Chemical Structure Software Development
The National Institute of Standards & Technology (NIST) seeks contractors that are capable of providing Software development and data analysis services to support the development of NIST Mass Spectral Libraries.
This announcement is not a Request for Proposals or Quotes (RFP/RFQ) and does not commit the Government to award a contract now or in the future. The information contained in this notice is a DRAFT only and, as such, is subject to change prior to issuance of a solicitation. No solicitation is available at this time. After results of this market research are obtained and analyzed, NIST may conduct a competitive or non-competitive procurement and subsequently award a contract. If at least two qualified small business sources are identified during this market research stage, this acquisition may be solicited as a small business set aside. NIST is seeking responses from all responsible sources, including large and small businesses (SB, SDB, WOSB, HUB Zone, SDVOSB and VOSB). This requirement is assigned a NAICS code of 541690 with a Small Business Size Standard of $15M in annual receipts. This notice seeks to identify any contractors that may be capable of performing NIST's requirements described below.
Interested business organizations that believe they may be capable of meeting NIST's requirements should respond to this notice with a narrative demonstrating their ability to meet NIST's requirements. Contractors may provide supplemental information at their discretion. Responses should be submitted to Grace.Parker@nist.gov by 5:00 PM ET on Tuesday, January 2, 2018.
NIST's potential requirements are described below:
The NIST Mass Spectral Library group requires assistance for improvements in the 2-D chemical structures and associated compound related information for enhancing the quality of its libraries. This consists of two separate tasks, each of which will have deliverables for each of three years.
1. The contractor shall develop and deliver Microsoft Windows based user-interface software for computer-assisted improvement of chemical structures in the NIST Electron Ionization (EI) library.
a. The contractor shall design the product, in consultation with NIST, for use by NIST staff and contractors for quickly and reliably examining and modifying 2-D chemical structures in its libraries. This will involve both structure ‘cleaning' (equalizing bond lengths and angles to create structures consistent with most structures already present in the library) and display of them symmetrically when possible. The contractor shall use International Union of Pure and Applied Chemistry (IUPAC) guidelines as well as NIST prior practice for producing good quality structures.
b. As input, this program shall use structures file in a standard text format (‘SDF' - a standard for multiple structure in ‘MOLfile' format), and output corrected structures to another file in the same format. The input files will be provided by NIST.
c. The user interface shall show original and proposed corrected structures, with the ability to ‘cut and paste' structures to allow corrections by NIST evaluators using available chemical structure drawing software (ACD ChemSketch or CambridgeSoft ChemDraw or custom software from the contractor).
d. Stereochemical improvements shall be proposed by the software based on tables of information extracted from internet sources of structure/names/Chemcial Abstracts Service Registry number and separate specific rules developed by the contractor.
e. ‘Cleaning' structures may use publicly available chemical structure software or such processing can be developed for this program. This must be done automatically (without user intervention) by the software. If publicly available software shall be utilized, the contractor must include in their response a discussion of any life cycle costs such as software licensing fees that may be applicable.
2. The contractor shall extract from publicly available sources chemical names, chemical class and other information for use in enhancing NIST mass spectral libraries and for ordering new compounds for NIST measurement.
a. The contractor shall build a database of all available discrete, covalently bonded chemicals from all openly available internet sources that contain information that may be used to match compounds in NIST libraries (chemical structure, InChI, major identifiers, chemical formulas, etc).
b. The contractor shall find all compounds of significance (defined as listed in a major non-mass spectral compilation of compounds important for science or commerce such as the Toxic Substances Control Act inventory, Wikipedia) that are not present in either the NIST EI or Tandem libraries (library data provided by NIST). This shall include all available information concerning the origin and importance of the compound identities. This deliverable shall be submitted in excel spreadsheet format. To execute this deliverable, the contractor shall extract chemical compound information from NIST libraries and process chemical compound information in chemical lists to generate a form compatible for NIST libraries/software. Processing implemented by the contractor shall de-salt compounds and reject mixtures or ambiguous compound identities.
c. For all compounds present in NIST libraries, the contractor shall provide all chemical information available from openly available internet sources, with quality control methods to limit of incorrect entries. This shall include any possible imperfections in the NIST library as well as commonly used names not present in the library.
Deliverables
Year 1
1. Task 1
a. 6 months: Deliver plans and preliminary version of software capable of correcting structures - using minimal level of stereochemical correction ( up to two stereocenters).
b. 12 months: Deliver working version 1.0 of software.
2. Task 2
a. 6 months: Provide excel spreadsheet for at least 6 major lists of chemicals of practical significance using as many web-based general lists as possible (PubChem, Chemspider, etc).
b. 12 months: Provide spreadsheet containing all compounds in the above lists that are not present in NIST libraries.
Year 2
1. Task 1
a. 6 months: Provide design and examples of software to add advanced stereochemical perception and to report relevant data available on the internet for each structure. Will also contain means of re-examining and correcting structure files process by Version 1.0.
b. 12 months: Provide version 2.0 of software with advanced stereochemical perception and internet reporting
2. Task 2
a. 6 months: Add 12 more lists of chemicals on internet lists for data access and relevance for acquiring data.
b. 12 months: Provide updated list of chemicals to be ordered and information to be added to NIST libraries.
Year 3
1. Task 1.
a. 6 months: Provide model of final version of structure correction software that may be used by customers of NIST libraries and which contain all available information for assisting correct stereochemical assignment
b. 12 months: Deliver version 3.0 of software, capable of being used by customers of NIST libraries and external evaluators, along with full documentation of its use
2. Task 2.
a. 6 months: Provide preliminary version designed to contain all available relevant data from internet sources that may be added to NIST libraries.
b. 12 months: Deliver final version of spreadsheet containing all available information to be added to NIST libraries
Reporting
Reports of progress and proposed designs should be delivered every two months for each task., The contractor shall provide the NIST TPOC with a description of the proposed plan and the contractor and TPOC shall reach an agreement on the method utilized prior to development of any software or data delivery.
Key Personnel Qualifications
The contractor shall have a minimum of a Master's degree in Chemistry. A doctorate degree is preferred. The contractor shall also possess at least 10 years of experience in computer programming for the processing of chemical structures, stereochemistry and names and the extraction and organization of this information from available sources on the internet.
Grace H. Parker, Phone 3019752345, Email grace.parker@nist.gov
