How to Master Benchling: Tips for Academic Users, from Academic Users

BY Lily Helfrich
January 22, 2020

If you’re like us, you have some big goals for the new year. A few of these goals involve helping you accelerate your research and centralize your research workflows on the cloud. Yours too? Check out these Benchling tips from users to get practical, actionable ideas for leveling up your research.

 

Benchling Notebook: Tips for keeping detailed and accessible notes on the cloud


Search your notes in a matter of seconds

“The search feature has saved me countless hours of searching through old entries by previous lab members or even my own entries! I can quickly pull up all the details with just a few keywords, and my PI loves how I can bring up results from months or years ago with just a few key strokes.”

— Marie, Lab Manager
University of Alabama at Birmingham


Plan your experiments intelligently — with to-do lists and colors

“Creating detailed “to-do” lists and checking them off helps me keep track of what I have already completed. I am still able to look back and search for those tasks in an organized manner!”

— Kendra, Graduate Student
University of California, Berkeley

“I plan out my experiments by color coding and labeling well plates.”

— Alison, Graduate Student
University of Virginia


Use (and reuse) tables to calculate recipes

“Use the (smart) table function to calculate all of the volumes of your reaction. Code a formula to auto-calculate the amount of water or a reagent needed in your reaction so you do not need to get a calculator out.”

— James, Postdoc
University of Western Australia

“I use the built-in spreadsheets for everything. They’re very easy to copy and paste from experiment to experiment, and it’s way easier to adjust volumes of reagents proportionally than in paper notebooks.”

— Shivam, Graduate Student
Stanford University


Link sequences to Notebook entries with @-mentions

“Hyperlinking a sequence to the Notebook and being able to search for a Notebook entry that contains that hyperlink is great.”

— Cholpisit, Graduate Student
University of Washington


 

Benchling Molecular Biology: Tips for centralizing sequence repositories and analysis tools


Keep all of your sequences — and their history — in one place

“For my molecular biology tools and constructs, I keep everything in Benchling. Each folder has specific constructs, and I know I can track versions and include all primers and annotations that I have updated over time. The very useful section lies in the description section, where I can detail what exactly has been updated in the newer version and why, or from what previous constructs a plasmid was assembled.”

— Kathryn, Graduate Student
North Carolina State University

“I enter all my oligos into Benchling so that I can just search my collection when I need to do a new PCR. This prevents me from double-ordering oligos.”

— Roman, Graduate Student
University of Colorado, Boulder


Use the Assembly Wizard to save time and make fewer errors

“The assembly tools make cloning more clear and ensure that I’m less likely to make small, mindless errors. Doing all of the cloning fully in silico is good initially, but the alerts from Benchling about restriction sites or other issues have saved me tons of time.”

— Eric, Graduate Student
Max Delbrück Center for Molecular Medicine


Generate and share feature libraries to simplify annotation

“We have our set of annotation features, which is shared among people in the lab and helps auto-annotate sequences. And every time we come across a useful feature sequence, we add it to the database.”

— Graduate Student
University of Montreal


Use Alignments to quickly analyze sequencing runs

“I upload multiple Sanger sequencing runs to display all the alignments across a plasmid simultaneously!”

— PI
University of Toronto

“The alignment tool for genotyping has helped me a lot. It makes it very easy to analyze many sequences all at once, easily identifying the sample that contains the correct mutation/insert.”

— Graduate Student
Utrecht University


 

Collaboration with Benchling: Tips for building a productive and organized lab


Generate share links to send experimental results to PIs and collaborators

“When I send my PI results from an experiment, I also send them the link to the Benchling Notebook entry. So, if they want to know specifics (concentrations, incubation times, reagents, etc.), they have a comprehensive entry of everything I have done. This also applies to collaborators outside our immediate lab — we often exchange samples or treatments with collaborators across the country (or even internationally), and it is helpful for them to see exactly what experimental steps were performed. There is very little confusion and no need to decipher handwriting on Benchling!”

— Marie, Lab Manager
University of Alabama at Birmingham


Reference collaborators’ sequences to prevent rework and reordering

“We now search for constructs across different lab groups, rather than reordering things.”

— Michael, Graduate Student
Imperial College London

“I always attach my primers to the DNA sequence I am working on. This makes it very easy to reuse or share primers with other people in the lab that may be working on the same constructs.”

— Postdoc
Johns Hopkins University


Take advantage of the Benchling Calendar to get a snapshot of your labmates’ work

“Being able to see collaborators’ Notebook entries through the Calendar makes it very handy to find and go over Notebooks of other people.”

— Adriana, Postdoc
Stanford University


Try using Benchling to run large lab course

“For the first time, I invited 35 students to keep an ELN in Benchling. This was the best choice I made this semester. Normally, I dread reading handwritten, image-stapled notebooks. However, this semester, every Notebook seemed professional, clear, and inviting. I also noticed students were more positive about their efforts and took more time to add photos and results. In writing assignments, I also loved the ability to hyperlink to a plasmid or cDNA I was discussing.”

— Harley, Adjunct Professor
University of Maryland


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Published by Lily Helfrich
VIEW ALL POSTS BY Lily Helfrich

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