Why Automation is Essential to Cell Therapy

When Karchem Consulting meets with your team to evaluate a system, we’re looking to make sure your systems are reliable and scalable. A huge component of this is automation. Cell therapy workflows are complex, data-dense, and highly sensitive to variation. 

“As organizations scale, manual processes don't scale with them. Automation enables a biotech to move from proof of concept to clinical and commercial readiness without changing its entire operation,” said Devan Shell, Ph.D., a consultant at Karchem. 

The smallest deviations in could have significant downstream impacts, but automation has the power to turn a manual process into a robust, manufacturing-ready pipeline.

Inefficient and Inaccurate: The Risk of Manual Processes 

Without automation, your lab faces compliance gaps, a broken Chain of Identity (COI), costly human errors, and scientists wasting valuable time on manual data wrangling instead of the high-impact science that matters. 

In many labs, flow cytometry outputs are exported as spreadsheets, renamed manually, uploaded into an ELN, and linked to a sample record by hand. Every one of those steps introduces risk.

Shell said the biggest risk isn't just inefficiency; it’s not knowing whether you can trust your own data. 

“Uncertainty around results reduces trust in the data, both internally and with regulators,” he said. 

Regulators don’t just evaluate your science — they evaluate your data integrity. Automation creates defensible, audit-ready records by design, not by cleanup.

In biotech, like many companies, wasted time means wasted money and resources. At Karchem Consulting, we want to make sure your time, money, and systems go further. Anywhere a scientist is manipulating files, data, or inventory is a prime candidate for automation, preventing costly re-runs of experiments caused by human error and lost data. 

“Sample Management and Instrument Data Capture especially can benefit from automation,” said Haley Gallagher, a consultant at Karchem. “Automating sample handoffs ensures context is never lost between teams, while direct instrument integration eliminates the risks of manual data transcription.” 

Bold Science With an Invisible System 

Karchem Consulting sits at the intersection between the physical lab and digital systems. We design workflows that align with how scientists actually work, imitating the in-lab workflow, while ensuring data flows cleanly between integrated instruments and digital platforms/ELNs/LIMS. 

For example, using programs like Benchling Connect, we help clients:

• Integrate instruments directly into Benchling run blocks + experimental templates

• Automate metadata capture and validation via background API usage

• Mass-register and transfer samples throughout the experimental workflow

• Ensure files, results, and entities stay in sync across steps

  
  

“Because we are former scientists, we design workflows that mirror how lab work actually happens, not just how engineers think it happens,” Gallagher said. 

The goal at Karchem Consulting is to make automation feel invisible so scientists can run their experiments while the system handles the rest.

Tackling Automation Misconceptions 

One of the most common misconceptions about automation is that it replaces scientists. In reality, it replaces repetitive tasks, allowing scientists to focus on experimental design and data interpretation. 

When Karchem Consulting comes in, we aren’t replacing your manual systems and leaving you to figure out where the human element comes in. Karchem will connect your systems, enforce rules, and eliminate manual transfers, so scientists can focus on what they do best. Team KC also knows that just because something can be automated, doesn’t mean it should be. Our team will analyze where automation is most applicable and where it delivers the greatest ROI, ensuring your time and efforts aren’t wasted. 

Another common misconception about automation is that it’s only relevant to large companies. Proper automation preparation can be critical for early-stage companies, where time and resources are already limited. It can often be far cheaper and easier to implement a digital foundation at the startup stage, so when you’re ready to automate, the transition is seamless. 

Regardless of company size, a desire to automate can sometimes reveal gaps in a data model that need to be addressed first. The use of automation should cement existing best practices. It can’t resolve the undefined ones. Without a strong data model, automation can be borderline impossible, or even damaging to your science. As Gallagher said, “If you can’t uniquely identify your cell lines and lots, no amount of downstream automation will save you from confusion.” 

For example, if you’re looking to automate the ingestion of result files, but are linking the result files somewhere or only recording one value in a notebook, rather than tracking results in a structured table, you have nothing to automate off of. Once our team is sure your system is ready for automation, Karchem will make sure your scientists understand the workflow and are trained on new processes. Even the best systems will fail if scientists aren’t trained and motivated to use them. 

“Start small, but design with the future in mind,” Shell said. “Choose systems, like Benchling, Revvity, and Labguru, that support extensibility, and partner with teams, like Karchem Consulting, that understand both the science and the informatics.” 

An Ongoing Process 

Automating your systems isn’t a one-and-done process. Team KC will stick with you as your lab grows, making sure you get the most out of your systems. Choosing to automate isn’t just a technical upgrade; it’s a strategic enabler to help your biotech and your science grow. In cell therapy, traceability, consistency, and speed are non-negotiable. When used properly, automation can become foundational to the success of your lab and your science, saving you time and avoiding the most expensive mistakes. 

Ready to transform your lab's data infrastructure? Contact us at Karchem Consulting today to get started.