NHGRI Scientific & Technical Support for Bioinformatics, DNA Sequencing, and Information Technology Infrastructure

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North American Industry Classification System (NAICS) Code 541519 Other Computer Related Services, Size Standard of $25 million. Project Title: NHGRI Scientific & Technical Support for Bioinformatics, DNA Sequencing, and Information Technology Infrastructure The Statement of Work a. Background. - The National Human Genome Research Institute (NHGRI) Office of the Director (OD) oversees general operations, administration and communications for the NHGRI. The Director's Office provides overall leadership, sets policies, develops scientific, fiscal and management strategies; assists in governing the ethical behavior of its employees, and coordinates genomic research for the National Institutes of Health (NIH) with other federal, private, and international programs. The Office also supports international meetings, workshops, and other activities essential to the efficient international coordination and exchange of large-scale genomic data. OD is divided administratively into the Office of Policy, Communications, and Education (OPCE), which develops policy on the ethical, legal, and social implications (ELSI) of human genome research and disseminates information about the NHGRI and the Office of Administrative Management, which provides administrative services and financial, personnel and grants management. The Division of Intramural Research (DIR) is one of the premier research programs working to unravel the genetic basis of human disease. NHGRI investigators, along with their collaborators at other NIH Institutes and various research institutions worldwide, have embarked on a number of high-risk efforts to unearth clues about the complex genetic pathways involved in human diseases. These efforts have used genomic sequence data from humans and other species to pinpoint hundreds of potential disease genes, including those implicated in cancer, diabetes, premature aging, hereditary deafness, various neurological, developmental, metabolic, and immunological disorders, and others. These studies have brought together NHGRI basic scientists and clinicians in collaborations aimed at developing better approaches for detecting, diagnosing, and managing these often-debilitating genetic disorders. The Office of the Scientific Director (OSD) provides leadership and managerial oversight for all research and related activities within the Institute's Division of Intramural Research. OSD creates and maintains a productive research environment through the effective management, coordination, and prioritization of NHGRI research activities. This is accomplished by providing overall scientific leadership and by overseeing activities that are central to the successful day-today operation of the NHGRI Intramural Program DIR also collaborates with other NIH Institutes and Centers, as well as with external academic and research institutions. DIR maintains a keen awareness of national and international research efforts in relevant program areas, advising the Director and staff on areas of emerging scientific areas relevant to the mission of NHGRI. The Division of Extramural Research (DER) provides scientific administration and management of the National Human Genome Research Institute's grants, cooperative agreements, and contracts programs. In consultation with the broad scientific community, DER supports funding for research, training and career development in genomics at sites across the nation. DER is also the focal point for international collaborations at the National Institutes of Health for genomic research. b. Purpose and Objectives. The purpose of this requirement is to provide support for Bioinformatics Scientific Programming, Technical Support of Scientific Equipment connected to the NHGRI Local Area Network (LAN), System Administration for Unix, Linux, Apple and Microsoft Windows Servers; Desktop Support, Network Infrastructure Support, Monitoring and Maintenance of IT Assets, after-hours and off-site Support, and Documentation and Technical Writing for the NHGRI Office of the Director (OD), the Division of Intramural Research (DIR), and the Division of Extramural Research (DER). c. Project requirements. The requirement will consist of Chief Information Officer (CIO) Support, IT Operations and Maintenance Services, Critical Infrastructure Protection and Information Assurance Support, and Software Development and Maintenance. The specific tasks are outlined below. Task 1 - Project Management Services. Provide the technical and functional activities at the contract level needed for program management of the requirement. This shall include productivity and management methods such as Quality Assurance, Configuration, Work Breakdown Structure, and Human Engineering at the contract level. Provide the centralized administrative, clerical, documentation and other related functions appropriate to this level. Prepare a Project Management Plan describing the technical approach, organizational resources and management controls to be employed to meet the cost, performance and schedule requirements throughout project execution. Provide a weekly progress review written report using a bullet and summary format for major efforts provided related to the project requirements. Provide a monthly status report monitoring the quality assurance, configuration management, and security management applied to the project (as appropriate to the specific nature of the requirement.) Task 2 - Bioinformatics Support. The objective is to provide expertise and assistance in bioinformatics and computational analysis in support of genomic research being performed by NHGRI Investigators and within DIR Research Core Facilities (the Cytogenetics and Microscopy Core, the Embryonic Stem Cell and Transgenic Mouse Core, the Flow Cytometry Core, the Genomics Core, and the Zebrafish Core). To that end, scientific programmers shall develop and implement computational tools for effective and efficient analysis of large-scale genomic data, to include sequence-based, structure-based, array-based, and proteomic data. Since many NHGRI Laboratories have similar needs, software solutions shall be developed as "generalized solutions" that can then be tailored to the specific needs of a specific NHGRI Investigator's research program. Staff under this task shall be housed within the DIR Bioinformatics and Scientific Programming Core. Scientific programmers shall also develop database solutions for the efficient archiving and retrieval of experimental data, including appropriate graphical user interfaces (GUI) to facilitate Use by scientific staff. This includes development of software to capture information being generated by high-throughput genomic instrumentation (e.g., sequence data, array-based data, in situ image data, and SNP genotyping data). Software and tools shall be developed aimed at converting legacy data to new platforms, as necessary. The successful contractor must have demonstrated expertise in the development and deployment of secure clinical database systems supporting IRB-approved clinical protocols generating genomic data; this includes medical sequencing data and other genotypic and phenotypic data being generated in the course of these IRB-approved clinical protocols. Demonstrated experience is required in programming in UNIX, Macintosh, and Intel-based environments, with a functional knowledge of relational database development, object-oriented programming, Oracle, MySQl, Sybase, C/C++, Perl, CGI, Java, JavaScript, SQl, HTML, CSS, and UNIX shell scripting. Familiarity with major public bioinformatics databases and associated tools is required. In order to facilitate scientific software usage across various platforms in a multi-user environment, the development of software using Web browsers as a graphical front-end is strongly encouraged. Bioinformatics expertise for projects requiring advanced, intensive data analysis being performed in NHGRI laboratories is required. This is to include the analysis of primary data being generated within NHGRI Laboratories, as well as for the mining of sequence, structural, expression, SNP-based genotyping, and proteomic data available in the public domain through third-party databases. Anticipated support will include, but is not limited to, active collaboration on scientific projects through the deployment of professional personnel. This will require a mixture of M.S. and Ph.D. level personnel with expertise in bioinformatics or computational biology. Support for the dissemination of scientific results to the biological community at-large through NHGRI DIR's research Web site shall be provided. In support of this goal, support for high-end graphics needs required for the proper communication of cutting-edge scientific findings, is required as needed. It is expected that modern system development environments, tools, and methodologies will be employed in accomplishing the aforementioned objectives. Anticipated support consists of the full range of software development support and maintenance tasks including, but not limited to, requirements definition, design, development, installation, maintenance, problem diagnosis and resolution, development, and enhancement of system and application software, as well as support for various scientific and programming services in use at NHGRI. It is expected that realistic project planning timetables incorporating development, beta-testing, portability, and troubleshooting are provided. The design and development of all applications, development tools, and user interfaces must be optimized for use with the unique architectural features of NHGRI's scientific computing environment. Furthermore, robust documentation for all software projects must be provided in a timely fashion and written in proper English. The ability to effectively use versioning control software (CVS or RCS) is critical. Given that the scientific programmers under this task interact closely with NHGRI Investigators, these programmers must possess excellent written and verbal communications skills, have a cooperative and service-oriented attitude, and always maintain a professional demeanor. Task 3 - DNA Sequencing Technical Support. The objective of this task is to support the NIH Intramural Sequencing Center (NISC). Established in 1997, the NISC is a multi-disciplinary genomics facility that emphasizes the generation and analysis of DNA sequence data. In addition to providing NIH investigators access to large-scale DNA sequencing services, NISC plays a major role in several high-profile genomic initiatives in its role as a member of the NHGRI Genome Sequencing Center Network. These include the Comparative Vertebrate Sequencing Initiative, the Encyclopedia of DNA Elements (ENCODE) Project, and the recently launched ClinSeq Medical Sequencing Initiative. Another objective of this task is to provide expertise and assistance in bioinformatics and computational analysis in support of this high-throughput DNA sequencing facility. NISC sequencing instruments run nearly 24 hours every day, with an expected yield of over seven million DNA sequences this year; the expectation is that output will increase over the coming years as additional economies-of-scale and improvements in efficiency are achieved. Production rates like these cannot be sustained or expanded without an extremely efficient, accurate, flexible and robust sample processing operation. Two critical components of such an operation are a laboratory Information Management System (UMS) for sample tracking and flow control, along with advanced laboratory robotics. Software design and engineering support for a specialized, custom LIMS that uses a Software Development Kit (SDK) provided by Cimarron Software, Inc is required. This platform provides for a flexible but standard graphical user interface that allows users ready access to workflow processes while facilitating sample tracking through extensive use of barcoding. Scientific programmers shall support and extend the current system, in order to meet evolving changes in DNA sequencing protocols. To accomplish this, scientific programmers shall be in frequent communications with laboratory and scientific personnel. An in-depth understanding of molecular biological protocols and DNA sequencing techniques are essential elements in achieving these goals. Engineering support shall also be provided for highly specialized robotic equipment. Effective design, implementation, and support are required in order to handle liquid reagents and thousands of DNA samples in tubes, 96-well, and 384-well plates on a daily basis in a reliable and extremely accurate fashion. Many of the processes employed at NISC require manipulation of liquid samples that are less than 1 micro-liter in volume. In order to insure optimal use of developing technologies, engineering staff will stay abreast of advances in robotics technologies by judicial attendance of relevant conferences and participation in education forums such as robotics user groups. Scientific engineering and programming staff will work to improve integration of robotic systems with the LlMS in order to reduce requirements for human manipulations, thereby increasing throughput and reducing handling errors. Demonstrated experience programming in UNIX, Macintosh, and Intel-based environments, with a functional knowledge of relational database development, object-oriented programming, Oracle, MySQl, Sybase, C/C++, Perl, CGI, Java, JavaScript, SQl, HTMl, CSS, and UNIX shell scripting is required. In order to facilitate scientific software usage across various platforms in a multi-user environment, the development of software using Web browsers as a graphical front-end is strongly encouraged. It is expected that modern system development environments, tools, and methodologies will be employed in accomplishing the aforementioned objectives. Anticipated support consists of the full range of software development support and maintenance tasks including, but not limited to, requirements definition, design, development, installation, maintenance, problem diagnosis and resolution, development, and enhancement of system and application software, as well as support for various scientific and programming services in use within NISC. Realistic project planning timetables incorporating development, beta-testing, portability, and troubleshooting are required. The design and development of all applications, development tools, and user interfaces must be optimized for use with the unique architectural features of NISC's scientific production environment. Furthermore, robust documentation for all software projects must be provided in a timely fashion and written in proper English. The ability to effectively use versioning control software (CVS or RCS) is critical. Given that the scientific programmers under this task interact closely with NHGRI Investigators, these programmers must possess excellent written and verbal communications skills, have a cooperative and service-oriented attitude, and always maintain a professional demeanor. Task 4 - Chief Information Officer (CIO) Support. Numerous laws, regulations, and policies have been enacted to include the Paperwork Reduction Act, the Computer Security Act, Presidential Decision Directive (PDD) #63, Government Performance and Results Act (GPRA), and the Clinger Cohen Act. In particular the Clinger Cohen Act of 1996 established the importance of the position and duties of the Chief Information Officer (CIO). The objective of CIO Support is to provide support to the CIO in the implementation of all laws, regulations, policies, and directives pertaining to NHGRI personnel and IT assets. Types of work to be performed under this task include but are not limited to: ~ Information Technology Architecture Support ~ Program Analysis (including Cost/Benefit Analysis and Cost Effectiveness Analysis) ~ Total Cost of Ownership (TOC) Studies ~ Stakeholders Analysis ~ Workforce Management ~ IT Organizational Development ~ Capacity Management ~ Information Assurance ~ IT Impact Analysis The Administrative Support under this task shall directly support the Program Manager, Project Manager, CIO, and ITB staff. Responsibilities include maintaining personnel and other files; preparing correspondence; and schedules; coordinating travel; assisting in the preparation of presentation graphics and supports the development of contract deliverables and reports by developing and updating graphic presentations to improve the quality and enhance the usability of these documents. Also, responsible for integrating presentation graphics generated with automated tools and the deliverable documents. Maintaining and updating the NIH accountable property inventory system for the ITB and NHGRI Data Centers. The Project Management / IT Business Development / Relationship Management shall design, develop, implement and manage solutions to information requirements. Support includes, but is not limited to the following: ~ Generate new designs (or modifications to existing designs); involvement in the refinement of or adaptation to existing installed and operational systems; ~ Meeting all requirements while maintaining cost, schedule, and architectural compliance; ~ Design, develop, implement, and manage information management systems with specific and detailed project designs that meet the technical requirements, and in accordance with industry project management guidelines; ~ Improve, enhance, and assist with the development of new network projects or refine and adapt existing projects, as needed; ~ Provide support in managing the development of agency Web projects, content administrators, software developers, and/or designers ; ~ Gather/analyze client requirements, write/edit Web copy, work with internal/external resources on design, coordinate with other internal and external IT services on development and work content approvals; ~ Coordinate/document all aspects of a project: develop/manage client request/review process, track all requests/changes, and adhere to a project time line; ~ Monitor and improve the NHGRI customers satisfaction in concert with the ITB technical teams; ~ Insure that technical teams follow industry best practices and serve as the mechanism to perform Quality Assurance testing of these best practices, reporting all findings to ITB management; ~ Collaborate with ITB technical teams in developing Memorandums of Understanding with members of the NHGRI community, as required; ~ Monitor the customer service awareness of the ITB technical teams, and survey the NHGRI user community both in person and via automated tools (i.e., Remedy) to gauge their satisfaction with ITB services; ~ Document and communicate business requirements of end-users and other stakeholders for the Government customer and the ability to capture documents and specifications using best practices of business analysis; ~ Adept in developing business process charts, (e.g., using Visio and conduct/fit gap analysis to document); ~ Experience facilitating meetings and coordinating all aspects of requirements management as well as commitment to Customer support; ~ Review IT-related Statements of Work; and ~ Manage Customer Relations by developing Standard Operating Procedures that improve the perception of customer service throughout the NHGRI community and monitoring the ITB usage of the Action Request System (i.e., NHGRI requests logged in the Action Request System) and generate detailed reports as required from the historical data in the Action Request System. Technical Report Writing Support includes writing and developing technical manuals and technical documentation that describes the "as installed" information technology infrastructure, the network topology and the installation details. The documentation shall reflect the physical and logical layout. Documentation will also include user manuals and training materials. The contractor should document each major application/task associated with the assigned project or task. This should consider the sequential aspects of the work to be performed from project/task commencement to finalization of the project/task. The contractor should document any changes or actions necessary to eliminate or minimize NHGRI devices and systems downtime. Task 5 - Information Systems Security Support. The task requires technical and administrative support to the NHGRI Information Systems Security Officer (ISSO) to assure compliance with all HHS, NIH, and NHGRI Information Security policies, procedures, and best practices. Actively monitor NHGRI systems for adherence to these policies and for potential vulnerabilities with NHGRI systems. The Information Systems Security Technical Support will analyze, define, and implement security requirements in a multi-platform environment. A non-exhaustive list of examples of the type of work to be performed by the Contractor hired under this task area involves: ~ Intrusion Detection and Prevention - Configure and monitor an intrusion detection and prevention system for abnormal activity and support security aspects of workstations, servers, backup or print operations; review audit trails and logs on a regular basis; and Research, test, and recommend new security products Malicious. ~ Activity Investigation - Lead the technical research in responding to incident alerts and identify, mitigate, and ultimately eradicate any malicious or suspicious activity operating on NHGRI information systems. ~ Vulnerability Detection and Prevention - Routinely scan all systems for vulnerabilities; Identify security upgrades, patches, and/or configuration re-mediation measures for the systems; Identify and notify management of available exploit code against known vulnerabilities; Provide assistance with corrections shown from system scans; Provide monitoring, scanning, and penetration testing, as allowed; and Provide security support for the network. ~ Crvpto Systems - Provide direction, security support and recommendations for use of encryption in support of Laptops, removable media, USB drives, terminal servers, firewalls, VPNs, PKI, as well support for using encrypted data and messaging. ~ Public Key Infrastructure - Provide support for Public Key Infrastructure and digital signature planning and implementation. ~ Electronic Messaging - Recommend methods of notification in the case of an emergency or E-mail messaging not being available; and Recommend and provide support for encrypted messaging, authentication, message integrity, and digital or electronic signature capability. ~ Intelligent. Automated Data Collection and Analysis - Analyze reports from the firewall and/or server logs, scans, or from other tools providing reporting capabilities, and treat them as deliverables within two days after they become available. Certification & Accreditation Support shall analyze, define, implement, and document security controls for "low", "moderate", and "high" categorized applications and or systems resulting in successful certification of required security controls. A non-exhaustive list of examples of the type of work to be performed under this task area are: Critical and Sensitive Infrastructure Asset Identification and Certification shall examine and determine sensitivity levels for systems; follow systems development life cycle plans; identify the administrative controls; identify the technical controls; identify the operational controls; conduct a formal risk assessment undergoing major changes, or expired accreditations; develop and or modify security plans; test all security controls for operability; develop contingency plans; perform e-Authentication assessment; and identify corrective actions in addressing vulnerabilities. Critical and Sensitive Infrastructure Asset Certification Documentation shall develop a Security Plan; identify the technical controls; identify the operational controls; conduct a formal risk assessment when undergoing major changes or in the event of expired accreditations; develop and or modify security plans; test all security controls for operability; develop contingency plans; perform e-Authentication assessment; and identify corrective actions in addressing vulnerabilities. Interview Stake Holders shall determine the application/systems administrative; technical; and operational controls. Risk Assessment Support Critical and Sensitive Infrastructure Continuity and Contingency Planning/Disaster Recovery shall write a contingency disaster recovery plan and research and recommend improvements for the backup system through exercises, simulations, testing the Contingency / Disaster Recovery plans; and attempting to break recommended or existing controls of systems. Risk Management (Risk and Vulnerability Assessment and Threat Identification shall update systems previously covered by Risk Assessments; provide Risk Assessments of systems not yet covered; and recommend controls for information assurance of accurate data and data integrity). Security Certification and Accreditation shall attempt to break the controls with penetration testing, as permitted by management; follow the Systems Life Cycle Management process, including the Certification and Accreditation process for applications and systems; Task 6 - Datacenter Operations. Facilities Management. The objective of this task is to provide Facilities Management for the NHGRI Data Centers at Two Democracy, Twinbrook, and Medical Center. Responsibilities include ensuring Data Centers are highly available by configuring, maintaining and regularly testing uninterruptible power supplies and environmental monitoring systems. Ensures HVAC systems are in operating condition, and under current service plans for preventative maintenance. Also coordinates with System Administrators, ITB Staff, and end users of the Data Centers the physical layout, safety, orderly storage of supplies, maintain spare parts inventory, documentation and general cleanliness of facilities. Currently Data Centers have various American Power Conversion (APC), rack mounted UPS, Symmetra; and NetBotz equipment. Systems Administration. The objective is to provide systems administration for all NHGRI servers and storage devices. System administration shall: Install and upgrade all servers with the latest OS patches and hot-fixes to provide a secure computing environment; Set up and maintaining network accounts and shared directories; Install and update all networked server hardware with the latest software and firmware provided by the manufacturer in variety of hardware configurations to provide a reliable hardware platform; Ensure that all configurations meet HHS minimum configuration management standards; Perform day-to-day LAN administration to fulfill the requirements of NHGRI users; Design, implement and maintain disaster recovery system for the NHGRI systems to provide a high availability network; Prepare system documentation on server configuration and standard operating procedures for all network administration tasks; Participate in management and execution of various network related projects; Troubleshoot all system problems and maintain the system in accordance with the manufacturer's recommended maintenance policy; Demonstrate programming and database management (DBA) skills in Oracle, MySQl, Sybase, and Microsoft Sql; Design, test, implement, maintain and administer databases/applications on Oracle, MySQl, Sybase, Microsoft SQl and similar database engines; Perform remedial maintenance after notification that equipment is inoperative; Setting up hardware and software for servers; Plan, implement, maintain, and document maintenance schedules for servers; and Plan, implement, maintain, and document back-up systems. Applications and Web Hosting coordinate and facilitate the use of Microsoft Internet Information Server (IIS), Microsoft Project Server, Microsoft Share Point, FileMaker Pro, Cold Fusion, and other technologies in support of the NHGRI mission. Specifically, applications and web hosting provide Web-specific technology support and guidance to NHGRI users in developing and maintaining web sites in a secure manner; Ensure that web servers have security and virus protection as recommended by the NHGRI IS Security Team; respond to requests to check Web servers for malicious software, hacks, intrusions, and similar suspicious activity; Provide a Web service hosting environment for NHGRI by maintaining Microsoft Windows 2003 servers, IIS, Apache, TomCat, Sal, FrontPage Extensions, shares, permissions; Serve as a central resource for system analyses, designs, and programming for NHGRI projects relating to scientific, clinical, and administrative data; Conduct analysis between currently available information technologies in the marketplaces and assesses, advises and designs systems to fill critical voids; Work on projects related to ITS R&D activities; Coordinate the work of other in-house specialists and outside contractors; Support databases/applications that include network automation tools, electronic documentation management systems, workflow applications, network management systems, and Web-based front-ends; Troubleshoot all systems supported and assisting customers and other support personnel on projects related to these systems; Provide web-trend reports for customers as scheduled; and Work with other members for C&A and POA&M. Task 7 - Workstation Support. The task provides in-person IT Support at all NHGRI facilities and as needed at NHGRI special events; provide remote-control and over-the-phone IT Support at all NHGRI facilities, telework, travel, and NHGRI special events. Core support hours are from 7:00 a.m. to 6:00 p.m., Monday through Friday, excluding official closings. Scientific Workstation duties include providing support for the scientific workstations NHGRI staff use in performing research in the Cytogenetics & Microscopy Core, Embryonic Stem Cell & Transgenic Mouse Core, Flow Cytometry Core, Genomics Core, Zebrafish Core, Bioinformatics and Scientific Programming Core, Inherited Disease Research Branch, NIH Chemical Genomics Center, and DNA sequencing facilities, as well as in NHGRI Intramural laboratories. These workstations typically are connected to dedicated scientific equipment on various hardware platforms (e.g., Intel, PowerPC, and SPARC processors) running proprietary versions of operation systems such as but not limited to (Microsoft: Windows XP Pro & 2007 Workstation, Server 2000 & 2003; Apple: OS 9, OS X, & Server OS X; Linux: Red Hat; Sun Solaris) connected to multiple VLANs within NHGRI. Commodity Desktop & Peripherals duties support for commodity desktops, laptops, Blackberry, printers, scanners, and other peripherals which NHGRLstaff use in performing their administrative functions/duties using typical Commercial of the Shelf (COTS) productivity applications for Web browsing, E-mail, word processing, developing spreadsheets, ...