Q A_for_RFP_No_NIHLM2013617.pdf

RFP No. NIHLM2013617 – Questions and Answers

IMPORTANT NOTE: The due date for submission of proposals is extended to 12:00pm local time on Wednesday, March 6, 2013.

1. No mention was made of the existing NIDDK website in the RFP. The description of task #6 states that a new website must be created. Please explain why the existing website may not be utilized, specifically, what does the current website not provide that NIDDK is looking for?

Answer 1: There is an existing Website at www.niddkrepository.org, which has both public and restricted access pages. The NIDDK is open to bids that propose creation of a new Website, use of the existing architecture and design, or retention of some features and re-design of others. The proposal should describe the planned approach and provide justification in terms of efficiency, functionality and/or cost.

2. If the existing website can be used, please explain the details of the website (language, database, web server software) that are required to operate and maintain it.

Answer 2: The current Website has been built using J2EE and a Struts Framework, with custom-built Java code. It is hosted on an Oracle 10g Application server (version 10.1.2.0.2), Microsoft Windows. The underlying datasets contributed by clinical studies are hosted in an Oracle 11g database Enterprise Edition (11.2.0.2.0), Microsoft Windows.

3. Task #6 states that the website must be “established” within two months of award. Given the scope of requirements described in the task this timeline seems unreasonable for a website constructed de novo. Please define what NIDDK means by “established” in the context of this task.

Answer 3: The NIDDK will support a transition period of reasonable length, but no longer than two months, to ensure seamless continuity. The proposal should propose a well-justified plan for transition. If the proposal plans the construction of a new Website, there must be a description of the continuity of the Repository will be maintained.

4. The RFP does not mention the HHS Enterprise Performance Life Cycle (EPLC). Is adherence to the EPLC required for this project?

Answer 4: Adherence to the EPLC is not required for this project.

5. As hosting is required by the RFP, please provide size estimates for the databases described in tasks 1-4. Also, what platform are the databases?

Answer 5: The size of the stored legacy databases is approximately 15GB. The size of the current Repository administrative databases, outlined in tasks 3-8, is approximately 10GB.

The data are stored in an Oracle 11g Application server, Enterprise Edition (version 11.2.0.2.0).

http://www.niddkrepository.org/

6. There is no mention of a transition from the current contractor. Please provide a timeline for transition from the current contractor, and if the timelines for deliverables in the RFP are inclusive or exclusive of this period.

Answer 6: The NIDDK will support a transition period of reasonable length, but no longer than two months, to ensure seamless continuity. The proposal should propose a well-justified plan for transition. If the proposal plans the construction of a new Website, there must be a description of the continuity of the Repository will be maintained. The timelines for deliverables will be adjusted so that they begin with the receipt of the corresponding existing data and materials from the incumbent.

7. Please provide specifications for the labeling used in task 4.b.

Answer 7: The Repository requires that each sample have a physical or electronic three-digit prefix specific to the study site. The Repository is responsible for assigning those unique prefixes. There is no other labeling requirement or uniform labeling specifications.

8. Is historical information available, or are there projections, of the annual number of outgoing data requests, outgoing specimen requests, and new incoming data and specimen collections?

Answer 8: Data requests – there were 49 complete data requests in 2012, and 37 in 2011.

Sample requests – there were 120 sample requests in 2012, and 163 in 2011. The NIDDK anticipates that data requests will increase steadily (5-20%) per year and that sample requests will remain at approximately the existing levels.

Specimens are received every day by the NIDDK Repositories as part of ongoing studies.

Approximately 30 – 60 new datasets will be received over the course of the 5-year contract.

9. The RFP references the posting of data collection, other forms, manuals of operation and other documents on a website in a searchable format. Are these documents currently in formats that are readily accessible or convertible to search formats or are they, for example, historical PDFs from photocopies and hand-annotations?

Answer 9: The forms and manuals received from studies are typically received as electronic documents. In the case of the oldest legacy studies, the documents may be in non-searchable forms, although this is not generally the case. The existing collection can be viewed at https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp#A2ALL.

10. Will the current website and database hosted by the incumbent be transferred to the new contractor? Per Task 6.d, NIDDK intends the Contractor to develop a new site to replace the current repository site and clarification on the transfer and short-term support of the current will assist in proper planning and estimation of this task.

Answer 10: The NIDDK will support a transition period of reasonable length, but no longer than two months, to ensure seamless continuity. The proposal should propose a well-justified plan for transition. If the proposal plans the construction of a new Website, there must be a description of the continuity of the Repository will be maintained.

https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp#A2ALL

11. How many gigabytes occupy the current repository databases and files?

Answer 11: The size of the stored legacy databases is approximately 15GB. The size of the current Repository administrative databases is approximately 10GB.

12. How does the current repository website process user authentication? Does it use an LDAP or Active Directory that is shared with other incumbent projects or is it stand alone and will be transferred to the new contractor?

Answer 12: The authentication process is a stand-alone that was created by the current Repository contractor. It is not shared with any other project. The information will be shared in order to ensure a seamless transition. A DES encryption algorithm is used to encrypt account passwords and Secure Socket Layer (SSL) encryption is used for web-based communications.

13. Will any government-owned hardware be transferred? If so, please provide a list and description.

Answer 13: No hardware will be transferred.

14. Task 5 asks for a library of blank informed consent forms. Is the incumbent also maintaining a database of the consent status of each stored specimen?

Answer 14: The incumbent maintains a database with information about each consent from each study (or protocol within a clinical studies network) and from each site. Samples are related to the consents by their site identifier prefix (see response to question 7). Thus, all samples from a specific site and a specific study (or protocol) are covered by a single consent.

In studies in which individual participants were offered options with respect to future research on samples, such as opting out of all genetic research, that information is provided for each individual by the study itself as part of the clinical dataset.

15. Is the Specimen Repository capable of exchanging changes to the specimen inventory through a web service? If not, what type of files will be provided and what will their content be (e.g. full inventory versus transactions).

Answer 15: When updates are provided to the inventory by the other NIDDK Repositories, they are provided as an update of change transactions through https uploads.

16. Please describe the current site number and specimen number assignment algorithms.

Answer 16: Please see question 7.

17. How many NIDDK-sponsored studies are conducted per year?

Answer 17: There are currently approximately 40 ongoing NIDDK multi-site clinical studies, of which 4 are clinical study networks with multiple protocols. Fewer than five new studies are initiated each year.

18. How many databases does the NIDDK data repository use and what software tools are used to maintain them?

Answer 18: Please see answer to question 19 below.

19. What is the current hardware and software inventory used in the production setup?

Answer 19:

Hardware Description Hardware/ Operating System

Remarks

Dell PowerEdge 2850 with Red Hat Enterprise Linux ES Release 4

3 server farms are used to host the Oracle 10g application server

Dell PowerEdge R610 with Red Hat Enterprise Linux ES Release 5.9

Hosts the Oracle 11g database

Software Description Operating System/Application Remarks Oracle 10g Application server, version number is 10.1.2.0.2, Microsoft Windows

Hosts the Web application.

Oracle 11g database Enterprise Edition, version number is 11.2.0.2.0 , Microsoft Windows

Hosts Repository data

Custom built Java code The website is built using J2EE on a Struts Framework

Firmware Description

• Dell Server System BIOS A04.

• Dell Service System BIOS 1.1.0.

20. Page 56 refers to a “Single Principal Investigator/Project Director,” but pages 6-7 and Section M refer to only a “Project Director.” Are these positions the same?

Answer 20: Yes.

21. Task 1 calls for testing the validity of electronic databases from completed studies. Can you please provide details on the databases, i.e., are they RDBMS, XML-based, or structured files?

Answer 21: Electronic databases from completed studies can be provided in a variety of formats, but the large majority are submitted in SAS. Please refer to https://www.niddkrepository.org/niddkdocs/resources/Archive%20Requirements_2012-02- 16.pdf for details on current submission requirements for databases.

https://www.niddkrepository.org/niddkdocs/resources/Archive%20Requirements_2012-02-16.pdf

22. Please confirm that the current system, including all source files, will be transitioned from the incumbent to the contractor who is awarded the contract resulting from this RFP.

Answer 22: All data and source files will be transferred from the incumbent to the new Contractor.

23. To enable bidders to prepare the most responsive proposals in response to the RFP, please provide all system documentation related to the current system.

Answer 23: Please see the answer to question 19.

24. To ensure sufficient data integration resources are planned for, please provide guidance on the expected number and size of new studies whose data will need to be added to the NIDDK data repository during the period of performance o of this contract.

Answer 24: Approximately 30 – 60 new datasets will be received over the course of the 5-year contract. These datasets will be of a variety of sizes, depending on the complexity of the data collection specific to the study. Most of the studies have fewer than 3000 participants.

25. From objectives section: "Receive and test the validity of electronic databases from completed studies, and maintain the stored databases" Can you provide some examples of these electronic databases? Is there an effort to harmonize data elements and electronic datasets across studies to allow cross-study data explorations?

Answer 25: It is not possible to provide actual copies of examples, because access to the databases is restricted to approved researchers. However, it is possible to gain understanding of the types and complexities of databases received by viewing the descriptions of existing databases and the associated public data at https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp.

A specific effort has been made to harmonize the datasets, after they are received, by identifying values for a set of common variables, as described in task 2. This has permitted the searches across studies that are available at https://www.niddkrepository.org/niddk/jsp/pqt/pqtMainPage.jsp. The underlying data files will be transferred from the incumbent to the contractor.

26. “Curate data to derive study metadata and descriptive variables that permit Web-based searches of the entire inventory using keywords and other features of samples and datasets.”

How is the study metadata delivered to the NIDDK data repository?

Answer 26: Each study delivers archival data to the Repository electronically. The archival data includes both raw datasets, with all the variables collected by the study as well as analytic datasets that were used to develop specific publications. In addition, the studies deliver their forms, manuals of operation and procedures, and protocols. Study metadata and variables corresponding to a set of common variables are derived by curators at the Repository, as described in Task 2.

https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp https://www.niddkrepository.org/niddk/jsp/pqt/pqtMainPage.jsp

27. Task 2: “Link phenotypic data to high-density genotyping data stored in the dbGAP (database of Genotype and Phenotype) or comparable database.” Will the requests for genotype data go directly to dbGAP or go through NIDDK data repository? If the requests come to NIDDK data repository, do we need to use the data access policies of dbGAP or will data access policies be set up for the data repository independent of dbGAP?

Answer 27: All requests for dbGAP data are handled through dbGAP by NIDDK staff and do not go through the Repository.

28. Task 8: “Provide a system for requesting databases and/or samples, for distribution of databases and/or stored samples to investigators granted access by the Project Officer.” Will the system(s) be maintained at the contractor site or at NIDDK? If at contractor site, will they need to be mirrored on NIDDK servers?

Answer 28: The systems for requesting and distributing databases and/or samples will be maintained at the contractor site and will not be mirrored on NIDDK servers.

29. What about legacy data? Will the past datasets/systems be delivered to the new contractor in a timely manner along with documentation? What is the estimated amount of legacy data?

Answer 29: The NIDDK will support a transition period of reasonable length, but no longer than two months, to ensure seamless continuity. The proposal should propose a well-justified plan for transition with proposed timeframes for receipt of the legacy data and accompanying documentation. The legacy databases are a total of approximately 15GB in size.

30. How many sites are expected to submit data to the NIDDK data repository?

Answer 30: Approximately 30 – 60 new datasets will be received over the course of the 5-year contract. In addition, at this time approximately 35 studies and 4 clinical study networks with multiple protocols are submitting samples.

31. Do we need to track modifications to patient consents during the course of the project?

How will this be coordinated with dbGAP which also stores patient consents?

Answer 31: The NIDDK works with the studies directly to collect data about consents. If there are modifications to the consents during the course of an ongoing study, the new version will have to be included within the Informed Consent database. However, it is the responsibility of the study to record which version of the consent was signed by each participant.

32. What types of data will be submitted? Case report forms, genetic experiment data, study protocols, signed consents, Publications, Others?

Answer 32: Each study delivers archival data to the Repository electronically. The archival data includes both raw datasets, with all the variables collected by the study as well as analytic datasets that were used to develop specific publications. In addition, the studies deliver their forms, manuals of operation and procedures, protocols and key publications.

Please see https://www.niddkrepository.org/niddkdocs/resources/Archive%20Requirements_2012-02- 16.pdf for details.

It is not possible to provide actual copies of stored datasets, because access to them is restricted to approved researchers. However, it is possible to gain understanding of the types and complexities of databases received by viewing the descriptions of existing databases and the associated public data at https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp.

High density genotyping or sequencing data are stored within dbGAP and not delivered to the Repository. However, small amounts of genotyping data, such as genotyping of key Single Nucleotide Polymorphisms, may be stored by the Repository.

NIDDK will provide blank informed consent forms.

33. Are all the biosamples housed in one location, therefore requiring data updates from one facility on a regular basis?

Answer 33: The large majority of the biosamples are stored in two locations. Over seven million biosamples are stored at the NIDDK Biosample Repository. Genetic samples from approximately 70,000 unique individuals are stored at the NIDDK Genetics Repository. A single legacy collection from the FIND study is stored at a third location, but that collection is complete.

34. What are the current data format requirements for data submission to the DCC?

What format are the current datasets available in? Is the DCC responsible for providing any format at an investigator’s request (i.e. CSV, SAS, SQL, etc)?

Please see https://www.niddkrepository.org/niddkdocs/resources/Archive%20Requirements_2012-02- 16.pdf for the current data format requirements for submission. In general, the studies provide the datasets in SAS, although the proposal should describe plans to accommodate alternative formats. Some parts of datasets may also be received as .csv files.

Answer 34: In general, the Repository provides SAS files. If a requester requires a different format, the Repository will consider that as an additional data manipulation and will charge fees as appropriate.

https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp

35. How many sites currently transmit genetic data to the central repository?

Answer 35: High density genotyping or sequencing data are stored within dbGAP and not delivered to the Repository. However, small amounts of genotyping data, such as genotyping of key Single Nucleotide Polymorphisms, may be stored by the Repository. Fewer than 5 studies have submitted these small genetic datasets to the Repository.

36. Are there any formal processes currently in place for investigators to request the data (i.e. a portal or application to request data)?

Answer 36: The current policies and procedures for requesting datasets can be found at https://www.niddkrepository.org/niddk/jsp/request/instruction.jsp .

37. Who handles the cost component associated with a request for biosamples?

Answer 37: The Repository is responsible for handling the cost component associated with requests for biosamples. However, the estimates and final costs are calculated by the Biosample and Genetic Repositories. More details can be found in Task 8f.

38. Are all data received by the DCC de-identified?

Answer 38: Yes.

39. Do Data Use Agreement (DUA) and Material Transfer Agreement (MTA) templates already exist?

Answer 39: Yes. The Sample and Data Use Certification used for those who are requesting samples can be found at https://www.niddkrepository.org/niddkdocs/resources/NIDDK_Sample_Data_Distribution_A greementFINAL.pdf. The Data Use Certification used for data requesters is similar. The MTA for submitting samples can be found at https://www.niddkrepository.org/niddkdocs/resources/MTA_receiving_biosamples_to_distr ibuteFINAL.pdf.

40. Is there any incurred cost to the investigator for derived datasets?

Answer 40: Although there is no cost for receiving datasets, there is a charge if more than two hours of statistician support is required for a request. The policy and pricing can be found at https://www.niddkrepository.org/niddk/jsp/public/cost.jsp .

41. How are eligible studies identified for integration to the DCC database?

Answer 41: The NIDDK identifies eligible studies, which generally are NIDDK-funded multi-site clinical studies or trials.

42. What is the expected turn-around time of a dataset or database to a requesting investigator?

Answer 42: As detailed in Task 8b, “When investigators are granted access by the Project Officer for the requested data, the Contractor shall transmit the requested data within 2 weeks of NIDDK approval.”

https://www.niddkrepository.org/niddk/jsp/request/instruction.jsp https://www.niddkrepository.org/niddkdocs/resources/NIDDK_Sample_Data_Distribution_AgreementFINAL.pdf https://www.niddkrepository.org/niddkdocs/resources/NIDDK_Sample_Data_Distribution_AgreementFINAL.pdf https://www.niddkrepository.org/niddk/jsp/public/cost.jsp

43. Is there a requirement of all databases to be accompanied by study element descriptors and data collection protocols? Will data collection tools be provided to the DCC in addition to consent forms and approval letters for each study?

Answer 43: Please see https://www.niddkrepository.org/niddkdocs/resources/Archive%20Requirements_2012-02- 16.pdf for the current data format and document requirements for submission. The forms used for data collection will be provided by the studies.

44. Would the government please clarify the order in which the documents of the business proposal are expected to appear? In the Business Proposal Instructions, Item 2 (Proposal Cover Sheet – pg 58) requires that it should be listed on the first page of the pricing proposal, and Item 4 (Certified Cost or Pricing Data – pg 60) has those instructions as well.

Answer 44: Items 2 and 4 are separate proposal instruction requirements. Offerors must address the requirements of paragraphs 1-9 under Item 2 (Proposal Cover Sheet – pg 58-59) on the first page of their pricing proposal. Offerors must address the requirements of paragraphs A-H under Item 4 (Certified Cost or Pricing Data – pg 60-61) within their submission of Certified Cost or Pricing Data.

45. Are there page limits to the proposal submission?

Answer 45: There are no page limits.

46. In Section L – Instructions, Conditions, and Notices to Offerors – there was no information regarding an estimate of effort. Please provide an estimate (labor hours or FTEs), for example, “for guidance purposes only, not to be considered restrictive for proposal purposes.”

Answer 46: The level of effort estimate for this procurement, for guidance purposes only and not to be considered restrictive for proposal purposes, is estimated at 5.5 FTEs per year.

47. In addition to the above items, if possible, please provide uniform cost assumptions to be used for proposal purposes.

Answer 47: There are no uniform cost assumptions to provide. Offerors should propose all costs necessary to support their proposal.

48. What are the current staff levels maintained by the incumbent?

Answer 48: See answer to question 46.

49. In the RFP's Attachment 2, Proposal Intent Response Sheet, does the deadline of “earliest practicable date” mean this form is optional or can it be included with the proposal submission?

Answer 49: Please submit your Proposal Intent Response Sheet to Mr. Richard E. Bailey at baileyrichard@mail.nih.gov no later than February 27, 2013. The purpose of this form is to assist the Government with internal planning. It is not required.

mailto:baileyrichard@mail.nih.gov

50. Section L, p. 45 refers to the “first page of the proposal”; however, p. 51 refers to the first page of each volume. Can the first page of the Technical Volume be considered the first page of the proposal?

Answer 50: It is recommended that the technical proposal consist of a cover page, a table of contents, and the information requested in the technical Proposal Instructions and as specified in SECTION J List of Attachments.

51. Page 56 refers to a “Single Principal Investigator/Project Director,” but pages 6-7 and Section M refer to only a “Project Director.” Are these positions the same?

Answer 51: Yes.

52. The links provided on February 4th to Attachments 13, 14, and 15 do not work. Can the Government please supply the correct links?

• Attachment #13 Commitment to Protect Non-Public Information Contractor Agreement http://ocio.nih.gov/docs/public/Nondisclosure.pdf

• Attachment #14 Roster of Employees Requiring Suitability Investigations http://ocio.nih.gov/docs/public/Suitability-roster.xls

• Attachment #15 Employee Separation Checklist http://ocio.nih.gov/nihsecurity/Emp-sep-checklist.pdf

Answer 52: Attachments #13, #14 and #15 are accessible via FebBizOpps under the link ALL FILES Attachments #3-#15, posted February 4, 2013.

53. Should the Section 508 Product Assessment Template be completed and submitted with the proposal?

Answer 53: Yes.

54. Can we add other labor categories beyond what is mentioned in the evaluation criteria?

Government expects any software engineers also to perform the work?

Answer 54: Yes.

55. Is there an independent government cost estimate (IGCE) available for this effort?

Answer 55: The IGCE is not available.

END OF QUESTIONS and ANSWERS DOCUMENT.

http://ocio.nih.gov/docs/public/Nondisclosure.pdf http://ocio.nih.gov/docs/public/Suitability-roster.xls http://ocio.nih.gov/nihsecurity/Emp-sep-checklist.pdf