Upstream Bioprocessing · FlexBIO at Heriot-Watt University, Edinburgh
Pilot-scale fermentation and cell culture, from first inoculation to 300 litres.
2L → 300L Bioreactor range Four microbial scales · Two mammalian scales
6 Organism types Bacteria · Yeast · Fungi · Algae · Plant · Mammalian
CL2 Containment Level 2 Separate microbial & mammalian suites
TRL 3–6 TRL range supported Proof-of-concept to pilot validation
Contact: scaleup@ibioic.com
FlexBIO provides upstream bioprocessing services across the full development scale range from 2L process development through to 300L pilot-scale demonstration runs for bacteria, yeast, filamentous fungi, algae, plant cells, and mammalian cell lines.
Background
What is upstream bioprocessing?
Upstream bioprocessing is everything that happens inside the bioreactor; inoculation, cell growth, product accumulation, and harvest. It is where the biology meets the engineering, and where the fundamental economics of a bioprocess are determined: how much product you make, how fast, and how consistently.
At laboratory scale, upstream processes run in shake flasks and small stirred vessels where variables like mixing, aeration, and heat transfer are easy to manage. These variables become considerably more complex as you move to pilot scale. The oxygen transfer rate changes. Substrate gradients emerge. Mixing times extend. Heat removal becomes a material constraint. These are not academic concerns, they are the practical reasons why a process that works at 2L can behave differently at 30L or 300L, and why piloting at an appropriate scale is not optional for any commercialisation pathway.
FlexBIO exists to give UK and international biotech organisations access to the infrastructure, equipment, and expertise needed to navigate this transition reliably, without the capital expenditure of building and staffing a pilot facility of their own.
Capabilities
FlexBIO upstream capabilities at a glance
FlexBIO operates a fully equipped upstream bioprocessing platform at the John Coulson Building, Heriot-Watt University, Edinburgh. The facility supports the full TRL 3–6 development range, from early proof-of-concept through to pilot-scale validation runs that generate investor-, partner-, and regulator-ready data.
Bioreactor scale range
2L Development scale
Process characterisation, parameter mapping, initial optimisation. Available for both microbial and mammalian workstreams in dedicated CL2 suites.
Microbial & Mammalian
7L Small pilot scale
First scale step for microbial processes. Identifies early transfer effects before committing to larger runs.
Microbial
15L Mammalian pilot scale
Pilot-scale confirmation runs for CHO, HEK293, stem cells, and other mammalian lines. Mixing, shear sensitivity, and kLa assessment at relevant volume.
Mammalian
30L Mid-pilot scale
Robust scale-up confirmation. Used in the Certificate of Upstream Bioprocessing training course and for client process validation runs.
Microbial
Culture formats
Batch
Straightforward, cost-effective runs for process validation, inoculum preparation, or demonstration batches across all scales.
Fed-batch
Most common format for high cell density and elevated product titres. Feeding strategies developed and optimised to your organism's kinetics.
Continuous & perfusion
Chemostat and ATF perfusion for sustained culture with continuous product removal. Pilot-scale experience for mammalian and microbial applications.
Organisms we work with
Bacteria
E. coli, B. subtilis, Streptococcus sp.
High-density fed-batch experience; E. coli standard expression and inclusion body workflows
Yeast
S. cerevisiae, P. pastoris
Methanol-induction protocols for P. pastoris; ethanol tolerance work for S. cerevisiae
Filamentous fungi
Fusarium sp., Aspergillus sp.
Morphology management; viscosity-aware aeration strategies
Microalgae
Various species
Photobioreactor and heterotrophic fermentation options available
Plant cell cultures
Various expression systems
High-value compound production; shear-sensitive culture management
300L Full pilot scale - flagship vessel
One of Scotland's largest publicly accessible pilot fermenters. CL2 certified, fed-batch and batch operation, continuous centrifugation integration. Delivers the data investors, regulators, and manufacturing partners require.
Microbial | Flagship
Mammalian cell lines
CHO, HEK293, stem cells, Vero, NS0
Dedicated CL2 mammalian suite; ATF perfusion; viability monitoring throughout
If your organism is not listed, contact us. Our team has worked across a wide range of production hosts and can advise on suitability before any commitment is made.
Feedstocks and media
FlexBIO supports a wide range of media and feedstock types from standard defined media and complex nitrogen sources to industrial substrates, lignocellulosic biomass, and waste streams or by-products. For organisations working with alternative feedstocks as part of a circular economy or industrial biotechnology strategy, our team has direct experience in translating bench-scale process conditions to pilot scale using non-standard inputs.
The team
The FlexBIO upstream team
The people running your fermentation matter as much as the equipment they use. FlexBIO's upstream bioprocessing team combines deep practical knowledge of microbial and mammalian fermentation with hands-on experience of scale-up across a diverse range of organisms and products.
The team is led by the Upstream Bioprocessing Manager and supported by Senior Upstream Bioprocessing Scientists with specialist expertise in fermentation process development, analytical monitoring, and downstream integration. The Biofacilities and Operations Manager oversees the facility, safety, and quality systems that underpin every campaign.
All client projects are managed under full confidentiality. Intellectual property ownership remains with the client throughout, and FlexBIO does not retain rights to processes or products developed in the facility.
Why it matters
Why pilot scale matters and when you need it
The TRL gap between a validated laboratory process (TRL 3–4) and pilot-scale demonstration (TRL 5–6) is where many bioprocesses stall. Capital cost, access to equipment, and the absence of in-house expertise at pilot scale mean that organisations often delay this step — or skip it entirely, attempting to move directly from bench to industrial scale. This rarely ends well.
Running at pilot scale exposes the mixing, aeration, heat transfer, and substrate distribution effects that are simply not visible at bench scale. It is at this stage that you discover whether your feeding strategy survives the transition, whether your strain performs under industrially relevant oxygen transfer conditions, and whether your downstream processing assumptions hold at volume.
The business case for generating this data early is clear:
Investor conversations
Pilot-scale yield data from an independently operated facility is a fundamentally different proposition from lab-scale extrapolations. It transforms your investment case from a projection into a demonstration.
Manufacturing partner discussions
A 300L dataset gives contract manufacturers confidence in your process. Scalability becomes proven rather than theoretical - a material difference in technology transfer negotiations.
Regulatory submissions
Pilot-scale process characterisation data supports CMC sections of regulatory submissions, IND and IMPD documentation, and technology transfer packages for GMP manufacture.
Grant applications
UKRI, Innovate UK, and Horizon Europe all value demonstrated TRL progression. A FlexBIO scale-up run documents a concrete, independently generated TRL step-change that strengthens funding applications.
How it works
The FlexBIO upstream service in practice
Every upstream project at FlexBIO begins with a free, no-obligation technical consultation. Our bioprocess engineers will ask about your organism, your current scale, your process history, your product and its characteristics, and what you need the scale-up run to demonstrate. From that conversation, we advise on the most appropriate scale, culture format, and engagement model, and provide a detailed project proposal within five working days.
Building a process from scratch
If you have a laboratory-scale process in shake flasks or small bioreactors but have not yet run in a controlled stirred tank system, FlexBIO can build it from first principles at pilot scale. This includes bioreactor selection and parameter mapping from your laboratory data, media preparation and sterilisation, inoculum development and seed train management, and iterative optimisation of pH, dissolved oxygen, temperature, and agitation. Feeding strategy development for fed-batch cultures and full online and offline analytical monitoring are included throughout.
Transferring an existing process
If you have an established process at one scale and need to demonstrate performance at the next, FlexBIO provides structured scale-up confirmation runs with full data packages. We identify the critical process parameters driving performance at your current scale, propose appropriate translation criteria for the target scale — including volumetric power input, kLa, and mixing time — and run the confirmation campaign with milestone reporting built in.
What every campaign delivers
✓Complete process logs with online parameter traces (pH, DO, temperature, agitation, airflow, feed rates)
✓Offline biomass and metabolite data throughout the culture run
✓Product titre measurements at defined sampling points
✓Written technical report summarising process performance against agreed objectives
✓Milestone-structured interim reporting for research services contracts
✓Reports formatted for investor data rooms, grant applications, regulatory dossiers, or partner due diligence packs on request
Evidence
Scale-up in practice - selected case studies
FlexBIO has supported upstream scale-up across a range of organisms, sectors, and scales. The following examples illustrate the breadth and practical nature of the team's work.
Biomanufacturing · UKRI Launchpad
Enzyme Production Scale-Up for Cyclodextrin Biomanufacturing
NCIMB partnered with FlexBIO to transition bench-scale enzyme production from static flask cultures to a controlled fermentation system, enabling access to pilot-scale capability without building their own facility.
Mammalian · Cultivated meat
Livestock iPSC Culture Scale-Up for Cultivated Meat
An academic research team used FlexBIO's mammalian suite to scale up induced pluripotent stem cell cultures. The project advanced cell line development and directly enabled additional funding to be secured.
Industrial chemistry · Oxford Biotrans
Twin Fed-Batch Scale-Up in 15L Bioreactors
Oxford Biotrans used FlexBIO's twin fed-batch system to test additional parameters for process improvement in a chemical biotransformation, demonstrating how parallel pilot-scale runs accelerate development timelines.
Healthcare · University of Bristol
Media Development & Probiotic Culture Scale-Up to 22L
FlexBIO resolved a media compatibility issue blocking commercialisation of a probiotic Streptococcus thermophilus strain, developing a new formulation that maintained cell growth and enabled a viable product to progress.
Training
Upstream bioprocessing training courses
FlexBIO is a recognised bioprocess training centre of excellence through the RESILIENCE programme. For organisations whose teams need to build upstream skills alongside a service project - or for individuals seeking hands-on training independently - FlexBIO offers practical, industry-focused courses delivered by the same team that runs the facility.
Certificate of Upstream Bioprocessing
Theory and practice of microbial and mammalian cell cultivation, bioreactor operation, SIP sterilisation, inoculation, monitoring, and harvest. Hands-on experience at 30L scale. Aimed at early career professionals building an upstream foundation.
3 days
From £2,100
Pilot-Scale Upstream Bioprocessing: 300L Bioreactor Training
For experienced practitioners: process design, parameter translation, online monitoring, and harvest strategies at 300L. Participants operate the 300L vessel directly. Bridges laboratory knowledge with industrial-scale application.
4 days
From £2,500
BioProcess360: Integrated Upstream and Downstream Bioprocessing
End-to-end view of the biomanufacturing workflow: cultivation of a recombinant protein in a 30L bioreactor, followed by purification using centrifugation, homogenisation, TFF, and chromatography. Ideal for those seeking a complete process perspective.
5 days
From £2,800
Applied Skills in Mammalian Cell Bioprocessing
Core competencies in mammalian cell line cultivation: cell line maintenance, media preparation, aseptic technique, and bioreactor operation at up to 1.5L scale. Theory and practical lab sessions combined.
3 days
From £2,100
Academic and start-up discounts are available across all courses. Bespoke training programmes can be designed for organisations requiring customised content or on-site delivery. Contact scaleuptraining@ibioic.com to discuss options.
How to engage
Three ways to access FlexBIO's upstream services
FlexBIO offers three engagement models, designed to match the project scope, timeline, and in-house expertise of different types of organisation. All models include IP protection and full confidentiality as standard, and SME-discounted rates are available across all three.
Direct-Use Access
Your team works in the FlexBIO facility using our equipment, with our technical staff on-site for supervision and support. Best suited to organisations with existing upstream expertise who need pilot-scale infrastructure they do not own.
Best for: teams with in-house expertise · equipment access without CapEx · cost-sensitive programmes
Short-Duration Service
Our bioprocess engineers operate the equipment on your behalf for a defined, bounded scope of work. Suitable for organisations without dedicated process development resource, or those needing rapid turnaround results.
Best for: startups needing investor data · defined single-stage experiments · fast turnaround
Research Services Contract
A structured multi-stage engagement with defined work packages, milestone sign-off, interim reviews, and a comprehensive final report. For longer development programmes, CMC data generation, and regulatory-adjacent projects.
Best for: CMC development · IND/IMPD data · longer scale-up programmes
Related content
Explore linked topics
This page covers FlexBIO's upstream bioprocessing services in full. For more detail on specific aspects, explore the pages below.
Mammalian Cell Process Development
CHO, HEK293, stem cell scale-up in detail
Analytical Services
Online/offline monitoring and CMC data
300L Pilot-Scale Fermentation
Specs, use cases, and booking info
Equipment Portfolio
Full technical specifications
Downstream Processing Services
Harvest, purification, and final form
Scale-Up Case Studies
Project examples across organisms and sectors
Common questions
Frequently asked questions
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FlexBIO supports bacteria (E. coli, B. subtilis, and others), yeast (S. cerevisiae, P. pastoris, and others), filamentous fungi, microalgae, plant cell cultures, and mammalian cell lines including CHO, HEK293, stem cells, Vero, and NS0. If your organism is not listed, contact us to discuss suitability before any commitment.
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The largest vessel is a 300-litre stirred tank bioreactor — one of Scotland's largest publicly accessible pilot fermentation vessels — operating under Containment Level 2 with integrated continuous centrifugation. For mammalian cell culture, the largest scale is 15L in the dedicated mammalian CL2 suite.
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Both. FlexBIO can take an organism and build a process from first principles at pilot scale, or take an existing bench-scale process and support its transfer and scale-up confirmation at a larger vessel. The initial technical consultation will establish your starting point and the most appropriate approach.
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Yes. FlexBIO has experience with a range of industrial substrates beyond standard defined media, including complex nitrogen sources, lignocellulosic biomass, and waste or by-product streams relevant to circular economy and industrial biotechnology applications.
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Standard deliverables include complete process logs with online parameter traces, offline biomass and metabolite data, product titre measurements, and a written technical report. For research services contracts, milestone-structured interim reporting is standard. Reports can be formatted for investor data rooms, grant applications, regulatory dossiers, or partner due diligence packs.
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For 300L campaigns, we recommend contacting us 4–8 weeks before your desired start date to ensure availability and allow time for technical consultation and process preparation. For smaller-scale runs, lead times are typically shorter — contact us to check current availability.
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Yes. IP ownership remains with the client throughout all engagements. FlexBIO operates under full confidentiality and does not retain any rights to processes or products developed in the facility.
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Yes. Dedicated pricing tiers are available for startups, small businesses, and academic organisations across all three access models. Contact scaleup@ibioic.com for current rates.
Ready to start your
upstream scale-up project?
scaleup@ibioic.com · Response within 2 working days · Containment Level 2 · SME discounts available · Part of Pilots4U European open-access network