Using automation to build New Materials at the interface of Synthetic Biology, Material and Computer Sciences
The Leibniz-INM Accelerated Research Foundry (ARF) is a research and service automation laboratory developing methods at the interface between Biofoundries and Materials Acceleration Platforms (MAPs).
The facility is a modular, fully integrated system steered by dynamic scheduling software, with labware moved between instruments by a robotic arm travelling along a central track. Through research and service, we aim to grow into a versatile, modular self-driving laboratory (SDL): one platform that closes the design–build–test–learn loop across data, materials, organisms, biomaterials, automation and artificial intelligence.
Key technologies include an acoustic ejection liquid handler for nanoliter dispensing, a liquid-handling robot with an integrated illumination device for hydrogel photo-crosslinking and optogenetic induction of cells, and equipment for automated cloning and microbiological culturing.
The ARF is currently moving from its testing phase into operation.
Data
Materials
Organisms
Biomaterials
Automation
Artificial Intelligence
Staff
Core Technologies and Methods
Synthetic Biology automation
Automated workflows for molecular cloning, cell-biological screening, directed evolution and protein engineering for mammalian cells and both conventional and unconventional fungi and bacteria.
Material Sciences automation
Combinatorial matrix/polymer formulations, AI-guided formulations for the integration of chemical and biological building blocks in engineered living materials, high throughput physical characterization and efficient automated handling of volatile and viscous liquids
Instruments
Workflows are constructed using methods spanning several instruments, software and data structures. Users and collaborators are encouraged to discuss projects ahead of time
Liquid Handling & Modules
Hamilton STAR (liquid‑handling robot) (1)
Flexible pipetting (µL–mL) with deck‑integrated modules for prepare–process–analyze steps. Automates DNA assembly, PCR setup, media prep, sample normalization, and plate replication. Open API and labware variety make it the central orchestration hub within the Foundry.
Key Modules within the HAMILTON STAR deck:
Colony picker (EasyPick) (2)
Automated selection of microbial colonies based on size/shape/intensity criteria. High‑throughput picking into destination plates for cloning and library construction. Reduces human variability; integrates with growth tracking and downstream PCR.
OptoWell illumination device (3)
Programmable illumination for hydrogel photo‑crosslinking and optogenetic induction. Temporal light control to trigger polymerization or gene circuits in‑well. Synchronizes with pipetting to create complex, time‑resolved protocols.
Other modules (not shown):
Tilter
Controlled plate tilting for gentle mixing, phase settling, or bubble mitigation. Improves assay uniformity before reads or imaging.
Shaker
Orbital/linear shaking for mixing reagents, cell suspensions, and enzymatic reactions. Supports consistent kinetics across plates during incubation or after dispensing.
Heater
On‑deck heating for rapid incubations, enzyme reactions, and temperature ramps. Shortens cycle times between dispense and reaction.
Cooler
On‑deck cooling/cold blocks to protect temperature‑sensitive reagents and cells. Stabilizes pre‑PCR and protein workflows in extended automated runs.
(1)
(2)
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Nanoliter Dispensing
Labcyte/Beckman Echo 650 (acoustic liquid handler)
Nanoliter, tipless acoustic dispensing enables precise, contamination‑free reagent transfer. Ideal for miniaturizing screens, DNA assembly, and combinatorial formulations. Rapid reformatting between plates supports on‑the‑fly experimental design updates.
Analysis
CytoFLEX (flow cytometer) (1)
High‑parameter flow cytometry for rapid, multiplexed cell and particle phenotyping. Quantifies fluorescence and scatter to track expression, viability, and population shifts in DBTL loops. Compatible with multiwell plate loaders for hands‑off runs via the robotic arm.
(1)
Tecan Spark Cyto Microplate Reader (imaging multimode) (2)
Multimode plate reading (absorbance/fluorescence/luminescence) plus live‑cell imaging. Kinetic assays with environmental control support time‑course measurements during automated campaigns. Scriptable protocols for high‑throughput screening that integrate with scheduling software.
(2)
Manipulation
4titude a4S Sealer V2 (plate sealer) (1)
Heat seals microplates (PCR, assay, storage) for evaporation control and contamination prevention. Consistent, barcode‑traceable sealing across varied plate types for robust unattended workflows. Suited for pre/post‑incubation and transport by robot without sample loss.
(1)
Tecan Spark Cyto Microplate Reader (imaging multimode) (2)
Automated removal of adhesive/heat seals from microplates with minimal agitation.
Preserves sample integrity and prevents cross contamination when transitioning steps.
Facilitates rapid access before dispensing, washing, or reading.
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Cytomat 2 C/4XX LiN B1 STD (automated incubator) (3)
Compact, walk‑away incubation with precise thermal control and gentle plate handling. Suitable for microbial growth, enzymatic reactions, and post‑seeding equilibration. Integrates with central scheduling to stage plates between unit operations.
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Cytomat 10 Hotel PH B1 (automated incubator/hotel) (4)
High capacity, robot accessible storage and incubation of plates at controlled temperature/humidity. Rapid plate exchange with barcoding for sample tracking and schedule driven retrieval. Stabilizes conditions for cell culture, enzyme reactions, and long kinetic assays.
(4)
Centrifuge SBS 300 Robotic (plate centrifuge) (5)
Robot‑loadable centrifugation of SBS‑format plates for pelleting, phase separation, and clearing. Programmable speeds/ramps for sensitive samples (e.g., cells, droplets, hydrogels). Critical for normalization steps before reading, cloning, or washing.
(5)
BioTek ELx405 Washer (plate washer) (6)
Automated washing of 96/384‑well plates for ELISAs, cell‑based assays, and bead workflows. Configurable dispense/aspirate patterns reduce residuals and protect delicate monolayers. Enables repeatable assay prep before Spark Cyto reads.
(6)
T-Robot automated thermal cyclers (PCR and other molecular biology reactions) (7)
High precision temperature control for PCR, qPCR prep cycles, and isothermal steps. Supports plate formats for parallel amplification in cloning and library prep workflows. Robot loadable lids/blocks for continuous, unsupervised runs.
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Spinnaker Robot Arm (track mounted) (8)
Central pick and place robot linking instruments along the main rail/track. Moves plates, tips, lids, and consumables between modules under dynamic scheduling. Enables fully integrated, lights out workflows across the Foundry.
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Steering Software
Momentum Dynamic Scheduling Software (1)
Real‑time scheduling engine coordinating all instruments and the Spinnaker robot arm. Optimizes plate routes, resolves resource conflicts, and ensures continuous operation. Adapts to delays or failures, enabling robust, lights‑out automation. Central “brain” of the Foundry, linking design inputs to physical execution.
(1)
Hamilton VENUS Software (for Hamilton STAR) (2)
Advanced protocol development environment for Hamilton STAR robotics. Provides scripting, error handling, and complex conditional logic for pipetting workflows. Integrates on‑deck modules (OptoWell, shaker, heater, cooler, colony picker) into unified protocols. Exposes APIs for higher‑level orchestration by Momentum.
(2)
Work with us
We host Master’s students on projects spanning automated cloning and screening, formulation, and characterization of engineered living materials — good training in laboratory automation, experimental design and data handling. We also support PhD candidates and postdocs applying for their own funding: if you want to build a project at the interface of biological and materials automation, we will help you shape the proposal and host you once it is funded. Get in touch early, since most schemes have long lead times.
Publications
Rabahi, Soraya | Maurin, Lucie | Marachlian, Emiliano | Guendel, Fabian | Mikdache, Aya | Quintero-Castillo, Keinis | Di Donato, Vincenzo | Riou-Ramon, Jessica | Kurup, Akshai J. | Salloum, Yazan | Gros, Gwendoline | Diabangouaya, Patricia | Garcia-Baudino, Camila | Medina-Yánez, Ignacio | Hersen, Pascal | Banderas, Alvaro | Levraud, Jean-Pierre | Lutfalla, Georges | Del Bene, Filippo | Feijoo, Carmen | Eberl, Gerard | Sumbre, German | Boekhorst, Jos | Brugman, Sylvia | Hernandez, Pedro P.
DOI:
The gut microbiota, immune system, and enteric nervous system interact to regulate adult gut physiology. However, the mechanisms establishing gut physiology during development remain unknown. We report that in developing zebrafish, enteroendocrine cells produced interleukin-22 (IL-22) in response to microbial signals before lymphocytes populated the gut. In larvae, IL-22 shaped the gut microbiota, increasing Lactobacillaceae abundance and ghrelin expression to promote gut motility. Impaired motility and ghrelin expression were restored in il22−/− zebrafish by transfer of microbiota from wild-type zebrafish or by introducing only Lactobacillus plantarum. IL-22–deficient mice also had impaired gut motility and reduced ghrelin expression in early life, indicating a conserved function. Thus, before immune system maturation, enteroendocrine cells regulate early-life gut function by controlling the microbiota through IL-22.
Banderas, Alvaro | Hofmann, Maud | Cordier, Céline | Le Bec, Matthias | Elizondo-Cantú, M. Carolina | Chiron, Lionel | Pouzet, Sylvain | Lifschytz, Yotam | Ji, Wencheng | Amir, Ariel | Scolari, Vittore | Hersen, Pascal
DOI:
During mating in budding yeast, cells use pheromones to locate each other and fuse. This model system has shaped our current understanding of signal transduction and cell polarization in response to extracellular signals. The cell populations producing extracellular signal landscapes themselves are, however, less well understood, yet crucial for functionally testing quantitative models of cell polarization and for controlling cell behavior through bioengineering approaches. Here we engineered optogenetic control of pheromone landscapes in mating populations of budding yeast, hijacking the mating-pheromone pathway to achieve spatial control of growth, cell morphology, cell-cell fusion, and distance-dependent gene expression in response to light. Using our tool, we were able to spatially control and shape pheromone gradients, allowing the use of a biophysical model to infer the properties of large-scale gradients generated by mating populations in a single, quantitative experimental setup, predicting that the shape of such gradients depends quantitatively on population parameters. Spatial optogenetic control of diffusible signals and their degradation provides a controllable signaling environment for engineering artificial communication and cell-fate systems in gel-embedded cell populations without the need for physical manipulation.