Bioinformatics services

(i) This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. (ii) The solicitation number is HHS-NIH-NIDA-SSSA-CSS-2017-429 and the solicitation is issued as a competitive Request for Quotation (RFQ) with a set-aside restriction for Women-Owned Small Business Concerns Eligible Under the Women-Owned Small Business Program. This acquisition is for a commercial item or service and is conducted under the authority of the Federal Acquisition Regulation (FAR) Part 13-Simplified Acquisition Procedures; FAR Subpart 13.5-Simplified Procedures for Certain Commercial Items; and FAR Part 12-Acquisition of Commercial Items, and is expected to exceed the simplified acquisition threshold. (iii) The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular FAC Number/Effective Date: 2005-94,2005-95 effective January 19, 2017. (iv) The NAICS code applicable to this requirement is 518210 - Data Processing, hosting, and related services with associated business size standard $32,500,000.00. (v) Background The National Institute of Mental Health (NIMH) is one of 27 Institute Centers at the National Institutes of Health (NIH) committed to making important discoveries that improve health and save lives. NIMH is the lead federal agency for research on mental disorders. The mission of NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery, and cure. The Human Genetics Branch (HGB) at the NIMH in the division of Intramural Research Programs (IRP) seeks to determine the human genetic variation that contributes to the risk for mood and anxiety disorders such as bipolar disorder and panic disorder, so that better methods of diagnosis and treatment can be developed. The Section on the Genetic Basis of Mood and Anxiety within the HGB studies the genetic basis of major mental illnesses. A critical component of this mission involves the generation and analysis of big data, including genome-wide association, exome sequence, whole-genome sequence, and sequence of RNA derived from cells and tissues. The analysis of such data requires expertise in bioinformatics methods, including data handling, quality control, annotation against existing databases, and analysis of relationships with disease outcomes. Purpose and Objective: NIMH IRP HGB requires contractor support services to satisfy operational objectives through performance of bioinformatics services. These services are needed for analysis of data generated within the HGB. This acquisition is a recompete of Previous Contract: Bioinformatics Services; Contract Number: HHSN271201100470P; Award Date: 7/15/2011; Total Amount of Contract Award: $527,217.60; Contractor Name: NIRMALA AKULA. Project Description: Independently and not as an agent of the Government, the contractor shall furnish all the necessary services, qualified personnel, materials, equipment, and facilities, not otherwise provided by the Government as needed to the subject requirement. Specifically, the contractor must be capable of providing the subject supply in accordance to the following specifications hereby stated as the Government's Essential Features: 1. Collaborate with laboratory, clinical, and computer scientists to define and design informatics projects of value to the Section. 2. Perform quality control and analysis of SNP, next-generation sequencing, and microarray data obtained from humans and model organisms. 3. Perform biological network and pathways analyses on sets of SNPs and genes that are being identified in ongoing studies. 4. Apply physical mapping, functional, and disease annotation to sets of SNPs identified in genome wide studies. 5. Design and apply existing computer systems and databases to organize, analyze, and mine large-scale DNA and RNA sequencing data. 6. Work independently and with a team of computer specialists, biologists, and clinicians to develop and maintain databases of genetic and biological data. 7. Create code in R, Perl, and Unix and provide documentation and support to users where needed. 8. Troubleshoot operational errors and decide what action is needed. 9. Collect, assemble, and curate publicly-available data with appropriate respect for rules governing data use and dissemination. 10. Maintain a laboratory notebook describing the work accomplished in sufficient detail to allow others to replicate the work. 11. Maintain associated computer files, printouts, and other documents in an orderly fashion. Contractor shall possess experience of or related to the following certifications, license or other expertise required. Personnel requirements: 1. Knowledge of Computers and Electronics (e.g. processors, chips, electronic equipment, and computer hardware and software) to work effectively in a computationally-intensive field 2. Experience in using Perl or Python to process or convert biological data 3. Experience in using open-source statistical tools as implemented in R and MATLAB 4. Experience with UNIX/LINUX-based high-performance computing environments 5. Experience with using publicly available data repositories, such as GenBank, Ensembl and PubMed 6. Experience in next-generation sequencing data processing, including quality control, variant filtering, and annotation 7. Experience in data mining techniques, including pathway analysis, text mining, and multivariate data visualization. 8. Experience with existing bioinformatics applications and programming including RNA analysis tools such as TopHat, BowTie, DESeq, and WGCNA. 9. Ability to use scientific rules and methods to solve problems. 10. Ability to implement programming techniques for writing computer programs for bioinformatic purposes. 11. Ability to employ written comprehension and verbal communication to read, understand and transmit information and ideas presented in technical biomedical publications and at scientific or professional meetings DELIVERABLES. 1. Reports of processing of DNA and RNA sequence data results 2. Biological and functional annotation of DNA and RNA sequence data 3. Analysis-ready data files for a variety of biomedical applications 4. Biological pathways and networks derived from available data 5. Scripts, macros, and computer programs that carry out routine tasks quickly and accurately Period of Performance: The anticipated period of performance for this requirement will be effective on or around June 26, 2017 through June 25, 2018 for one base year period of performance containing the option to exercise two (2) additional one-year periods of performance. Contractor shall perform the work at a government facility located at 35 Convent Drive, Bethesda, MD 20814. Work will be performed up to 40 hours per week during normal business hours 8am-5pm, Monday-Friday, excluding Federal holidays. Overtime cost may be authorized if approved in advance. The Government anticipates a Fixed Price type of contract for a commercial item acquisition will be made as a result of this solicitation. TRAVEL Travel is required. The contractor will occasionally be required to travel to other surrounding locations in support of the tasks described in this statement of work. Approved travel cost shall be a reimbursable expense. Prior to incurring any travel expenses, contractor personnel must obtain written authorization from the Project Officer that approves approximate travel, dates, expected duration, origin and destination, purpose, estimated costs and the number and names of personnel traveling. Contractor expense reports shall be prepared and processed in accordance with the Federal Travel Regulation (FTR) at GSA.gov. GOVERNMENT-FURNISHED EQUIPMENT The Government shall furnish the contractor with badge access and working space in a federally controlled facility, desk, phone and computer equipment to carry out the tasks associated with this statement of work. DATA RIGHTS The National Institute of Mental Health shall have unlimited rights to and ownership of all deliverables provided under this contract, including reports, recommendations, briefings, work plans and all other deliverables. This includes the deliverables provided under the basic contract and any optional task deliverables exercised by the contracting officer. In addition, it includes any additional deliverables required by contract change. The definition of "unlimited rights" is contained in Federal Acquisition Regulation (FAR) 27.401, "Definitions." FAR clause 52.227-14, "Rights in Data-General", is hereby incorporated by reference and made a part of this contract/order. INFORMATION SECURITY REQUIREMENTS: Contractor will abide by the terms of the applicable Information Security Program requirements of any resulting contract to this solicitation. The Information Security Program Requirements applicable to this solicitation is included as an attachment. (vi) The provision at FAR clause 52.212-1, Instructions to Offerors - Commercial Items, applies to this acquisition. The following is provided as an addendum to FAR clause 52.212-1, Instructions to Offerors. Inspection and acceptance will be performed at a Federal facility located at 35 Convent Drive; Bethesda, MD 20892. (vii) The provision at FAR clause 52.212-2, Evaluation - Commercial Items, applies to this acquisition. The following is an addendum to 52.212-2. (a) The Government will award a contract resulting from this solicitation to the responsible offeror whose offer conforming to the solicitation will be most advantageous to the Government, price and other factors considered. Price is an unscored component. Technical Evaluation criteria when combined are significantly more important when compared to price. Each quotation will be evaluated in strict conformity with the evaluation factors, utilizing written critiques. The evaluation will be based upon the demonstrated capabilities of the prospective contractor in relation to the needs of the project as set forth in the RFQ and will use an adjectival evaluation rating scheme based on the following responses: Excellent (Risk level: Very low); Good (Risk level: Low); Acceptable; Marginal (Risk level: High); Unacceptable (Risk level: Very high); Neutral (Risk level: Neutral). The following factors shall be used to evaluate offers equally weighted: (1) Personnel Qualifications. Offerors must demonstrate their knowledge and professional experience as it correlates to the experience outlined in the statement of work under contractor's experience. Proposal must include either a CV or a resume that clearly details offerors relevant experience and knowledge of the subject matter. Offeror must provide evidence of possessing M.S. or Ph.D. in bioinformatics, computational biology, or related field; Five (5) years of experience in genetics and genomics; Strong background in both computational and life science; Biological laboratory experience. (2) Technical Approach. Ability to achieve the essential government features identified in this solicitation. Offerors shall submit a response with documented evidence of possessing the technical knowledge, qualifications, capability and management structure needed in successfully performing this requirement. Offerors shall clearly indicate possessing an understanding and goals of the work, including creativity and thoroughness shown in executing the objectives of the work and specific tasks, and planned execution of the project. Offeror's ability to address anticipated potential problem areas, and creativity and feasibility of solutions to problems and future integration of new processes will be evaluated. (3) Organizational Experience. The offeror must submit with their proposal a list of the last three contracts completed during the past two years and / or contracts awarded currently in process that are similar in nature to the work scope. Contracts listed may include those entered into by the Federal Government, agencies of state and local governments and commercial concerns. Newly formed entities without prior contracts should list contracts and subcontracts as required above for such key personnel. For each contract, subcontract, or reference include: (i) Name of Contracting Organization; (ii) Contract Number (for subcontracts, provide the prime contract number and the subcontract number); (iii) Contract Type; (iv) Total Contract Value; (v) Description of Requirement; (vi) North American Industry Classification System(NAICS) Code. Price. Offerors must include a completed Price Quote with their response to this RFQ. Offerors shall submit a price quote for each period of performance with the following: Number of hours proposed; Fully loaded fixed-price hourly rate; Total price proposed; All other relevant information and documentation that the item(s) quoted meets the salient physical, functional, or performance characteristics as specified in this solicitation. (b) Options. The Government will evaluate offers for award purposes by adding the total price for all options to the total price for the basic requirement. The Government may determine that an offer is unacceptable if the option prices are significantly unbalanced. Evaluation of options shall not obligate the Government to exercise the option(s). (c) A written notice of award or acceptance of an offer, mailed or otherwise furnished to the successful offeror within the time for acceptance specified in the offer, shall result in a binding contract without further action by either party. Before the offer's specified expiration time, the Government may accept an offer (or part of an offer), whether or not there are negotiations after its receipt, unless a written notice of withdrawal is received before award. (viii) The provision at FAR Clause 52.212-3, Offeror Representations and Certifications Commercial Items, applies to this acquisition. (ix) The provision at FAR Clause 52.212-4, Contract Terms and Conditions-Commercial Items, applies to this acquisition. An addendum to FAR Clause 52.212-4, Contract Terms and Conditions-Commercial Items, Offeror Representations and Certifications Commercial Items, applies to this acquisition. The addendum includes the following FAR Clauses, provisions, terms and conditions hereby referenced: (a) 52.217-6 Option for Increased Quantity (Mar 1989); (b) 52.217-9 Option to Extend the Term of the Contract (Mar 2000). (x) FAR clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders-Commercial Items, applies to this acquisition and is included as an attachment. The following clauses in full text are applicable to this acquisition and will be incorporated into any contract resulting from this acquisition. 52.217-5 Evaluation of Options (July 1990) Except when it is determined in accordance with FAR 17.206(b) not to be in the Government's best interests, the Government will evaluate offers for award purposes by adding the total price for all options to the total price for the basic requirement. Evaluation of options will not obligate the Government to exercise the option(s). (End of provision) (xi) There are no additional contract requirement(s) or terms and conditions applicable to this acquisition. (xii) The Defense Priorities and Allocations System (DPAS) are not applicable to this requirement. (xiii) Responses to this solicitation must include sufficient information to establish the interested parties' bona-fide capabilities of providing the product or service. Responses to this solicitation must include clear and convincing evidence of the offeror's capability of fulfilling the requirement as it relates to the technical evaluation criteria and a price proposal. Offerors must include a completed copy of the provision at 52.212-3, Offeror Representations and Certifications Commercial Items, with their offer, or provide a copy of the valid certifications registrations and Representation and Certifications from the System of Award Management (SAM) applications at www.SAM.gov, which may be indicated on the Offeror's cover sheet. In addition, the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size must be included in the response. All Offerors must have an active registration in the System for Award Management (SAM) www.sam.gov." All responses must be received no later than the date specified in this announcement. Late responses will not be accepted. All responses must reference solicitation number HHS-NIH-NIDA-SSSA-CSS-2017-429. Responses must be submitted electronically to contact@example.gov and contact@example.gov. Facsimile responses will not be accepted. For information regarding this solicitation, contact Hunter Tjugum by email at contact@example.gov or by phone at +1 (555) 000-0000.