Mini SOW_Tethys-PAMGuard Integration Study_NT-22-05a.docx

STATEMENT OF WORK

Incorporating PAMGuard into the Tethys Passive Acoustic Data Metadata System – San Diego State University Component

INTRODUCTION

Tethys is a passive acoustic monitoring metadata database system designed to organize and store acoustic metadata ( http://tethys.sdsu.edu). Tethys has been developed over many years through joint BOEM-Navy funding. The data schema (rules that govern how data is organized) were designed to permit representations of acoustic metadata that are comparable across long time frames by providing a consistent format. A set of schemata have been developed for describing instrumentation, effort, detections, and localizations. In addition to the standard reporting fields, the schema permits the addition of user-defined information, thus letting passive acoustic monitoring (PAM) practitioners define their own information such as referencing physical oceanographic and meteorological data to help in the analysis and interpretation of the acoustical observations.

The Tethys metadata system has been adopted as the community standard by NOAA’s National Center for Environmental Information (NCEI), now serving as the permanent archive of raw marine acoustical observations. This study, in conjunction with an ongoing, companion project funded by the Navy’s Living Marine Resources (LMR) Program, is the final increment in Tethys’ development, bringing Tethys to maturity to give NCEI a reliable, user-friendly metadata tool that also meets the needs of scientists and natural resource managers wanting to make secondary user of the archived data.

PAMGuard, the software package that this study seeks to incorporate into Tethys, is a semiautomated, open-source software for real-time acoustic detection and localization of cetaceans and other marine species from mobile platforms. It can also be used as a stand-alone tool for analysis of previously collected acoustical observations. With the recent efforts at standardizing and optimizing the methods of acoustical measurements from moving platforms, PAMGuard has become a preferred tool in the collection and analysis of marine acoustical data and is the most common software used for BOEM permitted geological and geophysical surveys with PAM requirements in the GOM. Tethys integrated with PAMGuard affords metadata documentation concurrently with data collection rather than at a post-processing stage when important details may be forgotten or misrepresented. In addition, this study includes creating a programmer’s interface for the integrated package that will allow adding future functionality to Tethys without requiring a major overhaul of the core program.

STUDY OBJECTIVES

(1.) Integrate PAMGuard into the Tethys metadata system with a user-friendly interface for the combined packages enabling metadata documentation concurrently with data collection.

(2.) Add improved functionality for batch processing of large offline datasets (data previously collected from ship-based surveys, drifters, fixed archival recorders, gliders, etc.).

(3.) Develop an interface to other programming languages so that detection, classification, and localization (DCL) algorithms written in the MATLAB or Python programming languages can be called from within PAMGuard. This will enable the integrated package to acquire additional functionality without needing a major overhaul of the core of the integrated package.

SCOPE of WORK A. General Program Scheduling:

The Contractor shall complete the tasks identified herein in accordance with the period of performance and deliverable due dates located in Section F – Deliveries or Performance.

B. Tasks:

All tasks shall be conducted in accordance with the schedule specified in Section F. The Contractor is responsible for editing and proofreading all material in order to submit products of superior quality to BOEM.

1. Conduct a Planning Meeting

The Contractor shall attend a planning meeting with BOEM. BOEM will prepare an agenda, and the meeting will last no longer than 3 hours. The meeting shall include at a minimum the Principal Investigator on this project at the University of Saint Andrews and the Principal Investigator at San Diego State University who will be collaborating on this contract through a separate, cooperative agreement awarded by BOEM. Any additional personnel working on this project that the two Principal Investigators would like to include may attend the planning meeting. BOEM will review the obligations under this contract, and the contractor will present an overview of their integration plans to ensure that federal agency requirements are incorporated into the final software design. Following this meeting, the Contractor shall prepare a meeting summary outlining all the items discussed and listing any issues that need to be clarified later.

2. Establish a Steering Committee for User Feedback

Working collaboratively with the Principal Investigator at the University of Saint Andrews, and drawing from scientists at the U. S. National Oceanic and Atmospheric Administration (NOAA) and the U. S. Navy who have prior experience with the use of PAMGuard, form a Steering Committee of users that are willing to be advisors and beta-testers to give user feedback at appropriate stages of this project. If deemed appropriate by the Principal Investigator at the University of Saint Andrews and the Principal Investigator at San Diego State University collaborating on this project, other experienced PAMGuard users may be added to the steering committee.

3. Integrate PAMGuard with the Tethys Database Working collaboratively with the Principal Investigator at the University of Saint Andrews, integrate the Tethys into PAMGuard. Utilize the Steering Committee as needed during critical phases of the software integration.

4. Add Improved Functionality for Batch Processing of Large Offline Datasets Working collaboratively with the Principal Investigator at the University of Saint Andrews, enhance the already existing batch processing functionality. Utilize the Steering Committee as needed during critical phases of the software development.

5. Develop an Interface to Other Programming Languages Working collaboratively with the Principal Investigator at the University of Saint Andrews, build Matlab and Python programmers’ interfaces in PAMGuard to both Matlab and to Python: Matlab to provide an easy algorithm prototyping environment; Python to allow access to modern Machine Learning Algorithms (MLA’s). Utilize the Steering Committee as needed during critical phases of the software development.

6. Document the Enhanced, Tethys-integrated PAMGuard System

Working collaboratively with the Principal Investigator at the University of Saint Andrews, complete and legible documentation of the resultant integrated and enhanced PAMGuard system shall be incorporated into the online PAMGuard help files. Additionally, develop online tutorials for user self-training available through the PAMGuard website. Utilize the Steering Committee to critique the readability and helpfulness of the documentation and the tutorials.

Data Management

Section 508 of the Rehabilitation Act of 1973 (found at 29 U.S.C. 794d) requires access to and use of information by individuals with disabilities. A deliverable such as electronic reports (ex: PDF files) to be placed on the web (either on the agency's web server or the company's), video footage, or other electronic data such as flash drives to be distributed, are subject to Section 508 guidelines. Simplified, this means that PDF files need to be formatted so that they are "readable" by assistive technology devices such as screen readers. Video footage, if any produced, must be closed captioned. flash drives which contain HTML, PDF, or word processor files must be assessable.

Program Management

The Contractor shall designate a Principal Investigator who assumes the responsibility to ensure the successful planning and conducting of this project. The Contractor shall operate under a Management Plan as set forth in the Contractor’s technical and cost proposals and as agreed to in any subsequent modifications.

Meetings, Work Items, Reports, and Other Deliverables

The following deliverables shall be submitted, and meetings held in accordance with the schedules specified in Section F. The Contractor is responsible for editing and proofreading all material in order to submit products of superior quality to the BOEM.

Bi-monthly Status Reports:

Information about the progress made on this effort shall be provided in bi-monthly (every other month) status reports. The Status Reports will be used to support and validate invoices for expenses incurred during this project. The Status Reports will be due on the first of every other month and may be submitted via e-mail. Status Reports may be bulleted comments in whole or in part and shall contain the following items:

1. a summary of work accomplished, and overall progress made in each task of the contract, identifying any changes to the schedule (advances or delays);

2. a summary of any significant problems encountered during the preceding two (2) months, including an assessment of their probable impact on the project and statements of corrective actions taken or proposed; and

3. anything else of relevance to the project.

All correspondence pertaining to this Contract and prepared by the Contractor shall be sent to the ESP Contact, the COR, and the CO. Correspondence pertaining to this Contract, received by the Contractor (excluding correspondence to and from BOEM) shall be copied and sent to the ESP Contact, the COR, and the CO. All correspondence shall be clearly marked with the Contract number on the first page.

Summary of Planning Meeting

Within 2 weeks following the Planning Meeting, described in Task 1., the Contractor shall prepare a summary as explained in Task 1. Any changes that might affect the contract are subject to approval in writing by the BOEM Contracting Officer and COR.

Final Report and Technical Summary and Footprint

The Contractor shall prepare a Final Report, Technical Summary, and Footprint according to the instructions presented here -- https://www.boem.gov/environment/environmental-studies/report-specifications/esp-report-and-footprint-specifications .

A complete Draft Final Report and Draft Technical Summary shall be submitted to BOEM for review and comment. BOEM will review the documents for accuracy and scientific validity and will provide the Contractor with written comments based on the review. Upon reviewing BOEM's comments on this material, the Contractor shall correct all omissions or deficiencies resulting from nonconformance to the contract requirements. The Contractor shall also make additions, revisions, or corrections relating to data interpretation, judgments, or recommendations that have been mutually agreed upon between BOEM and the Contractor. If the Contractor does not agree with BOEM's findings, discussions shall be held with the COR to resolve the disagreements. When all issues have been resolved, the Contractor shall submit a written response to the COR as to how the Contractor will address the findings in the final material submitted. This response shall be submitted by the due date specified in Section F. The BOEM will then have seven (7) calendar days to either approve or disapprove the response.

The Draft Final Report and Draft Technical Summary addressing all comments, as agreed upon, shall be submitted after receiving BOEM’s approval of the response letter. Electronic files (prepared in IBM-compatible MS Word and Adobe PDF files) shall be submitted according to scheduling in Section F. The Contractor shall not provide copies of this Report, nor any subsequent revisions prepared during the review process, nor data contained within, nor any portions thereof, to any parties not specifically designated in the listing below prior to final acceptance by BOEM. If a need arises to do so, the Project Manager must obtain the written approval of the CO.

The Final Report and Final Technical Summary shall incorporate all changes to the Draft Final Report and Draft Technical Summary as requested by BOEM. Electronic files (prepared in IBM-compatible MS Word, Adobe PDF and/or database files) shall be submitted according to scheduling in Section F. The Contractor shall not provide copies of this Report, nor any subsequent revisions prepared during the review process, nor data contained within, nor any portions thereof, to any parties not specifically designated in the listing below prior to final acceptance by BOEM of the Final Report. If a need arises to do so, the Project Manager must obtain the written approval of the CO.

Scientific Integrity

Scientific integrity is vital to Department of the Interior (DOI) activities under which scientific research, data, summaries, syntheses, interpretations, presentations, and/or publications are developed and used. Failure to uphold the highest degree of scientific integrity will result not only in potentially flawed scientific results, interpretations, and applications but will damage DOI’s reputation and ability to uphold the public’s trust. All work performed must comply with the DOI Scientific Integrity Policy posted to http://www.doi.gov, or its equivalent as provided by their organization or State law.

Section C

DELIVERIES OR PERFORMANCE

TERM OF THE CONTRACT

The period of performance (POP) of this contract is anticipated to be forty-eight (48) months. The project period shall encompass all tasks from initial planning, through and including BOEM’s final acceptance of all deliverables.

PLACE OF PERFORMANCE

Work will be performed at the Contractor’s location except as specified below.

MEETINGS, REPORTS, AND OTHER DELIVERABLES

The following deliverables shall be submitted and meetings shall be held in accordance with the schedules specified below . The Contractor is responsible for editing and proofreading all material to submit products of superior quality to the BOEM.

POST-AWARD PLANNING MEETING AND SUMMARY

The Contractor shall attend a Post-Award Planning Meeting as soon as possible after contract award but no later than one (1) month after award via conference call or webinar. BOEM will provide an Agenda one (1) week or earlier before the meeting. BOEM will review the obligations under this contract, and the contractor will present an overview of their software integration plans to ensure that federal agency requirements are incorporated into the final software design. Within two (2) weeks following the meeting, the Contractor shall prepare a meeting summary outlining all the items discussed and listing any issues that need to be clarified later.

BI-MONTHLY PROGRESS REPORTS

All relevant information about the progress made on this effort shall be provided in bi-monthly (every other month) progress reports as described above. The reports are due to BOEM on the first of every-other month and be submitted to the ESP Contact, the COR, and the CO.

FINAL REPORT AND TECHNICAL SUMMARY

The Contractor shall submit draft and final-version Final Reports and Technical Summaries to BOEM for review as described in section above. These documents shall be submitted to the ESP Contact, COR, and Contracting Officer according to the schedule shown below.

JOURNAL PUBLICATIONS AND ORAL PRESENTATIONS

The Contractor shall collaborate with COR on all manuscripts intended to be published in journals and all abstracts or summaries prepared for oral presentations based on this contract. All associated tables and figures shall be included and sent to the COR for a courtesy review prior to formal submission. All such publications and oral presentations shall contain an acknowledgement of BOEM funding that reads as follows: "Study funding was provided by the U.S. Department of the Interior, Bureau of Ocean Energy Management, Environmental Studies Program, Washington, DC under Contract Number [TO BE PROVIDED AT TIME OF AWARD]." An acknowledgement page with the above statement shall be incorporated into any PowerPoint slides for oral presentations. Publication is strongly encouraged.

SCHEDULE AND DISTRIBUTION OF DELIVERABLES

Deliverable products shall be submitted to the addresses shown in Section F.5 in accordance with the following schedule.

CO

ADDRESSES FOR DELIVERABLES

COR - Contracting Officer's Representative

James Price Division of Environmental Sciences U. S. Bureau of Ocean Energy Management (BOEM) 45600 Woodland Road, Mail Stop VAM-OEP Sterling Virginia 20166 U. S. A.

e-mail: james.price@boem.gov voice: 703-787-1641

ESP - Environmental Studies Program Contact

Shane Guan Division of Environmental Sciences U. S. Bureau of Ocean Energy Management (BOEM) 45600 Woodland Road, Mail Stop VAM-OEP Sterling Virginia 20166 U. S. A.

e-mail: shane.guan@boem.gov voice: 703-787-1444

CO – Contracting Officer

Paula Barksdale Acquisition Operations Branch U. S. Bureau of Safety and Environmental Enforcement 45600 Woodland Road, Mail Stop: VAE-AMD Sterling, VA 20166 U. S. A.

e-mail:

voice:

DES – Chief, Division of Environmental Sciences Rodney Cluck Division of Environmental Sciences U. S. Bureau of Ocean Energy Management 45600 Woodland Road, Mail Stop VAM-OEP Sterling VA 20166 e-mail: rodney.cluck@boem.gov voice: 703-787-1087

BBSS – Chief, Branch of Biological and Social Sciences, Division of Environmental Sciences

Brad Blythe Division of Environmental Sciences U. S. Bureau of Ocean Energy Management 45600 Woodland Road, Mail Stop VAM-OEP Sterling Virginia 20166 U. S. A.

e-mail: brad.blythe@boem.gov voice: 703-787-1636

OTHER DELIVERABLE REQUIREMENTS

The Contractor shall adhere to Section 508 of the Rehabilitation Act of 1973 (found at 29 U.S.C. 794d), which requires access to and use of information by individuals with disabilities. A deliverable such as digital reports (ex: PDF files) to be placed on the web (either on the Agency's web server or the company's), video footage, or other digital data such as CD-ROMs to be distributed, are subject to Section 508 guidelines. Simplified, this means that PDF files need to be formatted so that they are "readable" by assistive technology devices such as screen readers. Video footage must be closed captioned. CD-ROMs which contain HTML, PDF, or word processor files must be assessable.