HTP-APP_RFP_Attach 3_Conceptual Design Report.pdf

S814057-CDR-01, R0

Microbial Molecular Phenotyping Capability (M2PC) Conceptual Design Report

October 2023

Author: ET Black Burns & McDonnell Engineering Company, Inc.

Concurred: DJ De Smet JT Hickman GM Wellsfry

Approved: SS Paulsen S Thevuthasan DM Mans

Prepared for the U.S. Department of Energy under Contract DE-AC05-76RL01830

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Revision Table

Revision Number Date Changes ADM-CM-055-Temp-02, R0

0 10/12/2023 Initial Issue

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Acronyms

Acronym Term/Phrase/Name

ACS Access Control System

AHU Air handling Unit

AISC American Institute of Steel Construction

AMCA Air Movement and Control Association

ANSI American National Standards Institute

ASHRAE American Society of Heating, Refrigeration, and Air Conditioning Engineers

AWS American Welding Society

BAS Building automation system

BER DOE Office of Biological and Energy Research

BSC Biosafety cabinet

BSL Biosafety Level

BMP Best Management Practices

CA Compressed air

CDR Conceptual Design Report

CRAH Computer Room Air Handling

CRSI Concrete Reinforcing Steel Institute

DBTL Design Build Test Learn

DI Deionized

DOE Department of Energy

DOE SC Department of Energy – Office of Science

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EcoFAB Fabricated Microbial Ecosystems

EF Entrance facility

EGB Electrical ground bus

EMSL Environmental Molecular Sciences Laboratory

FACS Fluorescence Activation Cell Sorting

FC Foot-candle

FDC Fire Department Connection

HVAC Heating, ventilation, and air conditioning

IBC International Building Code

IFC International Fire code

IESNA Illuminating Engineering Society

IMC International Mechanical Code

IPC International Plumbing Code

ISC Intelligent System Controller

KPPs Key Performance Parameters

LAN Local area network

LED Light-emitting diode

LEFs Lab exhaust fans

LIMS Laboratory Information Management System

M2PC Microbial Molecular Phenotyping Capability

MALDI Matrix Assisted Laser Desorption/Ionization

MNS Mission Need Statement

NFPA National Fire Protection Association

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NRC Noise reduction coefficient

OD Optical Density

OMB Office of Management and Budget

OSDP Open Supervised Device Protocol

PPE Personal Protective Equipment

PNNL Pacific Northwest National Laboratory

PNSO Pacific Northwest Site Office

RMW RMW Architecture & Interiors

RO Reverse osmosis

SBB Secondary Bonding Busbar

SBC Secondary Bonding Conductor

SDK Software Development Kit

TBB Telecommunication Busbar

TEC Total Estimated Cost

TR Telecom room

UPS Uninterruptible power system

VAV Variable air volume

VFDs Variable frequency drives

WS&H Worker Safety & Health

Zymergen Zymergen Corporation (Zymergen, Inc.)

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Contents Revision Table ............................................................................................................................................... i Acronyms ...................................................................................................................................................... ii

1.0 Executive Summary

1.1 Background Statement, Mission Need

2.0 Design Approach

2.1 Functional Requirements

2.2 Cost Estimate

3.0 Project Description

3.1 Preliminary Project Assumptions

3.1.1 Geographic Siting and Location

3.1.2 Interfaces with Existing and Planned Acquisitions

3.1.3 Standardization Requirements

3.1.4 Goals for Limitations on Recurring or Operating Costs

3.1.5 Affordability Limits on Investments

3.1.6 Stakeholder Considerations

3.1.7 Technology Status and Engineering

3.1.8 One-for-One Replacement

3.2 Short-Form Project Description

3.3 Key Stakeholders

3.4 CDR Project Team Members

3.5 Key Performance Parameters

4.0 Analysis of Alternatives

4.1 Overview

4.2 DOE Site Selection

4.3 Lifecycle Cost Analysis

5.0 Integration

6.0 Experimental and Automation Capabilities

6.1 Introduction

6.1.1 Automation Conceptual Design Report Structure

6.1.2 Definitions

6.2 System-wide Design Considerations

6.2.1 Hardware Design Guiding Principles

6.3 Software Considerations

6.3.1 Software Design Guiding Principles

6.4 Operations

6.4.1 Operations Guiding Principles

6.4.2 BSL-2 Considerations

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6.4.3 BSL-2 Controlled Containment

6.4.4 Non-BSL-2 Work in the BSL-2 Controlled Enclosure

6.5 Core Scientific Functions

6.5.1 Media

6.5.2 Cultivation

6.5.3 Design Guiding Principles

6.5.4 Sample Preparation

6.5.5 Analytical Capabilities

6.5.6 Strain Engineering

6.6 Organisms of Speical Interest

6.6.1 Soil Microbes

6.6.2 Filamentous Fungi

6.6.3 Photosynthetic Microbes

6.7 Anaerobic Microbes

6.8 Facility Integration Requirements

7.0 Facility Conceptual Design Summary

7.1.1 Codes and Standards

7.1.2 Building Coes and Standards

7.2 Site Selection

7.2.1 Climate Analysis

7.2.2 Buildable Area

7.3 Site Development and Systems

7.3.1 Site Grading

7.3.2 Parking Area/Roadways

7.3.3 Walkways, Walls, Entry Plaza

7.3.4 Landscape Development

7.3.5 Paving

7.3.6 Site Furnishings

7.4 Civil Engineering

7.4.1 Site Placement

7.4.2 Site Utilities

7.4.3 Master Plan Integration

7.5 Architectural

7.5.1 Design Narrative

7.5.2 Scope Considerations

7.5.3 Architectural Systems

7.6 Laboratory Planning

7.6.1 Laboratory Planning Approach

7.6.2 Laboratory Types

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7.6.3 Biosafety Level Spaces

7.7 Office Planning

7.7.1 Office Areas

7.8 Structural

7.8.1 Introduction

7.8.2 Wind/Seismic Load /Resisting System

7.8.3 Floor Vibrations

7.8.4 Design Loading Criteria

7.8.5 Deflections/Serviceability Limits:

7.8.6 Material Strengths

7.9 Mechanical Systems

7.9.1 General

7.9.2 Existing EMSL Infrastructure

7.9.3 Base Design Requirements

7.9.4 Laboratory Supply Air Ventilation and Distribution System

7.9.5 Laboratory Supplemental Cooling System

7.9.6 Laboratory Exhaust System

7.9.7 Non-Laboratory Supply Air Ventilation and Distribution System

7.9.8 Interstitial Space Heating and Cooling System

7.9.9 Preheat/Precool Energy Recovery – Air to Air Passive Heat Pipe

Exchangers

7.9.10 Chilled Water Service

7.9.11 Heating Hot Water Service

7.9.12 Process Chilled Water Loop

7.9.13 Automation Laboratory

7.9.14 Mass Spectrometry, Analytics Laboratory

7.10 Plumbing Systems

7.10.1 General

7.10.2 Water Systems

7.10.3 Wastewater Systems

7.10.4 Laboratory Gas Systems

7.11 Electrical Systems

7.11.1 Electrical Service

7.11.2 Electrical Distribution System

7.11.3 Electrical Load Estimates

7.11.4 Electrical Metering

7.11.5 Grounding System

7.11.6 Electric Vehicle Charging Stations

7.11.7 Lightening Protection System

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7.11.8 Building Lighting Systems

7.11.9 Daylighting Controls

7.11.10 Emergency Egress Lighting

7.11.11 Fire Detection and Alarm

7.12 Network and Communications

7.12.1 Introduction- PNNL Standards

7.12.2 Design Qualifications

7.12.3 Backbone Cabling

7.12.4 Telecommunications Rooms

7.12.5 General Construction of the Telecommunication Rooms

7.12.6 Structure Requirements of Telecommunications Rooms

7.12.7 Mechanical Construction Requirements of Telecommunications

Rooms

7.12.8 Electrical Construction Requirmenents of Telecommunciation Rooms

7.12.9 Telecommuication Racks and Cabinets

7.12.10 Sire Management

7.12.11 Grounding

7.12.12 Horizontal Communications Pathways

7.12.13 Telecommunications Outlets

7.12.14 Wireless Access Points

7.12.15 Public Address/Paging System

7.12.16 Mass Notification/Distributed Antenna

7.12.17 Audio / Video Systems

7.12.18 Electronic Security System

8.0 Operations and Maintenance Considerations

9.0 Building Code Analysis

9.1 Assumptions

9.2 Applicable Codes and Standards

9.2.1 Building Code

9.2.2 Fire Prevention Codes

9.2.3 Life Safety Code

9.2.4 Hazardous Materials

9.2.5 Accessibility Code

9.3 Use and Occupancy

9.4 Special Use or Occupancy

9.5 Building Heights and Areas

9.5.1 Proposed Code Building Area

9.5.2 Allowable Height

9.5.3 Allowable Numbers of Stories

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9.5.4 Allowable Floor Areas

9.5.5 Mixed Use and Occupancy

9.6 Type of Construction

9.6.1 Construction Classification

9.6.2 Building Elements

9.7 Fire and Smoke Protection Features

9.7.1 Fire Barriers

9.7.2 Fire Walls

9.7.3 Smoke Partitions

9.7.4 Vertical Openings

9.7.5 Incidental Uses

9.8 Interior Finishes

9.8.1 Wall and Ceiling Finishes

9.8.2 Floor Finishes

9.9 Fire Protection Systems

9.9.1 Fire Apparatus Access Roads

9.9.2 Fire Water and Hydrants

9.9.3 Sprinkler System

9.9.4 Fire Detection and Alarm

9.9.5 Smoke Detection

9.9.6 Standpipes

9.9.7 Portable Fire Extinguishers

9.10 Means of Egress

9.10.1 Design Occupant Loads

9.10.2 Number and Types of Exits

9.10.3 Common Path, Dead-End, and Travel Distance Limits

10.0 Preliminary Cost Estimate

10.1 Automation Equipment Cost Basis

10.2 Integration Cost Basis

10.3 Facility Cost Basis

11.0 Summary Schedule

12.0 Preliminary Risk Screen

12.1 Risks

13.0 Preliminary Acquisition Strategy Assumptions

14.0 Environmental Health and Safety

14.1 Preliminary Identification of Unusual Cultural or Biological Considerations

14.1.1 Security Approach

15.0 Quality Assurance Approach

16.0 Sustainability and Energy Efficiency

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16.1 Sustainability Approach

16.1.1 Compliance with Executive Orders

16.1.2 Sustainability Features

16.1.3 Impact on PNNL Site Sustainability

Appendix

APPENDIX A : EQUIPMENT LIST AND COST ESTIMATE

APPENDIX B : FACILITY PROGRAM

APPENDIX C : FACILITY ROOM DATA SHEETS

APPENDIX D : FACILITY DESIGN DOCUMENTS

APPENDIX E : FACILITY CONCEPTURAL DESIGN DRAWINGS

APPENDIX F : FACILITY COST ESTIMATE

APPENDIX G : GUIDING PRINCIPLES

APPENDIX H : M2PC INTEGRATION COST ESTIMATE

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Tables Table 4.1-1 Five Alternatives Identified and Analyzed Table 6.8-1 Summary of power recommendations for the M2PC facility Table 7.5-1 Scope Considerations Table 7.9-1: Laboratory AHU Schedule Table 7.9-2: Lab Exhaust Fan Schedule Table 7.9-3: Heat Pipe Energy Recovery Performance Table 7.9-4: Chilled Water Coil Schedule Table 7.9-5: Heating Hot Water Coil Schedule Table 7.11-1: Space Lighting Levels Table 7.12-1: Quantity of Communication Outlets Table 9.3-1: Building Use and Occupancies Table 9.6-1 Building Elements Table 9.8-1 Interior Finishes Table 9.9-1 Hazard Classification Table 9.10-1 Number and Types of Exits Table 9.10-2 Common Path, Dead-End, and Travel Distance Limits Table 10.1-1 Automation Equipment Cost Estimates Table 10.3-1 Facility Cost Estimate Table 10.3-2 Scope Considerations Table 11.2-2 Facility Timeframe

Figures Figure 6.3-1 Illustrative software stack. Arrows show direction of communication Figure 6.4-1 Wall Opening Within the walls of BSL-2 Figure 6.6-1 An EcoFAB Plate Figure 7.2-1 Site 1 Figure 7.2-2 Site 2 Figure 7.2-3 Site 5 Figure 7.5-1 The potential facility detailed floor plan Figure 11.1-1 Schedule of M2PC Project Duration

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Microbial Molecular Phenotyping Capability (M2PC) Conceptual Design Report 1

1.0 Executive Summary

1.1 Background Statement, Mission Need

The Department of Energy (DOE) Office of Biological and Energy Research (BER) approved a Mission Need Statement (MNS) on April 14, 2021, that describes capability gaps centered around an incomplete and constrained genome annotation. This gap limits the ability to understand and model the range of activities and function of individual microbes, engineered microbial consortia with bio-industrial potential or ecological relevance, and microbial communities from natural soil environments. The number of microbial isolates and chassis microbes interrogated is expanding rapidly given the advances in next generation genome sequencing and engineering capabilities. In contrast, the throughput capabilities to assess the phenotypes of these microbes accurately and expediently is quite low and the range of function of these microbes in engineered or natural systems is very limited. The pace of scientific advances, especially those within the biotechnology arena broadly, and BER’s scientific interests specifically, requires accurate phenotyping capabilities and a throughput capacity well beyond those currently available. New high throughput phenotyping approaches for a broad range of microbes and microbial communities are needed to develop sufficient mechanistic understanding of microbial activity and function across a wide range of species in the environment and in engineered consortia.

A significant gap exists in the ability of the scientific community to identify proteins and biochemical pathways of unknown function in microbes at the single cell to microbial community-scales, in part because microbial phenotypes change rapidly due to environmental factors and perturbations. There is an urgent need for experimental and analytical capabilities that systematically inform (1) gene-encoded function, (2) development of inexpensive and high-throughput gene manipulation across taxa, (3) linkages of genotype to phenotype, (4) expansion of work at the single-cell level, and (5) elevation of experimental studies to ecosystems of relevance to DOE.

To address this gap, a new, flexible, high throughput research capability that encompasses direct integration of automated multi-omics analysis, biomolecular and cellular imaging, and functional biological assays at timescales relevant to biological processes is proposed. The resultant BER research capability for Microbial Molecular Phenotyping (M2PC) that is broadly available to the scientific community as part of a DOE/SC User Facility will fulfill this mission need.

The purpose of this Conceptual Design Report (CDR) is to identify a design concept that fulfills the mission need and aids in establishing an appropriate cost range for the project in order to achieve CD-1 per DOE Order 413.3b.

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2.0 Design Approach

Functional requirements were developed to meet the Mission Need by Pacific Northwest National Laboratory (PNNL) R&D staff and the PNNL M2PC project team. Based upon these requirements, and multiple workshops with PNNL, Burns & McDonnell, RMW Architecture & Interiors (RMW), and Zymergen Corporation (Zymergen) developed equipment and associated space requirements to deliver the project goals. Programming efforts obtained information centered around delivering automated research and equipment requirements. These capabilities and equipment drove space types, space sizes, infrastructure utility (plumbing, gas piping, electrical, etc.), equipment, adjacencies, circulation, and collaboration opportunities.

The M2PC facility must integrate into the PNNL campus and will provide research and technologies that leverage existing research and infrastructure capabilities of the Environmental Molecular Science Laboratory (EMSL).

The M2PC facility will provide a modern showcase facility attached to the existing EMSL facility that is commensurate with the state of the art, high throughput biological automation processes taking place within. The capabilities provided will maximize the Research & Development (R&D) output, as well as foster communication and collaboration between the staff within the building, between M2PC and other facilities at PNNL, and with external research partners. A critical functional requirement of the M2PC that was identified throughout the workshop centered on the flow of data into, within, and out of the M2PC. EMSL, JGI, KBase, and the National Microbiome Data Collaborative (NMDC) were key resources that the M2PC must interact with seamlessly in both the provisioning of data analyses as well as experimental planning efforts.

The design will provide a broad degree of flexibility to support advancing future automation technologies, adapt to requirements for those technologies, and allow virtual access. Since phenotyping microorganisms requires a wide mix of diverse capabilities, the automation technologies will involve a wide mix of interconnected capabilities which greatly expands the experimental design space. As such, this high level of interconnectivity is a core design principle for the complete automated capability and allows for the rapid development of new workflows without the need for physical work cell reconfiguration. The facility design for this automated capability will use PNNL-developed standard laboratory modules and open flexible spaces to facilitate a reduction in potential renovation costs as labs are re-purposed or reconfigured to meet advancing technology demands in the future. For this, the M2PC must include the computing infrastructure (hardware, software, space, and operational staff) to facilitate these connections to the other BER resources, ensure their permanence, and broadly support the user community about experimental planning, data analyses, and coordination with EMSL, JGI, KBase, and NMDC within M2PC operations.

EMSL is positioned to facilitate the partnerships required for planning, capturing, and executing the correlative genomic sample collection and integrating into the analytical phenotyping platforms being designed in M2PC through the long-standing FICUS (Facilities Integrating Capabilities for User Science) program. Through FICUS, EMSL and the JGI have already established metadata workflows, operational logistics, and sample ID tracking. EMSL has a complete BER-focused computational infrastructure within the User Facility, including a state-

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Microbial Molecular Phenotyping Capability (M2PC) Conceptual Design Report 3 of-the-art HPC, associated long-term/permanent data archive, optical networks, data management, and associated IT and software engineers to optimally support the infrastructure. In addition, more than sufficient computing space exists for future expansion to meet the computing needs M2PC would require as designed.

As high throughput automation is the core component of the facility, attention to innovation, machine learning, and overall sustainability shall be incorporated into the M2PC. Areas of focus will be building siting and envelope configuration, materials usage, an easily reconfigurable format, and energy-efficient mechanical and electrical technologies.

2.1 Functional Requirements

Following approval of a Mission Need Statement, PNNL design staff began working with EMSL research staff and scientific communities through science workshops to ascertain more detailed requirements for an automated molecular phenotyping process. Many of the identified processes and capabilities of microbial research currently exist on the PNNL campus in traditional research methodologies. The M2PC aims to automate those processes at a scale beyond what exists at any other facility nationally. To accomplish this, the M2PC needs to be capable of high throughput, 24-hour, microbial production and assaying. As target microbes are identified and selected for further study, they will be transferred to high precision anylytical instruments within the M2PC facility or to other labs within EMSL, such as electron microscopy, high resolution mass spectrometry and nuclear magenetic resonces spectroscopy.

As such, the M2PC facility will include the ability to produce and analyze a broad range of microbes in a high throughput automated system. Initial requirements to meet the Mission Need Statement include achieving the following minimum functional requirements:

• The ability to demonstrate high throughput culturing with a minimum of 500 Design Build Test Learn (DBTL) strain starts per week.

• The ability to demonstrate high throughput culturing with a minimum of 100 microbiome strain starts per week.

• The ability to demonstrate high throughput assaying and phenotyping with a minimum of 1,000,000 data points per month.

• Demonstrate the ability to remotely design and execute culturing, assaying, and phenotyping.

• Provide an open, flexible, laboratory space to house and support automated equipment lines. This space is envisioned as approximately 12,000 square feet that can accommodate approximately 200 self-contained interconnected discreet automated instruments arranged to perform defined processes.

• Provide support spaces necessary to operate the automation lab. These should be programmed and planned based upon PNNLs standard laboratory module. They include short-term waste storage, centralized supplies and consumable accumulation, autoclave/glass-wash, sample prep cold room, freezer storage, automation equipment parts storage, and automation equipment development and testing and assembly area.

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• Provide between 4 to 10 touchdown workstations outside of the laboratory space for temporary work and meetings for M2PC staff.

• If sufficient funding is available, the M2PC could also contain o Non-automated high-end mass spectrometer(s) and associated lab space.

o Non-automated screening and high-resolution cryo-electron microscopes (cryo-

EM) that will occupy available space in the existing EMSL Q-wing.

o Non-automated high-end nuclear magnetic resonance (NMR) spectrometer(s) and associated lab spaces.

• The project shall also o Provide an extension to the existing EMSL facility that compliments the existing aesthetic.

o Provide a direct connection to the existing EMSL facility for circulation of staff and transportation of samples and supplies.

o Provide a broad degree of flexibility to support the ever-changing research projects and advancement in technology.

o Identify energy-efficient approaches and incorporate sustainable materials and methods (i.e., high-performance sustainable building principles)

Through space programming meetings and following peer review sessions and research, a tabular space program was created that focuses more on actual sizes and spaces required. The space program fulfills the intent of the Mission Needs Statement and creates a design baseline for the project. Detailed room data sheets and space program information are contained in Appendix C.

2.2 Cost Estimate

Regarding automation instruments, majority of these are off the shelf instruments that need to be assembled together in an automated loop. The cost for design, fabrication, installation and commissioning/acceptance testing of individual mobile systems with sample transport devices and collections are provided by Zymergen, Inc. and the basis can be found in Appendix A.

The integration cost estimate and scope were developed using recent examples of similar work at

PNNL.

The facility cost estimate is built up of direct labor and materials based off engineering sketches and layouts. Take-offs from the information is priced using the latest in-house prices and recent similar jobs as well as market feedback anywhere possible. Indirect costs are then applied on the coversheet to the direct costs and are either percentages or job cost build ups. See Appendix F for further details of each account.

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3.0 Project Description

3.1 Preliminary Project Assumptions

3.1.1 Geographic Siting and Location

The PNNL Campus around the EMSL facility had numerous sites that were evaluated in depth during CDR planning. Siting considerations included the ability to leverage existing research capabilities, proximity to existing utility infrastructure, the ability to leverage existing laboratory facility support spaces, future flexibility, site access, vibration impacts (on existing and the proposed facility), and architectural integration into the campus. See Section 4.2 of this document for the site selection criteria, analysis, and conclusion.

3.1.2 Interfaces with Existing and Planned Acquisitions

The proposed M2PC is articulated in and integrated with the overall PNNL Campus Strategy. A Memorandum of Understanding or equivalent will be prepared to ensure that any off-project interfaces, including relocation of existing or newly acquired equipment, are optimized.

3.1.3 Standardization Requirements

The project will be executed in accordance with applicable Public Laws, Executive Orders, Office of Management and Budget Circulars, Federal Property Management Regulations, and DOE Orders.

3.1.4 Goals for Limitations on Recurring or Operating Costs

The project’s objectives include creating a flexible automation design and accompanying facility spaces to allow for efficient reconfiguration to meet the scientific needs of today and the future.

Doing so in a federal asset on the PNNL Campus would limit reconfiguration costs and maximize research capabilities.

3.1.5 Affordability Limits on Investments

The primary TEC for the project will be accommodated within the planned out-year budgets of the Office of Science Biological and Energy Research Programs, subject to annual Congressional appropriations.

3.1.6 Stakeholder Considerations

The primary affected stakeholders include program management staff within the DOE Office of Science Biological and Energy Research programs, as their programs will be directly improved by the project’s outcomes. All stakeholders have been engaged and will continue to be engaged and consulted in the planning and analysis of the respective options, including programming of specific facilities. See 3.3 for the Key Stakeholders list.

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3.1.7 Technology Status and Engineering

The proposed work for the research automation and facility portions of the project will be accomplished with existing technology, robotics, programming, and facility technologies. This is not a one-of-a-kind capability. The project will use existing developed technology for both the automation equipment and facility; therefore, no research and development will be required.

3.1.8 One-for-One Replacement

The Office of Management and Budget "Reduce the Footprint" policy was reviewed and confirmed that demolition of federal space is not needed. The lab currently occupies a considerable amount of leased and private space. PNNL is committed to the intent of the policy, using existing space when available, and vacating space no longer required. This is further described in the M2PC Project Execution Plan.

3.2 Short-Form Project Description

The proposed project mission is to deliver high throughput automated equipment and specialized analytical equipment to meet the mission need. The facility will be approximately 49,095 square feet of enclosed space. Laboratory and support spaces will be single story with mechanical interstitial space. Initial programming indicates a minimum need for one automation bay and 10 lab modules. A minimum of 6 open office workstations will be included.

An automation laboratory will provide an open floor plan with highly flexible overhead utility layout. Support laboratory spaces will be based on a PNNL standard modular design, which provides for flexibility and can be adaptable to inevitable changes in research needs in the future.

In addition to the Automation laboratory, add alternate capabilities include dedicated mass spectrometry and NMR suites, totaling up to 4 additional lab modules.

A lobby space adjacent to the automation laboratory will serve as the main entrance to the facility while providing views into the automation laboratory. A direct connection from the lobby will be provided to the EMSL facility primary corridor for circulation of personnel.

Where capacity allows, existing EMSL services will be extended to the facility from the EMSL mechanical room. Services not provided from EMSL will be provided in new electrical, mechanical, and roof top spaces. The EMSL shipping and receiving area will serve this facility via a secondary circulation connection between EMSL and the facility.

3.3 Key Stakeholders

Name Title Paul Bayer Federal Program Manager Ron Gallagher Federal Project Director Douglas Mans EMSL Director Angus Bampton M2PC Project Advisor

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3.4 CDR Project Team Members

Name Title Sam Paulsen PNNL, Battelle Project Manager Theva Thevuthasan PNNL, Battelle R&D Project Manager Eliot Black PNNL, Battelle Technical Lead/Architect Matt Youngblood Zymergen Katie Kerpedjiev Zymergen Will Serber Zymergen Peter Kelly Zymergen Matthew Myers Zymergen Kari Jensen Burns & McDonnell, Lead Civil Anthony Gianpetro Burns & McDonnell, Lead Mechanical David Adams Burns & McDonnell, Project Manager Jeff Dew Burns & McDonnell, Lead Fire Protection Robert Heiller Burns & McDonnell, Lead Electrical Steve Worthington RMW, Lead Architect Hallie Travis RMW, Job Captain Stanley Lew RMW, Laboratory Planner

3.5 Key Performance Parameters

This CDR delivers on the draft Key Performance Parameters (KPPs), as they are envisioned prior to CD-1. Draft KPPs are listed in the Preliminary Project Execution Plan. In addition, the draft KPPs are captured within the functional requirements (section 2.1) related to high throughput culturing, assaying, and phenotyping, as well as the ability to remotely design and execute processes. No KPPs are envisioned as being associated with the conventional facility.

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4.0 Analysis of Alternatives

4.1 Overview

In preparation for CD-1, a formal DOE Analysis of Alternatives (AoA) was performed to select the preferred alternative from five options identified in the Mission Need Statement. Only two of these options were identified as viable during initial screening.

Table 4.1-1 Five Alternatives Identified and Analyzed

Alternative Viability Nonviable Description

1 Maintain Status Quo Nonviable This alternative is nonviable because it does not address the mission need.

2 Standalone Viable

3 Expansion Viable

4 Virtual Facility Nonviable This alternative is nonviable because automation levels 3 and 4 are needed for the M2PC capabilities that currently do not exist at DOE SC facilities.

5 Collaborate with Others Nonviable This alternative is nonviable because multiple collaborating facilities that would participate in hosting the M2PC would need to interact with multiple facilities to accomplish a task. The existing policies and policy differences between different user facilities and federal agencies add additional complications. These challenges do not help address the science gap described in the MNS.

4.2 DOE Site Selection

As part of the AoA process, an Analysis of Alternative Study Plan was developed to select the best DOE site for the M2PC. According to the Geographic Siting and Location requirements of the MNS, a DOE Site was to be selected by evaluating existing and relevant DOE SC User Facilities. Requirements for selection included sufficient expertise, capabilities, and management; proximity to existing facilities with multi-omics, structural biology, cellular imaging, and other microbial research capabilities; and existing space utilization planning.

The selected site for the two viable alternatives, based upon the above criteria, was the EMSL facility at the Pacific Northwest National Laboratory.

4.3 Lifecycle Cost Analysis

In performing the AoA, a Life Cycle Cost Analysis (LCCA) was executed to determine the net present value of the viable alternatives. A constant-dollar analysis based on the real interest rate obtained from the Office of Management and Budget (OMB) Circular A-94 Appendix C (November 2020 revision) was used for discounting constant-dollar flows. The study period for

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Microbial Molecular Phenotyping Capability (M2PC) Conceptual Design Report 9 the LCCA was 50 years, with a base year of 2023. Expenses analyzed associated with the New Facility Construction and Automated R&D Equipment included:

• Construction Cost

• Design, fabrication, purchase, installation, and commissioning of R&D automation equipment.

• Direct operations and maintenance (O&M).

• Research Operations.

• Productivity Loss

• Office moves

• Demolition at the end of useful life.

The expansion alternative resulted in the lowest net present life cycle cost for both facility construction and R&D automation equipment. Therefore, an expansion to EMSL was selected and approved by the AoA.

In order to select the best site around the EMSL facility, a detailed site selection was performed in S814057-RPT-14, Site Selection Study for Microbial Molecular Phenotyping Capability. The results of that study are summarized in Section 7.2 below.

5.0 Integration

This CDR includes two major components: R&D Experimental Automation Capabilities and the physical facility that will house these capabilities. A key focus of this CDR, and overall project, is integration of these two components. For CDR development, the Automation Team (Zymergen) coordinated utility, laboratory space, support space, and other requirements with the facility concept team led by Burns and McDonnell. This partnership, and associated inputs and outputs from each product are fully integrated into the conceptual design report and are captured in the estimated cost range.

Coordination is also paramount during the installation of the equipment and connection to the facility infrastructure. The integration scope includes design and installation of utility extensions (compressed gas, electrical, chilled water, local exhaust ventilation, etc.) from the facility to the automation and other R&D equipment that is installed after facility construction is completed.

This integration phase is accounted for in development of the cost range as a separate cost element (Section 10.3). Battelle will lead the integration effort to ensure the design, installation, testing, and commissioning of both the automation equipment and facility deliver on the mission need.

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6.0 Experimental and Automation Capabilities

6.1 Introduction

The microbial molecular phenotyping capability (M2PC) facility is envisioned to be a highly autonomous, high throughput phenotyping facility that allows researchers to develop a mechanistic understanding of biological activity and function across a broad range of microbes, microbial communities, and experimental conditions.

Such a capability has never existed at this scale before, in large part because of the breadth of the experimental landscape required to assess it. Enormous increases in scale and reductions in costs of genotyping workflows have been achieved in part due to the linear nature of these workflows.

However, unlike genotyping workflows, phenotyping workflows are highly non-linear and less amenable to traditional principles of scaling. In order to obtain relevant phenotyping information, an organism must both be: induced into the right physiological state by manipulating its cultivation conditions; and interrogated with one or several analytical techniques, each likely requiring unique sample preparation. A complete phenotyping experiment may require that each of the thousands of genotypes possible in a single organism are exposed to unique combinations of all of these factors.

To phenotype in high throughput is thus a challenge of diversity in addition to a challenge of throughput. Never before has an autonomous facility connected the wide range of instruments and capabilities necessary to enable this broad experimental search, nor has this capability been paired with a software that is flexible enough to manage samples traveling through the full diversity of experimental paths.

6.1.1 Automation Conceptual Design Report Structure

This part of conceptual design report was prepared by Zymergen, while integrating requirements, inputs, and outputs with Burns & McDonnell and the Battelle project team. It begins with a discussion of the high-level attributes necessary to develop a high throughput phenotyping facility.

The overall scientific needs of the capability are broken into five dynamically interconnected core scientific functions. The conceptual design describes the specific design guiding principles in each of these five areas:

• Media

• Cultivation

• Sample Preparation

• Analytics

• Strain Engineering

Specific considerations necessary to handle niche organisms and/or experimental conditions are highlighted separately.

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6.1.2 Definitions

6.1.2.1 Automation System Terms

● Integrated Device- A laboratory instrument that is capable of receiving samples delivered automatically by a centralized transport system.

● Pod- A collection of integrated devices grouped together to reduce transport distance or concentrate a particular utility common to those devices

● Automation system- A system of connected integrated devices that can perform one or many laboratory workflows. The automation system is organized into discrete Pods, but all Pods are interconnected.

● M2PC Facility- The collection of labs and support spaces located in the new facility being built for the M2PC program. Includes the Automation system.

● Protocol- Reusable sequences of automated steps with a common set of parameters that can be scheduled together. One or more protocols may be combined in sequence, with supporting data and human interaction steps, to make up a biological workflow.

● Workflow- A collection of biological process steps to be performed in a specific order to achieve a meaningful chemical or data end product.

● Protocol run- An individual instance of a protocol that is scheduled and realized as physical actions. Multiple protocol runs can occur simultaneously.

● SBS format- Scientific labware matching the standard dimensions set out by the Society For Laboratory Automation And Screening- SLAS (the former name of this organization was Society of Biomolecular Screening (SBS)).

● Intrinsic Safety- A principle that it is better to have a device that cannot harm a user in the first place than a protection mechanism around a harmful device. Originally employed in electrical system design, this concept is now commonly applied in other disciplines such as robotics (Steijn, Wouter & Luiijf, Eric & Beek, Dolf. (2016).

Emergent risk to workplace safety as a result of the use of robots in the work place (R11488). Report prepared by TNO for the Netherlands Ministry of Social Affairs and Employment).

● Offline- Devices that are not fully integrated into the automation system. These devices typically require manual transport of samples between them and other offline devices or the automation system.

● BSL-2- Biosafety level 2. A set of considerations defined by the CDC and NIH for working with “agents associated with human disease and that pose moderate hazards to personnel and the environment”

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6.2 System-wide Design Considerations

6.2.1 Hardware Design Guiding Principles

6.2.1.1 Interconnecitvity

Phenotyping microorganisms requires a wide mix of capabilities; therefore, as many diverse capabilities should be fully and dynamically interconnected as possible. This high level of interconnectivity is a core design principle for the automated system. In practice, this high interconnectivity not only allows for the rapid development of new workflows without the need for physical work cell reconfiguration but also reduces the number of instruments needed to execute a wide range of workflows. Dynamic assignment of instruments across the system should be seamless and should not impair or slow the execution of a protocol in a way that compromises the experiment (i.e.. a sample must arrive at an instrument on the other side of the automation system quickly enough that the overall throughput of the workflow is not meaningfully reduced as compared to routing to an adjacent instrument).

A wide mix of interconnected capabilities also greatly expands the experimental design space that is explorable for each system being studied- leading to the unlocking of massive amounts of fundamental knowledge across greater microbial systems.

It is not feasible or practical to integrate 100% of devices within the facility into the automated system. The integrator should recognize this by including easy offramps from the automated processes to manually operated ones. The operations and instruments that are not integrated into the complete automation system should be specifically highlighted.

6.2.1.2 Sterility

The nature of M2PC’s proposed biological workflows necessitates that a sterile environment is maintained wherever viable samples are present. As a result, appropriate environmental control measures are recommended to protect samples from contamination. This likely includes HEPA filtered enclosures surrounding most integrated devices and covered transport passageways for any instrument-to-instrument connection systems.

6.2.1.3 Safety

The M2PC facility is intended to be staffed by research and support personnel who likely will not have prior experience with, or qualifications for maintaining, installing, or interacting with industrial robotics. As a result, all elements of the automated system relating to sample transport should satisfy at least one of the following criteria:

1. sourced from within the life science space;

2. certified ‘collaborative’ as defined under ISO/TS 15066:2016 or an equivalent recognized standard

3. selected or engineered to provide a standard of “Intrinsic Safety,” both for operators and for maintenance personnel.

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Intrinsically hazardous industrial robots and transport mechanisms should be avoided throughout M2PC, regardless of the installation of protections such as those defined under industry standards such as ISO 10218-1:2011 and ISO 10218-2:2011. This is for the benefit of providing intrinsically safe conditions for system maintenance personnel.

Physical access to the inside of work cells, enclosures, or other spaces occupied by automation equipment should be mechanically or electrically limited to approved technical personnel.

Access to these spaces should be dynamically granted to support personnel without interrupting the work of adjacent instruments. For example: it should be possible for support personnel to replace consumables or remove waste during active system operation without stopping the execution of workflows at the system-level or pod-levels and without exposing the support personnel to equipment that might create a physical hazard. Additionally, any instrument or instrument control unit within a work cell or enclosure should be able to be removed or serviced without stopping the execution of workflows.

6.2.1.4 Reconfigurability and Flexibilty

Scientific technology changes quickly, and a key factor for the successful operation of this facility will be the ability to easily expand and integrate emerging technologies and adapt to new workflows. With that in mind, the automated system should have the ability to quickly switch out devices from the system or expand the entire system by adding additional devices with minimal downtime or redesign work. In addition the workflow mix on the system is expected to change over time, so ‘locked in’ device arrangements specific to some workflow that exists today should be avoided.

6.2.1.5 High Uptime

For a user facility, high-uptime is critical because down-time can result in damage to time-sensitive samples, backup of work, and missed timelines. The hardware should promote a high uptime by having the following characteristics:

• Fast equipment exchange- The system should allow for exchanging equipment without needing extensive reconfigurations and/or reteaching of instrument locations.

• Continued operations in the event of a power failure- The facility that houses the automation should support the operations with sufficient standby and UPS power systems so that work would continue in the event of a power failure.

6.2.1.6 Hardware Conceptual Approach

With the above design guiding principles in mind, Zymergen recommends that any implementation adhere to the following conceptual architecture:

6.2.1.7 Pods

Instruments that commonly work together as part of a single workflow should be grouped together to form ‘Pods’. These pods should be designed to reduce transportation distance and to concentrate particular and/or special utilities together (for example, in the case of BSL-2 controlled operations - see the BSL-2 Considerations section below for more details).

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6.2.1.8 Automation System

Pods should be linked together to form a complete automated system. Samples, contained in SBS format labware, should move automatically and dynamically between instruments and between pods. When scheduling, devices within a pod should be preferentially chosen to minimize transport distance, however utilizing devices in other pods should still be possible to maximize the benefits of interconnectivity.

Instruments should be housed in enclosures or work cells that are designed with safety, ergonomics, and serviceability in mind. These housings should include standardized data and utility connections. It is strongly recommended that new instruments be interchangeable into these standard form factors with only minor updates and at minimal expense. Adherence to this modular approach to hardware design would allow system architects to quickly retire old instruments and replace them with new ones (with equivalent or different functions), which in turn facilitates easy adoption of emerging technologies.

Where possible, the mass spectrometry instruments should be located near the entrance to the service corridor so that pumps and chillers that can generate a lot of noise and heat can be removed from the main lab and placed in the service corridor. In addition, specialty gasses for the mass spectrometers will be located in the service corridor, so this will reduce the gas transportation distance. Media/support instruments should be located close to the lab entrances for easy access to the media prep and consumables support spaces.

6.3 Software Considerations

6.3.1 Software Design Guiding Principles

6.3.1.1 Parameterization

Protocols that will run on the system should be designed to be fully parameterizable. This allows a user of the system the widest possible design space from which to create an experiment by allowing each parameter of a protocol to be varied.

6.3.1.2 Interleaved and Dynamic Scheduling

The M2PC facility is recommended to run a high mix of workflows at a high throughput across shared equipment. The scheduling software used should be capable of receiving and scheduling new protocol run submissions while the system is already in the process of executing existing protocol runs. In addition, the software should support human interaction with storage devices during protocol run execution to allow for the manual addition or removal of labware. Further, the system should be capable of running multiple protocol runs of different types simultaneously, interleaving protocol runs to maximize system throughput.

The system shall be capable of dynamically rescheduling in response to new protocol run submissions, addition/removal of labware, and errors/slowdowns/accelerations resulting from physical execution of protocol runs. Because the system requires multiple instances of certain devices to accomplish the throughput necessary, it should also be possible to dynamically re-route samples to any instance of a given device based on availability at time of scheduling.

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6.3.1.3 Reconfigurability

Reconfiguration of the system should be just as easy to achieve in software as was described in the hardware guiding principles. A reconfigured physical system should be able to be updated accordingly within the software system within minutes, using a graphical user interface.

6.3.1.4 Security and Safety Considerations

Several different types of personnel are expected to interact with automation systems in the M2PC with different objectives. The software should therefore be capable of supporting different user classes for the system. Permission to perform specific actions on the system, such as programmatically reconfiguring the system, submitting protocol runs, starting/pausing system execution, and controlling individual devices could be granted based on membership in certain user class groups.

In addition to these security considerations, ideally the software system would work with hardware to ensure the safety of personnel who may physically interact with the system.

6.3.1.5 Error Recovery and Remote Resolutions

To facilitate error identification, the software system should be capable of emitting error messages that are easily consumed by external tools used for monitoring and alerting purposes.

In addition, the system should be designed to facilitate remote error recovery whenever possible, such as remotely restarting and re-initializing devices. Finally, in the event that a protocol run is deemed non-recoverable, the system should facilitate the ability to cancel and clean up individual protocol runs without affecting the execution of any concurrent protocol runs.

6.3.1.6 High Uptime

For a user facility, high-uptime is critical because down-time can result in damage to time-sensitive samples, backup of work, and missed timelines. The scheduler should enable the following characteristics:

● Low downtime during routine maintenance- The scheduler should allow work to continue progressing while an individual…