FBO_Combined_synopsis-solicitation_Amendment_One_9-1-15.pdf

NIHOLAO-OA-0082415 – Professional Support Services

Amendment One (1)

09/01/2015

Amendment One (1) to Combined Synopsis/Solicitation: NIHOLAO-OA-0082415 is issued on September 1, 2015. The Purpose of this Amendment is to:

1) Correct formatting and numbering sequence in the RFP and SOW.

2) Revise the SOW to include Optional Task 2 – Linkage of Technology Transfer Data with NIH Awards.

This is a combined synopsis/solicitation for commercial services prepared in accordance with the format in FAR 12.6 and 13.5 as supplemented with additional information included in this notice. The incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2005-83.

THIS ANNOUNCEMENT CONSTITUTES THE ONLY SOLICITATION AND A SEPARATE

SOLICITATION WILL NOT BE ISSUED. The solicitation number for this acquisition is NIHCC-R-002023 and is being issued as a Request for Proposal (RFP). The NAICS Code for this solicitation is 541990 and the Small Business Size Standard is $14.0 Million. This will be awarded as Time and Materials, 100% Total Small Business Set-Aside. The Government intends to issue one Contract award.

The National Institutes of Health (NIH) has a need to procure Subject Matter Expertise services within the Division of Program Coordination, Planning, and Strategic Initiatives Office.

BACKGROUND AND OVERVIEW:

As part of the NIH Reform Act of 2006, NIH established the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI) within the Office of the Director (OD). The Division’s mission includes:

• Identifying emerging scientific opportunities, rising public health challenges, and scientific knowledge gaps that merit further research.

• Developing and applying resources (databases, analytic tools, and methodologies) and producing specifications for new resources in support of portfolio analyses and priority setting in scientific areas across NIH.

• Assisting the NIH to address areas of emerging scientific opportunities and public health challenges effectively.

• Planning, supporting, and providing technical assistance in the development of program evaluations comprising:

o NIH-wide program and project evaluations o Planning and reporting required by the Government Performance and Results Act

(GPRA) and other government-wide performance efforts.

The Division also coordinates research and activities related to research on AIDS, behavioral and social sciences, women's health, disease prevention, dietary supplements, and research infrastructure, as well as incorporating all of the functions of the former Office of Portfolio Analysis and Strategic Initiatives (OPASI) and supporting cross-cutting, trans-NIH programs that require participation by at least two NIH Institutes or Centers (ICs) or would otherwise benefit from strategic planning and coordination.

The Office of Portfolio Analysis (OPA) was established within DPCPSI in 2011 to provide NIH staff with multiple services, including consultations, training in the use of portfolio analysis tools, and software development. Additional information about OPA can be found at http://dpcpsi.nih.gov/opa/index.

http://dpcpsi.nih.gov/opa/index

SCOPE

OPA anticipates the need for a broad spectrum of support to fulfill its mission and programs.

Support includes, but is not limited to the following areas:

• Tactical and strategic planning efforts for tool and process enhancements, which may include but are not limited to evaluating methods, tools and materials currently in use at NIH, developing needs assessments and business requirements, and developing new software and training materials.

• Software development activities may involve creating, modifying, and using technology to assist with automated content analysis, biomedical natural language processing, high-volume text and data mining, large-scale search and information retrieval, supervised and unsupervised machine learning, as well as data visualization, statistical modeling, and simulation, among other tasks.

• Planning, development and implementation of training programs, to include classroom as well as virtual training, which provide NIH staff with the knowledge and skills to use computational tools for analyzing and evaluating the NIH research portfolio, among other activities.

A. OBJECTIVES/PURPOSE

The objective of this Statement of Work (SOW) is to acquire Professional and Subject Matter Expertise services to assist OPA, and potentially other DPCPSI offices, in all subject areas related to portfolio analysis. The professional services will include planning, analysis, engineering, design, development, documentation, implementation, and operation and maintenance support for projects in all stages of their life cycle. The work requirements also include activities related to project management, administration, technical research and analysis, system documentation, database administration, end-user training, curriculum development, and operational support for specific information system applications, among other activities.

B. TASKS

The contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities not otherwise provided by the Government, as needed to perform task assignments at the direction of the Contracting Officer's Representative (COR). Tasks performed may include:

TASK AREA 1 - SCIENTIFIC RESEARCH AND ANALYSIS

The contractor shall provide scientists having a PhD or other degree(s) in fields such as molecular cell biology, bioinformatics, mathematics, statistics, computational linguistics, or other areas of research determined by the COR, in order to support research activities and priorities of the NIH. Such activities may include but are not limited to applying computational linguistic, biological, and statistical expertise to the qualitative and quantitative scientific analysis of NIH and other scientific program portfolios. Such expertise requires not only substantial prior experience working with NIH-internal data schemes, tables, and queries, but a deep understanding of existing OPA-specific tools and processes for linking, deduplicating, normalizing, encoding, and searching NIH funded and unfunded grant data, as well as interpreting the scientific content with respect to the qualified personnel’s biomedical and scientific expertise.

The work may also involve providing scientists having a PhD or other degree(s) determined necessary by the COR who shall participate in trans-NIH analyses and therefore must have broad scientific expertise including, but not limited to, basic biological, translational, and clinical research, as well as knowledge and demonstrated experience working with international research data sets and agencies such as Wellcome Trust, among other data sets and agencies.

The work may further involve providing scientists having a PhD or other degree(s) in fields such as molecular cell biology, bioinformatics, mathematics, statistics, computational linguistics, or other areas of research determined by the COR, who will be involved in the collection, organization, analysis, preparation, processing, and reporting of large volumes of scientific information, as well as conducting primary research to generate data or validate data already collected and/or published, while supporting knowledge exchange with other entities for effective use of scientific portfolio analysis resources, among other tasks.

The work may further involve providing scientists with a PhD or other degree(s) in mathematics or statistics together with a minimum of 7 years’ experience in carrying out statistical analyses to perform a variety of quantitative analysis activities involved in the collection, organization, and analysis of large volumes of scientific content. The statistician will have detailed working knowledge of and demonstrated prior experience working with NIH data systems, as well as demonstrated experience applying statistical software packages such as SAS and SPSS to provide analysis and policy advice to NIH leadership.

The contractor shall also actively participate in activities such as tactical and strategic planning efforts for tool and process enhancements and collaborate with staff in support of efforts to develop research proposals and strategies for implementing and disseminating research results as well as developing and writing articles and communicating findings through conference presentations, scientific publications, and project reports.

TASK AREA 2 - CONTENT ANALYSIS SOFTWARE DEVELOPMENT

The contractor shall provide qualified personnel with a PhD or other degree(s) determined necessary by the COR in computational linguistics or related fields who have comprehensive experience designing and implementing quantitative approaches to large-scale biomedical content analysis, including but not limited to the application of statistical natural language processing techniques to scientific literature, next-generation representation of semantic content, vector-based representation of the content of NIH grants, developing and implementing efficient concept extraction and entity recognition software, and the integration of such techniques and approaches with content analysis tools currently in use at NIH such as IN-SPIRETM and R-based clustering and classification scripts, among other software tools.

The contractor shall provide qualified personnel who have detailed working knowledge of how content analysis tools currently in use at NIH such as IN-SPIRETM convert documents into the mathematical vectors used in clustering algorithms as well as a detailed knowledge and prior experience preparing NIH-internal data for use in such tools, among other knowledge and experience producing scripts, tools, and software appropriate for NIH-specific content analysis.

The contractor shall further provide qualified personnel who have detailed working knowledge of and demonstrated prior experience working with data systems such as the NIH IMPACII data environment including table structure, SQL queries, and data processes; retrieving and parsing individual parts of NIH grant applications such as abstract, specific aims, public health relevance, summary statement; substantial expertise with batch PDF-to-text conversion, character encoding, name disambiguation, data linking and deduplication; and comprehensive experience with NIH systems such as QVR, RCDC, SPIRES, clinicaltrials.gov, RePORTER and ExPORTER.

The contractor shall further provide qualified personnel with demonstrated experience downloading and parsing patent data files, clinical trials data files, grants from non-NIH agencies, and publications as well as linking these external records to NIH projects and publications using automated text mining techniques. Examples of relevant text mining experience include extracting NIH project numbers from free text patent fields and accounting for variation in how project numbers are written as well as extracting and structuring citation information from patent data files and linking these citations to internal NIH citation databases, among other tasks.

The contractor shall provide qualified personnel with demonstrated experience producing software tools and scripts suitable for use by NIH staff for content analysis, including but not limited to Python and/or Java scripts and programs for retrieving and analyzing NIH and other scientific content from document-oriented databases such as Solr and MongoDB. In addition, the contractor shall have demonstrated experience producing web-based search applications, including Solr-based search and drill-down web applications among other software applications.

Furthermore, the contractor shall have comprehensive working experience with other methodologies related to automated content analysis and NIH-specific software development experience, including but not limited to those for artificial intelligence, machine learning, information retrieval, data mining, biomedical natural language processing, and clustering and classification algorithms and packages such as LibSVM, IN-SPIRETM, OpenNLP, Python NLTK, and OpenNLP Maximum Entropy modeling, among other technologies.

The contractor shall further have demonstrated knowledge of various software development platforms, systems and technologies including, but not limited to: Java, Python, R, Perl, C/C++, HTML, XML, JSON, SQL command and in-line programming, JavaScript, JSP, SVN, Bootstrap, Eclipse, web services, MongoDB, and Lucene/Solr.

TASK AREA 3 - BIOMEDICAL DATA LINKING

The contractor shall provide qualified personnel with comprehensive experience designing and implementing quantitative approaches to large-scale structured and unstructured biomedical data linking, including but not limited to automated techniques for name disambiguation, entity resolution, PI matching, organization deduplication, content similarity, as well as cross-data source record matching. This work may also involve providing scientists with a PhD or other degree(s) determined necessary by the COR in computational linguistics or related fields with advanced computer programming skills and NIH-specific data linking experience, including linking patents, news releases, publications, and clinical trials to NIH grants through text mining or data mining techniques, as well as heuristic and statistical machine learning-based approaches to name disambiguation, PI matching and entity resolution among other tasks determined by the

COR.

Furthermore, the contractor shall have demonstrated working experience with NIH-specific data cleaning and a demonstrated understanding of how data quality impacts data analysis. This work may involve providing qualified personnel with demonstrated experience in determining NIH-specific stopword lists, automatic detection and correction of character encoding issues, and automatic determination of non-content textual portions of NIH grant applications, among other data cleaning tasks.

TASK AREA 4 - TRAINING AND CURRICULUM DEVELOPMENT

The contractor shall provide qualified and experienced personnel with a PhD or other degree(s) determined necessary by the COR in molecular cell biology or related fields with substantial and demonstrated NIH-specific training experience who can apply this experience to supporting education, training, and outreach activities, including but not limited to the design, development, and delivery of instructor-led training programs. This work may also involve providing scientists with a PhD or other degree(s) determined necessary by the COR in molecular cell biology or related fields with substantial and demonstrated NIH-specific training experience who can apply this experience to the generation of in-house training materials and instructor guides for blended-learning solutions such as web-based training, and execution of new technologies to enhance the training curricula, including but not limited to e-learning, among other tasks.

The contractor shall further have demonstrated experience of developing and delivering portfolio analysis training classes for NIH staff. These classes should include, but are not limited to training in the use of IN-SPIRETM, Sci2, Guess, and Cytoscape. The contractor should also have demonstrated knowledge of relevant DPCPSI-specific tools and their configuration, as well as software required for generating blended learning materials including, but not limited to, Camtasia, WordPress, WP Courseware, and Event Espresso among other relevant software packages.

TASK AREA 5 - SOFTWARE DEVELOPMENT/ANALYSIS

The contractor shall provide qualified personnel with an MS or other degree(s) determined necessary by the COR in biotechnology, computer science or related fields who have detailed working knowledge of and demonstrated prior experience working with such NIH data systems as the IMPACII data environment including table structure for both IMPPRD and IRDPRD;

SQL queries, and data processes; and comprehensive experience with NIH systems such as QVR, RCDC, SPIRES, clinicaltrials.gov, RePORTER, and ExPORTER.

The contractor shall further provide qualified personnel with demonstrated expertise writing IMPACII SQL queries and extracting, processing, cleaning and exporting IMPACII data into formats such as CSV and other formats suitable for processing by existing OPA data processing routines, including but not limited to OPA-specific Python scripts. Examples of relevant IMPACII queries include calculating funding amount, extracted text, summary statements, and grant images among other queries.

The contractor shall provide qualified personnel with demonstrated experience producing software tools and scripts suitable for use by OPA staff for data analysis, including but not limited to Python and/or Java scripts and programs for retrieving and analyzing NIH and other scientific content from PostgreSQL, IMPACII, and Solr. In addition, such personnel shall have demonstrated experience installing, querying, and modifying Solr schemas as well as experience linking a document-oriented database such as Solr to IMPACII, among other skills.

Furthermore, the contractor shall have comprehensive in Python scripting and application development, including but not limited to web frameworks such as Flask and Pyramid as well as Python application deployment using Docker, Ubuntu, nginx, and PostgreSQL among other technologies.

TASK AREA 6 - PROGRAM MANAGEMENT

The contractor shall provide a program manager to be the principal point of contact for activities under this SOW. The contract's program manager will receive direction from the COR and then delegate assignments, as necessary. For each assigned task, the contractor shall provide appropriately qualified staff to provide program management, budget control and reporting, as required. It is the contractor's responsibility solely to manage, monitor and report progress on all task assignments under this SOW. This task is largely to fulfill business functions of the company related to the contract.

Program management activities shall also include staff direction, quality assurance and quarterly program reviews. The contractor shall be knowledgeable about and provide the technical and functional activities necessary for the management of this SOW and resulting task assignments.

On a monthly basis, the contractor shall provide the COR with a brief written summary of all activities, their status, and expected activities for the upcoming month. The Monthly Project Status Report shall include a list of all task assignments performed the previous month, open issues and recommended solutions, risks and constraints that have emerged, and plans for the next reporting period.

OPTIONAL TASK 1 – GLOBAL DATA DELIVERY & CITATION DATABASE

The contractor shall maintain an NIH-focused citation matching system that addresses current problems with access to and dissemination of citation data. The Contract also requires providing NIH with data, updated monthly, as described herein. The system will comprise two main components and data:

1. A citation database, which

a) pairs PubMed/MEDLINE content with CrossRef citation data

b) identifies Direct Object Identifiers (“DOIs”) with PubMed ID’s (“PMIDs”) for the references in CrossRef, and

2. An easily understandable user interface designed to support use by non-technical NIH personnel and potentially other users across the research community.

3. Data, as described below, including global data (biomedical research awards made by other federal, private sector, and international sources, and patents associated with those awards).

Description of the System Data: The primary citation data within the system will come from CrossRef (http://www.crossref.org/), “an association of scholarly publishers that develops shared infrastructure to support more effective scholarly communications. [Their] citation-linking network today covers over 67 million journal articles and other content items (books chapters, data, theses, technical reports) from thousands of scholarly and professional publishers around the globe.” CrossRef data provided by the contractor shall include:

• Information collected and regularly updated from CrossRef Member Publishers, such as title, journal information, publication type, and list of citations (http://www.crossref.org/oai-handler_sample.xml), and

• Digital identifiers, which point to the location of articles stored online by participating CrossRef members.

All data are to be housed either at NIH or at a location specified by NIH. Contractor will develop and deliver to NIH for use and dissemination without restriction algorithms, source code, database schemas, installation instructions, and the instructions for compiling and executing the source needed to:

• Access CrossRef data files

• Parse CrossRef data files

• Map PubMed Ids to CrossRef document identifiers

• Derive citation counts from the CrossRef data

• Derive additional citation metrics as defined by OPA from the CrossRef data

• Populate database tables

In addition, NIH will own all of the PubMed/MEDLINE to CrossRef mapping data generated by contractor, and this mapping data will be delivered to NIH as one of the deliverables of this contract. The database will physically store in-house (not link out to a virtual repository) citation data from a minimum of two sources, e.g., CrossRef, their affiliates and libraries, and the mapping data created by contractor. NIH will have exclusive rights to the data under FAR clause 52.227-17 Rights in Data—Special Works. In addition to citation data, the development plans for the citation matching system also include making it interoperable with patent data provided by NIH from sources such as iEdison, USPTO, or commercial entities in a format(s) provided by OPA. The architecture and approach for interoperability for patent data, and other data sets, will be vetted with OPA staff and leadership as part of the project plan.

The date range for the data from the sources will be all available historic data. No data contain PII or other commercially sensitive information. NIH’s receipt of future data beyond the termination of this contract will be contingent upon a future agreement procuring the additional data. Database and Interface: The database will integrate with an internal DPCPSI system via a standard programming API such as the Java Database Connectivity (JDBC) API.

Functionality also includes:

• Web-based user interface. Password/protected access not required for NIH users.

• Queryable (key words, filtering on one or many data elements) by the public through an interface and directly to the database through NIH

• Query “save” feature

• Standard reporting feature, as defined by NIH

• Data exports in format(s) specified by NIH http://www.crossref.org/ http://www.crossref.org/oai-handler_sample.xml

• Data display in format(s) specified by NIH

• Allow for at least 1000 concurrent users to query and download data without service degradation

• Interface and data returns and display to be 508 compliant

• Interface and data returns and display operate successfully in multiple browsers (Safari, Chrome, IE, Firefox, etc)

• 99% required uptime, not including maintenance, with performance standards (e.g., query time) to be specified by NIH at a later time.

Vendor will provide database and data hosting options to NIH. Hosting will include stage/production environment consistent with NIH and other federal requirements.

Database will be scalable to include future data updates (not replacing existing data but supplementing), patent data, and possibly other sources of data.

Use of Database and Data After Contract Expiry: Independent of and not governed by this SOW, NIH intends to make the database, interface, and all raw data widely available within the NIH free of further fees, licensing, or use restrictions. NIH also intends to make the database, interface, and raw citation data available to the public. In order to support these outcomes, contractor will ensure that all algorithms, software, software dependencies, and data mappings created by this project will be delivered under an open source license and available at no additional cost throughout the NIH community, via OPA. Additionally, both OPA and contractor agree to make all algorithms, software, software dependencies, and data mappings open source beyond NIH (in accordance with PubMed and cost-free CrossRef license agreements) so that the software and data mapping could be shared by NIH externally.

OPTIONAL TASK 2 – LINKAGE OF TECHNOLOGY TRANSFER DATA WITH NIH

AWARDS

The Contractor shall provide intellectual property (IP) data to NIH, including but not limited to transferred technologies and products, patent filings, licensing activities, and startup creation and continuation, and financial disclosure data from technology transfer offices at U.S. institutions that receive NIH funding. Work may involve data purchases, data scraping, and/or data mining of web content from Technology Transfer Offices and relevant resources or another resourceful way of efficiently and responsibly obtaining and updating the information.

Description of the System:

Data Deliverables: Data are to be delivered under this contract. As directed by the COR, the deliverable must be project-level or investigator-level data, which means that each reported transferred technology, patent filing, licensing activity, startup, etc., will be linked to one or more specific NIH-funded extramural projects and investigator(s). The data will be delivered to the NIH’s Office of Portfolio Analysis (OPA) in the data format and structure, coverage, and quality as specified by the COR. At a minimum, the data components will comprise the following:

Each NIH awarded project and investigator will be linked with available

a) Published and/or issued patents,

b) Licensing activities,

c) Spinoffs from particular investigator(s) or patent(s), and associated public financial disclosure data, and

d) Historical invention or inventor profile. The date range will be all available historic data captured by the Contractor’s methodology.

For all data, algorithms, and other deliverables created by the contractor, NIH will have exclusive rights to the data under FAR clause 52.227-17 Rights in Data—Special Works.

Acceptability of Delivery Data delivered by the Contractor should meet the OPA’s specifications on data format and structure, coverage, quality, and time of deliverables. As the minimum performance criteria, the delivered data should cover at least 95% of NIH benchmark dataset, less than 0.5% of missing rate, and less than 0.5% of mas-matched records (i.e. association of invention with grants or investigators).

Remediation Acceptance Guideline:

If the deliverable is not acceptable to NIH, the Contract has up to 30 days to make corrections and re-deliver the data in OPA specified format and structure, coverage, and quality.

Specific Tasks The Contractor will be responsible for data quality control and data validation according to assessment standards developed by the COR. To ensure successful use of this data, the methodology development will be implemented in two phases in a timely manner, as summarized below.

Database and Interface: The database will integrate with an internal DPCPSI system via a standard programming API such as the Java Database Connectivity (JDBC) API.

Functionality also includes:

• Web-based user interface. Password/protected access not required for NIH users.

• Queryable (key words, filtering on one or many data elements) by the public through an interface and directly to the database through NIH

• Query “save” feature

• Standard reporting feature, as defined by NIH

• Data exports in format(s) specified by NIH

• Data display in format(s) specified by NIH

• Allow for at least 1000 concurrent users to query and download data without service degradation

• Interface and data returns and display to be 508 compliant

• Interface and data returns and display operate successfully in multiple browsers (Safari, Chrome, IE, Firefox, etc)

• 99% required uptime, not including maintenance, with performance standards (e.g., query time) to be specified by NIH at a later time.

Vendor will provide database and data hosting options to NIH. Hosting will include stage/production environment consistent with NIH and other federal requirements.

Database will be scalable to include future data updates (not replacing existing data but supplementing), patent data, and possibly other sources of data.

Use of Database and Data After Contract Expiry: Independent of and not governed by this SOW, NIH intends to make the database, interface, and all raw data widely available within the NIH free of further fees, licensing, or use restrictions. NIH also intends to make the database, interface, and raw citation data available to the public. In order to support these outcomes, contractor will ensure that all algorithms, software, software dependencies, and data mappings created by this project will be delivered under an open source license and available at no additional cost throughout the NIH community, via OPA. Additionally, both OPA and contractor agree to make all algorithms, software, software dependencies, and data mappings open source beyond NIH (in accordance with PubMed and cost-free CrossRef license agreements) so that the software and data mapping could be shared by NIH externally.

C. PLACE OF PERFORMANCE :

National Institute of Health (NIH) Office of Portfolio Analysis/DPCPSI/Office of the Director Building 2 Bethesda, MD 20892-1352

FOB: Destination

National Institute of Health (NIH) Office of Portfolio Analysis/DPCPSI/Office of the Director Building 2 Bethesda, MD 20892-1352

D. PERIOD OF PERFORMANCE:

Base Period: Specific dates to be completed upon award: September 30, 2015 through September 29, 2016 (base period), with four (4) one (1) year options:

Option Period 1: September 30, 2016 through September 29, 2017 Option Period 2: September 30, 2017 through September 29, 2018 Option Period 3: September 30, 2018 through September 29, 2019 Option Period 4: September 30, 2019 through September 29, 2020

E. LINE ITEM AND PRICES:

Contract Line Item Number Title

Hours Hourly Rate Total

Line Item 0001 Scientific Analyst 2000 $ $ Line Item 0002 Data Scientist 2000 $ $ Line Item 0003 Training Director 2000 $ $ Line Item 0004 Statistician 2000 $ $ Optional Tasks Line Item 0005 Data Scientist 6000 $ $

Line Item 0006 Scientific/Database Development 4000 $ $

Line Item 0007 Software Developer 2000 $ $ Line Item 0008 Travel $ Line Item 0009 Other Direct Costs $

Total Base Period $

Item Number Title

Hours Hourly Rate Total

Line Item 0001 Scientific Analyst 2000 $ $ Line Item 0002 Data Scientist 2000 $ $ Line Item 0003 Training Director 2000 $ $ Line Item 0004 Statistician 2000 $ $ Optional Tasks Line Item 0005 Data Scientist 6000 $ $

Line Item 0006 Scientific/Database Development 4000 $ $

Line Item 0007 Software Developer 2000 $ $

Total Option Period One $

Hours Hourly Rate Total

Line Item 0001 Scientific Analyst 2000 $ $ Line Item 0002 Data Scientist 2000 $ $ Line Item 0003 Training Director 2000 $ $ Line Item 0004 Statistician 2000 $ $ Optional Tasks Line Item 0005 Data Scientist 6000 $ $

Line Item 0006 Scientific/Database Development 4000 $ $

Line Item 0007 Software Developer 2000 $ $

Period Two $

Hours Hourly Rate Total

Line Item 0001 Scientific Analyst 2000 $ $ Line Item 0002 Data Scientist 2000 $ $ Line Item 0003 Training Director 2000 $ $ Line Item 0004 Statistician 2000 $ $ Optional Tasks Line Item 0005 Data Scientist 6000 $ $

Line Item 0006 Scientific/Database Development 4000 $ $

Line Item 0007 Software Developer 2000 $ $

Period Three $

Hours Hourly Rate Total

Line Item 0001 Scientific Analyst 2000 $ $ Line Item 0002 Data Scientist 2000 $ $ Line Item 0003 Training Director 2000 $ $ Line Item 0004 Statistician 2000 $ $ Optional Tasks Line Item 0005 Data Scientist 6000 $ $

Line Item 0006 Scientific/Database Development 4000 $ $

Line Item 0007 Software Developer 2000 $ $

Period Four $

Provide a time and materials price quote in accordance with the Statement of Work identified.

The price quoted will be evaluated taking into consideration any price reductions. A best value analysis will be performed taking into consideration the results of the technical evaluation, price evaluation, and the ability to complete the work within the Government's specifications.

The Government intends to make an award(s) to that offeror whose proposal provides the best overall value to the Government.

F. DELIVERABLES

a. Provide detailed documentation (electronic and hard copy) of all requested reports, proposals, policies, plans and data base proposals and/or revisions as specified in the

SOW.

b. All paper/hardcopy documents/reports submitted under this contract shall be printed or copied, double-sided, on at least 30 percent post consumer fiber paper, whenever practicable, in accordance with FAR 4.302(b).

c. Satisfactory performance of the final contract shall be deemed to occur upon performance of the work described in Statement of Work and upon delivery and acceptance by the Contracting Officer, or the duly authorized representative, of the following items in accordance with the stated delivery schedule.

d. Deliverables under this requirement will vary extensively, and the due dates for deliverable will also vary considerably. The COR will specify the deliverable needed and timeframe (quarterly or as requirements arise), as well as other requirements such as those involving confidentiality or security.

e. The items specified below as described in the reporting requirements shall be required to be delivered F.O.B. Destination, and in accordance with and by the timeframe of quarterly or as requirements arise.

Deliverables:

• Requirements documentation

• All source code

• Data procured by NIH and data exchange formats, data structure, definitions, etc

• Training materials and support information

• Database and documentation

• Quarterly progress reports

• Patent data incorporation

• Test plans

• Results of load tests

• Installation instructions

G. GOVERNMENT FURNISHED PROPERTY AND INFORMATION

The Government is responsible for:

a. Providing necessary facilities to support contract completion including desktop computer, facility management software and network services, printers, blackberry and software, software updates, and access and privileges to server files, data and an email. The Government will provide routine maintenance and software upgrades.

H. GENERAL INFORMATION

Contractor Responsibilities

a. The Contractor is responsible for:

b. Providing knowledgeable, fully-trained Contractor support services to perform the functions listed in the SOW, an average of 40 hours per work week, Monday through Friday, excluding holidays and any day declared an official Federal Holiday. Provide a minimum of three references that can speak to the Contractor’s abilities to perform the SOW requirements.

c. Being prepared to conduct on site, face-to-face discussions, if requested by the Government.

The Contractor shall be headquartered or have service locations within the Washington Metropolitan area. The Contractor shall work 40 hours a week. Contractor will not receive payment for vacation or Government holidays. Contractor will not receive extra pay for weekend work. Scheduling shall be made at least a week in advance and mutually agreed upon between the Government COR and the Contractor.

Confidential Treatment of Sensitive Information

The Contractor shall guarantee strict confidentiality of the information/data that is provided by the Government during the performance of the award if the Government has determined that the information/data that the Contractor will be provided during the performance of the award is of a sensitive nature.

Disclosure of the information/data, in whole or in part, by the Contractor can only be made after the Contractor receives prior written approval from the Contracting Officer. Whenever the Contractor is uncertain with regard to the proper handling of the information/data under the award, the Contractor shall obtain a written determination from the Contracting Officer.

Information Technology System Security Specifications

The Contractor agrees to comply with the IT systems security and/or privacy specifications set forth herein; the Computer Security Act of 1987; Office of Management and Budget Circular A-130, Appendix 3; Security of Federal Automated Information Systems, and the DHHS Automated Information system Security Program Handbook, which may be found at the following websites:

Computer Security Act of 1987: http://csrc.ncsl.nist.gov/secplcy/csa_87.txt

OMB A-130, Appendix III: http://csrc.ncsl.nist.gov/secplcy/a130app3.txt

DHHS AISSP Handbook: http://irm.cit.nih.gov/policcy/aissp.html

The Contractor further agrees to include this provision in any sub contract award pursuant to this award. Failure to comply with these requirements shall constitute cause for termination.

The Contractor shall be responsible for properly protecting all information used, gathered, or developed as a result of the SOW. The Contractor shall establish and implement appropriate administrative, technical, and physical safeguards to ensure the security and confidentiality of sensitive Government information, data, and/or equipment.

In addition, during all activities and operations on Government premises, the Contractor shall comply with DHHS, including Operational Division rules of conduct.

(a) Required IT Systems Security Training http://csrc.ncsl.nist.gov/secplcy/csa_87.txt http://csrc.ncsl.nist.gov/secplcy/a130app3.txt http://irm.cit.nih.gov/policcy/aissp.html

The Contractor shall assure that each employee has completed the NIH Computer Security Awareness Training (http://irtsectraining.nih.gov/) prior to performing any work under this award.

The Contractor shall maintain a listing by name and title of each individual working under this award that has completed the required security training. Any additional security training completed by Contractor staff shall be included on this listing. [The listing of completed training shall be included in the first technical progress report. See SOW status reporting requirements). Any revisions to this listing as a result of staffing changes shall be submitted with next required technical progress report.]

(a) Position Sensitivity Designations

The Government has determined that the following position sensitivity designations and associated clearance and investigation requirements apply under this award:

Level 5C: Sensitive – Moderate Risk (Requires Suitability Determination with

NACIC).

Contractor employees assigned to a 5C position with no previous investigation and approval shall undergo a National Agency Check and Inquiry Investigation plus a Credit Check (NACIC), or possibly a Limited background Investigation (LBI). These positions include:

• SPACE AND DATA SYSTEMS MANAGER

Contractor employees in AIS-related positions shall comply with the DHHS criteria for the assigned position sensitivity designation prior to performing any work under this award.

Contractor employees who have met investigative requirements within the past five years may only require an updated or upgraded investigation. Verifications of completed investigations (e.g. copies of certificates of investigations or security clearances), as well as requests for new investigations, shall be submitted to the COR.

(b) Commitment to Protect Sensitive Information

1. Contractor agreement

The Contractor shall not release, publish, or disclose sensitive information to unauthorized personnel, and shall protect such information in accordance with provisions of the following laws and any other pertinent laws and regulations governing confidentiality of sensitive information:

18 U.S.C. 642 (Criminal Code: Public Money, Property or Records)

18 U.S.C. 1905 (Criminal Code: Disclosure of Confidential Information)

Public Law 96-511 (Paperwork Reduction Act)

2. Contractor-employee non-Disclosure Agreements

Each Contractor employee who may have access to sensitive information under this award shall complete the Contractor Employee Non-Disclosure Agreement available on the NIH NITAAC Website.

http://irtsectraining.nih.gov/

A copy of each signed and witnessed Non-Disclosure agreement shall be submitted to the CO/COR prior to performing any work under the award.

I. GOVERNMENT HOLIDAYS

a. The Government hereby provides notification that Government personnel observe the listed days as holidays:

(1) New Year's Day (6) Labor Day

(2) Martin Luther King's Birthday (7) Columbus Day

(3) President’s Day (8) Veterans' Day

(4) Memorial Day (9) Thanksgiving Day

(5) Independence Day (10) Christmas Day

b. In addition to the days designated as holidays, the Government observes the following days:

(1) Any other day designated by Federal Statute

(2) Any other day designated by Executive Order

(3) Any other day designated by the President’s Proclamation

c. When any such day falls on a Saturday, the following Monday is observed. Except for designated around-the-clock or emergency operations, Contractor personnel will not be able to perform on-site under this contract with NIH on holidays set forth above. The Contractor will not charge any holiday as direct charge to the award.

d. It is understood and agreed between the Government and the Contractor that observance of such days by Government personnel shall not otherwise be a reason for an additional period of performance, or entitlement of compensation except as set forth within the award.

e. Nothing in this clause abrogates the rights and responsibilities of the parties relating to stop work provisions as cited in other sections of this contract.

J. EVALUATION AND AWARD:

In addendum to FAR 52.212-2; the following factors shall be used to evaluate offers.

I. TECHNICAL APPROACH and QUALIFICATION OF PERSONNEL

Submit evidence of experience and qualifications of the Contractor in:

A. Technical Capabilities – Score 30

The Offeror shall detail its technical capability to perform the required tasks identified in this statement of work. Technical capability must demonstrate the contractor's capabilities relevant to this requirement.

The contractor shall be evaluated for,

1. Understanding of the work, including creativity and thoroughness shown in understanding the objectives of the SOW and specific tasks, and planned execution of the project.

2. Demonstrated experience in applying computational linguistic, biological, and statistical expertise to the qualitative and quantitative scientific analysis of NIH and other scientific program portfolios.

3. Prior experience working with NIH-internal data and understanding of existing OPA-specific tools and processes, as well as interpreting the scientific content.

4. Evidence of experience producing software and scripts for biomedical content analysis using various platforms including but not limited to Python/ Java scripts, SQL queries, and Solr schemas for data collection and scientific content extraction from document-oriented databases.

5. Comprehensive experience in designing and implementing quantitative approaches to large-scale biomedical analyses, and integrating with other tools such as IN-SPIRETM and R-based clustering and classification scripts.

6. Experience in applying statistical methods in data analysis.

7. Demonstrated experience working with various data systems such as NIH grants data, USPTO patent data, clinical trials data files, and publications, as well as cross linking these records to NIH projects using automated text mining techniques.

8. Experience designing and implementing automated techniques for portfolio analysis, such as cross-data source record matching, name disambiguation, PI matching, organization deduplication, and content similarity.

9. Experience in scripting and application development including but not limited to using python/java scripts, web frameworks, Ubuntu, and PostgreSQL among others.

10. Ability to manage, monitor, and report progress on all task assignments under this SOW.

11. Have the knowledge and ability to meet the requirements set forth in Section 508 of the Rehabilitation act of 1973.

B. Training Capability – Score 25

1. Demonstrated experience in education, training, and outreach activities specifically targeted to the qualitative and quantitative analysis of the biomedical research landscape, including but not limited to the design, development, and delivery of instructor-led training programs.

2. Experience developing and delivering a course curriculum for training in the qualitative and quantitative analysis of the biomedical research landscape, including a web-based training portal to facilitate perusal of available offerings and online registration by interested students.

C. Organizational Experience – Score 25

1. Evidence that the organization has current capabilities, and for assuring performance of this requirement.

2. Evidence of supporting subcontractors, consultants and business partners will be considered.

3. Appropriate mix and balance of staff to meet all computational, analytical, and training requirements.

II. PAST PERFORMANCE

D. Past Performance – Score 20

1. The organization’s history of successful completion of projects; history of producing high-quality reports and other deliverables; history of staying on schedule and within budget.

2. The quality of cooperation of key individuals within your organization, and quality of cooperation and performance between your organization and its clients.

3. The organization’s specific past performance on prior similar tasks specified within this SOW.

III. PRICE

The proposed price will be evaluated but not scored. The price evaluation will determine whether the proposed prices are fair and reasonable in relation to the solicitation requirements.

Proposed prices shall be entirely compatible with the technical quotations.

Although price is the least important evaluation factor, it will not be ignored. The degree of importance of the proposed prices will increase with the degree of equality of the proposals in relation to the other factors on which selection is to be based.

FAR 52.212-3 Offeror Representations and Certifications—Commercial Items. (APR 2012)

The Government intends to evaluate proposals and, if necessary conduct discussions with all responsible Offerors within the competitive range. The award will be made to the Offeror whose proposal conforms to the terms and conditions of the solicitation and award may be made to other than the lowest priced or the highest technically rated offer.

Relative importance and trade-offs. The Government will base the determination of best value on performance, and the other evaluation factors identified elsewhere in this solicitation. The determination of best value also considers the relative importance of the evaluation factors.

Technical factors and past performance when combined are significantly more important than price. It is pointed out; however, should technical competence between Offerors be considered approximately the same, then price could become primary.

NIH will base its award decision using a best value analysis that results in the most advantageous acquisition for the Government. NIH’s acquisition strategy used to obtain best value may result in an award to other than the lowest priced, technically rated Offeror. Best value analysis spans a continuum from the lowest priced, technically acceptable proposal to those proposals in which tradeoffs between price, past performance, and each Offeror’s technical solution is evaluated.

This tradeoff process depends on the Government’s assessment of quality factors, including but not limited to past performance, compliance with solicitation requirements, technical excellence, management capability, personnel qualifications and prior experience, and price.

PROPOSAL SUBMISSION FORMAT:

***Proposal shall be in 3 volumes: 1 Technical, 2 Past Performance and 3 Price. The volumes shall be separate and complete. The volumes shall be separate and complete, so that evaluation of one may be accomplished independently of, and concurrently with, the evaluation of the other. No pricing information shall be provided in volume’s 1 and 2***

***The total number of pages for the technical quote shall not exceed thirty (30) pages, using 1” margins, single spaced, font type Time New Roman, and a font size of 12.

***The solicitation does not commit the Government to pay any cost for the preparation and submission of a quote or proposal. It is also advised that the Contracting Officer (CO) is the only individual who can legally commit and obligate the Government to the expenditure of public funds in connection with the proposed acquisition.

QUESTIONS DUE: Interested offerors shall submit questions electronically to Darlene.Johnon@nih.gov no later than September 2, 2015, 12:00 p.m. Eastern Standard Time.

Companies that previously submitted proposal may do so again. Collect calls will not be accepted. No Phone Calls Please.

PROPOSAL DUE: All proposals should be submitted electronically to Darlene.Johnson@nih.gov no later than September 11, 2015, 12:00 p.m. Eastern Standard Time.

PROVISIONS and CLAUSES:

The Full text of the Federal Acquisition Regulation (FAR) can be accessed on the internet at https://www.acquisition.gov/far/

The following provisions and clauses apply: FAR 52.212-1, Instructions to Offerors Commercial Items; FAR 52.212-2, Evaluation-Commercial Items; FAR 52.212-3 Offeror Representations and Certifications-Commercial Items; FAR 52.212-4, Contract Terms and Conditions Commercial Item; FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes Or Executive Orders--Commercial Items; FAR 52.217-8, Option to Extend Services; 52.217-9, Option to Extend the Term of the Contract; FAR 52.219-6, Notice of Total Small Business Set- Aside; FAR 52.219-8, Utilization of Small Business Concerns; FAR 52.219-13 Notice of Set- Aside of Orders; FAR 52.203-13, Contractor Code of Business Ethics and Conduct (APR 2010);

FAR 52.222-3, Convict Labor (JUNE 2003);…