Contact Points
The Section on Development and Affective Neuroscience (SDAN) is a laboratory at the National Institute of Mental Health (NIMH) designed to conduct brain imaging studies in children and adolescents. Such research requires the use of a diverse set of data collection methods, which lend themselves to the use of multivariate statistical approaches for analysis. Of particular interest is the use of Canonical Correlation Analysis (CCA) for the investigation of associations between a host of clinical and imaging variables. While CCA is available in a number of software packages, none is able to handle particularities of imaging data, which include reading and writing information from different file formats (NIFTI, GIFTI, CIFTI, MGH/MGZ, among others), handle masking of data, and crucially, producing valid statistical inferences. Recently, the SDAN participated in the development of a permutation test known to be statistically valid for CCA (Winkler et al., 2020; https://doi.org/10.1016/j.neuroimage.2020.117065). A general implementation is publicly available at https://github.com/andersonwinkler/PermCCA. However, to facilitate use with a broader context of imaging data, the implementation must be extended to handle reading and writing imaging formats, and other aspects that are specific to permutation tests, including the ability of conducting restricted permutations (Winkler et al., 2015; https://doi.org/10.1016/j.neuroimage.2015.05.092) as needed, for example, to analyze data from siblings such as in the Human Connectome Project (HCP) and the Adolescent Brain Cognition Development (ABCD) study, both of which are funded by the NIH, and the ability to conduct faster inference using valid statistical shortcuts (Winkler et al., 2016; https://doi.org/10.1016/j.neuroimage.2016.05.068).
The objective is to implement the method described by (Winkler et al., 2020; https://doi.org/10.1016/j.neuroimage.2020.117065) for permutation inference for CCA, allowing a diverse set of imaging file formats to be used as inputs and outputs, and to handle details specific to brain imaging, as well accommodate the possibility of multi-level block permutation as well as acceleration schemes.
GENERAL REQUIREMENTS
Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work.
SPECIFIC REQUIREMENTS
The Contractor shall:
- Implement Canonical Correlation Analysis as described in the above-mentioned publication, in a way that is compatible with both GNU Octave 5.0.0 or superior, and MATLAB (Mathworks, Inc) 2015a or superior.
- Implement reading and writing of imaging data using functions that already exist for the tool Permutation Analysis of Linear Models (PALM; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM).
- Condition the input data so as to render them amenable to CCA.
- Condition the outputs of CCA to be amenable for storage into imaging formats.
- Ensure that the implementation can be integrated into PALM.
LEVEL OF EFFORT
During the period of performance of one year from date of award, the contractor shall provide approximately 10 hours per week, not to exceed 495 labor hours.
GOVERNMENT RESPONSIBILITIES
The Government shall review activities and provide guidance and feedback, via electronic communication (email, conference calls). The government shall not provide computing resources (either hardware or software).
DELIVERY OR DELIVERABLES
Octave and/or MATLAB-compatible software produced by the contractor shall be made available to the Government. Software should be fully functional on a variety of test data provided by the Government. Coding should be clear, concise, profusely commented, and follow well known best MATLAB coding practices towards speed and memory management.
REPORTING REQUIREMENTS
Weekly software updates on a shared, private software repository with version control in a commercial platform (such as Github.com or Gitlab.com), to be agreed with the contractor, will act as reporting. The contractor is not required to submit additional written reports.
KEY PERSONNEL
Successful performance will require the contractor to be or work closely with a software developer with extensive programming skills which include MATLAB and/or Octave, and with the ability to develop highly efficient, vectorized code.
INFORMATION SYSTEM SECURITY PLAN
The contractor shall not have access to federal information systems. Software developed will be sent to the Government via electronic communication.
DATA RIGHTS
The NIMH shall have unlimited rights to, and ownership of all deliverables provided under this contract, including software and other computer scripts, data, reports, recommendations, briefings, work plans and any 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.
SECTION 508- ELECTRONIC AND INFORMATION TECHNOLOGY STANDARDS
The contractor shall comply with Section 508 of the Rehabilitation Act (29 U.S.C. § 794d), as amended by the Workforce Investment Act of 1998 (P.L. 105-220), August 7, 1998.
PUBLICATIONS AND PUBLICITY
The contractor shall not write or publish articles related to the production or as a result of the requirements of the SOW, unless in direct cooperation with the Government.
CONFIDENTIALITY OF INFORMATION
The government shall not provide to the contractor any information or data of a personal nature about individual(s) or proprietary information or data pertaining to an institution or organization which is confidential. The government reserves the right to publish software and/or data related to this SOW, at its own discretion, with or without participation of the contractor.
CONTRACTING OFFICER'S REPRESENTATIVE (COR)
- The Contracting Officer's Representative (COR) contact information:
- Courtney White
National Institute of Mental Health
Section on Development and Affective Neuroscience
31 Center Drive, Bethesda, MD 20892-2370
Phone: 301-443.8060
E-mail: courtney.white@nih.gov
- Courtney White
- The COR is responsible for: (1) monitoring the Contractor's technical progress, including the surveillance and assessment of performance and recommending to the Contracting Officer changes in requirements; (2) interpreting the statement of work and any other technical performance requirements; (3) performing technical evaluation as required; (4) performing technical inspections and acceptances required by this contract; and (5) assisting in the resolution of technical problems encountered during performance.
- The Contracting Officer is the only person with authority to act as agent of the Government under this contract. Only the Contracting Officer has authority to: (1) direct or negotiate any changes in the statement of work; (2) modify or extend the period of performance; (3) change the delivery schedule; (4) authorize reimbursement to the Contractor for any costs incurred during the performance of this contract; (5) otherwise change any terms and conditions of this contract; or (6) sign written licensing agreements.
- The Government may unilaterally change the COR designation for this contract.
Interested parties may identify in writing their interest and capability in response to this requirement. Responses to this notice shall contain sufficient information to establish the interested parties’ bona-fide capabilities for fulfilling the requirement and include: unit price, list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov.
All responses must be received by closing date and must reference the announcement. Responses may be submitted electronically to the attention of the contract specialist. Fax responses will not be accepted.
All responsible sources may submit a bid, proposal, or quotation which shall be considered by the agency.