Scientific Computing Support IDIQ Q A_Amendment 4.pdf

Scientific Computing Support IDIQ Q&A

SOL# 12-223-SOL-00010

Amendment 4

37. Attachment 3, Scientific Computing Technical Scenario #2 General - After 3 years, is there any issue with reimagining the workstation once the warranty is expired?

A: Sometimes scientists will obtain extended warranties or service agreements, so reimaging may not be possible at that time. It is not clear why there would be a need to reimage if the equipment had been functioning successfully.

38. Attachment 4, Technical Scenario 3: Data Normalization and Analysis -

How many columns do the input files have approximately?

A: There is wide variation into the number of columns in any dataset.

Generally, clinical data are obtained from product sponsors in support of their applications. An application consists of several domains of data (e.g., demographics, vital signs, adverse events) for clinical studies. Data from other types of studies for example, engineering, toxicology, social science experiments, genomic/genetics experiments and observational studies, are also obtained from sponsors. The number of variables depends on the specifics of the study ranges broadly. Typically the different domains of data are stored in separate data tables with a specified structure. Clearly document any assumptions upon which your scenario response is based.

39. Attachment 4, Technical Scenario 3: Data Normalization and Analysis -

When column names don’t match, but they are in reality the same, do we need to figure that out programmatically or a user will tell us the matching columns upfront?

A: It is expected that column names will match across data sets within a study. However, variables may be named differently across studies. For example, the unique subject identifier may be named “USJID” in one dataset and “SUBJNO” in another. It is expected that study protocols and meta-data information are generally available for each study. There will be situations in which a programmatic assessment or validation of data is needed. During the resolution of data quality issues there will be subject matter experts with whom you will interact to assist in resolving issues as they arise. Clearly

40. Attachment 4, Technical Scenario 3: Data Normalization and Analysis - Is the text found together with the data created by machines or by humans?

Could there be typos too?

A: Data may be generated using human interventions during documentation on a clinical case report form (CRF) or a survey questionnaire. There will also be data collected using devices to record data values. The data collection process and forms are generally accessible. There could be typographical and other errors. Clearly document any assumptions upon which your scenario response is based.

41. Attachment 4, Technical Scenario 3: Data Normalization and Analysis -

Any chance we could have a sample of data with several instances of problems?

A: Data samples are not readily available at this time.

42. Attachment 4, Technical Scenario 3: Data Normalization and Analysis -

What are the keys/attributes linking the input files?

A: There is a unique subject identifier (primary) and second keys to allow queries across the various domains of data. Clearly document any assumptions upon which your scenario response is based.

43. Attachment 4, Technical Scenario 3: Data Normalization and Analysis - Is the desirable outcome just a bigger/wider denormalized flat file integrating the input ones? Or is there any need to keep history of the data in a database/star schema, which could be easily accessible by the analytical applications, such as R and SAS? (The requirements don’t say anything about this possibility, but I just want to make sure they thought about it.)

A: Algorithms of varying complexity for transforming raw data into derived variable for analysis datasets which conform to the requirements of the analytical software, for example, SAS®, SUDAAN®, R/SPlus®, STATA®, Minitab®, or Matlab® are generally implemented. The process (audit trails) showing the derivation of raw data into a transformed analysis-ready dataset is expected to be documented and maintained. Clearly document any

44. Attachment 7, Past Performance Questionnaire - The document currently in the solicitation shows a due date of April 23, 2012 for the submission of the completed forms. Is FDA going to provide an updated form with the correct closing date?

A: The Attachment 7, Past Performance Questionnaire was correct in Amendment 2 to the RFP.

45. Would the government consider extending the due date for proposals by two weeks?

A: No.

46. Under Relevant Experience and Past Performance, should the offeror submit three projects for each of its proposed subcontractors or just three projects for the entire proposed team?

A: Three projects in total.

47. What are the font requirements for proposal text? The RFP only mentions text in graphics and charts.

A: Please see the response to question #23 posted in Amendment 3 to the

RFP.

48. May submitted proposals be printed single sided? This will more easily accommodate the requested tabbed sections.

A: In accordance with FAR 52.204-4, Printed or Copied Double-Sided on Postconsumer Fiber Content Paper, Offerors are required to submit paper documents that are printed or copied double-sided on paper containing at least 30 percent postconsumer fiber, whenever practicable, when not using electronic commerce methods to submit information or data to the Government.

49. Are each of the plans requested as part of the Management Approach included in the 50 page limit for Subfactor 2? Many of these plans can be quite long, for example the provided Subcontracting Template is 13 pages.

A: Each of the plans listed under Factor III Management Approach are included in the 50 page limit. One of the plans under Management Approach is a Sub-Contractor/Teaming Management Plan. This is not the same as the Small Business Subcontracting Plan Template, Attachment 9, which is a requirement of the Business Proposal (Volume II) only, not the Technical Proposal (Volume I).

50. Do data dictionaries exist for the data referenced in Attachment 4?

A: If this is an assumption in the scenario response it should be clearly documented. A data dictionary will not be provided by FDA for purposes of this RFP.

51. What filing systems or databases are used to house the data referenced in

Attachment 4?

A: The datasets are received in SAS transport file (open) format with information to link and retrieve information across tables. However, the data are not usually stored in a relational database management system. Clearly

52. What are expectations are there for a helpdesk or support center? Does

FDA require 24/7 support?

A: Helpdesk requirements will be defined in individual task orders. The requirements are not currently defined.

53. Will FDA provide CM tools?

A: Requirements will be defined in individual task orders.

54. Will FDA provide QA or issues tracking tools?

A: Requirements will be defined in individual task orders.

55. How will travel and other ODCs be costed into the proposal, if at all?

A: Travel and ODCs, if required, will be priced in individual task orders.

Pricing for travel and ODCs is not requested in Attachment 5, Pricing Worksheet.

56. Have scientific computing systems been evaluated against NIST controls?

A: Yes, when FDCC was first implemented.

57. Can FDA provide the master approved list?

58. Is the Scientific computing LAN being supported and monitored by OIM?

A: There is no separate scientific computing LAN. The network is supported and monitored by OIM.

59. Has any security assessment been started and completed on systems in the Scientific computing LAN?

A: Yes.

60. Page 47 (Organization of Proposal). We understand that Section 1.A, Section 1.B, and Section 1.C are limited to 10 pages each. Can you please confirm the total page count for Volume I (Technical Proposal) for Sections 1, Section 2, and Section 3 combined?

A: Please see the response to question #14 in Amendment 3 to the RFP.

61. On page 5 of the RFP, On the summary worksheet, we are required to propose a not to exceed % on any subcontractor and material expenses.

However, on page 51 we are required to propose a ceiling on Material Handling on ODCs and Subcontracts. Are we providing a percentage or a ceiling amount?

A: A percentage. Please also see the response to question #30 in Amendment 3 to the RFP.

62. On the Pricing Worksheet, is the column “Full Burdened Hourly Labor

Rate” to be a formula that sums Direct Rate column through FCOM/COM column?

63. Where do we add Travel Costs (if applicable)? Are Travel Costs estimated by each task order requirement?

A: Please see the response to question #55.

64. Section 33 – Instructions for Proposal Submission - Would the FDA consider a 2 week extension so that there is ample time to incorporate answers to questions into RFTOP responses?

65. Section 34. Organization of Proposal – Page 47 - Should each scenario response be on a separate CD, or can all three scenarios be submitted on the same CD?

A: Please see the response to question 34 in Amendment 3 to the RFP.

66. Section 35 – Instructions for Technical Proposal – Factor III Management

Approach – Page 49 -The Management Approach asks for five different plans as part of the response. Are all these plans included in the 50 page count for this section?

67. Attachment 1, Scientific Computing Support IDIQ—Statement of Work –

Page 24 - Section 6 – Deliverables section states that a final version of the PMP and QAP is due within 30 days of award. Will FDA issue a task order under the IDIQ for completion of the PMP and QAP?

A: No – The completion of the PMP and QAP are IDIQ deliverables.

68. Attachment 1, Scientific Computing Support IDIQ—Statement of Work –

Page 24 - Section 6 – Deliverables section states that “Also to be submitted with the proposal, a sample monthly progress report with examples of the type of risks and status updates expected to be reported under this contract.” This item is not listed in Section 35 – Instructions for

Technical Proposal. Where in the technical proposal should this be provided? Is it included in the page count?

A: Attachment 1, Section 6 of the RFP has been amended in Amendment #4 for remove the proposal instructions for a sample monthly progress report.

69. Attachment 4 – Scenario 3 (Data normalization and analysis) - What are the approximate number and type of fields to be normalized?

A: There is wide variation into the number of columns in any dataset.

Generally, clinical data are obtained from product sponsors in support of their applications. An application consists of several domains of data (e.g., demographics, vital signs, adverse events) for clinical studies. Data from other types of studies for example, engineering, toxicology, social science experiments, genomic/genetics experiments and observational studies, are also obtained from sponsors. The number of variables depends on the specifics of the study ranges broadly. Typically the different domains of data

70. Attachment 4 – Scenario 3 (Data normalization and analysis) - Will the

FDA provide a sample dataset or similar?

A: Sample datasets are not available at this time.

71. Attachment 4 – Scenario 3 (Data normalization and analysis) - What is the number of raw (source) datasets we should expect to receive?

A: The number of raw datasets that are associated with any particular analysis varies depending on the scientific question. Clearly document any

72. Attachment 4 – Scenario 3 (Data normalization and analysis) - Are contractors expected to provide descriptive or inferential statistical outputs?

A: Descriptive and inferential statistical outputs may be needed. For example, depending on the complexity of the situation the contractor may be involved in developing statistical models, simulation to support statistical inference or methodology development. Clearly document any assumptions upon which your scenario response is based.

73. Attachment 4 – Scenario 3 (Data normalization and analysis) - The RFP states the data is in the raw format and is provided without any machine validation. If data review and validation will not occur please advise how data discrepancies will be resolved (will revised datasets be provided to contractors)? Will validation rules be provided?

A: The data, as received by FDA, may not have been put through an FDA validation process. Although, sponsors conduct their validation and data quality assurance it is very common that the data received have errors. The contractor will collaborate with FDA staff to design strategies to resolve data discrepancies. Resolving certain discrepancies may include requesting additional datasets from sponsors. Clearly document any assumptions upon which your scenario response is based.

74. What is the current Level of Effort (LOE) and assigned labor categories for

Scenario 1 and Scenario 2?

A: The technical scenarios may or may not represent actual work currently being performed at FDA. If known, the current LOE and labor categories will not be released.

75. Can you provide a list of HPC servers/equipments, storage, network and a technical description including number of servers and technical specifications? Such information is needed to respond with an appropriate amount of information.

A: The HPC environment at FDA is very dynamic. Specific HPC environments and requirements related to HPC will be defined in individual task orders.

76. Please clarify the Government’s expectations for providing a draft PMP and a draft QAP given the page constraints for the proposal. (Section 6, page 24, states that: “Draft versions of the contract level Program Management Plan (PMP) and Quality Assurance Plan (QAP) shall be submitted with the Offerors proposal. Final versions of the PMP and QAP shall be delivered within 30 days of contract award.”)

A: Please provide all of the information required in Section 35 within the maximum page limits established in Section 34. The draft PMP and draft QAP requirements are described in Section 35 under Factor III Management Approach, (a) and (b).

77. Re Technical Scenario 1: Please clarify whether the HPC cluster environment referenced exists and simply needs to be supported, or whether, for scenario response purposes, FDA needs it to be expanded or built from scratch.

A: It already exists.

78. Re Technical Scenario 3: Approximately how many variables are contained in each dataset from the various organizations?

A: Generally, clinical data are obtained from product sponsors in support of their applications. An application consists of several domains of data (e.g., demographics, vital signs, adverse events) for clinical studies. Data from other types of studies for example, engineering, toxicology, social science experiments, genomic/genetics experiments and observational studies, are also obtained from sponsors. The number of variables depends on the specifics of the study ranges broadly. Typically the different domains of data

79. Re Technical Scenario 3: The RFP states the data is numeric. Does that mean continuous variables such as temperature/blood pressure or categorical such as 0/1 for Yes/No in which a data dictionary is needed to define the variables?

A: The data is numeric but is not limited to numeric. There are different data types used to store information values, for example, numeric, character, date and time variables. Datasets will typically include continuous variables such as temperature/blood pressure, height, weight; or categorical data such as 0/1 for Yes/No in which a data dictionary may be used to define the categories and the coding specifications. The data set may contain raw data or derived data. Clearly document any assumptions upon which your scenario response is based.

80. On Attachment 5, Labor Category Description worksheet, the Disaster Recovery Engineers 1 & 2 (SE30 and SE31; row 57 and 58) have the exact same description and minimum requirements qualifications. Was this FDA’s intent?

A: Attachment 5 Pricing Worksheet has been amended in Amendment 4 to correct the minimum requirements in the labor category descriptions.

81. On Attachment 5, Labor Category Description worksheet, FDA requests rates for SE35 - High Performance Computing Linux System Technician, SE36 - High Performance Computing Linux System Administrator, and SE37 - High Performance Computing Linux System Engineer. FDA has not included these labor categories on the Labor Category Descriptions worksheet. Will FDA be providing descriptions for these three labor categories?

A: Attachment 5 Pricing Worksheet has been amended in Amendment 4 to add labor categories descriptions for SE35-SE37.

82. Page 5 of the RFP, Section I. Pricing Schedule, Pricing Terms. The RFP states, “Any material handling fee proposed must be exclusive of any profit and of any costs that would normally be covered by the indirect rates applied to the direct labor rate.” Will the Government please clarify if prime contractors are restricted from including profit on subcontractor direct costs?

A: Offerors will propose one set of fully burdened labor rates. Task order pricing will be based on the negotiated IDIQ rates. The same rates will be used regardless of whether the work is staffed with the prime or a subcontractor’s employees. Additional material handling or profit will not be permitted on top of the negotiated fully burdened IDIQ rates if the position is staffed by a subcontractor.

83. Attachment 3, Scientific Computing Technical Scenario #2 General - Over what time period is the C drives on the instruments work stations filled?

A: The drives fill over time and at rates that vary due to the many variables that would affect the rate of accumulation of data, and added software, updates, etc. The C drive is only one logical, physical, or mapped drive any one of the systems may use, all drives are monitored for usage.

84. Please provide word versions of the following forms:

Intent Response Form Past Performance Questionnaire Commitment to Protect Non-Public Information Small Business Subcontracting Plan Template

A: All RFP attachments are provided in word versions in Amendment 4 to the

RFP.

85. Section II. 20.3. Physical Security Requirements for Releasing Non-Public

Information (RFP page 18), requires a physical security plan be submitted with our proposal. There are no instructions for this plan in Section IV.

Organization or Proposals. Please confirm if a physical security plan is required, and if it is part of the page limitation.

A: Section 20.3 is removed from the RFP in Amendment 4 to the RFP.

HSSAR clause 352.239-72 Security requirements for federal information technology resources (JAN 2010) defines requirements for contracts which include information technology resources or services in which the Contractor has physical or logical (electronic) access to, or operates a Department of Health and Human Services (HHS) system containing, information that directly supports HHS’ mission. This clause is located in Section 28 by reference.

86. Pg. 18 RFP Section 20.3 requires contractors to submit a physical security plan with the proposal. Confirm that the physical security plan is located in the Business Volume, therefore is not included in the page count.

A: Please see the response to question #85.

87. Page 18 of the RFP, Section 20.3: Physical Security Requirements for

Releasing Non-Public Information. The RFP states, “The contractor shall be required to submit a physical security plan with their proposal.” Will the Government please clarify where this plan should be submitted (i.e., volume, section) and the associated impact on page limitations?

A: Please see the response to question #85.

88. On Attachment 5, Labor Category Description worksheet, the descriptions and minimum requirements for the labor categories of SME3 - Subject Matter Expert 3 and SME4 - Subject Matter Expert 4 (rows 68 and 69) have the exact same description and minimum requirements qualifications. Was this FDA's intent?

A: FDA intent was to provide a range of SME labor rates available to the vendor so they may be able to competitively and effectively price SME LOE in each of the Task Orders.