QC_OF_ISOMERIC_CHEM_STRUCTURES_R1_8-2013.doc

TITLE: QUALITY CONTROL OF ISOMERIC CHEMICAL STRUCTURES IN THE NIST/NIH/EPA MASS SPECTRAL LIBRARY

SOLICITATION NO.: SB1341-13-RQ-0714

THIS IS A COMBINED SYNOPSIS/SOLICITATION FOR COMMERCIAL SERVICES PREPARED IN ACCORDANCE WITH THE FORMAT IN FAR SUBPART 12.6 – STREAMLINED PROCEDURES FOR EVALUATION AND SOLICITATION FOR COMMERCIAL ITEMS-AS SUPPLEMENTED WITH ADDITIONAL INFORMATION INCLUDED IN THIS NOTICE. FAR PART 13 SIMPLIFIED ACQUISITION PROCEDURES ARE UTILIZED IN THIS PROCUREMENT. THIS ANNOUNCEMENT CONSTITUTES THE ONLY SOLICITATION; QUOTATIONS ARE BEING REQUESTED AND A WRITTEN SOLICITATION DOCUMENT WILL NOT BE ISSUED. This solicitation is a Request for Quotation (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2005-69.***

*** The associated North American Industrial Classification System (NAICS) code for this procurement is 541511 with a small business size standard of $25.5M. This acquisition is 100% set-aside for small business***

***The National Institute of Standards and Technology (NIST) requires quality control of isomeric chemical structures in the NIST/NIH/EPA Mass Spectral Library.

***All interested small businesses may provide a firm fixed-price quotation for the following:

CLIN 0001: Contractor Performance of Requirements associated with Task 1 and Related Deliverable(s) outlined in the Statement of Work (SoW).

QTY: 300,000 ea.

CLIN 0002: Contractor Performance of Requirements associated with Task 2 and Related Deliverable(s) outlined in the Statement of Work (SoW) QTY: 1 job.

***The following is the Statement of Work (SoW):

Quality Control of Isomeric Chemical Structures in the NIST/NIH/EPA Mass Spectral Library

I. BACKGROUND

The Biomolecular Measurement Division (BMD) is in part charged with the development of the NIST Chemistry WebBook (http://webbook.nist.gov/chemistry/) and chemical databases (http://www.nist.gov/srd/nist1a.cfm) for the National Institute of Standards and Technology’s (NIST) Material Measurement Laboratory (MML). This includes, but is not limited to, the development of new methods that enhance the evaluation, and development of new software for this purpose.

II. PURPOSE AND OBJECTIVE

The purpose of this requirement is the extension of the chemical structure identification system for the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI, http://www.iupac.org/home/publications/e-resources/inchi.html ) and the application to identify compounds in NIST collections where stereochemical or tautomeric information in the name and structure do not precisely match.

The objective of this requirement is to find and organize for correction, stereochemical and tautomeric discrepancies between chemical names and chemical structures in the WebBook and in the Library.

III. SCOPE OF WORK

The Contractor shall provide information and software needed for efficiently correcting these problems. This pertains specifically to compounds with potential stereochemistry and tautomerism in the NIST Chemistry WebBook and in the NIST/NIH/EPA Mass Spectral Library.

There are approximately 300,000 different chemical structures among these two collections.

The Contractor shall develop annotated lists of discrepancies, techniques of the resolution, and produce software and computer files for automatically or manually verifying and correcting name/structure discrepancies in the WebBook and the Library using the structure-definitions of the NIST developed InChI code.

Based on the structure definitions in the WebBook and the Library, which are expressed in IUPAC InChI structure-processing code, the Contractor shall find discrepancies between names and geometrical and stereo isomers and tautomers.

The Contractor shall develop a program to identify these isomers from structures/names in the WebBook and in the Library, generate lists of name/structure files for such isomers, organize results to facilitate resolution of problems, and create software solutions to fix these problems in an efficient manner.

IV. SPECIFIC TASKS

Task 1: The Contractor shall check text-derived tautomeric information against structure-derived ones. The Contractor shall develop or enhance the software to account for numeration systems which are associated with important classes of tautomerism-able compounds. The Contractor shall organize the results into logical classes for either automated computer correction (with manual verification) or to facilitate manual correction by grouping similar problems together for further processing by software developed by contractor.

Task 2: The Contractor shall develop software for the automated or semi-automated resolution of the problems discovered (including Web-querying of external public databases), as related to tautomerism. The Contractor shall apply the software to corrections for compounds of various classes.

V. DELIVERABLES AND REPORTS

The Contractor shall produce annotated lists of structure/name discrepancies for geometrical and stereo isomers, as well as tautomers, along with an automated method for making corrections to the structures. This shall be based on structure descriptors defined by IUPAC InChI code and shall include all relevant compounds in the Webbook (25,000 compounds) and in the Library (approximately 375,000 compounds).

The Code shall be written in C or C++ for a Windows environment. Code shall be tested and be operational under Windows NT, 2000, XP, Vista and later Windows environment operating system releases. In all cases, code shall be compatible with the existing NIST MS Spectral Search Software code and the associated utility programs used to generate and maintain data and index files.

The data to be acquired under this project shall be delivered in a text format (as mol. Files, not images).

The successful demonstration, integration and documentation of a completed software tool for finding and annotating structure/name discrepancies shall serve as a report. The source code must be well structured, and be adequately commented (such as short descriptions of algorithm details and portability issues).

VI. DELIVERABLE DUE DATES

Documentation of tautomerism-able chemicals and identification discrepancies between a name and the structure – 6-months post award.

Software for automatic correction with manual verification and correction of tautomeric compounds – 12-months post award.

VII. PERIOD OF PERFORMANCE

The period of performance shall be September 30, 2013 through September 29, 2014.

VIII. PLACE OF PERFORMANCE

The place of performance shall be the Contractor’s facility.

IX. GOVERNMENT-FURNISHED PROPERTY, DATA AND/OR INFORMATION

NIST will provide names and structures of compounds of interest in an electronic form (“Chemical Editor” format and as mol. files: http://en.wikipedia.org/wiki/Chemical_table_file#Molfile ).

The NIST MS Spectral Search Software code will be provided to the Contractor post contract award.

X. PERFORMANCE REQUIREMENTS SUMMARY

XI. CONTRACTOR MINIMUM QUALIFICATIONS

The Contractor shall have a degree in chemistry and at least one year of experience in computational chemistry and one year of experience in molecular design for organic molecules using InChI.

***END OF STATEMENT OF WORK***

***INSTRUCTIONS TO OFFERORS / EVALUATION FACTORS***

***All vendors shall submit the following:

Technical Quotation (Vol. I), Past Performance/References (Vol. II) and a Business/Pricing Quotation (Vol. III), as three (3) separate electronic files. Incomplete quotations may be considered non-responsive and removed from further consideration. Quotations shall be clearly and concisely written as well as being neat, indexed (cross-indexed as appropriate) and logically assembled. All pages of each part shall be appropriately numbered and identified with the name of the offeror, the date, and the solicitation number. A one-page transmittal letter signed by an individual authorized to commit the organization shall be transmitted with the quotation to the Government. Each quotation shall be on 8.5” x 11” paper, in a commercially standard font, not smaller than 12 point font. Each page in the quotation shall be separately numbered. The quotation shall be limited to fifteen (15) single-sided, single-spaced pages (excluding the letter of transmittal, resumes, certifications, cover letter, letters of commitment, and past-performance information).

***Overall Arrangement of Documents*** Technical Quotation addressing all technical subfactors (Volume I) - No pricing information shall be included in the technical quotation

Past Performance/References (Volume II)

Business/Pricing Quotation (Volume III)

***VOLUME I: TECHNICAL***

NIST will evaluate quotations, based on the information submitted in support of these factors/subfactors:

***Technical SubFactor 1 Technical Approach

The offeror shall provide sufficient information to demonstrate its understanding of the complexities involved in developing and maintaining databases, and provide a concise, detailed, and thorough discussion of its ability to perform modeling of molecules including any potential risks and how these can be mitigated.

***Technical SubFactor 2 Organizational Experience

The offeror shall describe its general background, experience, and qualifications of the organization as it relates to a recent relevant project for the same or similar services. If subcontracting, the offeror shall also describe the relevant experience of any proposed subcontractors.

***Technical SubFactor 3 Key Personnel The offeror shall demonstrate that its key personnel have the qualifications to conduct the tasks described in the Statement of Work (SoW). Offerors shall include resumes along with a description of the experience and capability of the proposed key personnel. Descriptions shall address such items as the individual’s background, education, work experience, and accomplishments. In addition, it shall demonstrate the knowledge that key personnel have gained through any completed and ongoing efforts that are similar in nature and scope of this effort.

***VOLUME II: PAST PERFORMANCE/REFERENCES***

The offeror shall provide two (2) examples of past performance conducted within the last three (3) years of contracts for relevant work of a similar type and scope as the current requirement with federal, state or local governments and/or commercial customers. If the offeror has no relevant past performance it should include a statement to that effect in its quotation. The government reserves the right to consider past performance data obtained from sources other than those provided by the offeror in its quotation.

The description of each reference described in this section shall not exceed a half page. For each of the contracts, the offeror shall provide the following information:

· Contract number

· Client’s name and address and point of contact, including telephone number and e-mail address

· Dollar value

· Period of performance

· Narrative describing the requirement and its relevance to the current requirement

· Name of contracting officer or point of contact, telephone number and e-mail address

The offeror may include: a) past performance information regarding any problems encountered on the contracts described above and corrective actions taken to resolve those problems; and b) Any quality awards or certifications, letters of appreciation, commendations, industry recognition of excellence or special awards received with respect to performance of services. The offeror shall describe when the award, certification, etc. was received, and may provide as an attachment to this part.

***VOLUME III: PRICE***

1. Price - firm, fixed-price per chemical structure and for the developed software; the following tables shall be used for calculation purposes:

***PROPOSED LABOR CATEGORIES***

Task 1 – Check Text-Derived Tautometric Information…

1.

2.

Task 2 – Software Development

1.

2.

***OTHER DIRECT COSTS (ITEMIZE HERE):

***ALL OFFERORS SHALL PROPOSE A PAYMENT SCHEDULE FOR THE DELIVERABLES SPECIFIED IN THE STATEMENT OF WORK(SoW)***

***PROVISIONS / CLAUSES***

The full text of a FAR provision or clause may be accessed electronically at http://acquisition.gov/far/index.html

The following provisions apply to this acquisition:

52.212-1 Instructions to Offerors – Commercial Items

52.212-2 Evaluation – Commercial Items

52.212-3 Offerors Representations and Certifications- Commercial Items;

52.225-25 Prohibition on Contracting with Entities Engaging in Sanctioned Activities Relating to Iran – Representation and Certification

All interested offerors must be actively registered in the System for Award Management (SAM) website located at https://www.sam.gov and must complete annual representations on-line in SAM in accordance with FAR 52.212-3 Offerors Representations and Certifications- Commercial Items. If paragraph (j) of the provision is applicable, a written submission is required.

The following clauses apply to this acquisition:

52.217-8 Option to Extend Services;

52.227-17 Rights in Data—Special Works;

52.232-99 Providing Accelerated Payments to Small Business Subcontractors;

52.245-1 Government Property;

52.252-2 Clauses Incorporated by Reference;

52.212-4 Contract Terms and Conditions—Commercial Items;

52.212-5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders— Commercial Items including subparagraphs:

52.204-10 Reporting Executive Compensation and First-Tier Subcontract Awards;

52.209-6 Protecting the Government’s Interest When Subcontracting with Contractors Debarred, Suspended, or Proposed for Debarment;

52.219-6 Notice of Total Small Business Set-Aside 52.219-13 Notice of Set-Aside of Orders;

52.219-28 Post Award Small Business Program Re-representation;

52.222-3 Convict Labor;

52.222-21 Prohibition of Segregated Facilities;

52.222-26 Equal Opportunity;

52.222-36 Affirmative Action for Workers with Disabilities;

52.223-18 Contractor Policy to Ban Text Messaging While Driving;

52.225-13 Restriction on Certain Foreign Purchases; and 52.232-33 Payment by Electronic Funds Transfer-System for Award Management The following Department of Commerce (CAR) provision applies to this acquisition:

1352.213-70 Evaluation Utilizing Simplified Acquisition Procedures

The following Department of Commerce (CAR) clauses apply to this acquisition:

1352.201-70 Contracting Officer’s Authority;

1352.208-70 Restrictions on Printing and Duplicating;

1352.209-72 Restrictions Against Disclosure;

1352.209-73 Compliance with the Laws;

1352.209-74 Organizational Conflict of Interest;

1352.237-75 Key Personnel; and 1352.246-70 Place of Acceptance Department of Commerce Agency-Level Protest Procedures Level above the Contracting Officer is also incorporated. It can be downloaded at www.nist.gov/admin/od/contract/agency.htm ***This is an Open-Market Combined Synopsis/Solicitation for services as defined herein. The Government intends to award a Purchase Order as a result of this Combined Synopsis/Solicitation that will include the terms and conditions that are set forth herein. In order to facilitate the award process, ALL quotations shall include a statement regarding the terms and conditions herein as follows:

The Offeror shall state “The terms and conditions in the solicitation are acceptable to be included in the award document without modification, deletion, or addition.”

OR

The Offeror shall state “The terms and conditions in the solicitation are acceptable to be included in the award document with the exception, deletion, or addition of the following:

Offeror shall list exception(s) and rationale for the exception(s).

Offerors that fail to furnish required representations or information, or reject the terms and conditions of the solicitation may be excluded from consideration.

***Please note that this procurement is not being conducted under the GSA Federal Supply Schedule (FSS) program or another Government-Wide Area Contract (GWAC). If an Offeror submits a quotation based upon an FSS or GWAC contract, the Government will accept the quoted price. However, the terms and conditions stated herein will be included in any resultant Purchase Order, not the terms and conditions of the Offeror’s FSS or GWAC contract, and the statement required above shall be included in the quotation.

***EVALUATION***

The Government will award a purchase order resulting from this solicitation to the responsible offeror whose quotation, conforming to the requirements of the solicitation, is evaluated to be the Lowest Price Technically Acceptable (LPTA) quotation.

The Government intends to make a single award but reserves the right to make no award as a result of this solicitation.

The Government intends to evaluate quotations and award a purchase order without discussions with offerors. Therefore, the offeror's initial quotation should contain the offeror's best terms from a price and technical standpoint. However, the Government reserves the right to conduct discussions if later determined by the Contracting Officer to be necessary. The Government may reject any and or all quotations if such action is in the public interest.

Technical and Past Performance, when combined, are approximately equal in importance to evaluated price.

***EVALUATION CRITERIA***

***Technical ***Technical SubFactor 1 Technical Approach The Government will evaluate the offeror's technical approach based on the information contained in the technical quotation to determine the extent of its understanding of the requirements, including the soundness of the offeror's proposed methodology(s) to effectively meet and comply with the tasks outlined in the SoW.

***Technical SubFactor 2 Organizational Experience The Government will evaluate the offeror’s organizational experience example submitted, and if applicable, its subcontractor’s organizational experience example, to determine the extent to which the offeror’s, and if applicable, its subcontractor’s general background, experience, and qualifications demonstrate its ability to perform similar services.

***Technical SubFactor 3 Key Personnel

The Government will evaluate the offeror’s submitted resume(s) of the proposed key personnel to determine the extent to which their background, education, work experience, and accomplishments demonstrate their ability to effectively conduct quality control of isomeric chemical structures.

***Past Performance The Government will evaluate the offeror's past performance, and if applicable, its subcontractor past performance information to determine its relevance to the current requirements and the extent to which it demonstrates that the offeror has successfully completed relevant contracts in the past three (3) years. In assessing the offeror's, and if applicable, its subcontractor’s past performance, NIST may evaluate the quality, timeliness, and ability to control cost and schedule of the past work. The Government will assign a neutral rating to offerors with no relevant past performance in the past three years. Past performance will be evaluated by contacting appropriate references, including NIST references, if applicable.

***Price The Government will evaluate the offeror's proposed prices to determine whether the proposed prices comply with the instructions articulated above and are realistic, complete, and reasonable in relation to the solicitation requirements.

***Offerors shall e-mail their quotation to randy.schroyer@nist.gov so that it is received by the response date/time for this solicitation. It is the responsibility of the offeror to confirm NIST’s receipt of its quotation. Each quotation shall include sufficient data to allow the Government to determine the amount, realism and consistency of the quoted fixed price.

***All questions regarding this solicitation shall be submitted in writing via e-mail to the Contract Specialist, Randy Schroyer, at randy.schroyer@nist.gov no later than 5:00PM EST August 23, 2013.

***The due date and time for receipt of quotations is August 29, 2013 no later than 5:00PM EST.