Performance: Six (6) months from time of award.
B. Task Order Description / Statement of Work:
1) Provide at a minimum Large-Scale Single-cell Transcriptome Sequencing with the following baseline capability and capacity:
a. Meet or exceed the Illumina recommended minimum sequencing performance specifications: sequencing output per flow cell, quality scores, run time, sample throughput per year
b. Meet or exceed a minimum capacity of producing 1 trillion short sequencing reads per year with capability of scaling up to a maximum of 10 trillion short sequencing reads per year
c. Provide capability of sequencing a variety of single-cell transcriptome libraries at customized sequencing depths and read lengths
d. Provide sequential Just in Time secured/encrypted and high-speed transfer of sequence data in FASTQ format to the NIH BRAIN Initiative designated cloud-based archive(s) with Google, AWS, or Azure.
e. Provide correct and complete metadata for submission to the NIH BRAIN Initiative designated archive(s), including unique project sample identifiers and sequencing center.
2) Provide separate plans for Phase I (pilot studies) and Phase II of the task order as outlined in the Statement of Work (Attachment 3).
3) Utilize state of the art computational tools and algorithms for analysis
4) Provide personnel with expertise and experience in high throughput large-scale single-cell transcriptome sequencing, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)
5) Provide personnel with expertise and experience in aliquoting, labeling, shipping, and minimum acceptable standards for quantity and quality for samples submitted for sequencing
6) Provide personnel with expertise and experience in sample receipt, tracking, handling, and storage, including the use of an in-house Laboratory Information Management System (LIMS); develop and implement procedures for these activities
7) Provider must use seamless LIMS for contracted production and must provide real-time tracking by all production partners and this information must be available in real-time between production partners. BICAN investigators and NIH BRAIN Initiative staff must have the ability to identify where a sample is in production via communications
8) Provide personnel with expertise and experience in omics analyses and bioinformatics for data cleaning
9) Provide personnel with expertise and experience in the secure physical and electronic transfer of large quantities of omics data as well as securing in-house data
10) Provide data to the BICAN Project Office or its designee on request in a complete and timely manner
11) Provide encrypted raw and transformed cleaned data as well as the final transformed data and sequencing metadata
12) Provide a Final Manual of Operations within 30 days of task order initiation. Details in Reporting Requirements
13) Provide bi-weekly Status Reports to NIH staff and if requested, designated BICAN investigators. The bi-weekly Status Report shall summarize the status of the sequencing, the weekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements.
14) Communicate with NIH designated data coordinating center and data repository (archive) and the respective BICAN investigators and BRAIN Initiative staff to coordinate sample delivery and sample metadata.
15) Provide materials and information promptly and communicate with NIH staff, BICAN investigators, data coordinating center, and other contractors frequently and regularly
16) Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the sequence data
17) Maintain security guidelines that meet or exceed the current security best practices, including detailed description of requirements for security and encryption. This includes, but is not limited to:
a. all approved users have completed all required institutional computer security training, e.g. http://irtsectraining.nih.gov/, or the equivalent
b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard)
c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled
d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged, if necessary then they must be encrypted
e. updated anti-virus/anti-spyware/anti-malware software
f. security auditing/intrusion detection software, detection, and regular scans of potential data intrusions
g. strong password for file access and never shares it
h. All copies of the dataset must be destroyed whenever the NIH BRAIN Initiative program office requests destruction of the dataset
18) Provide secure backup of all data essential to the project, including but not limited to all sequence data generated (including raw data), study data received, sample tracking and storage information, and QC information
19) Provide shipping and handling of samples from BICAN investigators. Offeror will develop best practices for sample concentration and plating and QC testing of study with BICAN investigators and NIH BRAIN Initiative staff during Phase I.
20) Receive and process data and samples from BICAN studies, including receive, track, and store samples and accompanying data from BICAN designated studies in preparation for sequencing
21) Pilot QC of representative study samples during Phase I is expected to be within 7 days of the sample receipt
22) Complete sequencing and electronic delivery of appropriately cleaned and formatted data from all samples received (including quality control measures during production to identify sequencing errors and sample mix-ups) by end of task order period (6 months). Quality control methods should include appropriate controls. See technical acceptability criteria in item 1 above.
23) Perform appropriate QC for quantification, post library prep, on-instrument sequencing and transcriptomic build
24) Demonstrated support for completing transcriptomic data at 1, 3 and 6 months.
25) Participate in NIH BRAIN Initiative designated in person or virtual-meetings (1 or 2 during task order performance period) and conference calls dealing with data integration, formats, QC/QA, data deposition as designated by the BRAIN Initiative Program Office.
26) Provide a Draft Final and Final Report according to the details in the Reporting Requirements
27) When promising sequencing technologies are identified (examples may include changes in cost, increased information or density, or increases in accuracy or interpretation) and has been requested by the COR, the contractor shall prepare a technology evaluation proposal.
C. Deliverables:
See Deliverables identified in Article F.2., Deliveries (also described in Article C.2.), of the RFP.
Although data will not be produced under this sample task order, offerors shall describe their approach for providing all resulting genotyping or sequencing data and associated files to the BICAN Investigators and central data repositories.
D. Special Restrictions/Clearances/Clauses: See the following Articles in the RFP.
Article B.3. Advanced Understandings, Section H, and Section I.
E. Evaluation Criteria: See Section M of the RFP. Price is also a factor. The Offeror(s) price proposal will be evaluated for reasonableness. For a price to be reasonable, it must represent a price to the government that a prudent person would pay when consideration is given to prices in the market. Normally, price reasonableness is established through adequate price competition, but may also be determined through cost and price analysis techniques as described in FAR 15.404.
F. Response Due Date: Same date that overall proposal is due (see RFP).
TASK ORDER (TO)
Offerors are reminded that all terms and conditions of the IDIQ contract will apply to all task orders awarded.
Offerors shall submit a separate proposal within the general proposal for this Task Order as listed herein. In doing so, you are to provide a separate Technical Proposal and Cost Proposal (including documentation to support the proposed price).
Technical Proposal
1. Government Furnished Information/Equipment
The Contractor shall provide all necessary equipment for performance of the task order except for the Government furnished information identified in the RFP in Section J – List of Attachments.
2. Deliverables
See deliverable identified Article F.2., Deliveries (also described in Article C.2.), of the RFP.
3. Detailed Description Provide a detailed description of the approach for each task in accordance with the evaluation criteria in Section E above (be specific).
Cost Proposal The Contractor shall attach a detailed budget to identify all proposed costs.
ATTACHMENT 10
Task Area Three (3)
Task Order No. TBD Modification No: N/A TO Title: TBD Project Officer: TBD
Contract Task Area: Three (3): Large-Scale Single Cell Epigenome Sequencing
1) Provide at a minimum Large-Scale Single-cell Epigenome Sequencing with the following baseline capability and capacity:
a. Meet or exceed the Illumina recommended minimum sequencing performance specifications: sequencing output per flow cell, quality scores, run time, sample throughput per year
b. Meet or exceed a minimum capacity of producing 1 trillion short sequencing reads per year with capability of scaling up to a maximum of 10 trillion short sequencing reads per year
c. Provide capability of sequencing a variety of single-cell libraries at customized sequencing depths and read lengths
d. Provide sequential Just In Time secured/encrypted transfer of sequence and high-speed data in FASTQ format to the NIH BRAIN Initiative designated cloud-based archive(s) with Google, AWS, or Azure.
e. Provide correct and complete meta data for submission to the NIH BRAIN Initiative designated archive(s), including unique project sample identifiers and sequencing center.
2) Provide separate plans for Phase I (pilot studies) and Phase II of the task order as outlined in the Statement of Work (Attachment 3).
3) Utilize state of the art computational tools and algorithms for analysis
4) Provide personnel with expertise and experience single cell epigenomic sequencing, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)
5) Provide personnel with expertise and experience in sample receipt, tracking, handling, and storage, including the use of an in-house Laboratory Information Management System (LIMS);
develop and implement procedures for these activities
6) Provider must use seamless LIMS for contracted production and must provide real-time tracking by all production partners and this information must be available in real-time between production partners. BRAIN Initiative and BICAN investigators must have the ability to identify where a sample is in production via communication
7) Provide personnel with expertise and experience in epigenetic analyses and bioinformatics for data cleaning
8) Provide personnel with expertise and experience in the secure physical and electronic transfer of large quantities of data as well as securing in-house data
9) Provide data to the BRAIN Initiative Project Office or its designee on request in a complete and timely manner
10) Provide encrypted raw and transformed cleaned data as well as the final transformed data and sequencing metadata
11) Provide a Final Manual of Operations within 30 days of task order initiation. Details in Reporting Requirements
12) Provide biweekly Status Reports to the BRAIN Initiative Project Office and designated committees. The biweekly Status Report shall summarize the status of the single cell epigenomic analysis, the biweekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements
13) Communicate with NIH designated data coordinating center and data repository (archive) and the respective BICAN investigators and BRAIN Initiative staff to coordinate sample delivery and sample metadata.
14) Provide materials and information promptly and communicate with NIH staff, BICAN investigators, data coordinating center, and other contractors frequently and regularly
15) Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the sequence data
16) Maintain security guidelines that meet or exceed the current Security Best Practices, including its detailed description of requirements for security and encryption. This includes, but is not limited to:
a. all approved users have completed all required institutional computer security training, e.g.
http://irtsectraining.nih.gov/, or the equivalent
b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard)
c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled
d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged, if necessary then they must be encrypted
e. updated anti-virus/anti-spyware/anti-malware software
f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions
g. strong password for file access and never share it
h. All copies of the dataset must be destroyed whenever the NIH BRAIN Initiative program office requests destruction of the dataset
17) Provide secure backup of all data essential to the project, including but not limited to all sequence data generated, study data received, sample tracking and storage information, and QC information
18) Provide shipping and handling of samples from BICAN investigators. Offeror will develop best practices for sample concentration and plating and QC testing of study with BICAN investigators and NIH BRAIN Initiative staff during Phase I.
19) Receive and process data and samples from BICAN studies, including:
a. Receive, track, and store samples and accompanying data from BICAN designated studies in preparation for sequencing
20) Pilot QC of representative study samples during Phase I is expected to be within 7 days of sample receipt
21) Single cell epigenome data must begin to flow to the Government (NIH BRAIN Initiative designed data repository) within 14 days after receipt of samples
22) Demonstrate support for completing single cell epigenome sequence data at 1, 3, and 6 months.
23) Complete sequencing and electronic delivery of appropriately cleaned and transformed data (e.g. raw, processed, and segmented/interpreted) from all received (including QC/QA analysis) by end of the task order period (6 months). Quality control methods should include appropriate controls. See technical acceptability criteria in item 1 above.
24) Participate in NIH BRAIN Initiative designated in person or virtual-meetings (1 or 2 during task order performance period) and conference calls dealing with data integration, formats, QC/QA, data deposition as designated by the BRAIN Initiative Program Office.
25) Provide a Draft Final Report and Final Report prior to end of task order according to the details in the Reporting Requirements
26) When promising technologies are identified (examples may include changes in cost, increased information, or density, or increases in accuracy or interpretation) and has been requested by the COR, the contractor shall prepare a technology evaluation proposal.
See Deliverables identified in Article F.2., Deliveries (also described in Article C.2.), of the RFP.
approach for providing all resulting genotyping or sequencing data and associated files to the BICAN Investigators and central data repositories.
D. Special Restrictions/Clearances/Clauses:
See the following Articles in the RFP. Article B.3. Advanced Understandings, Section H, and Section I
E. Evaluation Criteria: See Section M of the RFP. Price is also a factor. The Offeror(s) price proposal will be evaluated for reasonableness. For a price to be reasonable, it must represent a price to the government that a prudent person would pay when consideration is given to prices in the market. Normally, price reasonableness is established through adequate price
Offerors are reminded that all terms and conditions of the IDIQ contract will apply to all task orders awarded.
Offerors shall submit a separate proposal within the general proposal for this Task Order as listed herein.
In doing so, you are to provide a separate Technical Proposal and Cost Proposal (including documentation to support the proposed price).
Task Area Four (4)
Task Order No. TBD Modification No: N/A TO Title: TBD Project Officer: TBD
Contract Task Area: Four (4): Large-Scale Single-Cell Multi-omics Sequencing
1) Provide at a minimum Large-Scale Single-cell Multi-omics Sequencing with the following baseline capability and capacity:
a. Meet or exceed the Illumina recommended minimum sequencing performance specifications: sequencing output per flow cell, quality scores, run time, sample throughput per year
b. Meet or exceed a minimum capacity of producing 1 trillion short sequencing reads per year with capability of scaling up to a maximum of 10 trillion short sequencing reads per year
c. Provide capability of sequencing a variety of single-cell libraries at customized sequencing depths and read lengths
d. Provide sequential Just In Time secured/encrypted transfer of sequence and high-speed data in FASTQ format to the NIH BRAIN Initiative designated cloud-based archive(s) with Google, AWS, or Azure.
e. Provide correct and complete meta data for submission to the NIH BRAIN Initiative designated archive(s), including unique project sample identifiers and sequencing center.
2) Provide separate plans for Phase I (pilot studies) and Phase II of the task order as outlined in the Statement of Work (Attachment 3).
3) Utilize state of the art computational tools and algorithms for analysis
4) Provide personnel with expertise and experience single cell multi-omic sequencing, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)
5) Provide personnel with expertise and experience in aliquoting, labeling, shipping, and minimum acceptable standards for quantity and quality for samples submitted for sequencing
6) Provide personnel with expertise and experience in sample receipt, tracking, handling, and storage, including the use of an in-house Laboratory Information Management System (LIMS);
develop and implement procedures for these activities
7) Provider must use seamless LIMS for contracted production and must provide real-time tracking by all production partners and this information must be available in real-time between production partners. BRAIN Initiative and BICAN investigators must have the ability to identify where a sample is in production via communication
8) Provide personnel with expertise and experience in epigenetic analyses and bioinformatics for data cleaning
9) Provide personnel with expertise and experience in the secure physical and electronic transfer of large quantities of data as well as securing in-house data
10) Provide data to the BRAIN Initiative Project Office or its designee on request in a complete and timely manner
11) Provide encrypted raw and transformed cleaned data as well as the final transformed data and sequencing metadata
12) Provide a Final Manual of Operations within 30 days of task order initiation. Details in Reporting Requirements
13) Provide biweekly Status Reports to the BRAIN Initiative Project Office and designated committees. The biweekly Status Report shall summarize the status of the single cell epigenomic analysis, the biweekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements
14) Communicate with NIH designated data coordinating center and data repository (archive) and the respective BICAN investigators and BRAIN Initiative staff to coordinate sample delivery and sample metadata.
15) Provide materials and information promptly and communicate with NIH staff, BICAN investigators, data coordinating center, and other contractors frequently and regularly
16) Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the sequence data
17) Maintain security guidelines that meet or exceed the current Security Best Practices, including its detailed description of requirements for security and encryption. This includes, but is not limited to:
a. all approved users have completed all required institutional computer security training, e.g.
http://irtsectraining.nih.gov/, or the equivalent
b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard)
c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled
d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged, if necessary then they must be encrypted
e. updated anti-virus/anti-spyware/anti-malware software
f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions
g. strong password for file access and never share it
h. All copies of the dataset must be destroyed whenever the NIH BRAIN Initiative program office requests destruction of the dataset
18) Provide secure backup of all data essential to the project, including but not limited to all sequence data generated, study data received, sample tracking and storage information, and QC information
19) Provide shipping and handling of samples from BICAN investigators. Offeror will develop best practices for sample concentration and plating and QC testing of study with BICAN investigators and NIH BRAIN Initiative staff during Phase I.
20) Receive and process data and samples from BICAN studies, including:
a. Receive, track, and store samples and accompanying data from BICAN designated studies in preparation for sequencing
21) Pilot QC of representative study samples during Phase I is expected to be within 7 days of sample receipt
22) Complete sequencing and electronic delivery of appropriately cleaned and transformed data
(e.g. raw, processed, and segmented/interpreted) from all received (including QC/QA analysis) by end of the task order period (6 months). Quality control methods should include appropriate controls. See technical acceptability criteria in item 1 above.
23) Perform appropriate QC for quantification, post library prep, on-instrument sequencing and transcriptomic build
24) Demonstrate support for completing single cell multi-omic sequence data at 1, 3, and 6 months.
25) Participate in NIH BRAIN Initiative designated in person or virtual-meetings (1 or 2 during task order performance period) and conference calls dealing with data integration, formats, QC/QA, data deposition as designated by the BRAIN Initiative Program Office.
26) Provide a Draft Final Report and Final Report prior to end of task order according to the details in the Reporting Requirements
27) When promising technologies are identified (examples may include changes in cost, increased information, or density, or increases in accuracy or interpretation) and has been requested by the COR, the contractor shall prepare a technology evaluation proposal.
See Deliverables identified in Article F.2., Deliveries (also described in Article C.2.), of the RFP.
approach for providing all resulting genotyping or sequencing data and associated files to the BICAN Investigators and central data repositories.
Section H, and Section I
E. Evaluation Criteria: See Section M of the RFP. Price is also a factor. The Offeror(s) price proposal will be evaluated for reasonableness. For a price to be reasonable, it must represent a price to the government that a prudent person would pay when consideration is given to prices in the market. Normally, price reasonableness is established through adequate price
Offerors are reminded that all terms and conditions of the IDIQ contract will apply to all task orders awarded.
Offerors shall submit a separate proposal within the general proposal for this Task Order as listed herein.
In doing so, you are to provide a separate Technical Proposal and Cost Proposal (including documentation
ATTACHMENT 11
Task Area Five (5)
Task Order No. TBD Modification No: N/A TO Title: TBD Project Officer: TBD
Contract Task Area: Five (5): Bulk Tissue Transcriptome and Epigenome Sequencing
A. Period of Performance: Twelve (6) months from time of award.
1) Provide state-of-the art transcriptome and epigenome sequence profiles from BICAN selected studies with the following baseline criteria:
a. Meet or exceed the Illumina recommended minimum sequencing performance specifications: sequencing output per flow cell, quality scores, run time, sample throughput per year
b. Provide capability of sequencing a variety of bulk transcriptome and epigenome libraries at customized sequencing depths and read lengths
c. Provide sequential Just In Time secured/encrypted and high-speed transfer of sequence data in FASTQ format to the NIH BRAIN Initiative designated data archive(s).
d. Provide correct and complete meta data for submission to the NIH BRAIN Initiative designated archive(s), including unique project sample identifiers and sequencing center.
2) Provide separate plans for Phase I (pilot studies) and Phase II of the task order as outlined in the Statement of Work (Attachment 3).
3) Utilize state of the art computational tools and algorithms, quantitation, and analysis
4) Provide personnel with expertise and experience in transcriptome profiling, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)
5) Provide personnel with expertise and experience in transcriptome and epigenome profiling.
6) Provide personnel with expertise and experience in sample receipt, tracking, handling, and storage, including the use of an in-house Laboratory Information Management System (LIMS); develop and implement procedures for these activities
7) Provider must use seamless LIMS for contracted production and must provide real-time tracking by all production partners and this information must be available in real-time between production partners. BRAIN Initiative and BICAN investigators, must have the ability to identify where a sample is in production via communications.
8) Provide personnel with expertise and experience in transcriptome sequence analysis and
9) Provide personnel with expertise and experience in the secure physical and electronic transfer of large-quantities of transcriptome sequence profile data as well as securing in-house data
10) Provide sequencing data to the BRAIN Initiative Project Office or its designee on request in a complete and timely manner
11) Provide encrypted raw and transformed cleaned data as well as the final transformed data and sequencing metadata
12) Provide a Final Manual of Operations within 30 days of task order initiation. Details in Reporting Requirements
13) Provide biweekly Status Reports to the BRAIN Initiative Project Office and designated committees. The biweekly Status Report shall summarize the status of the sequencing, the biweekly QC data, the weekly production, completeness, and quality metrics.
14) Communicate with NIH designated data coordinating center and data repository (archive) and the respective BICAN investigators and BRAIN Initiative staff to coordinate sample delivery and sample metadata.
15) Provide materials and information promptly and communicate with NIH staff, BICAN investigators, data coordinating center, and other contractors frequently and regularly
16) Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the transcriptomic sequence data
17) Maintain security guidelines that meet or exceed the current Security Best Practices. This includes, but is not limited to:
a. all approved users have completed all required institutional computer security training, e.g. http://irtsectraining.nih.gov/, or the equivalent
b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard)
c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled
d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged, if necessary then they must be encrypted
e. updated anti-virus/anti-spyware/anti-malware software
f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions
g. strong password for file access and never share it
h. all copies of the dataset must be destroyed whenever NHLBI requests destruction of the dataset
18) Provide secure backup of all data essential to the project, including but not limited to all sequencing data generated, study data received, sample tracking and storage information, and QC information
19) Provide shipping and handling of samples to and from the BICAN investigators. Offeror will develop best practices for sample concentration and plating and QC testing of study with BICAN investigators and NIH BRAIN Initiative staff during Phase I.
20) Receive and process data and samples from BICAN studies, including:
a. Receive, track, and store samples and accompanying data from BICAN designated studies in preparation for analysis
21) Pilot QC of representative study samples during Phase I is expected to be within 7 days of sample receipt
22) Sequencing data must begin to flow to the Government (NIH BRAIN Initiative designed data repository) within 14 days after receipt of samples
23) Complete sequence profiling and electronic delivery of appropriately cleaned and transformed data (e.g. raw, processed, and segmented/interpreted) from all received (including QC/QA analysis) by end of the task order period (6 months). Quality control methods should include negative controls, sample-independent and sample-dependent controls
24) Demonstrate support for completing transcriptome profile data at 1, 3, and 6 months
25) Participate in NIH BRAIN Initiative designated in person or virtual-meetings (1 or 2 during task order performance period) and conference calls dealing with data integration, formats, QC/QA, data deposition as designated by the BRAIN Initiative Program Office.
26) Provide a Draft Final Report and Final Report prior to end of task order according to the details in the Reporting Requirements
27) When promising transcriptome profile technologies are identified (examples may include changes in cost, increased information or density, or increases in accuracy or interpretation) and has been requested by the COR, the contractor shall prepare a technology evaluation proposal.
See Deliverables identified in Article F.2., Deliveries (also described in Article C.2.), of the RFP.
Investigator and central data repositories.
Section H, and Section I.
E. Evaluation Criteria:
See Section M of the RFP. Price is also a factor. The Offeror(s) price proposal will be evaluated for reasonableness. For a price to be reasonable, it must represent a price to the government that a prudent person would pay when consideration is given to prices in the market. Normally, price reasonableness is established through adequate price competition, but may also be determined through cost and price analysis techniques as described in FAR 15.404.
F. Response Due Date: Same date that overall proposal is due (see RFP)
Offerors are reminded that all terms and conditions of the IDIQ contract will apply to all task orders
Offerors shall submit a separate proposal within the general proposal for this Task Order as listed herein.
In doing so, you are to provide a separate Technical Proposal and Cost Proposal (including documentation
ATTACHMENT 12
Task Area Six (6)
Task Order No. TBD Modification No: N/A TO Title: TBD Project Officer: TBD
Contract Task Area: Six (6): Whole Genome Sequencing
A. Period of Performance: Twelve (6) months from time of award.
1) Provide at a minimum Whole Genome and Exome Sequencing of human, macaque, marmoset and mouse samples with the following baseline criteria:
a. Meet or exceed the Illumina recommended sequencing performance specifications: sequencing output per flow cell, quality scores, run time, sample throughput per year.
b. Provide capability of sequencing a variety of libraries at customized sequencing depths and read lengths
c. Provide sequential Just In Time secured/encrypted and high-speed transfer of sequence data in FASTQ format to the NIH BRAIN Initiative designated archive(s).
d. Provide correct and complete meta data for submission to the NIH BRAIN Initiative designated archive(s), including unique project sample identifiers and sequencing center.
2) Provide separate plans for Phase I (pilot studies) and Phase II of the task order as outlined in the Statement of Work (Attachment 3).
3) Utilize state of the art computational tools and algorithms for quantitation and analysis
4) Provide personnel with expertise and experience in metabolite profiling, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)
5) Provide personnel with expertise and experience in sample receipt, tracking, handling, and storage, including the use of an in-house Laboratory Information Management System (LIMS); develop and implement procedures for these activities
6) Provider must use seamless LIMS for contracted production and must provide real-time tracking by all production partners and this information must be available in real-time between production partners. BRAIN Initiative and BICAN investigators must have the ability to identify where a sample is in production via communication
7) Provide personnel with expertise and experience in omics analyses and
8) Provide personnel with expertise and experience in the secure physical and electronic transfer of large quantities of sequence data as well as securing in-house data
9) Provide data to the BRAIN Initiative Project Office or its designee on request in a complete and timely manner
10) Provide encrypted raw and transformed cleaned data as well as the final transformed data and sequencing metadata
11) Provide a Final Manual of Operations within 30 days of task order initiation. Details in Reporting Requirements
12) Provide bi-weekly Status Reports to the BRAIN Initiative Project Office and designated committees. The bi- weekly Status Report shall summarize the status of the metabolite profiling, the bi-weekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements.
13) Communicate with NIH designated data coordinating center and data repository (archive) and the respective BICAN investigators and BRAIN Initiative staff to coordinate sample delivery and sample metadata.
14) Provide materials and information promptly and communicate with NIH staff, BICAN investigators, data coordinating center, and other contractors frequently and regularly
15) Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the sequence data
16) Maintain security guidelines that meet or exceed the current security best practices, including detailed description of requirements for security and encryption. This includes, but is not limited to:
a. all approved users have completed all required institutional computer security training, e.g. http://irtsectraining.nih.gov/, or the equivalent
b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard)
c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled
d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged; if necessary then they must be encrypted
e. updated anti-virus/anti-spyware/anti-malware software;
f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions
g. strong password for file access and never share it
h. All copies of the dataset must be destroyed whenever NHLBI requests destruction of the dataset
17) Provide secure backup of all data essential to the project, including but not limited to all data generated (including raw data), study data received, sample tracking and storage information, and QC information
18) Provide shipping and handling of samples from BICAN investigators. Offeror will develop best practices for sample concentration and plating and QC testing of study with BICAN investigators and NIH BRAIN Initiative staff during Phase I.
19) Receive and process data and samples from BICAN designated studies, including:
a. Receive, track, and store samples and accompanying data from BICAN designated studies in preparation for sequencing
20) Pilot QC of representative study samples during Phase I is expected to be within 7 days of sample receipt
21) Sequence data must begin to flow to the Government (NIH BRAIN Initiative designed data repository) within 14 days after receipt of samples
22) Demonstrate support for completing single cell epigenome sequence data at 1, 3, and 6 months.
23) Complete profiling and electronic delivery of appropriately cleaned and transformed data from all received (including QC/QA analysis) by end of the task order period (6 months). Quality control methods should include negative controls, sample-independent and sample-dependent controls
24) Participate in NIH BRAIN Initiative designated in person or virtual-meetings (1 or 2 during task order performance period) and conference calls dealing with data integration, formats, QC/QA, data deposition as designated by the BRAIN Initiative Program Office.
25) Provide a Draft Final Report and Final Report prior to end of task order according to the details in the Reporting Requirements
26) When promising metabolomic technologies are identified (examples may include changes in cost, increased information or density, or increases in accuracy or interpretation) and has been requested by the COR, the contractor shall prepare a technology evaluation proposal
See Deliverables identified in Article F.2., Deliveries (also described in Article C.2.), of the RFP.
approach for providing all resulting sequencing data and associated files to the BICAN Investigators and central data repositories.
Section H, and Section I.
E. Evaluation Criteria:
See Section M of the RFP. Price is also a factor. The Offeror(s) price proposal will be evaluated for reasonableness. For a price to be reasonable, it must represent a price to the government that a prudent person would pay when consideration is given to prices in the market. Normally, price reasonableness is established through adequate price competition, but may also be determined through cost and price analysis techniques as described in FAR 15.404.
Offerors are reminded that all terms and conditions of the IDIQ contract will apply to all task orders
ATTACHMENT 13
Task Area Seven (7)
Task Order No. TBD Modification No: N/A TO Title: TBD Project Officer: TBD Date Prepared:
Contract Task Area: Seven (7): Novel Omics Profiles for 500 samples up to maximum capacity (to be proposed in increments of 1,000)
NOTE #1 TO OFFERORS: This task requires obtaining omics sequencing profiles that are novel to the BICAN program. Measures can include characterization of any transcriptome and epigenome changes in cell type and state whether transitory, permanent, or mutable.
Sequencing approaches and library types may include but are not limited to: a) RNA isoform long-read sequencing, b) subcellular compartment RNA sequencing, c) ribosome sequencing, and d) DNA hydroxymethylation sequencing. Novel Omics profile data following cleaning, QC/QA, and assembly must be securely transmitted to NIH BRAIN Initiative designated partners/data archive(s).
1. Provide state of the art omics profiles that measure changes in cell state whether transitory, permanent, or mutable for designated BICAN samples and indicate potential sample sources
2. Incorporate methodologies to increase accuracy and enhance detection
3. Incorporate quality measures to minimize false discovery rates
4. Utilize sample preparations to maximize the utility and efficiency of the samples
5. Utilize state of the art computational tools and algorithms for task omics identification, quantitation, change in state, and analysis
6. Provide personnel with expertise and experience in task omics profiling, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)
7. Provide personnel with expertise and experience in preparing samples for task omic profiling
8. Provide personnel with expertise and experience in sample receipt, tracking, handling and storage, including the use of an in-house Laboratory Information Management System (LIMS); develop and implement procedures for these activities
9. Provider must use seamless LIMS for contracted production and must provide real-time tracking by all production partners and this information must be available in real-time between production partners. BRAIN Initiative and BICAN investigators must have the ability to identify where a sample is in production via communication
10. Provide personnel with expertise and experience in task omics analyses and bioinformatics for data cleaning
11. Provide personnel with expertise and experience in the secure physical and electronic transfer of large quantities of task omics data as well as securing in-house data
12. Provide data to the BRAIN Initiative Project Office or its designee on request in a complete and timely manner
13. Provide encrypted raw and transformed cleaned data as well as the final transformed data and sequencing metadata
14. Provide a Final Manual of Operations within 30 days of task order initiation. Details in Reporting Requirements
15. Provide bi-weekly Status Reports to the BRAIN Initiative Project Office and designated committees. The bi- weekly Status Report shall summarize the status of the task omics profiling, the bi-weekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements
16. Communicate with NIH designated data coordinating center and data repository (archive) and the respective BICAN investigators and BRAIN Initiative staff to coordinate sample delivery and sample metadata.
17. Provide materials and information promptly and communicate with NIH staff, BICAN investigators, data coordinating center, and other contractors frequently and regularly
18. Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the task omics data
19. Maintain security guidelines that meet or exceed the current security best practices, including detailed description of requirements for security and encryption. This includes, but is not limited to:
a. all approved users have completed all required institutional computer security training, e.g. http://irtsectraining.nih.gov/, or the equivalent
b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard)
c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled
d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged, if necessary then they must be encrypted
e. updated anti-virus/anti-spyware/anti-malware software
f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions
g. strong password for file access and never share it
h. All copies of the dataset must be destroyed whenever NHLBI requests destruction of the dataset
20. Provide secure backup of all data essential to the project, including but not limited to all data generated (including raw data), study data received, sample tracking and storage information, and QC information
21. Provide shipping and handling of samples from the BICAN investigators. Offeror will provide best practices for sample processing and will initiate pilot QC testing of study samples within 30 days of task order initiation
22. Receive and process data and samples from BICAN designated studies, including:
a. Receive, track, and store samples and accompanying data from BICAN designated studies in preparation for task omics profiling
23. Task omics profiling data must begin to flow to the Government (NIH BRAIN Initiative designated data repository within 30 days after receipt of samples
24. Complete task omics profiling and electronic delivery of appropriately cleaned and transformed data (e.g. raw, processed, segmented/interpreted data, and region of interest data) from all received (including QC/QA analysis) by end of the task order period (6 months). Quality control methods should include negative controls, sample-independent and sample-dependent controls
25. Participate in NIH BRAIN Initiative designated in person or virtual-meetings (1 or 2 during task order performance period) and conference calls dealing with data integration, formats, QC/QA, data deposition as designated by the BRAIN Initiative Program Office.
26. Provide a Draft Final Report and Final Report prior to end of task order according to the details in the Reporting Requirements
27. When promising technologies corresponding to the omics task submitted are identified (examples may include changes in cost, increased information, or density, or increases in accuracy or interpretation) and has been requested by the COR, the contractor shall prepare a technology evaluation proposal
See Deliverables identified in Article F.2., Deliveries (also described in Article C.2.), of the RFP.
Investigator and central data repositories.
Section H, and Section I.
E. Evaluation Criteria: See Section M of the RFP. Price is also a factor. The Offeror(s) price proposal will be evaluated for reasonableness. For a price to be reasonable, it must represent a price to the government that a prudent person would pay when consideration is given to prices in the market. Normally, price reasonableness is established through adequate price
F. Response Due Date: Same date that overall proposal is due (see RFP)
Offerors are reminded that all terms and conditions of the IDIQ contract will apply to all task orders
File details come from the government source that posted it. Updated .