HTP-APP_Industry Day Presentation.pdf

M2PC Project Overview

Sam Paulsen Project Manager

Agenda

Project Organization

Plan: Scope, schedule, and budget

Project Status

Challenges

Documentation to Review

Approved scope: Key performance parameters

*The planning basis was refined from CDR to align with the threshold KPPs

Description of Scope *Threshold KPP Objective KPP

Demonstrate HTP culturing of microbial isolates and consortia

Capacity to operate M2PC with 500 strain experiments per week

Capacity to operate M2PC with 2000 strain experiments per week

Capacity to operate M2PC with 100 microbiome experiments per week

Capacity to operate M2PC with 500 microbiome experiments per week

Demonstrate HTP assaying and phenotyping of microbial isolates and consortia

Capacity to operate M2PC to obtain 1,000,000 multimodal analytical measurements per month

Capacity to operate M2PC to obtain 3,000,000 multimodal analytical measurements per month

Provide capability for remote planning and operations

Demonstrate that remote users can run pre-defined EMSL protocols to be executed autonomously within M2PC across culturing, assaying, and analyses

Demonstrate that remote users can perform dynamic experimental intervention with help from EMSL staff by modifying an executed protocol during the experimental timeframe

Facility 24,500 sq. ft. 50,000 sq. ft.

Scope statement: Provide a high-throughput microbial molecular phenotyping capability and a facility that houses and supports the capability.

M2PC Acquisition Strategy (and Facility) – Procurement Lead Garrett Hyatt – Acquisition Lead Specialist

High-Throughput Phenotyping – Procurement Lead Samantha Ernst – Acquisition Lead Specialist

Integration of the two procurements is key Working to a single, integrated schedule

• High-throughput phenotyping specifications will include integration with design build contractor. Includes facility constraints.

• Design

• Install

• Facility specifications will include integration with the high-throughput phenotyping contractor. Defines facility constraints.

• Design

• Construction

M2PC requires two major procurements

The M2PC will be a single facility focused on microbial molecular phenotyping

It requires two major procurements to complete

Solicitations timed to support award shortly after CD 2/3

Automation laboratory facility coordination

N

Characteristic Value/Constraint Comments

Automation lab size 12,000 ft2

Utilities location Fed from Overhead

120V & 208V Power Defined density in P- Spec

Actual locations will be adjusted during design

Exotic power Not provided HTP-APP contractor would need to provide transformers for exotic power

CA, N2, Vac Defined density in P- Spec

Actual locations will be adjusted during design

Vacuum exhaust, direct exhaust, snorkels

Defined density in P- Spec

Actual locations will be adjusted during design

Heat load TBD BTU/hr Verified during design

Partnering with facility contractor

• Design & schedule

• Facility requirements for the system

Automation laboratory facility coordination

M2PC Project R&D Technical Overview

Theva Thevuthasan Project Manager

Performance Requirements

Agenda

Various Requirements

KPPs and KPPs - Stretch Goals

System Testing and Training

Performance Requirements/ Specifications

Key performance parameters requirements

Science core functions

General system requirements

Scheduling software requirements

Safety requirements

Testing, training and operations

Mission needs

Science workshop

Design Guiding Principles

Discussion w/ potential users

Conceptual design

Science Core Functions

Five dynamically interconnected core scientific functions are required as foundations to formulate the concept to achieve those KPPs:

• Media

• Cultivation

• Sample preparation

• Analytical capabilities

• Strain engineering

Project KPPs

KPP# KPP title KPP threshold, minimum requirement

KPP 1

Demonstrate HTP culturing of microbial isolates and consortia

(i)Capacity to operate M2PC with execution of 500 new strain experiments per week.

(ii)Capacity to operate M2PC with execution of 100 new microbiome experiments per week.

KPP 2

Demonstrate HTP assaying and phenotyping of microbial isolates and consortia.

Capacity to operate M2PC to obtain 1,000,000 multimodal analytical measurements per month.

KPP 3

Provide capability for remote planning and operations.

Demonstrate that remote users/operators can run pre-defined EMSL protocols to be executed autonomously within M2PC across culturing, assaying, and analyses.

Minimum throughputs required to meet the project scope requirements

KPPs Stretch Goals Increase throughputs within the available contract cost

Stretch Stretch Title Stretch Requirement

#1

Exceed Threshold KPP#1 and KPP#2 by 25%

KPP #1(i): Provide a minimum of 850 strain experiments per week

KPP #1(ii): Provide a minimum of 200 microbiome experiments per week

KPP #2: Provide a minimum of 1,500,000 multimodal analytical measurements per month.

#2

Exceed Threshold KPP#1 and KPP#2 by 50%

KPP #1(i): Provide a minimum of 1250 strain experiments per week

KPP #1(ii): Provide a minimum of 300 microbiome experiments per week

KPP #2: Provide a minimum of 2,000,000 multimodal analytical measurements per month

#3

Exceed Threshold KPP#1 and KPP#2 up to Objective KPPs

KPP #1(i): Provide 2000 strain experiments per week

KPP #1(ii): Provide 500 microbiome experiments per week

KPP #2: Provide 3,000,000 multimodal analytical measurements per month

KPP 1 Testing

Strain Experiments

•Constructing mutant plasmids to create a test panel

•Transforming plasmids to create engineered microbial strains

•Cultivating strains across different media, nutrient/metals & carbon sources, temperatures, pH, etc. - analyzing their growth

Example

•Construct 500 single or multiple gene knockout/up-regulated constructs

•Use 12 replicates of each

•Grow each in 4 media types with 2 different carbon sources

•Test growth at multiple time points

•Total of 500 “experiments” performed in 500 96-well plates at multiple time points

Microbiome Experiments

•Creating communities of one or more unique microbes in varying proportions and a variety of media/growth conditions

•Perturbations - temperature range, pH range, various metal ion concentrations, primary or secondary metabolites and different carbon and/or nitrogen sources.

KPP 2 Testing

Multimodal Analysis

• Capturing scientifically relevant data

- during the growth of microorganisms

- functional responses associated with experimental perturbations

- after sample processing/preparation

Example

• Various spectroscopy and spectrometry measurements can be carried out to characterize the growth and processed samples.

• Cell characteristics including cell size, cell count and cell cycle can be measured using spectral and image cytometry.

• Characterization using Gas chromatography (GC) or Liquid chromatography (LC) coupled with UV, fluorescence detection (FLD), mass spectrometry (MS), or refractive index detection (RID) to detect the chemical components.

• Characterization using automated microscopy.

General requirements Minimum requirements for the complete system

Modular

• Replace broken or old instruments

• Incorporate emerging technologies

• Minimize system downtime

Flexible

• Flexibility to move instruments

• Flexibility to move processes

Expandable

• Adaptable for future technologies

• Expand the components with minimum disturbance minimum

Scheduling software requirements

Scheduling Software

• Parameterization of protocols

• Interleaved dynamic scheduling – protocols run in parallel

• Error recovery – location of the error and remote resolutions

• Reconfiguring - updated accordingly within the software system within minutes

• Security and Safety - accessibility by operators and different classes of users

• High uptime and Simulation – should be able to simulate a workflow

• Operable with EMSL data management and LIMS system

Scheduling software needs to interact with:

• EMSL LIMS – L7 Enterprise Science Platfrom

• Experimental intention tools

• Design engine – combine LIMS information with experimental intentions

• Data processing engine - Data produced by the system would be ingested and processed before loading the results back into the LIMS

Safety measures

Environmental Safety and Health

Bio Safety - BSL-2

Robotics Safety (intrinsically safe per consensus standards)

Electrical safety

NRTL, UL, CSA … certified instruments and electrical components

Testing, training and operations

System testing

• Factory acceptance testing

• Functional testing (Installed)

• KPP verification testing (Witnessed by 3rd Party Commissioning Agent and Battelle team)

Training to our staff

• Number of staff

• Length

One-year operations

• Warranty for one year

• Consumables for one year

Hardware redundancy

• 5%?

RFI Overview

Samantha Ernst

HTP-APP RFI Package

• Request for Information (RFI)/Sources Sought

• Technical Brief

• DRAFT Request for Proposal (RFP) including Draft Contract

• Draft Proposal Submission Requirements

• Draft Evaluation Criteria

• Draft Price Proposal Worksheet

It is currently publicly posted to:

• SAM.gov

• PNNL’s Acquisition Supplier Portal (ASP)

Will be used to gather market research, gauge interest from potential offerors, and potentially refine our Request for Proposal (RFP) for the

M2PC HTP-APP

M2PC HTP-APP - RFI Overview

Acquisition Strategy & Characteristics

• Procure a fully operational system that is designed, fabricated, installed, and tested.

• System includes software, integration hardware, BSL-2 enclosure(s), OTS equipment

• HTP-APP and facility design proceeds concurrently, each informing the other throughout the design process

• Facility construction will have a “ready for equipment” milestone that triggers the ability to start installation of the

HTP-APP

• 3rd Party Commissioning Agent for HTP-APP to verify system meets capability and throughput requirements

• Procured by Battelle via separate subcontract

M2PC HTP-APP

Acquisition Strategy

Acquisition Strategy & Characteristics cont.

• Firm Fixed Price Contract with Set Price between $40M and $50M

• Minimum requirements plus stretch goals that can be met within the set contract amount are the basis for award

• Two-Step, Best Value, Source Selection

• Proposals Evaluated in accordance with an approved Source

Selection Plan (SSP) and established Evaluation Criteria in the

RFP

• 2 Phase Review and Approval required by DOE-PNSO &

DOE HCA-IRB

• Acquisition Plan & Request for Proposal

• Contract Award

M2PC HTP-APP

Acquisition Strategy

M2PC HTP-APP

Source Selection

Source Selection

Approach: Two-Step, “Best Value”, Source Selection

Step 1: Review and Evaluation of all Offerors Received Verify Mandatory Go/No-Go Requirements are Met Evaluate & Score Step 1 Technical Proposals – no concept Top 3 Offerors Advance to Step 2

Step 2: Evaluation of Highest Qualified Offerors Conduct Oral Presentations/Interviews Evaluate & Score Step 2 Technical (conceptual design) and Price

Proposals Stipends to the unsuccessful Step 2 Offerors

Basis of Award: Best Value Contract award will be made to the Offeror with the highest evaluated proposal for Step 2 who’s determined to be the “best value"

Draft Request for Proposal (RFP)

Key Elements and Structure Scope Overview Basis of Award o 2-Step, Source Selection o Stipends (for Step 2 Unsuccessful Offers) o Set Contract Price and Funding Profile

Proposal Submission Instructions Evaluation Criteria o Mandatory Go/No-Go Requirements o Technical o Pricing – Inclusion of Stretch Goals

Additional Instructions/Information Attachments – Not provided with Draft RFP o Performance Specification o General Requirements o Conceptual Design Report (Reference Only)

Draft Contract o Contract Clauses & Requirements o Terms and Conditions

M2PC HTP-APP

Draft Request for Proposal

RFP will be finalized following the receipt of RFI responses and Draft RFP comments

Following DOE approval of the RFP, it will be broadly shared & publicly posted via:

• SAM.gov

• PNNL’s Acquisition Supplier Portal (ASP)

• Email to RFI Respondents

Request for Proposal (RFP) / Solicitation

Challenges / Areas of Interest

• Interest and Capability Statements

• Commerciality

• Proposal Durations – 20 business days for Step 1 and 30 business days for Step 2 and validity period

• Stipends – amount

• Progress Payments –milestones vs.

schedule of values

• Evaluation Criteria – clear, sufficient and appropriate?

• Funding Constraints

• Stretch Goals – evaluation and pricing

RFI Response

• Thoroughly review the RFI and Technical Brief

• Provide company capability statement and responses to items 1 though 6

Draft RFP Comments

• Thoroughly review the Draft RFP and associated attachments

• Provide comments/responses to items 1 through 12

Submit via email to Samantha.Ernst@pnnl.gov

Due by 4:00pm Pacific Time on June 11, 2024

15 Page Maximum

RFI & Draft RFP Response Requirements mailto:Samantha.Ernst@pnnl.gov