Opentrons E-Books

Opentrons e-books, organized by subject and scientific application

You can find all Opentrons e-books here, organized by subject and scientific application. We will be adding more all the time, so keep checking this page!

If you’re looking for something that’s not on this page, please email us at

Documentation by Subject:

Lab Automation

EXCERPT: Let’s consider what makes a good workflow for automation—and what doesn’t. The key general concepts can be applied to almost any protocol. To get started, review “Figure 3: Your Workflow is a Good Candidate for Automation if...” table below and compare that to the workflow you’re considering for liquid-handling automation. If all five features in the table are true for a common workflow in your lab, you should automate it! If some of them are not true for the workflow you are considering, it is probably most practical to stick to manual pipetting. Let’s think about these features in a bit more detail. First, you should aim for an automation solution that will easily accommodate the liquid volumes you use most often in your workflows…

EXCERPT: SCENARIO: A principal investigator plans to expand the number of researchers in her academic lab, but is hesitant to purchase a liquid handler because it might not be used. REALITY: Most laboratory equipment sits idle most of the time. But it’s not the fault of any individual liquid handler; it’s often just the nature of the industry. As many as 25 percent of labs using these tools are engaged in highly complex projects that take time to activate, and labs may not have the time to set up these tools. Also, some automation solutions are only set up to do one protocol, making it difficult or even impossible to switch applications when needed by the lab. Other tools are so complicated that only one or two members of the lab have the expertise to use them, causing all lab members to rely on those few to keep the tools running. And, frankly, some workflows just can’t be automated...

EXCERPT: Thanks to its versatility and variety of applications, life scientists have a range of benefits to reap from open-source. As an example, open-source enables wet lab devices’ features to be fine tuned for particular assays, or even modified wholesale enough to create entirely new ones such as turning a liquid handler into a colony picker. Imaging expert Eric Greenwald of the University of California, San Diego did exactly that: he created an opening in his OT-One, added legs, and mounted it to an inverted microscope. Greenwald uses this combined liquid handling–imaging system with fluorescent sensors to study how drugs impact biochemical signaling in living cells. Another example is customizing the operation of a device. With just a few pieces of high-precision 3D-printed parts, a gear system and some screws, most any scientist can make a gripping device. Greenwald did exactly this, building a gripping device to move petri dishes on the deck of his OT-One...

Documentation by Application:

NGS Library Prep

EXCERPT: scientists benefit from a collection of savings when using automation to create an NGS library. When preparing a library by hand, for example, new technicians must train for days which, including training, reagents, and time, can cost a lab tens of thousands of dollars. Plus, preparing an NGS library by hand takes time—lots of time. In three days, an experienced technician probably prepares eight libraries. On the other hand—actually, with mostly no hands—an automated NGS preparation kit cranks out up to 24 libraries in just one day. That means that in one 5-day week of work, a technician could prepare about 13 libraries with the manual method—or 120 with low-cost automation. So even in just one week, the increase in output really makes a difference...

EXCERPT: The protocols that get the most out of integrating a thermocycler are complex, involving multiple sub-protocols before and after an incubation or PCR step. Let’s look at a next-generation sequencing (NGS) library preparation protocol as an example. By automating only the pipetting and magnetic bead handling steps in the workflow, you take approximately ⅔ of the work off your hands. That's the enzymatic prep (fragmentation + a-tailing, etc.), cleanups, indexing, and pooling steps, which can be done by an OT-2 liquid handling robot and the Opentrons Magnetic Module. Without a thermocycler on the deck of your robot, a person (or another, more expensive robot) has to physically move the prepared reactions into the thermocycler. After the amplification is complete, they also need to physically retrieve the samples—taking them off of the thermocycler and putting them back on the robot for the final magnetic and pipetting steps...

NGS Library Prep Workflow Breakdown With Automated Thermocycler
NGS Library Prep Workflow Breakdown With Automated Thermocycler

Nucleic Acid Extraction

EXCERPT: 1) Streamlined extraction process. Accurate and consistent pipetting with an automated protocol helps to achieve uniformity in key sample processing steps such as lysis, washing, and elution. 2) Less manipulation, less contamination. Fewer manual handling and pipetting steps reduce the threat of external contamination and sample-carryover risk, whether or not the protocol is executed in a sterile workspace. 3) Throughput and scope.  With automated nucleic acid extraction you can process larger sample numbers with greater speed, thus increasing your throughput. This also creates an opportunity to broaden the scope of your research…


EXCERPT: The COVID-19 pandemic exposed a major deficiency of traditional labs: most were unable to quickly pivot from their routine operations to meet the rapidly escalating needs of a global health crisis. Their designs and procedures—equipment, supply chains, workflows, and more—were unable to scale to meet the urgent need for diagnostic testing. But some innovative labs were able to quickly ramp up to meet the demand. By mid-2020, the Pandemic Response Lab in Manhattan, many hospital clinics in Europe, and scores of others around the world had overhauled their operations to process thousands of test samples each day, in some cases starting from scratch. How? They embraced the newest generation of laboratory automation—the cornerstone of which are liquid handling robots from Opentrons that are user-friendly, open-source, and perhaps most important, affordable.

Again, if you’re looking for something that’s not on this page, please email us at