Attach 1 SOW_DCCPS Biomedical Computing.pdf

Division of Cancer Control and Population Sciences Biomedical Computing Support Draft Statement of Work (SOW)

Scope

The Contractor shall perform Information Technology (IT) and biomedical computing services required by programs and projects in the Division of Cancer Control and Population Sciences (DCCPS), National Cancer Institute (NCI). Specifically, the Contractor shall provide support that fits into the eleven task areas. They are:

Task Area 1. Project Management/Core Services Task Area 2. Data Management Task Area 3. Computer Programming Task Area 4. Computing Infrastructure Services Task Area 5. Website Development Task Area 6. Systems Design and Development Task Area 7. Reports and Manuscripts Preparation Task Area 8. Statistical Methodology and Program Support

Requirements

The Contractor, as an independent entity and not as an agent of the Government, shall provide the necessary resources (except for those specifically designated as Government-furnished, which is not anticipated for this requirement) to accomplish tasks of the type set forth below.

Task Area 1. Project Management/Core Services

1. Project Management

a. Overall Contract Management

The Contractor shall provide overall management, integration and coordination of all task order activities, including the management and coordination of activities carried out under subcontracts. The Contractor shall provide all technical and administrative infrastructure to ensure the efficient planning, initiation, implementation and timely completion of all projects carried out under this task order. Additionally, the Contractor shall meet at regular intervals with the Contracting Officer’s Representative (COR) in face-to-face and/or virtual meetings monthly to review contract performance and discuss project management issues.

The Contractor shall deliver a Project Management Plan draft, within sixty business (60) days after start of contract, coordinate and initiate revision meetings with COR to refine the Project Management Plan and deliver a final version of the Project Management Plan thirty business (30) days after draft. Additionally, as agreed upon with COR, the Project Management Plan shall include but not be limited to:

i. Contact list and organizational chart

ii. Project milestones, strategy and roadmap

iii. Project risks and assumptions

iv. Estimated timelines for each component of the project plan.

b. Individual Project Management

As agreed upon with COR and project lead(s), the Contractor shall set up time with appropriate NCI project staff members to define individual project management needs and provide project management activities as agreed upon with the project lead(s).

2. Travel and Meetings

As directed by the COR, the Contractor shall attend virtual meetings and/or travel to conferences, meetings, offsite registry trainings for tasks including but not limited to staffing presentation and demonstration booths, providing presentations and demonstrations on projects, and providing technology workshops. The number of people for travel to the meetings will vary depending on the requirements and as such, the Contractor shall provide an estimate of required staff for travel to the COR and appropriate NCI project personnel for review and approval prior to travel.

Task Area 2. Data Management

1. Surveillance, Epidemiology, and End Results (SEER) Program Data Management and Maintenance

a. SEER DATA SUBMISSIONS: The population-based tumor registries participating in the

SEER Program submit routine data submissions to NCI twice during the calendar year, during November and February. Special data submissions, such as the National Childhood Cancer Registry (NCCR) data and linkage file or other one-time data submissions, may also be required. These submissions contain records on individual cancer cases. The Contractor is responsible for applying the edits defined by the COR and constructing the basic analytic files for NCI. The following describes the current basic procedure the Contractor shall follow for processing the November SEER data submissions. A similar process shall be followed for February without edit checks. These processes may evolve, as needed, and the COR and appropriate NCI staff will oversee all data flow to SEER through ongoing project management tasks as outlined Task Area 1.

i. The Contractor shall receive data submissions from the registries to a secure submission site as designated by the COR. The secure submission site is a secure web portal that would be developed and maintained by the Contractor as agreed upon with COR. Registries will utilize this web portal to securely transfer data to the Contractor. If problems arise during file transfer from the registry, the Contractor shall communicate them to NCI staff so that a resubmission can be requested by SEER program from the registry.

ii. The Contractor shall use the SEER Edit/Update Program to process the SEER files.

The Contractor shall deliver summary tabulations describing any errors found, and other statistics, reports and graphs produced by the SEER Edit/Update Program, and associated programs, to NCI staff. NCI staff will review these reports and communicate any changes needed to the Contractor. Similarly, if the registries have any special requests for the content of their own error reports; these shall also be communicated to NCI staff. After receiving instructions from the NCI staff on the production of the error reports, the Contractor shall produce the reports using the Error Report Program and send them to the registries.

iii. The registries will be expected to correct the errors and resubmit their files. The Contractor shall process these corrected submissions in the same manner as the original submission.

iv. After NCI staff determines that the files can be used for analytic purposes, the

Contractor shall recode variables. A list of variable definitions can be found, although the recodes are not limited to this list, on https://seer.cancer.gov/analysis/.

v. After recoding the files, the Contractor shall make them available to the NCI staff through SEER*Stat (See Task Area 6. Systems Design and Development) or other agreed upon location such as the NCI data enclave.

b. MAINTENANCE OF THE SEER PROCESSING SYSTEM EDITS: The Contractor shall maintain edits involving program modification and testing as requested by NCI staff.

Changes shall be made throughout the year as problems are discovered, or the need for new edits are realized, with the bulk of the changes occurring around the time of the routine data submissions in February and August. The Contractor shall also provide additions and modifications to the routine reports generated by the edit programs.

c. MAINTAIN SECURE File Transfer Protocol (FTP) SITE: The Contractor shall maintain the secure site utilized for electronic data transmissions between the SEER Registries and NCI. The FTP site is developed and maintained by the Contractor as agreed upon with

COR.

d. DOCUMENTATION: The Contractor shall prepare, as needed, and keep up-to-date written policies and procedures for all SEER data processing activities. Drafts of all new procedures shall be provided to the COR for review and obtain written approval prior to implementation. Copies of the documentation shall be made readily available and provided to the COR upon request.

e. ANALYTICAL FILES: The Contractor shall create and/or update a number of subsets of the full SEER data to support analysis of the data by both NCI and the non-NCI researchers, as directed by the COR. These files shall be made available to the researchers through the SEER*Stat software.

2. Mortality Processing

The Contractor shall make changes to the programs for updating of new National Center for Health Statistics (NCHS) county codes, changes to the recodes, and addition of new fields to the original data or recoded data. The Contractor shall update all documentation for all phases of mortality processing.

The Contractor shall process U.S. mortality data files annually using the following procedures:

a. As directed by the COR, the Contractor shall select a subset of cancer only deaths from the file of all deaths and shall process this file using the Mortality Recode Program.

b. The Contractor shall append this new file with files (both total U.S. and SEER) from previous years.

c. The Contractor shall produce a set of tables for use in verifying the accuracy of the data received, as directed by the COR.

d. The Contractor shall prepare new SEER*Stat mortality databases for both NCI and public use.

3. Census/NCI Population Processing The Contractor shall transfer the population estimates received from the U.S. Census Bureau to the local computer systems (NCI’s and/or the Contractor’s) used for this contract. The Contractor shall develop files from these data sources for use by SEER*Stat. The Contractor shall maintain documentation on the procedures used to transfer and develop the files and the files received.

4. SEER-CMS

The Contractor shall complete the linkage of the SEER data with Centers for Medicare & Medicaid Services (CMS) data. This shall require developing methods to concatenate cases.

The Contractor shall work with the NCI, the CMS, and designated Contractors to consolidate individuals between the existing linkages and persons to be added. The Contractor shall, under the direction of the COR, develop four research databases; three pertain to Medicare data: SEER-Medicare, SEER-Medicare Health Outcomes Survey (SEER-MHOS) and SEER- Consumer Assessment of Healthcare Providers and Systems (CAHPS) and one pertains to Medicaid: SEER-Medicaid.

1. Create and maintain the linked databases. The Contractor shall update the SEER-CMS linkages annually (e.g., add new years of data and/or new persons to the databases) through activities including, but are not limited to:

a. Maintain linkage tracking systems that can be accessed by NCI, the Contractor, and other NCI-designated entities. These tracking databases shall be maintained by the Contractor.

b. Sign confidentiality agreements with each participating cancer registry in order to receive and compile personal identifiable information (PII), including names, dates of birth and social security numbers, from the registries (e.g., requires accessing data via SEER*DMS or receiving data via a secure portal managed by the Contractor, if a registry is not on SEER*DMS).

c. Sign confidentiality agreement with CMS to serve as NCI’s data custodian.

d. Assess the quality of the identifiers prior to sending a standardized consolidated file to

CMS to be linked with the Medicare and Medicaid master enrollment files.

e. Receive data from CMS via secure delivery, and securely store the received data.

f. Assess linkage quality (e.g., calculate match rates) and exclude persons based on data anomalies and other exclusion criteria, under the direction of the COR.

g. Perform data cleaning activities to ensure quality of the linked data;

h. Process the linked data to create the finalized versions of the databases, including, but not limited to, grouping the data into the four separate research databases and encrypting restricted variables (e.g., identifiers for small geographic areas and for included person and/or providers), recode variables and create new variables and scaled scores. The COR will provide guidance concerning the confidentiality of small geographic areas and health care providers identified from the database.

i. Link and maintain additional data, including, but not limited to, data from non-SEER registries or other databases, such as Census data or the Area Resource File.

j. Support the development of public facing websites pertaining to the four databases (e.g., update web content summarizing the available data and how to obtain the data), the webpages serve as a source of information for outside investigators to understand and obtain the data, as well as some technical support questions. The Contractor shall respond to the COR requests for additions and modifications to the existing webpage.

k. Maintain the publicly available web-based sample size calculators for each of the databases.

l. Maintain the customized SEER*Stat databases that contain variables created from the SEER-CMS databases.

2. Create resources for the research community, including but not limited to data codebooks, manuals, code libraries (ICD-9, ICD-10, CPT, HCPCS) for cancer related conditions and procedures. The Contractor shall then make these resources available to the research community by posting them on the SEER-CMS webpages.

3. Process requests for access to the SEER-CMS data, which are made available to approved investigators through an application process. The Contractor is responsible for, but not limited to, the following:

a. Maintain and manage database-specific request tracking systems that can be accessed by NCI, the Contractor, and other NCI-designated entities. These databases shall be maintained by the Contractor.

b. Serve as the point of contact for the submission of SEER-Medicare and SEER- Medicaid data applications and manuscripts that result from the analyses of these data.

Triage the applications and manuscripts to the appropriate multi-tiered review teams and track the progress of data requests from application submission, through application review, and if approved through signing of Data Usage Agreement, data processing and shipping, submission of any associated manuscripts, and finally closing of the project at completion).

c. Restrict access to the SEER-CMS data, and related documents including data applications and resulting manuscripts to authorized users.

d. Prepare project specific cuts of the databases once the research applications have been approved and ship the data to the requestor (e.g., restrict released data to approved cancer sites, specific years and/or claim types and years).

e. Develop cost structures to cover the data processing and shipping costs that are incurred for creating SEER-CMS project-specific data request. Cost structures shall consider programming complexity to create the data request (e.g., how many variables across how many files need to be considered to define the inclusion/exclusion criteria for the request) and the resulting size of data files that are to be shipped to the requestor. The Contractor shall discuss the cost structures with the COR prior to implementation. The Contractor shall directly invoice the requestor for the incurred data processing and shipping costs. The current cost structures for the SEER-CMS linkages are available at:

a. SEER-Medicare: Cost of Acquiring SEER-Medicare Data (cancer.gov)

b. SEER-MHOS: Cost of Acquiring the SEER-MHOS Data (cancer.gov)

c. SEER-CAHPS: Cost of Acquiring SEER-CAHPS Data (cancer.gov)

d. SEER-Medicaid: Cost of Acquiring SEER-Medicaid Data (cancer.gov)

4. Conduct SEER-CMS analyses as directed by NCI, with approval of the COR. These analyses will include, but are not limited to, creating analytic files and/or conducting bivariate and multivariate statistical analyses, summarizing results in publication quality tables, graphs, and slides. The Contractor shall track time spent on SEER-CMS analyses using branch specific cost codes.

5. SEER-HUD

The Contractor shall complete the linkage of the SEER data with HUD data. This shall require developing methods to concatenate cases. The Contractor shall work with the National Cancer Institute, the Department of Housing and Urban Development (HUD), and designated Contractors to consolidate individuals across files and years.

https://healthcaredelivery.cancer.gov/seermedicare/obtain/cost.html https://healthcaredelivery.cancer.gov/seer-mhos/obtain/cost.html https://healthcaredelivery.cancer.gov/seer-cahps/obtain/cost.html https://healthcaredelivery.cancer.gov/seermedicaid/obtain/cost.html

1. Create and maintain the linked database. The Contractor shall maintain and update the SEER-HUD linkage through activities including, but are not limited to:

a. Maintain linkage tracking system that can be accessed by NCI, the Contractor, and other NCI-designated entities. This database shall be maintained by the Contractor.

b. Sign confidentiality agreement with HUD in order to receive data from HUD including

PII via secure delivery, and securely store the data.

c. Compare the PII from HUD and from SEER (e.g., using the PII data used to create the

SEER-CMS linkages) to identify overlapping persons (e.g., using Match*Pro software).

d. Assess linkage quality (e.g., calculate match rates) and exclude persons based on data anomalies and other exclusion criteria.

e. Create the SEER-HUD database, which will include the SEER variables and administrative enrollment in housing assistance variables from HUD. Wherever applicable identified persons who are in SEER-CMS and SEER-HUD and ensure restricted variables are appropriately encrypted (e.g., identifiers for small geographic areas).

f. Perform data cleaning activities to ensure quality of the linked data.

g. Support the development of public website (e.g., create and update web content summarizing the available data and how to obtain the data).

h. Create and maintain a publicly available web-based sample size calculator.

i. Create and maintain a customized SEER*Stat database that contains variables created from the SEER-HUD linkage.

2. Create resources for the research community, including but not limited to data codebooks, manuals, code libraries. The Contractor shall then make these resources available to the research community by posted them on the SEER-HUD webpage.

3. Process requests for access to the SEER-HUD data, which will be made available to approved investigators through an application process similar to SEER-CMS. The Contractor is responsible for, but not limited to, the following:

a. Maintain and manage database-specific request tracking system that can be accessed by NCI, and other NCI-designated entities. These databases shall be maintained by the Contractor.

b. Serve as the point of contact for the submission of SEER-HUD data applications and manuscripts that result from the analyses of these data. Triage the applications and manuscripts to the appropriate multi-tiered review teams and track the progress of data requests from application submission, through application review, and if approved through signing of Data Usage Agreement, data processing and shipping, submission of any associated manuscripts, and finally closing of the project at completion.

c. Restrict access to the SEER-HUD data, and related documents including data applications and resulting manuscripts to authorized users.

d. Prepare project specific cuts of the databases once the research applications have been approved and ship the data to the requestor (e.g., restrict released data to approved cancer sites, and/or specific years of data).

e. Develop a cost structure to cover the data processing and shipping costs that are incurred for creating SEER-HUD project-specific data requests, like the above-mentioned SEER-CMS cost structures. The cost structure shall consider programming complexity to create the data request (e.g., how many variables across how many files need to be considered to define the inclusion/exclusion criteria for the request) and the resulting size of data files that are to be shipped to the requestor. The Contractor shall discuss the cost structure with the COR prior to implementation. The Contractor shall directly invoice the requestor for the incurred data processing and shipping costs.

4. Conduct SEER-HUD analyses as directed by NCI, with approval of the COR. These analyses will include, but are not limited to, creating analytic files and/or conducting bivariate and multivariate statistical analyses, summarizing results in publication quality tables, graphs, and slides. The Contractor shall track time spent on SEER-HUD analyses.

6. Data linkages

The Contractor shall link the SEER data to various sources as requested by the COR. The linkage specifications shall vary based on the data source to be linked. Linkages may require the Contractor to acquire the data to be linked. The Contractor shall:

a. Develop the linkage process. The linkage process may require:

i. The Contractor to receive automated data feeds or a regularly scheduled submission at specified intervals from the data provider.

ii. Consolidate records identified from a finder file.

iii. Create additional variables or flags resulting from the linkage results as directed by

NCI.

iv. Use code libraries to identify cancer-related treatment and/or conditions and procedures that appear in insurance or pharmacy claims or other sources.

v. Enable support through collaboration with additional analytics partners particularly those having an existing platform that can support the required analysis.

b. Coordinate with NCI investigators, as directed by the COR, data delivery, format and documentation.

c. Establish and manage any required legal agreements.

Task Area 3. Computer Programming

1. Quality Assessment and Control Analyses The Contractor shall, under technical direction of the COR:

a. Support and conduct analyses to develop SEER Program Benchmarks Development activity;

b. Support and conduct analyses required by SEER Quality Audits activity;

c. Support analyses necessary to conduct focused in-depth audits;

d. Conduct data analyses as part of the development of tools for corrective actions, tools field testing, and verification of corrective actions outcomes;

e. Support and conduct analyses to study the effect of automation, such and consolidation automation.

Analysis support refers to preparation of analysis files including selection of an analytic dataset, de-identification procedures, building new variables, and any related data management activities, including the transfer of a de-identified dataset to NCI. Analysis conduct means conducting descriptive and inferential statistical procedures, including tabular and graphical presentation of results.

2. Quality Assurance Analyses The Contractor shall:

a. Support and conduct analyses for SEER reliability studies.

b. Support and conduct analyses for the Surveillance Research Program (SRP) feasibility studies.

For these activities, analysis support refers to maintenance and update of the SEER Reliability software, and data management steps related to data upload and creating analytic dataset out of participants’ responses. Analysis conduct means conducting descriptive and inferential statistical procedures, including tabular and graphical presentation of results.

3. Patterns of Care (POC) Studies The Contractor shall assist with the POC studies, which is a congressionally mandated annual evaluation of the dissemination of state-of-the-art cancer therapy and diagnostics into community oncology practice. During each annual POC study, a sample of cancer cases are identified using SEER*DMS or via a secure portal managed by the Contractor, if a registry is not on SEER*DMS, to have additional information abstracted from their medical charts. The Contractor shall:

a. Provide editing assistance for the data manuals and data forms of these annual studies.

b. Develop, maintain and train users on the abstracting software (POC*Abs), which must be customized each year to meet the annual POC study aims. The annual software is then provided to the participating cancer registries along with an annual training session.

c. Provide data editing, key entry, computer editing, problem resolution support for the capture and maintenance of the data. Edit specifications to be applied to the data are to be developed by the Contractor and analyses performed with approval by the COR.

These analyses will include, but are not limited, to tabulations, frequencies and other standard statistical approaches.

d. Provide International Classification of Disease-10, Clinical Modification (ICD-10-CM) coding services for the Patterns of Care studies. It is essential that the ICD coding of co-morbid conditions be consistent over all the Patterns of Care studies. As a quality control measure, a subset of data will be coded a second time. The results of these duplicate coding shall be compared to assess the accuracy of the ICD coding patterns.

e. Develop and maintain POC*Explorer, an interactive website allowing access to aggregated data from certain POC studies.

f. Conduct POC analyses as directed by NCI, with approval of the COR. These analyses will include, but are not limited to, creating analytic files and/or conducting bivariate and multivariate statistical analyses, summarizing results in publication quality tables, graphs, and slides. The Contractor shall track time spent on POC analyses using branch specific cost codes.

g. Provide the POC data to outside requestors, with approval of the COR and the POC program lead.

4. Large research networks (e.g., Population-based Research to Optimize the Screening

Process (PROSPR), Improving the Management of symPtoms during And following Cancer Treatment (IMPACT) and Accelerating Colorectal Cancer Screening and follow-up through Implementation Science (ACCSIS)). To support these networks the Contractor shall:

a. Create web-based systems for receiving, maintaining, and sharing the data generated by the different research projects and coordinating centers.

b. Run quality control analyses on the data to ensure consistency.

c. When deemed appropriate by NCI, with approval of the COR, assist with creating plans for the analyses and dissemination of these data.

5. Cohort Consortium The Contractor shall provide project support for a database of consortium project activities and centralized repository for consortium data by updating, maintaining, and fielding technical questions regarding the NCI Cohort Consortium Project Hub, which is a searchable electronic data management system designed to track and report on the activities of NCI Cohort Consortium projects and project groups in an efficient manner and to automate the proposal process for new NCI Cohort Consortium projects, including the electronic submission, review, tracking, and reporting of progress reports and project proposals.

6. COnsortium of METabolomics Studies (COMETS) Analytics The Contractor shall support the maintenance and expansion of COMETS Analytics to include:

a. Maintain functionalities of the COMETS Analytics working version (e.g., v2.0);

b. Coordinate with front-end developers to optimize function outputs that help streamline development of front-end interface;

c. Develop new functionalities for 2.1 release (survival analysis, conditional regression, pathway analyses, etc.) and future releases;

d. Incorporate unit tests for older and new functionalities;

e. Update documentation on the public COMETS Analytics R package; and

f. Ensure package builds without errors and can be deployed on different system (e.g., GitHub Actions).

7. Metabolomics Project Hub The Contractor shall develop an electronic data management system (project hub) to track and report on activities of the Metabolomics Project Hub. This project hub will either be cloned from or integrated within the existing Cohort Consortium Project Hub.

8. Diet History Questionnaire (DHQ)

a. The Contractor shall manage the DHQ respondent and researcher website, update the DHQ architecture, and consider updates and alternative options for DietCalc.

b. Computing Infrastructure Maintenance and Support: The Contractor shall manage the DHQ Help Desk, provide system administration functions (i.e., help desk support) to support the continuing operation of the computing infrastructure for DCCPS researchers and the Contractor’s staff who assist DCCPS researchers.

c. The Contractor shall assist with all aspects related to the migration of DHQ to the cloud.

d. The Contractor shall review the EGRP DHQ website for accuracy on a regular/ongoing basis.

9. Dietary Assessment

a. The Contractor shall continue in the development, support, and modification of the of Food

Frequency Questionnaires (FFQs) such as the National Institute of Health American Association of Retired Persons FFQ, NCI’s Diet History Questionnaire, and NCI’s Prostate, Lung, Colorectal and Ovarian (PLCO) FFQ as needed. This may require analysis of individual food consumption data in national surveys; e.g., Continuing Survey of Food Intakes by Individuals (CSFII) 94-96 and the National Health and Nutrition Examination Survey (NHANES).

b. The Contractor shall provide analyses as needed to further develop and/or validate the Automated Self-Administered 24-hour dietary recall (ASA24), traditional interviewer-administered 24-hour dietary recalls, FFQs short dietary assessment tools/screeners and a daily checklist of food consumption. These analyses shall provide extensive demographic and descriptive analyses, as well as detailed statistical modeling to assess validity using demographic, biomarker and dietary data. Tasks shall include, but not be limited to the creation of extensive analytic files and statistical analyses. Analyses shall include, but not be limited to data from the following validation and evaluation datasets: the Food and Eating Assessment Study (FEAST) and the Food Reporting Comparison Study (FORCS), the Eating at America’s Table Study (EATS), and the Observing Protein and Energy Nutrition (OPEN) Study. Some analyses may require examination of individual food consumption data in national surveys; e.g., the National Health and Nutrition Examination Survey (NHANES).

10. Dietary Monitoring

a. The Contractor shall provide analyses on a range of topics related to dietary monitoring using data from the most recent cycle of the National Health and Nutrition Survey (NHANES) or other surveys such as the California Health Interview Survey (CHIS), the Continuing Survey of Food Intakes by Individuals (CSFII), the Diet and Health Knowledge Survey (DHKS), or the NHANES I Epidemiologic Follow-up Study (NHEFS).

b. Analyses may include assessing food and nutrient intakes in relation to both dietary recommendations and health objectives and assessing trends in these dietary components over time. Survey data may also be examined to address methodological questions in dietary assessment. Tasks shall include, but not be limited to the creation of extensive analytic files and statistical analyses as required.

c. The Contractor shall provide analytic support to create nutrient and food pattern equivalents databases for food frequency questionnaires (and including associated 24-hour recall validation sub-study data) and to assess dietary intakes of various demographic groups as required.

d. The Contractor shall provide analyses of data related to estimating the distributions of usual intakes of foods and nutrients in a univariate or multivariate context. These shall include analyses of data from various surveys as well as simulations.

11. NHANES I Epidemiologic Follow-up Study (NHEFS)/ National Health and Nutrition Examination Survey (NHANES) Databases

a. The Contractor shall provide data processing and secondary data analysis of these public use databases. Studies may involve risk factor surveillance and examination of specific risk factors relative to site specific cancer outcomes. The Contractor shall generate code to develop and validate diet quality indices. The Contractor shall generate analytic data files from the larger public use files as requested by the COR. These data may also be used to produce nutrient databases for the Diet History Questionnaire (DHQ) or other dietary assessment instruments (as mentioned under Item G above).

b. The Contractor shall provide analyses of designated years of NHANES data, including but not limited to, reported risk behaviors, accelerometer data, biomarkers and other physiological measures with the range of covariates available from the NHANES.

c. The Contractor shall work with NCI investigators to obtain approval to link mortality datasets from the National Center for Health Statistics and perform analyses of the linked data.

d. The Contractor shall develop R code (a set of steps with code) that can be included on an NCI website to download, unzip, and merge raw accelerometer data files from the 2011- 2014 National Health and Examination Survey (NHANES), the 2012 NHANES National Youth Fitness Survey, and other NHANES survey that gather accelerometer data.

12. National Collaborative on Childhood Obesity Research (NCCOR) Measures Registry and

Catalogue of Surveillance Systems

a. The Contractor shall develop and maintain websites for the various programs and branches within DCCPS, as directed by the Project Officer(s). To accomplish this task the Contractor shall meet with the NCI investigators to develop the system requirements for future enhancements and additions.

b. Develop prototypes of the WWW page modifications utilizing currently available computer resources.

c. Provide access to the data entry pages for updates and additions of new measures and systems.

d. Improve the webpages and searching tools based on feedback from the users.

13. National Institute of Heath-American Association of Retired Persons (NIH-AARP) Diet and Health Cohort Study The Contractor shall provide analyses using both the total cohort and the calibration study participants. Analyses for this study will include descriptive data on nutrient and food intakes as well as risk factors by demographic characteristics. Calibration study analyses include modeling for calibration/validation, as well as other statistical analyses, to assess error in dietary assessment methods. Various outcome analyses using diet as the independent variable may also be conducted.

14. IDATA Study/MEASURE

The Interactive Diet and Activity Tracking in AARP (IDATA) Study and the Multi-cohort Eating and Activity Study for Understanding Reporting Error (MEASURE) are related initiatives conducted to assess the measurement error properties of diet and physical activity assessment instruments against biomarkers and other reference measures. The MEASURE study includes three studies, IDATA and two Harvard studies (the Men’s and Women’s Lifestyle Validation Studies). Data elements common to all or some of the studies include food frequency questionnaires, diet records, 24-hour dietary recalls, accelerometers, anthropometry, demographics resting metabolic rate, physical activity questionnaires, physical activity 24-hour recalls, and biological measures from doubly labeled water and 24-hour urine, saliva and fasting bloods. The Contractor shall provide analyses of IDATA and MEASURE data including but not limited to creation of analytic files, variable creation, data linkage and harmonization, data documentation, calibration and other statistical modeling. The creation and maintenance of a Web portal for investigators to access data may also be required.

15. Health Information National Trends Survey (HINTS)

The Contractor shall assist with the data management and analysis of HINTS data, which are nationally representative nationally representative data about the American public’s knowledge of, attitudes toward, and use of cancer and health-related information. HINTS data are used to monitor changes in the rapidly evolving fields of health communication and health information technology and to create more effective health communication strategies across different populations. The Contractor shall:

a. Run relational checks and other quality control analyses on the databases to ensure consistency of primary measures.

b. Maintain version control over the HINTS public databases and publish release notes when changes are made, as directed by the COR.

c. Recode data and create new variables, as needed, and develop tabular output from statistical analyses.

d. Specific analytic support to include, but not limited, to data error remediation re-analyses;

trends analysis on e-cig harm perceptions; creating tables of results of Healthy People 2030 objectives; and geo-code data linkages (e.g., with ACS data).

16. Tobacco Use Supplement to the Current Population Survey (TUS-CPS) Data

The Contractor shall support:

1. Data analysis and dataset review and documentation.

2. Analysis for a TUS-CPS military tobacco use paper.

3. Refreshing a National Survey on Drug Use and Health (NSDUH) analysis with TUS-CPS data.

17. Smoking Cessation at Lung Examination: The SCALE Collaboration The Contractor shall:

a. Manage a portal for resource sharing and data upload.

b. Create user accounts to access the portal.

c. Provide database management, housing shared data and releasing data for cross-project research that involves data from more than one of the 8 SCALE funded projects.

d. Provide checks of uploaded data, e.g., range checks to ensure that uploaded data are correctly coded.

Task Area 4. Computing Infrastructure Services

The Contractor shall provide computer system administration and resources to support analytic processing, client/server applications, web server applications, and file transfer options in a secure, firewall-protected environment. The resources shall be configured as a networked system of computers such that services and resources are distributed across multiple specialized servers.

Redundancy shall be designed and built into the systems for all mission-critical services and components. To ensure reduced impact on government time and monies the Contractor shall provide written evidence that Contractor owns and/or maintains and operates directly (not through a subcontractor) 1) a non-federal and non-cloud data center and 2) a redundant non-federal and non-cloud data center for security and back-up of systems. Both data centers should have SOC 2 Type 2 audits and be maintained directly by the contractor.

Additionally, Government will give preference for Contractors that can show they have the following conditions currently:

1) Show their ability to host systems that process health records and/or health registry systems that provide services for at least 10 organizations across different regions across the United States

2) The systems that are hosted in #1 above have existing High to Medium level Federal Authority to Operate (ATO) clearances

3) The systems that are hosted in #1 are hosted within both a data center and a redundant data center as specified above to provide redundant security controls

4) The systems that are specified in #1 have been hosted and maintained by the Contractor directly for a period of no less than 5 years.

The Contractor may provide narratives that show the above conditions to produce clear evidence that Contractor has existing ability to host and maintain numerous healthcare or health registry systems that have medium to high level ATO clearances in an infrastructure that aligns with standard redundant data center practices.

Additionally, the Contractor shall establish and maintain appropriate security controls as required or requested by the federal government, including but not limited to the Federal Information Security Modernization Act of 2014 (FISMA) controls specified under the federal Authority to Operate (ATO) as granted by the National Cancer Institute’s (NCI’s) Information Systems Security Officer (ISSO), SOC Type 2 level controls and other controls as agreed upon with COR, for the aforementioned resources, infrastructure, and administration.

The contractor shall withing 30 days of award of contract provide written evidence of existing ATO as granted by NCI’s ISSO or if ATO is currently not in place provide a written project plan for establishing the ATO as granted by NCIs ISSO.

The Contractor shall provide services that include but are not limited to:

1) Provide technical support (help desk) for users of the computing facility during business hours, between 8am and 5pm Eastern time.

2) Monitor the performance of the computing environment for capacity planning.

3) Provide enhancements to the performance of the computing environment.

4) Maintain hardware and software as necessary.

5) Renew licenses for all software installed on the infrastructure.

6) Purchase new software as required to support the DCCPS mission.

7) Develop new software as required to support the DCCPS mission.

8) Provide enhancements to existing software to support the DCCPS mission.

9) Monitor and audit for the physical, network, and user-level security of the system and resources.

1. General Computing Infrastructure Requirements As agreed upon with COR, the Contractor shall support the computer center infrastructure for overall computing resource needs which shall include but not be limited to the following minimum specifications:

1) Existing one data center and a recovery data site that are not federally owned and operated.

2) In addition to a physical location of a non-federal data center and a non-federal physical location recovery data site, if the contractor is also using a cloud solution, then the cloud service provider must be FedRAMP certified at the moderate/moderate/moderate level or as agreed upon with COR.

3) Perform ongoing federal and non-federal security assessments as agreed upon with

COR.

4) A full backup plan and disaster recovery testing for all mission critical applications and data.

5) A data archival system to safely store at least 200 TBs of content off-line.

6) A least a 10 gigabit/sec internal connection between both datacenters.

7) A firewall and intrusion detection system (IPS) for each Internet connection.

8) A least a 1 gigabit/sec Internet connection at each datacenter.

9) Daily backup is off-site, automated, reliable, secure, and scalable.

10) Scalable and capable of supporting up to hundreds of biostatisticians, statistical programmers, and systems developers in addition to the Contractors staff.

11) Support the Vmware, Linux, and Windows operating systems on at least 400 servers.

12) A least 300 TBs of active data storage for all data types including but not limited to unstructured “flat files”.

13) As agreed upon with COR, all storage shall have encryption that aligns to federal security standards.

14) At least 256 CPU cores and 1 TB RAM for computationally demanding software (e.g.

Match*Pro, Joinpoint, SEER*Prep).

15) A least 64 CPU cores (64-bit) and 512 GBs RAM for statistical packages (e.g. SAS, R, Stata).

16) Sufficient Input/Output (I/O) for the SAS workspace(s) to keep the associated CPU wait times < 15% on average.

17) A least 10 SAS workspace resources > 3 TBs in size.

18) A least 2 SAS workspace resources that are at least 7 TBs in size.

19) At least 5 TBs flash-based data storage and relational database services for

PostgreSQL

20) Provide at least 48 CPU cores (64-bit) and 1 TB RAM for PostgreSQL.

21) Provide at least 12 specialized development servers for tasks such as continuous integration for large scale development efforts such as the Surveillance, Epidemiology, and End Results Data Management System (SEER*DMS).

22) Include production and development Web services supporting PHP, Java, Plone, Drupal, and Django technologies. This should include 3 TBs of data storage for the production environment.

23) Have the ability to produce (burn and print/label) up to 40 thumb drives per week.

24) Have 24/7 availability. Regular maintenance procedures that impact the use of the resource shall be performed during nights or weekends and with at least 48 hours’ notice to users.

25) Ensure limited and controlled physical access to the computing resources.

26) Include built-in redundancies for all mission critical services and components.

27) Provide data encryption in transit and/or at rest to protect sensitive information as required.

28) Provide data center-wide disk backups including virus detection processes

29) Ensure multi-factor authentication is utilized for network access

In addition to the above specifications the Contractor shall:

1) Have an existing ATO or an ATO granted within the last 5 years for their existing technical infrastructures that are managed on non-federal (neither owned nor managed by the federal government) data centers.

2) Provide through detailed previous experience, at least 3 use cases, a proven track record of creating numerous direct data connections between healthcare facilities and their clients. The data connections should include the transport of both PII and non-PII data. The Contractor must be the primary Contractor that created the direct data connections between Healthcare facility For this requirement the Contractor shall provide the following details in the narrative for each use case:

i. Facility Type

ii. Facility Name

iii. Type of legal agreement set up between contractor and healthcare facility

iv. Type of health records (e.g. pathology records, claims records, etc.)

v. Whether the data was PII or non-PII

vi. Number of health records transferred annually by

vii. Type of technology utilized for transfer (e.g. SFTP, Direct Transfer Tool, etc.). Note, the direct connection cannot include a manual process of transfer (i.e. letter, fax, or email type transfers) or paper based transfers.

3) Provide through detailed previous experience, a proven track record of connecting data solutions for Central Cancer Registries, at least 10, at scale. Scale here refers to data solutions that were implemented for at least 10 Central Cancer Registries that were able to handle data imports of at least 200,000+ records per year per registry.

4) Provide through detailed previous experience, the ability to support the full lifecycle of both Research Health Information Systems and Operational Health Information Systems. A Research Health Information System is a system that supports the intake, processing, storage, and output of health information for research specific uses, which may or may not include Personally Identifiable Information (PII). An Operational Health Information System is a system that supports the intake, processing, storage, and output of health information specific for cancer surveillance operations, which does include PII. The fully lifecycle support may include but not be limited to; a) requirements gathering and analysis, b) direct development and refinement of system, c) maintenance and management of the system including troubleshooting and client support, d) storage and security of the systems, and e) development and support for automatic and ad-hoc data output and reporting functionalities.

Note: NCI requires that cloud solutions be deployed and managed within the federal NCI’s managed cloud environment (ex: Cloud One). If the Vendor specifies use of any cloud product or solution in accomplishing the above tasks with their proposal, the Vendor shall provide acknowledgment and written agreement to deploy their cloud solution within the NCI managed cloud environment.

2. SEER*DMS Specific Infrastructure Requirements In addition to the above requirements for computer resources to support overall program computing requirements, the Contractor shall also provide non-federally owned computer center infrastructure resources specifically for SEER*DMS computing requirements. These resources shall also continually adhere to Federal Security controls, as outlined above and as agreed upon with COR. The computer center infrastructure for SEER*DMS shall include but not be limited to the following minimum specifications:

1) Supports the VMware, Linux, and Windows operating systems on at least 100 servers.

2) Provide at least 100 TBs of active data storage for all data types including but not limited to unstructured “flat files”.

3) Ensures the availability of at least 96 CPU cores and 512 GBs RAM for the Department of Energy (DOE) Labs APIs

4) Ensures the availability of relational database services for PostgresSQL with at least 20

TBs flash-based data storage.

5) Provides at least 140 CPU cores and 5 TB RAM to VMware for the Linux virtual servers.

Task Area 5. Website Development

The Contractor shall develop and maintain websites for all Programs within DCCPS, as directed by the Task Order. To accomplish this task the Contractor shall:

1) Meet with the Federal NCI investigators to develop the system requirements for future enhancements and additions.

2) Develop prototypes of the WWW page modifications utilizing currently available computer resources.

3) Provide access to the sample home page to a limited number of NCI users for testing purposes.

4) Improve pages and searching tools based on feedback from the NCI investigators.

5) Update pages with new data on an ongoing basis for tools such as the Measures Registry.

1. PLONE Site Development

The Contractor shall develop standard Plone sites as the need is identified and as directed by the COR. The Contractor shall develop the Plone sites using the standard Plone software.

2. CANQUES (Cancer Query Systems)

The Contractor shall maintain and enhance CANQUES under the technical direction of the

COR.

3. State Cancer Profiles Website The Contractor shall provide system development and maintenance support for the State Cancer Profiles project.

a. The Website is to be maintained so that it is compatible with NCI standards and so that it is conformant with Section 508 of the Rehabilitation Act of 1173, as amended.

b. The "Contact Us" email account shall be monitored and responded to.

c. The system shall be modified to include new cancer statistics as requested by the COR.

d. Options for the display of the analytic results are to be incorporated as requested by the

COR.

e. The underlying databases are to be updated as the data are made available to the public. Most data will be available for update on an annual basis but may not be available at the same time.

4. Genetic Simulation Resource (GSR) website

The Contractor shall host and maintain the Genetic Simulation Resource on the Contractor’s computing infrastructure. The Contractor shall also perform any modifications to the GSR under the technical direction of the COR. This may include, but is not limited to, the following:

a. Search and obtain or create appropriate glyphs for each GSR certification type and implement CSS styling; update content and glyphs on pages that refer to these certifications.

b. Update website package listing view and template (Django web development).

c. Implement client-side table…