HTP-APP_RFP_Amendment 2.pdf

RFP 843396

January 20, 2025

RFP 843396: AMENDMENT No. 2

Amendments/Changes/Clarifications

Project: Microbial Molecular Phenotyping Capability (M2PC)

High-Throughput Automated Phenotyping Platform (HTP-APP)

RFP ISSUE DATE: December 9, 2024

RFP No. 843396 is hereby modified with the following:

This amendment revises the RFP to formally include the specified due date:

Step 2 Question Due Date: 4:00 pm PT, March 7, 2025

1. The Question Due Date for Step 2 proposals has been added and and shall be 4:00 pm PT, March 7, 2025.

This amendment also provides Offeror questions and Battelle’s answers. See attachment HTP-APP_RFP_Amendment

2_Q&A.

End of Amendment 2

The above stated revisions are the only changes being made at this time.

Failure to acknowledge receipt of this amendment with submittal of your Offer could be cause to reject your offer. All other requirements of the RFP remain as originally stated.

Thank you, Samantha Ernst

Senior Contract Specialist cc: File, Bidders List

Attachments:

1. HTP-APP_RFP_Amendment 2_Q&A

RFP 843396

Amendment 2

Questions and Answers

General Response 1: The proposed system is intended to enable new R&D workflows and is not a system to automate existing production workflows. To be successful, it is more important to support a variety of capabilities than to hit specific throughput numbers/performance metrics in any one capability. Criteria, where provided throughout the performance specification, are to define lower boundaries for capacity and quality so vendors can propose a solution that meet the KPPs.

General Response 2: Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification.

Refer to Appendix A for the deliverable schedule. For the the proposal, base calculations on the example workflows given in the Performance Specification Appendix D.

General Response 3: A detailed conceptual design is not being evaluated as part of the Step 1 proposal. The Step 1 proposal concept should indicate the high-level approach and solution unique to the proposed contractor/contractor team. Step 1 proposals will be evaluated against the Step 1 criteria defined in the RFP (e.g., past performance, past project experience, technical approach to solving the problem, management systems, key personnel, teaming approach).

General Response 4: Detailed questions about Offeror’s proposed solutions cannot be commented on as part of the RFP process. The design solutions presented by the Offeror in the proposals will be evaluated versus the source selection criteria. The Offeror shall meet the minimum performance criteria in the P-spec, and in the conceptual design included in the Step 2 proposal, describe how the Offeror’s proposal optimizes and exceeds the minimum criteria in their best value proposal.

General Response 5: Where feasible, the contractor is encouraged to provide capabilities to exceed the minimum base requirements defined in the Performance Specification.

General Response 6: Many of the questions posed are in excess of the amount of detail needed to complete the Step 1, high-level, concept and approach to performing the HTP- APP design. Offeror’s that are selected for Step 2 proposals will have a chance to submit questions commensurate with the detail necessary to develop the Step 2 conceptual design as part of their proposals.

Question Answer # How long should the devices run independently? How long should the machines work per day (8h/12h/24h)?

For proposal purposes (and KPP throughput calculation/models), assume the system will run for 24 hours straight for 7 days a week, inclusive of planned down-time.

Actual operational parameters will be refined after contract award during definitive design.

The proposal has throughput requirements, but these are not set in the context of a system or instrument uptime. What instrument uptime assumption should be used, recognizing that no real-world system has 100% uptime. It will be beneficial for offerors to have uniform guidance on this such that apples-to-apples comparisons may be made given that actual estimates/measurements of system uptime could not yet be provided at this early stage.

For proposal purposes (and KPP throughput calculation/models), assume the system will run for 24 hours straight for 7 days a week, inclusive of planned down-time.

Actual operational parameters will be refined after contract award during definitive design.

Throughput requires an understanding of timing, and timing requires an understanding of the specific workflow. While we recognize processes in the strain engineering such as gene editing or CRISPR, DNA or RNA extraction and library preparation for sequencing as possible workflows, depending on the specific commercial kits selected (or homebrew protocol utilized), the times for running these workflows could vary significantly depending on the assumptions made in the model based on which workflows are used as the reference, thus altering the achieved throughput. Are there reference kits representative of the desired workflows you could suggest, such that offerors can calculate their estimates of throughput based on a uniform set of inputs enabling an apples-to-apples comparison of vendor proposals?

The HTP-APP should be able to accommodate multiple strain engineering methods. Provide details of the method and assumptions you use to make your calculations in the Step 2 proposal, if applicable.

Please define your meaning of experiment.

Could you provide more clarity on the example provided for the first KPP of 500 new strain experiments per week and what is defined as an experiment?

In the example "500 single of multiple gene constructs are created", is each attempt to create a single, new gene construct considered an experiment?

The documents say a “total of 500 experiments” performed in 500 96-well plates at multiple time points. Is each plate considered an experiment or is each individual well considered an experiment?

If there are different constructs within a single 96-well plate (for example, 8 strains at 12 replicates or 8 strains/plate), is each construct considered its own experiment?

Refer to the strain experiment definition included in the table included in P-Spec Section 4.1.1.

Each attempt to create a single, new gene construct IS NOT considered an experiment.

In the specific example cited, each plate would be considered an experiment.

Appendix D and this example are provided to aid the Offerors in appropriately sizing and scoping the system. This is not inclusive of all capabilities required in the performance specification. Refer to General Response 1.

Can we get more details on what the lab is defining as the input and the type of labware it will be in? For example, when creating new constructs, are the starting bacteria stored in frozen 96-well plates or tubes? Are the oligos and plasmids stored in tubes or plates? Any other material starting labware we need to be aware? What conditions do the inputs need to be stored?

Assume plates and tubes in SBS format racks will be used on the system in an automated fashion, and non-SBS format containers will be loaded onto the system manually (e.g. 1L glass media bottles).

See section 4.3 for more details.

Samples and reagents need to be kept stable, see section 4.3 for storage requirements for each science core function.

Do Offerors need to be set up as an approved vendor prior to submitting "Intent to Propose"?

No. Offerors do not need to be set up as an approved vendor prior to submitting their "Intent to Propose". The successful Offeror will receive an invitation to register in the PNNL Vendor portal during the contracting award process, and no action is required before the invitation is sent.

For Step 1, could you provide the rubric on which the technical submittals are being evaluated?

No rubric will be provided. However, the following technical evaluation criteria are all of equal significance and importance: Past Performance/Project Experience, Design Concept and Technical Approach, Management Systems, Key Personnel, and Teaming Approach.

For Step 1, what technical information is needed and being evaluated to assess concept throughput?

A detailed conceptual design is not being evaluated as part of the Step 1 proposal. Indicate with the step 1 proposal the high-level approach and solution unique to the proposed contractor/contractor team.

Given the scale of this project, will Battelle visit the selected Offerors to understand their level of experience in the integration of equipment, approach to Program Management, and ability to execute complex/large scale programs?

Site visits are not planned as part of the Step 1 or Step 2 evaluation.

In-Person interviews will be performed with the top 3 Offerors as part of Step 2. This will include interviews and software demonstrations.

"At least 1/3 of the cultivation incubators shall be fully integrated with the automation system" does this mean that the automation provider must supply equipment in in the scope of the automation?

What other equipment should be supplied that will not be directly connected with the main automation units?

The contractor shall provide incubators necessary to achieve the performance metrics committed to in the contract. At least 1/3 of the incubators shall be integrated to the automation system, and those that are not included in the integrated shall be provided offline.

"Systems capable of real-time ODs, so that growth kinetics can be observed without disturbing the physiology, are acceptable" is this required for every culture and in 96 well plates? What does it mean to not disturb physiology?

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

Who will be responsible for getting new consumables into the system?

The contractor is responsible for demonstrating KPPs and completing the acceptance testing, including necessary consumables.

After system acceptance, operators will manually load consumables.

Are the Offerors responsible to provide the offline equipment that is referenced (e.g., 4.3.3.7.10)?

The offeror is not responsible for providing offline NMRs, High Field FTIS MS, or Cryo EM’s. The offeror is responsible to enable the ability to prepare samples for existing tools at EMSL.

Could you provide information on the level of staffing of the laboratory during the Monday-Friday workweek, and also how the laboratory is staffed on the weekend or after hours?

Is the automation to run 24/7?

For the purpose of Step 1 proposal, refer to previous responses. 14

Are the servers for electronic data storage part of scope? Outside of the HTP-APP requiring storage capacity to operate the system components, devices, and software, data storage will be supplied by existing EMSL data infrastructure storage. Refer to the P- Spec. Examples 4.5.10 and Appendix E.

In section 4.1.1 of the Performance Specification our understanding is that the KPP around "500 New Strain Experiments" is to have sufficient capacity to construct 500 strains (and that phenotyping those strains is the focus of the KPP in 4.1.2 around 1,000,000 data points). However, the example provided mentions having 500 96-well plates. Is the requirement that we construct 500 new strains or test 500 plates? Similarly, is the stretch goal to construct 1000 strains or to test 1000 plates?

Refer to previous response regarding the similar topic. 16

From reading the RFP, it appears that the Battelle team require the integration partner to be more than just an integrator; with Battelle suggesting the integrator to be responsible for device selection, device training, and scientific outcomes (biological testing). Can you please comment on whether we have understood this correctly.

Refer to P-Spec section 2.2.1 and 4.2.7 for requirements for the contractor to collaborate with Battelle throughout the design process.

The scientific outcomes are not part of the project. However, there are exemplar workflows, functional testing, and KPP verification testing that will run specific known biological workflows to prove the system operates as intended/designed.

What is the Battelle team’s role in this automation initiative? Please describe the ideal relationship between Battelle and its integration partner.

Refer to P-Spec section 2.2.1 and 4.2.7 for requirements for the contractor to collaborate with Battelle throughout the design process.

Refer to the General Requirements document (S814057-SPEC-01) for required coordination meetings between the HTP-APP contractor, the facility contractor, Battelle, and others.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule

For integration projects it is common for scientists, who are experts in their field, to confirm that devices meet scientific requirements.

Can you please confirm if the Battelle team will take ownership of the final device selection?

Refer to P-Spec section 2.2.1 and 4.2.7 for requirements for the contractor to collaborate with Battelle throughout the design process.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule

The system design, including device selection, will be a collaborative effort between the Battelle team and the selected HTP-APP contractor. Battelle will approve the final design; however, meeting the KPPs and performance metrics committed to in the Step 2 proposals/contract is the responsibility of the HTP-APP contractor.

Typically our clients are responsible for the device methods to support their science. Our expectation is that Battelle staff will be responsible for method creation on devices to be integrated, please confirm (note that we understand the requirement to provide training for Battelle employee enablement).

Requirements are defined in the Performance Specification and other RFP documents. Refer to the sections in the performance specification related to software requirements (e.g., 4.4, 4.5). The requirements in the P-Spec and general requirements document will govern, and in this case, they appear to differ from the stated expectation.

Can you please elaborate on the ideal LIMS integration approach. For example, we can provide the API to allow Battelle to self-integrate, LIMS integration and design requirements are covered in detail in the performance specification.

or we can work with L7 (or others as needed) to directly integrate.

We want to plan resourcing accordingly, and your response will help.

If we identify a more economical option to meet requirements for under $47m will that be advantageous?

The contractor is encouraged to provide capabilities to exceed the minimum base requirements, including stretch goals, defined in the Performance Specification, to achieve the best system possible for $47M.

While it is clear the contract is a fixed price, is there an opportunity to include a change order (or equivalent) if the project scope changes during the duration of the partnership? For example if Battelle request a third party device type and quantity to change during the implementation phase how would that be handled under the fixed price approach?

Should a change to the contract requirements or project scope be determined necessary, it may result in a change order in which case a firm fixed price proposal will be required, evaluated, and negotiated and a subsequent contract modification will be issued.

Will this be a single PO, or multiple POs against each milestone funding schedule?

This will be a single PO/Contract, multiple POs will not be issued. 24

Please elaborate on the surety requirement. In our experience, the customer should pay into the surety to demonstrate sufficient funds are available to pay for the multiphased project. If we’re understanding correctly, Battelle are expecting the integrator to incur project cost, and put $3m into a surety. What is the intent of the surety?

Offerors who advance to Step 2 are required to furnish a bid bond/guarantee in the amount of $3M as part of their Step 2 Volume IV proposal. Battelle is requiring this as a means to ensure the Offeror has the financial means to accept the project and to provide a guarantee that the Offeror will perform the contract if selected.

Section 7 doc “BATTELLE MEMORIAL INSTITUTE, PACIFIC

NORTHWEST DIVISION'S REQUEST FOR PROPOSAL NUMBER 843396.

“Funding is not fully obligated”. If no one wins the award, does everyone receive a stipend for their Phase 2 bid response

Although not anticipated, if no one were to win and no subsequent contract was awarded, then all 3 Offerors who submit technically acceptable Step 2 proposals would receive the stipend.

Can you please comment on the staffed hours at Battelle such that we can plan operator involvement with the system to those times?

Refer to the General Requirements document paragraph 1.4.A. 27

Can you please confirm that it is acceptable to run the automation in non-staffed times to meet throughput goals?

Refer to previous, similar discussions on this topic. 28

Will there be opportunities to ask additional questions if we move towards step 2?

Yes, additional questions can be submitted prior to Step 2, however, all questions and answers will be provided to all Offerors who made it to Step 2.

We would like to propose that the KPP testing is based on the integrated automation success, where the right steps are performed at the right time. Not, based on biological test. Please confirm this approach is acceptable.

The requirements for KPP verification testing, and performance metrics committed to in the proposal, are clearly outlined in the Performance Specification.

We would like to clarify throughput requirements. KPP1 for example says 500 new strain experiments, and 100 new microbiome

Both are needed to satisfy the requirements.

experiments. Can you clarify whether both are needed per week, or whether it is either.

If we make a proposal with a set of assumptions, which includes devices, it is unclear to us how the input from the Battelle team will change the final proposal. For example, the 60% design package is the first time the device list is “final” from a Battelle perspective. Can you please clarify how Battelle plans to handle cost impactful changes?

The conceptual design in the proposals will be judged for technical scoring; however, it is recognized that further design development is necessary due to the project complexity. After award, the definitive design will be developed, that will be designed to the price and performance metrics in the contract.

If Battelle modifies the scope, a change order would be processed to cover the price differential. Refer to previous response regarding change orders.

There is no reference to anaerobes in the RFP. Can we confirm that is intentional?

This is intentional. This platform will not include anaerobic workflows.

Can the Battelle team comment on whether there are any owned devices that can be (or should be) integrated, vs buying all new devices. Depending on the response, please elaborate on which devices, models and qty’s.

All devices integrated into the HTP-APP shall be new (no used equipment) and shall be provided by the HTP-APP vendor.

In the conceptual design report the Mass specs are proposed to be integrated without human intervention (robotic). In the RFP, there is no requirement to directly integrate without human intervention. Is that intentional? We have solutions for both approaches, and want to align with Battelle’s ideals.

The conceptual design report is not part of the requirements basis.

Refer to P-Spec paragraph 4.3.5 for integrated mass spectrometer requirements.

There is no reference to the EcoFAB plate in the RFP. Can we confirm that is intentional?

The conceptual design report is not part of the requirements basis.

Refer to the performance specification for system requirements.

When is the Hazard form due back, can we assume this is part of the step 2 evaluation response?

The Hazard form is due back as part of Step 2 Volume IV Business Proposal.

When is the bid guarantee due? The bid guarantee is due as part of Step 2 Volume IV Business Proposal.

Is it possible to be part of 2 bids. For example, there may be a scenario where we would bid on the entire project as one option, and as an alternative option we may be a subcontractor to another entity bidding.

Yes. That is acceptable. 39

Who (scientist, Automation engineers, Lab Mangers, etc) will be running the system, and ultimately responsible for its success following successful SAT?

P-Spec Sections 4.8.2 and 4.8.3 clearly state the contractor is responsible to operate the equipment during installation, functional testing, KPP verification testing, and on-site commissioning.

4.3 Science Core Functions

4.3.1 Media

Topic Question Answer # Bulk media or bulk media components will be formulated by hand outside the M2PC system and needed amount can be transferred to the media science core function capability in M2PC

What volume(s) of bulk media are we expecting?

See General Response #3 regarding the content of Step 1 proposals.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

Bulk media or bulk media components will be formulated by hand outside the M2PC system and needed amount can be transferred to the media science core function capability in M2PC

What is min and max range volume of the 12 individual media components?

Definitive design details will be developed after contract award and in accordance with the design process

Offline capabilities shall include supplement addition, subsequent storage, transfer of appropriate media under experimental conditions.

In what format/container/labware would it be delivered in? Are we looking at bags and/or bottles of media stored in a refrigerator with a tube that delivers the amount to a reservoir on the liquid handler?

Where feasible, the contractor is encouraged to provide capabilities to exceed the minimum base requirements defined in the Performance Specification.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

The media dispensing capability in M2PC system should have the ability to explore a wide parameter space of media conditions.

Can PNNL be more specific here? Are we looking at mixing a couple of new media formulations or something more in the lines of Design of Experiments?

We are looking to perform “Design of Experiments” style formulations on the HTP-APP. We expect a variety of liquid media dispensing capabilities included in the HTP-

APP.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

The media dispensing capability should have the ability to use SBS format plates and tube racks with up to total of 1 mL volume

For the tubes, will these be individual tubes (e.g. test tubes, 50mL Falcon, 15mL centrifuge, etc) or will these be screw cap tubes secured in a SBS format (rack of 96, or 48, or 24 tubes). If Screw Cap tubes, will you want the ability to remove and then replace the caps for long term storage or down the line processing capabilities?

Tubes will be in an SBS footprint rack. Caps (internal/external threading) may be used.

Where feasible, the contractor is encouraged to provide capabilities to exceed the minimum base requirements defined in the Performance Specification.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the design deliverable schedule

Media dispensing capability in M2PC system should have both the ability to bulk dispense a single media type into many plates and different media type and composition to every well or every plate.

This (I’m assuming) can be managed with two pipetting tools (96MPH and Independent Channels) and disposable (but reusable and potentially washable) tips. Both tools have a range of 1uL to 1000uL.

Definitive design details will be developed after contract award and in accordance with the design process

Bottles of fully prepared media, or media components could be placed on the media dispensing capability, and the system could then dispense media into the correct plates and wells based on the experimental needs.

Again needing to know the volumes of fully prepared media and the labware and/or containers that would be holding/storing this media.

Definitive design details will be developed after contract award and in accordance with the design process

The media dispensing capability in M2PC system should house a waste processing device, which will be the main location where waste will be collected from the system. The waste collection should include solid and solvent waste collection capabilities.

I expect a possibility of three different waste paths: standard (media and other aqueous waste), solvents, solid (tips and maybe plates if needed)

Definitive design details will be developed after contract award and in accordance with the design process

The media dispensing capability in M2PC system should have the following features: -ability to blend different media composition from at least 12 independent media or

What is meant by this? Does the system actually have to physically attach a barcode label to a piece of labware? Or are you looking to track

Where feasible, the contractor is encouraged to provide capabilities to exceed the minimum base requirements defined in the Performance Specification.

media component sources into individual wells in the sample plates (different volume of each input).

- ability to affix barcodes to 4000 consumables/week various labware (tubes, plates, troughs, etc) by scanning the barcodes already found on the labware. Will the barcodes be 1D or 2D? For the tubes (if found in SBS racks) my assumption is that these will be 2D barcodes found on the bottom of each tube. Is a rack of 96 tubes considered a single barcode or 96 individual discreet barcodes?

Barcode type and application is part of the design solution.

Definitive design details will be developed after contract award and in accordance with the design process

- ability to wash and dry 1000 tip boxes/week.

What would the wash cycle look like? Just a water rinse? Water with detergent? Water-detergent, followed by rinse with an organic solvent? Just an organic solvent rinse? Will all tips be washed and reused, or just some?

Definitive design details will be developed after contract award and in accordance with the design process

- ability to store at least 600 tip boxes and 600 plates simultaneously.

What are the sizes of the tips/tip boxes? What are the sizes of plates? Will the plates have lids? Do you need random access to each stored labware or can they be stacked? You need Storage for 600 of each yet you still want to be able to wash 1000 tip boxes? Will the tip boxes be washed and then placed in Storage? The numbers seem a bit off here but maybe not as we really don’t know what the process flow looks like.

Definitive design details will be developed after contract award and in accordance with the design process

- ability to dispense 5uL-1500uL media/well into 1000 96 well plates/week.

Easily met with the 96MPH and Channels. Top range is 1000ul but we can make two dispenses for the 1500ul target dispenses.

Definitive design details will be developed after contract

- seal all plates with breathable or solid seals.

Will you need both breathable and foil seals? Will only labware that is going to storage or off the system need to be

Definitive design details will be developed after contract sealed? Will there be a need for a Peeler as well? How many plates will need sealing in any given week?

- ability to sort system waste by separating liquid waste streams and removing solvents from plates and strong in waste canisters

Again, expect that two separate liquid waste streams and a single (or possibly two) solid waste streams/containment will be adequate here.

Definitive design details will be developed after contract award and in accordance with the design process

- ability to store solid wastes What solid wastes besides tips are we expecting here? What volume are we expecting?

Definitive design details will be developed after contract award and in accordance with the design process

- tips ready for disposal are separated from their recyclable bases

My assumption is that you’d like to collect tip boxes for recycling. Will this hold true for any tips that are washed and then placed back in the tip boxes for drying? What is the volume of tip boxes you’ll need storage for?

Definitive design details will be developed after contract award and in accordance with the design process

- waste sorting for BSL-2 workflows needs to be separated and stored within a BSL-2 controlled enclosures

Are we looking at protecting the experiment or the operators? I suspect all we need to do is protect the experiment. If this is the case then CAP (Clean Air Protection – Positive Pressure HEPA Filtered Air) can be added to the project in lieu of a full BSC II Enclosure saving $100’s of thousands of dollars.

Will the entire process (includes storage of plates and tips) need to be inside BSC II? Or do we just need protection when there is open media/reagents?

See General Response 4.

washes and dries 1000 units of labware/week, including tip boxes and plates.

How many times can a plate be washed before it is considered consumed?

See General Response 4 and 6.

washes and dries 1000 units of labware/week, including tip boxes and plates.

Will washed plates require fresh barcodes

See General Response 4 and 6.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

(Kim – This was blank?) Do you anticipate needing to relabel plates mid biological batch or will the initial label track the labware the entire time?

See General Response 4 and 6.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to

4.3.2 Cultivation

Topic Question Answer # M2PC cultivation capability should include a large bank of incubators to grow organisms in and should also include equipment to inoculate plates

How many different temperatures will be needed with these incubators? How many plates will be required for each temperature? Will all cultures require agitation (shaking)? What are the sizes of the plates to be used (specifically what height)?

See General Response 4 and 6.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

M2PC cultivation capability has the ability to create experimental diversity, so that a wide range of environmentally relevant parameter space can explored including cultivation temperatures, light exposures, humidity changes, various gas concentrations and shaking speeds.

Please provide a table with the maximum number of plate positions needed for each incubation variation (temp, light, humidity, gas, shaking). Without this information we cannot estimate the number and type of incubators.

See General Response 4 and 6.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

In M2PC cultivation capability, some portions of cultivation equipment need to

Will plates in the offline incubation be included in the automation

The Offeror shall provide incubators necessary to achieve the performance metrics committed to in the contract. At least 1/3 of the be offline to provide the capacity and experimental conditions needed to satisfy multiday cultivations using a combination of offline and online capabilities during varying times to avoid inefficiencies. At least, 1/3 of the capability or more should be fully integrated with the automation system.

portion? Or will they be kept completely separate? Requiring the capability to introduce new labware/cultures half-way through a cultivation process significantly increases the complexity of the project.

incubators shall be integrated to the automation system, and those that are not included in the integrated shall be provided offline by the Offeror.

In M2PC cultivation capability, some portions of cultivation equipment need to be offline to provide the capacity and experimental conditions needed to satisfy multiday cultivations using a combination of offline and online capabilities during varying times to avoid inefficiencies. At least, 1/3 of the capability or more should be fully integrated with the automation system.

Do all incubators need a shaking function?

See General Comments 4 and 6

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

• The cultivation capability should have the ability to use SBS format plates and tube racks with up to total of 1 mL volume.

• The location of an individual plate both between and within incubators shall be tracked so that an individual plate can be removed at a given time, based on experimental needs.

The cultivation capability should have a colony picker to transfer colonies on solid substrates such as agar plates or biofilms to liquid media or other solid substrates.

What are the parameters of colony picking? Is there an established colony picker that is currently being used and is considered acceptable for this project?

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

Refer to P-Spec Appendix F: “Key microbial types identified for inclusion in the M2PC include eukaryotic and prokaryotic systems with focus on bacteria, archaea, fungi, extremophiles, algae, and synthetic and natural consortia. As such, the functional requirements should include to the greatest extent possible the capabilities and infrastructure to culture under conditions relevant to these species.”

M2PC cultivation system should have the ability to monitor growth kinetics without disturbing the physiology.

What are the parameters of growth management monitoring? Is there a particular Reader that is currently being used in the manual process that is considered acceptable to the automated process? (there are

See General Response 4 and 6.

Definitive design details will be developed after contract award and hundreds of readers that meet the need of “monitor growth kinetics”)

• M2PC cultivation system should have the ability to remove a plate from an incubator, measure the optical density (OD), and return the plate to an incubator within 10 minutes or have some capacity for real-time ODs so that growth kinetics can be observed without disturbing the physiology.

In M2PC capability, BSL-2 controlled organisms will need to be inoculated within appropriate physical containment.

Will you require the entire integrated platform to be enclosed in BSC II or just those devices that have access to the unsealed (unlidded) plates?

Refer to P-Spec Section 4.6.2 for BSL-2 requirements. The portions of the system requiring BSL-2 protection depend upon the Offeror’s design solution.

The cultivation capability in M2PC system should have the following features: - ability to simultaneously cultivate 500 medium well plates SBS format plates and tube racks.

How many different cultivation parameters (temp, humidity, shaking, light, etc.) are needed? Will all 500 plates be kept in the same cultivation environment? Or will the numbers vary? If so, how many should be planned for? (i.e. 5 incubators each with a 100 plate capacity)

See General Response 4 and 6.

Definitive design details will be developed after contract award and

- ability to inoculate 750 plates/week. Please describe the inoculation steps. This is needed prior to determining potential throughput.

See General Response 4 and 6.

Definitive design details will be developed after contract award and ability to centrifuge the liquid if necessary Will plates be lidded or sealed? What is the g requirement for centrifugation of the plate lids?

See General Response 4 and 6.

Definitive design details will be developed after contract award and ability to provide orbital shaking with up to a 3mm throw and be able to shake up to 1000rpm.

How long will the plates need shaking? Short period of time or continuous? How many plates will need to be shaken simultaneously?

See General Response 4 and 6.

Definitive design details will be developed after contract award and ability to provide controllable illumination preferably with proper mitigation of heat transfer to the cultivation plates.

Please explain further. See General Response 6.

The light parameters and temperature should be independent cultivation variables that can be controlled by the system.

At least 1/3 of the cultivation incubators shall be fully integrated with the automation system

Why do only a 1/3rd of the incubators need to be attached to the automated system? Do you expect manual intervention to move labware between the different incubators?

See previous response for similar question.

Provide cultivation capability to create experimental diversity so that a wide range of environmentally relevant parameter space can explored, including cultivation temperatures, light exposures, humidity changes, various gas concentrations, and shaking speeds

Have the specific requirements for cultivating challenging microorganisms, as well as microbial and microbiome communities, been thoroughly evaluated? This includes the need for precise environmental conditions, such as maintaining anaerobic environments. It should be determined whether regulation of the atmosphere and other parameters in the entire automated system or in some components is necessary*.

Considerations should also include extended incubation periods.

See General Response 4 and 6.

The system does not include anaerobic environments.

Definitive design details will be developed after contract award and

Is the installation of bioreactors planned? For the growth of consortia under controlled conditions, specialized bioreactors may be necessary to allow precise control of parameters such as pH, oxygen levels, and nutrient supply.

See General Response 5 and 6. 75

4.3.3 Sample Preparation

Topic Question Answer The M2PC sample preparation capability should accommodate wide range of sample preparation techniques to satisfy the sample requirements for a wide range analytical techniques.

Please provide examples of sample preparation techniques.

Sample preparation requirements are in P-Spec section 4.3.3. 76

Many of the techniques used during sample preparation can produce splashes and aerosols and should therefore be contained within BSL-2 controlled physical biological containment while sample preparation techniques that don’t form aerosols can be kept outside the BSL-2 enclosures.

If performed properly splashes and aerosols should not be created. It is our contention that BSL-2 containment is a requirement due to the characteristics of the cells/viruses/bacteria that are part of the experiment not due to pipetting technique. Should we just assume two liquid handling platforms, one with BSL- 2 and one without?

See General Response 4.

Refer to P-Spec Section 4.6.2 for BSL-2 requirements. The portions of the system requiring BSL-2 protection depend upon the Offeror’s design solution.

The BSL-2 controls will be fully developed during design and will be informed by each contractor’s concept.

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

The sample preparation capability in M2PC system should have the following features:

- ability to seal 3500 plates/week.

- ability to perform 3500 stamps/week with transfer volumes of 5-250uL.

- ability to perform hit-picks/cherry-picks (well to well transfers, rather than full plate transfers)

- ability to peel 3500 plates/week.

- ability to bulk dispense solvent/buffer into 3500 plates/week selecting from at least 6 solvents/buffer with 50-1000uL dispense volume.

- ability to centrifuge 2000 plates/week, It is all but impossible to assemble a system that meets the above throughput requirements without knowing the overall process flow. A single sealer can certainly seal 3500 plates per week if it is continuously loaded with plates and seals but I expect the plates need to be processed and manipulated by other components of the system making them not available for continuous sealing activities.

See General Response 1 and 4.

- ability to shake plates.

ability to support enzymatic reactions, there should be capacity to statically incubate plates with at least 3 temperature options

What are the three temperatures? How many plates per temperature? How long is the incubation phase?

See General Response 6 79 ability to provide (i) Bead Beater, with ability to add automatically add metal beads to a plate, (ii) Positive pressure device, (iii) Sample concentrator, (iv) Fraction Collector and (v) Well-based stirring to mix up individual wells of a plate capabilities (consider having >1 device if the device is slow).

Is there an existing bead beater device that is currently in use in the manual process? What are the operating parameters for this step. Please provide a more complete definition of the process flow here.

See General Response 1 and 6 ability to perform sample preparation for various offline capabilities including NMR, high field FTIR MS, and cryo electron microscopy.

Is there more information you can provide here? Odd sized labware can make this potentially unachievable.

See General Response 3 and 6

Sample preparation capability shall have bead beaters capable of automatically adding metal beads to a plate, positive pressure device, sample concentrator, fraction collector, and well-based stirring to mix individual wells of a plate.

Do the bead beaters need to be cleaned in an automated fashion?

See General Response 5 and 6 82

Sample preparation capability shall have the capability to lyophilize plates. The contractor shall determine if this capability is an integrated automation or offline standalone system.

How many plates are expected to be lyophilized each week?

See General Response 6

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance

4.3.4 Strain Engineering

M2PC Strain Engineering capability should be able to do each transformation attempt, e.g. a single well of a plate, represents the start of building a new microbial strain with a unique genome.

Please provide a more detailed description of this process.

See General Response 6

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

- ability to perform heating and shaking. How many heating and shaking positions will be needed? How long is the incubation/shake time? What temperature, speed. Orbit?

See General Response 6

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

ability to perform liquid handling using a special liquid handler to support nanoliter volume hit picking required to set up PCR reactions in addition to the other liquid handlers to meet the requirements.

Please provide additional information on this process: what is the source labware? What is the type and volume of source material? What is the volume of the hit-pick? Is the dispense volume the same as the hit-pick volume? What is the destination labware? Are there other reagents in the destination labware? Please provide a more complete description of this process.

See General Response 6

Definitive design details will be developed after contract award and in accordance with the design process outlined in the performance specification. Refer to Appendix A for the deliverable schedule.

some of the additional instruments which need to be integrated are the following:

colony picker, incubator space, -20C plate storage, late peelers, plate sealers, plate readers, centrifuges and liquid handlers

Please provide more information on what is needed here. All of these can be included/integrated but how are we supposed to choose the correct ones and the correct number of these devices?

Refer to General Response 2, 3, and 6.

perform thermocycling using automation-compatible thermocyclers to support strain build and for cell lysis before DNA extraction.

Are there any requirements for cleaning the thermocyclers between plates?

See General Response 5 and 6. 88

4.4 Remote Planning and Operation

Software shall have security controls in place, such as authentication and authorization via Keycloak to enable single sign-on for remote users to log into the system and execute their work.

Are there any expectations on additional restrictions/lockouts for remote access users versus on-site access users to the system software? (i.e. a remote access user can only do X, where an on-site access user can do X, Y, Z, etc.)

Refer to P-Spec sections 4.4. and 4.5. 89

Remote users shall be able to submit work, monitor progress, and review data.

Remote users shall be able to kick-off protocols remotely by specifying which samples/parameters to use with a given protocol. Protocols kicked off by remote users must interleave with protocols running in parallel.

4.5 Automation System Control Software Design

Scheduling software shall have interleaved protocols capable of running multiple protocol runs of different types simultaneously, interleaving protocol runs to maximize system throughput.

Can there be business rules governing which protocols can be interleaved and how, or is any protocol expected to work at any time, regardless of the current capacity of the system?

Refer to section 4.4 and 4.5 for software controls.

Software shall include collaborative configuration management tools.

Could you define collaborative configuration management tools?

Collaborative configuration management tools allow users to work together to automate and manage system configurations across various environments, enabling collaboration through shared configuration code and centralized management.

The software shall integrate with existing relevant EMSL software infrastructure including but not limited to LIMS architecture (enterprise L7 platform) for experiment, workflow, and sample

Could you provide more information on the “enterprise L7 platform” LIMS system in its current implementation?

LIMS integration and design requirements are covered in detail in the metadata capture, and EMSL’s data storage archive. Integrated experimental systems shall support or manage the capture of instrument performance, sample ID, analytical results in real-time or near real-time, instrument calibration, and quality control information, and associate these data with parallel data and metadata stored on EMSL’s LIMS system.

Software shall include the option to automatically put unused/unscheduled instruments into sleep mode or turn them off to conserve energy without compromising integrity and be able to bring them back online when needed without operator intervention.

For instruments without remote power control (i.e. device must be in

“automation mode” to receive commands), is the expectation that a secondary power control is added to facilitate this control?

4.9 Training

Advanced, on-site, hands-on training on the entire equipment capability shall be provided to Battelle staff for a minimum of 2 weeks (a minimum of four Battelle employees are required for each topic, but the same employees do not have to learn each topic)

A minimum of 4 Battelle scientists will need to be trained in various areas over the course of 2 week on site training. Has a maximum number been defined? We propose no more than 8

See General Response 4

Minimum requirements are defined in the Performance Specification.

Once the system is accepted, do you expect the contractor to continue to train new

Battelle scientists, or is it expected that the already trained Battelle scientists will be able to onboard new trainees?

Training after system completion, not defined in the contract, is outside of the project scope.

4.10 Consumables

Contractor shall submit a list of consumables that are needed for 1 year of operations at the KPP threshold level of activity and maintenance of the complete system. At minimum, include the manufacturer, brief description, part number, quantity, and cost.

Are there any limitations or preferences for consumables utilized within the system based upon cost/availability/previous experience?

See General Response 4. 96

Contractor shall submit a list of consumables that are needed for 1 year of operations at the KPP threshold level of activity and maintenance of the complete system. At minimum, include the manufacturer, brief description, part number, quantity, and cost.

What kind of plates will be used? 96-well, 384-well, and 1536-well formats

See General Response 4. 97

4.11 System Backup and…