The Basics of Benchling

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Getting Set Up on Benchling

Benchling is a cloud-based software platform that requires an internet connection. We recommend using Google Chrome for optimal performance on Benchling but do support other browsers like Firefox and Safari.

Sign up for a free Benchling account

Use this link to sign up for your free Benchling account. We recommend that you use a school email address when signing up. You can always switch out the email address that you use to login to Benchling later. If you were instructed to join an Organization on Benchling as part of a research group or course, you can do this upon signing up or later after you've signed in.

Finish Benchling Onboarding tutorials for more space

After signing up, each user will be asked what aspect of Benchling they would like to immediately explore: Notebook or Molecular Biology. Each of these applications of Benchling come with their own task list that upon completion, will award you 1 GB of additional space. Note: There are additional tutorials to find that award you space for learning more about Benchling.

Benchling Navigation

Benchling is organized through a central Navigation Bar located on the left side of the screen. Hover over each icon to display its name and click into it to open its contents. You can can close each side panel by clicking on the highlighted icon again.

Home (and the Calendar) 🏠 🗓

The Benchling logo icon will open the Home panel, where you can find your most recent files that you've opened. You can expand this section to access different views of your projects, including daily, 2-week and monthly calendar views.

Projects 💼

The briefcase icon takes you to the Projects panel, where you can create new folders, entries, and protocols, or access your notebook and sequence files. You can search for a project by name, and filter by projects shared with your instructor, a student peer, or organization. Your projects are listed in alphabetical order by default but you can sort them by other parameters as well.

Expand your Projects view by clicking on the ">" at the top right of panel. The resulting expanded view allows you to work with files in bulk which is great for reorganizing or transferring files. You can collapse the expanded view again by clicking on the arrow on the top right corner of the screen.

In order to navigate backwards in Projects (e.g. return to the top level Projects Folder from a project that you've navigated to), simply follow the breadcrumbs trail through the Project / Folder titles.

Search 🔍

The magnifying glass icon will navigate you to the "Search" feature on Benchling that allows you to comb through your data on Benchling. Similar to the "Projects" panel, you can specify parameters such as file type (notebook entries or sequence files) or specific Projects. Additionally, you can set more granular filters or input keywords to help narrow down your search.

You can further sort and organize your search results for better viewing and you can save your search filters and keywords to expedite future queries.

Create ➕

The plus (+) icon allows you to globally create any Benchling file type including: projects, notebook entries, protocols, sequences (DNA and protein), oligos, CRISPR guide RNAs, and more. Note: There are additional ways to create files depending on the file or side-panel that is open.

External Data 💾

The folder icon takes you to the External Data section. You can connect Box, Dropbox, OneDrive or Google Drive accounts to Benchling. Files from these external accounts can be previewed and then dragged directly into the relevant notebook entries.

User Profile 🧑‍🔬👩‍🔬

At the bottom-left of your screen, you will see a circular icon with your initials (or a preview of an image). Navigate to this menu for additional features such as "Templates" and "Organizations" but most importantly for "Settings". You can change your name, your primary/recovery email, institution, and designate a lab. You can also upload a profile picture to use.

Benchling Workspace

Beyond our central main navigation, Benchling displays a unique Workspace depending on certain file type(s) that you create or work on. We'll go over a quick tour of the interface for the most commonly used file types.

Entries and Protocols 📓

Notebook entries are used free-form to plan experiments and record data. Each entry has a formatting toolbar above the entry and you can create a read-only share link to share your entry. If you hover over the icons in local toolbar to the right of the screen, you can access the "History" and "Information" features for this file.

Protocols utilize a standard template for writing up experimental protocols that can then be added into a Notebook entry. They are similar to entries but are more rigid and structured. Some key differences are the formatting toolbar has different functionalities and there is an additional method to discuss protocols on Benchling.

DNA / Protein Sequences and Oligos 🧬

DNA sequences can be created free-hand or imported using external databases. Each DNA sequence has various sub-tabs changing your view of the sequence or displaying other information. You can modify and analyze your sequence and in addition to read-only share links, you can copy your own version of the sequence to work off of. Navigating to the local toolbar to the right of the screen, you can access the following features which have their own sub-menus:

  • Annotations

  • Digests

  • Primers

  • History

  • Alignments


  • Information

Protein sequences can also be created free-hand or imported using external databases . Each protein sequence has sub-tabs that analyze biochemical properties or display specific information. You can modify and analyze your sequence and in addition to read-only share links, you can copy your own version of the sequence to work off of. Navigating to the local toolbar to the right of the screen, you can access the following features which have their own sub-menus:

  • Annotations

  • History

  • Alignments

  • Information

Oligos are stored single-stranded DNA sequences that are typically used as primers that bind other complementary DNA sequences. Each oligo will display general primer properties and include all hyperlinks to any DNA sequences that it has been attached to on Benchling. For oligos, you can only access the "Information" icon.

Workspace Tips

Tip #1. Discover powerful sub-menus and learn convenient shortcut keys

Depending on where your cursor is positioned and the file that you're working on, you will find using "right-clicks" on Benchling will bring up important sub-menus that make certain processes more convenient. Combining this with existing keyboard shortcuts on Benchling will save you time and transform your Benchling experience.

Use these on DNA sequences to edit & copy bases faster, on tabs to close other files simultaneously, or on Projects / Folders for quicker access.

Tip #2. Customize your views and workspace when appropriate

You can declutter your Projects panel view by hiding specific Projects you don't use often. If you want to remove a Project, Folder, or file made by mistake, you can also archive them so they do not show up.Use the Split Workspace button to view multiple sub-tabs on your screen at the same time. When Split Workspace is enabled, you can drag and drop sub-tabs to each half to customize which sub-tabs are open to view.

Tip #3. Use the Benchling Help Center to search for quick answers

At the bottom-right of your screen, click on the blue "?" button that will direct you to the Benchling Help Center. You can find easy and quick tutorials on specific biology concepts or find answers to general questions about your Benchling account.

Congrats! You've finished learning the Basics of Benchling.

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