Contract Research Services

Datasets from biological processes are usually subject to diverse biological or experimental effects, making them challenging to analyze with traditional statistical methods. Bayesian statistical methods are not only perfectly suited to deal with this challenge, but they also enable us to minimize the number of experiments required to screen large parameter spaces. All the while these methods are key to obtaining statistically robust and reproducible results from which you can make data-driven decisions.

We can provide the necessary expertise to apply Bayesian data analysis to tackle your research question!

Your Input

• Research question where assay results or parameter spaces are subject to diverse biological/experimental effects (can also be as part of a regular bioproces campaign)
• Clear understanding of what key performance indicator you are interested in

Our Output

• Tailored data analyses that factor out mixed effects to quantify your KPI with uncertainty
• Accelerated exploration of higher-dimensional parameter spaces to locate your best-performing strain or bioprocess parametrization
• Distilled-down summaries that your stakeholders can make decisions from

How we deliver

The first step is understanding your research question which is most efficiently done by a discussion between your and our domain experts. From the shared understanding of your needs, we'll draft a project outline that accounts for anticipated modeling needs.

Bayesian modeling at this scale is often times just one of the building blocks of a project, and we're happy to include it as part of a more comprehensive offer for an end-to-end campaign.

For many customers, lab-scale stirred-tank bioreactor (STR) experiments are still the benchmark for validation of the results from the AutoMBR experiments. To increase data output and reproducibility, we connect STRs with our automation capabilities. Our AutoSTRs are built on four-fold parallelised laboratory-scale bioreactor setups (1.0 L Eppendorf) and are used for bioreactor scale and validation experiments and in-depth kinetic and phenotypic analysis. Integration into the robotic platform provides the same process flexibility (e.g. 24/7 sampling) and data quality as the AutoMBR. The AutoSTR offers online DO, pH, and offgas-analysis. Via automated sampling, optical density and cell dry weight are determined at-line.

In addition, further manually operated bioreactors (1.0–3.8 L Eppendorf and 30 L Infors) can be used for process development and scale-up experiments.

Your Input

• 1-12 strains or process conditions to be tested
• Current protocol for cultivation process
• Research question or KPI to focus on

Our Output

• Detailed characterization of selected conditions in bioprocess time series and KPIs under scalable bench-top STR bioprocess conditions
• Comprehensive data set including DO, pH, offgas-analysis, at-line optical density, cell dry weight, and sample analysis tailored to your project.

How we deliver

First we will schedule a call with your bioprocess experts to precicely understand your situation, such that we can quickly arrive at a project outline that fits your needs.

Next we'll draft a project outline including the appropriate work packages for tech transfer and downstream analytics.

Once your order is confirmed we'll get to work, starting with strain- and tech transfer. Finally we'll deliver milestone-based insight updates and a final report including summarized results on the performance of your top strains!

Microliter-scale experiments have the potential to speed-up strain characterization and process development due to the increased throughput compared to lab-scale stirred tank bioreactors (STRs). However, setting up valuable experiments that mimic your STR-process requires a solid scale-down and knowledge about the potential and limitations of such micro bioreactor systems (e.g. BioLector by Beckman coulter). With our extensive knowledge about chances and pitfalls of micro-scale cultivations, we enable you to gain as much process insights as possible from your microcultivation experiments without making all the costly mistakes on your own. Together, we can set-up scale-comparable cultivation protocols and analyze your experiments regarding comparability.

Your Input

• Clearly specified needs (e.g. setting up microscale process from scratch or scale down from an STR-protocol)
• Current protocol for cultivation process either from MTP or STR
• Initial dataset from cultivation growth- and production parameters (if applicable).
• Further datasets that are generated during protocol validation

Our Output

• Suggestions and advice on establishing the right microscale cultivation parameters for your bioprocess
• Microscale cultivation protocol tailored to your research question

How we deliver

First we will schedule a call to precicely understand your situation, such that we can quickly arrive at a project outline that fits your needs. Once your order is confirmed, we will get to work and analyze your dataset with respect to the questions or schedule a meeting to get all necessary information for our task. In accordance with the project outline and coordination with your subject matter experts we will conduct 1-on-1 support and deliver a tailored microcultivation protocol. After you performed 1-2 test runs with the new protocol, we will assess the collected data and refine the protocoll, if necessary. Finally we will be available for further improvement after protocol validationd in your lab.

Powerful devices such as the BioLector or high throughput liquid handlers create vast amounts of high-resolution data that can be difficult to analyze. For distilling quantitative and reproducible results, postion- or batch effects must be accounted for. Working with big time series datasets of bioprocess upstream or assay reaction kinetics, we have developed tools like bletl or calibr8 as well as advanced modeling techniques by which we can distill insight from these datasets with unprecedented depth. If you need support for analyzing the time series of a complex assays or bioprocesses, we can support you with state of the art data analysis and 1-on-1 sessions to speed up your analysis workflow.

Your Input

• Clearly specified needs (e.g. hours of 1-on-1 support, analysis of a given dataset)
• Dataset to be analyzed (e.g. raw BioLector file, unprocessed assay kinetics) including relevant process and layout parameters

Our Output

• Python-based data analysis workbook
• Analysis report incl. figures, conclusions
• Tabular summary of extracted key performance indicators

How we deliver

First we will schedule a call to precicely understand your situation, such that we can quickly arrive at a project outline that fits your needs.

Once your order is confirmed, we will get to work and analyze your dataset with respect to the questions or key performance indicators that you require.

In accordance with the project outline and coordination with your subject matter experts we will deliver a Python-based data analysis notebook and or conduct 1-on-1 support sessions.

Finally we will be available for further iteration if needed.

Without analytical technologies, our bioprocess improvements could not be revealed. Therefore it is an integral part of our contract research. With mass spectrometry, high-performance liquid chromatography (HPLC) and biochemical assays, we quantify intra- and extracellular target molecules. Our automation platform allows us to implement various enzymatic and kinetic assays to quantify substrates or target molecules, tailored to your need.

We're happy to include this building block as part of a more comprehensive offer for an end-to-end campaign.

Your Input

• SOP for quantification of the target molecule as a reference (if available)
• Data about expected concentration range and reference samples if applicable

Our Output

• Quantification of target molecules with uncertainty estimates

How we deliver

First we will schedule a call with your experts to precicely understand your situation, such that we can quickly arrive at a project outline that fits your needs.

Next we'll draft a project outline including the appropriate work packages for tech transfer and establishment of the analytics.

Once your order is confirmed we'll get to work. Finally we'll deliver milestone-based insight updates and a final report including summarized results on the performance of your top strains!

Characterization of bioprocesses in higher throughput can be challenging without the right tools. Our unique AutoMBR technology combines the well known Beckman Coulter BioLector for parallelized microscale cultivation in batch or fed-batch mode with Tecan liquid handling robots, enabling us to conduct parallelized bioprocess characterization, screening or optimization experiments with maximum information gain.

Through online monitoring (biomass, pH, DO, fluorescence), optional pH control, and substrate feeding we can run these small-scale experiments under production-relevant conditions while gathering tons of relevant signals. Our integration into lab robotics brings the flexibility to adapt to specific process requirements (e.g. sampling and dosing), and third party integrations offer additional functionalities beyond the ordinary, such as at-line microscopic imaging of your samples.

With these workflows we can provide the throughput you need to find the best producer strains and process conditions so you don't get surprised by the first scale-up runs!

Your Input

• 1-96 strains to be characterized
• Current protocol for cultivation process either from MTP or STR
• Research question or KPI to focus on

Our Output

• Identification of top performing strains
• Detailed characterization of top performer bioprocess time series and KPIs under scalable bioprocess conditions

How we deliver

AutoMBRs are one of the our important tools, and they come in many flavors depending on the specific research question. Therefore we'll first schedule a discussion with your bioprocess experts to understand exactly what your're looking for.

Next we'll draft a project outline including the appropriate building blocks for library preparation and downstream analytics.

Once your order is confirmed we'll get to work, starting with strain transfer and feed them into our higher-throughput characterization workflows. Finally we'll deliver milestone-based insight updates and a final report including summarized results on the performance of your top strains!

Working with high-throughput platforms requires developing and adopting software for automation systems or data analysis. We leverage open source software and also contribute to the community by publishing some of the software that was developed at the Forschungszentrum Jülich. bletl and robotools are notable examples of our software projects that gained widespread adoption in the microcultivation and liquid handling community.

We recognize that powerful tools require expertise, therefore we understand that you may need tailored support for using our software to its full potential. Or maybe you have encountered limitations and need support for debugging or bugfixing?

Your Input

• Clearly specified needs (e.g. hours of 1-on-1 support, feature/bugfix work, training workshop)
• If applicable: Datasets to reproduce e.g. software bugs that you encountered (can be anonymized)
• If applicable: Confidential access to your code/dataset

Our Output

• Problem-solving tailored to your needs
• Code contributions/changes to publicly available, open-sourced licensed Python libraries

How we deliver

First we will schedule a call to precicely understand your needs, such that we can quickly arrive at a project outline that fits your needs.

Once your order is confirmed, we will get to work and make the necessary code or content preparations.

In accordance with the project outline and coordination with your subject matter experts we will deliver new software releases, training workshops or 1-on-1 support sessions.

Finally we will be available for further iteration if needed.