The Cloud Software Stack for the Modern, Collaborative Academic Biology Lab

BY Lily Helfrich
January 21, 2020

Managing laboratory data, especially biological data, is no small task. Biological data is complex; scientists have to design intricate biological entities and trace sample lineage, and they have to capture multi-step, multi-day experimental processes. Not to mention, modern biologists need to track experiments of increasing throughput and capture results of various types and formats. More frequently, this work requires a computer — for everything from designing DNA sequences to storing large data files.

And yet, many academic labs are still transcribing notes by hand, keeping traditional paper notebooks while half of their data lives disconnected on their desktop or online. Even when paper notebooks are a scientists’ true source of truth, they end up collecting dust on a shelf or in an unorganized bin that makes it nearly impossible for lab members to find and reference old experiments. If you ask biologists why they still keep paper notebooks, they often can’t really explain it; it’s just what they’ve always done. Old habits die hard.

Modern, highly collaborative labs have seen the paper notebook tradition break down and have switched to the cloud. They have also seen that it’s not enough to switch to desktop-based tools. Like paper, desktop-based software leaves data — and people — disconnected.

Cloud-based software helps scientists do what they once did on paper each day: take notes for a specific date and an experiment, record and reference protocols, display data analysis, and link results to notes. But could-based software also captures complete version control with timestamped audit trails, automatically backs up data, and makes data accessible from anywhere in real-time. Scientists even record data faster on the cloud, which means their results are more accurate and their experiments are more reproducible.

But perhaps the cloud’s biggest impact on research is the way it has enhanced scientist collaboration. Paper, desktop-based spreadsheets, individual emails — they’re all static. When they’re shared, they might not be up-to-date. On the cloud, there’s one version and it’s up-to-date, so everything can be shared with a simple link and searched with a few keystrokes. Data is better centralized. Lab members and collaborators can communicate instantly. Lab-wide repositories and general protocols can be edited by the many people who contribute to them.

Today’s most productive and collaborative labs have adopted software that helps them work faster, together. Here’s what their foundational software stack looks like:

Google Drive or Dropbox: File Storage and Collaborative Editing

A cloud-based storage platform is required for every lab. Given the magnitude and the variety of results that scientists generate — from huge imaging datasets (which scientists need to keep in their entirety, even if they only need a few of them for their notes and a publication) to extensive sets of sequencing files, adopting a reliable, cloud-based storage solution is inevitable. Adopting such a solution also provides a place to store important publications for reference or for journal clubs, and to store and edit work-in-progress: presentations for lab meetings, posters for conferences, grant applications, a draft of a paper.

Cloud-based storage, editing, and collaboration platforms like Google Drive and Dropbox are critical components of the modern academic lab’s software stack. Academic institutions recognize this too, often providing their scientists access to these tools. Like other cloud-based tools with search and link sharing, they ensure real-time access to information and enable better lab-wide collaboration.

Benchling: The Wet Lab Repository

Benchling is a lab’s source of truth for the design, analysis, and records of wet lab experiments. Each lab member captures their day-to-day lab work on Benchling: they write and edit protocols, make calculations and capture results in Notebook entries, design and analyze sequences — plasmids, Sanger sequencing results, primers, CRISPR guides. Together, the lab organizes their research into Benchling projects, maybe one for each person or one for each research area. Other projects might function as repositories: repositories of the lab’s commonly used protocols and repositories of specific sequences, like primers or plasmid backbones, preventing lab members from re-transcribing protocols or reordering sequences.

When these projects are shared with the lab’s Benchling organization, the experimental data is accessible by the entire lab. PIs and mentors review experimental plans and data in detail with their students in real-time. Each lab member shares individual projects or Benchling files with relevant external collaborators. Anyone who wants to find a specific sequence or protocol can search for the most recent version by name. And when a lab member needs to link a file stored in Google Drive or Dropbox to a Benchling entry, they can connect their Google or Dropbox account to Benchling directly.

Slack: More Productive Group Conversations

In today’s workplace, including in academic labs, Slack is replacing email for all internal communication. Like other cloud-based tools and unlike email, Slack is made for teams — teams where people are working on different schedules or in different places. Labs have always known this kind of team: there’s always someone traveling for a conference, someone else across campus in the core facility, a collaborator on the other side of the world, a grad student coming in at 6am to run an experiment and postdoc leaving at midnight. It comes with little surprise, then, that many labs have embraced Slack. Slack makes it easy for lab members to communicate on the fly, to quickly share links (to files in Google, sequences in Benchling, or papers in journals), and to search and reference lab-wide discussions.

Labs set up Slack “channels” for specific discussion topics. Most labs start with an announcements channel, a place where they can share information relevant to the entire lab, such as lab meeting agendas, upcoming seminars, or timing for a lab safety inspection. Many labs have had success fostering productive scientific discourse with Slack: for example, they might create a channel to share recent, relevant publications and another to source feedback on presentations, posters, and figures. Slack can also be an operational tool, where labs create a scheduling channel to help coordinate and swap time at laboratory equipment and an inventory channel to clear up any confusion about the whereabouts of particular reagents or supplies. And of course, all labs need a channel for sharing fun news and science memes.

Academic labs that have adopted tools like Slack, Google Drive, Dropbox, and Benchling have done so because these tools not only enhance group productivity and communication, but also improve group morale. As we enter the new decade, it’s about time for other labs to follow their lead, let go of paper, and embrace the cloud.


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Published by Lily Helfrich
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