Protocols

A protocol is a detailed, operational guide your lab uses to perform a method. Think “how we run PCR in this lab”, not the published method itself. Protocols live in their own library, separate from your notes, and can be tagged, linked and searched like anything else in Bower. Bower has two kinds of protocol:

• Structured protocols are laid out as sections and numbered steps. The values in each step, such as temperatures, volumes and times, are pulled out so you can check them, and every version is kept. Approve a version and it’s locked, so a record of a run always matches what the protocol said at the time.
• Note protocols are plain written documents in the rich text editor, like a note.

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Creating a protocol

1. Click Protocols in the left rail to open the protocol library.
2. Click New protocol.
3. Choose Structured protocol or Note protocol.

For a structured protocol, choose how to start:

• Attach a file. Pick a PDF or Word (.docx) document. Bower reads the steps out of it and lays them out as a structured protocol. You can correct anything it gets wrong afterwards.
• Start from scratch. You get an empty protocol and add the steps yourself.

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While Bower reads your document

The protocol page shows Reading your document while the import runs. A long protocol takes a few minutes, and you can leave the page while it works. In the library, the protocol shows Importing until it’s done. If Bower can’t find enough procedural detail to lay out as steps, the page says so and shows its reason. You can ask in the chat to try again and pull out whatever it can. If the import fails partway, delete the protocol and import the document again.

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Turning a note protocol into steps

Open the note protocol and click Structure it. Bower reads the document and builds a structured version alongside it. When it’s ready, click Open it. The original document isn’t changed.

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The protocol page

At the top are the protocol’s title and its version bar: the state of the version you’re viewing (for example draft or approved), and its name. Click the name to give the version your lab’s own name, like “Rev C”. A protocol imported from a file links back to it. Below that:

• Parameters are the values your lab chooses each time, with their allowed range or options and a default.
• Method holds the sections, lettered A, B, C, and their steps, numbered A.1, A.2, B.1. Steps that don’t belong to a section are listed under Other steps. Use Expand all or Collapse all to open or close every section at once.

Each step has its title, its text, and sometimes a short explanation of why it matters. Pictures, videos and files attached to the step appear below it. The panel beside the method holds Acceptance criteria, Materials & equipment, Recipes, Safety, Troubleshooting, Review notes and Other details.

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Editing steps and sections

While a version is a draft, you can edit it in place:

• Click Add step or Add section.
• Drag a step by its handle to reorder it, or to move it into another section. Move up, Move down and Move into do the same without dragging.
• Hover over a step and click Remove step to delete it.
• Use a section’s actions to merge it into the one above, or to remove it.
• Click Add media on a step to attach a picture, video or file. Removing it from the step keeps the file itself.

Changes save automatically. Use Undo and Redo at the top of the page, or Cmd+Z and Shift+Cmd+Z.

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Extracted values

When Bower imports a protocol, it marks each value it finds in the steps, such as 37 °C, 5 mL or 10 min, as a highlighted chip, and records how confident it is in each one. A value it isn’t sure about, that no one has checked yet, is highlighted in a warning color with a dashed underline. Check it against your source before you rely on it. Click a value to see the wording it came from (The document said …) and correct it: the amount (or a range), the unit, what kind of value it is, and whether it’s exact, approximate, or “until”. Click Remove: not a value if Bower marked something that isn’t a value. To add a value by hand, click Insert a typed value in the step’s toolbar, or type / and choose Value. Reagents and equipment Bower recognizes are underlined. Hover over one to see what Bower took it to be.

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Versions and approval

Every structured protocol keeps its versions. When a version is ready to use at the bench, click Approve this version. When you approve a version, you can name its state if your lab calls it something other than “approved”. To change an approved protocol, click New version. Bower copies it into a new editable draft, and the approved version stays the one people run until the new one is approved. Once a protocol has more than one version, a Versions list appears beside the method. It marks the current version and the one you’re showing; click any version to open it. You can also jump to the list from the protocol’s menu with Version history.

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Working on a protocol together

If a colleague saves a change to a step while you’re editing the same step, Bower doesn’t overwrite either change. A banner appears on the step: click Review to compare the two, then Keep mine or Use theirs. Until you choose, your version isn’t saved, and Bower asks before you leave the page.

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When something doesn’t come through

An import can miss things: a table it couldn’t read, or a whole part of the protocol such as the materials list. When it does, a notice at the top of the page lists what’s missing, with the page of the source where it knows it. Check those parts against your original document. If a protocol is longer than Bower can load at once, the page tells you it isn’t the whole method.

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The protocol library

The protocol library lists every protocol in your workspace, with its title, collection, tags, who created it, and when it was created and last updated. Structured protocols carry a Steps badge. While an import runs, or if it found no steps or failed, the row says so. Search, sort, and filter by collection, tag, or creator. Select several protocols to act on them together.

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Managing and exporting a protocol

A structured protocol’s ⋮ menu holds access, version history, moving, deleting, and export to PDF or Word. See Protocol menu and export.

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Linking protocols to notes

Protocols become more useful when linked to the notes they relate to. Use the link entity feature to connect a protocol to relevant notes, samples, or collections. This makes it easy to trace which protocol was followed for a given set of observations.

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The Protocols page in the redesigned workspace

If your workspace has the redesigned workspace view, the protocol library looks and works like the workspace’s List view.

• Two tabs. The page heading has two tabs: Protocols, the library itself, and Protocol runs, every run of a protocol with the notes, photos and recordings captured during it. Protocol runs is what other pages call the Capture Stream.
• The top bar holds the workspace search and the New protocol button.
• The toolbar under the heading holds the protocol search box, the Collection, Tags and Created by filters, and a Sort menu.
• Each row shows the protocol’s name, collection, tags, who created it, and when it was created and last modified.

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Finding your way back

When you open a protocol from the list, the top of its page shows a trail such as Protocols / PCR setup, with in and the protocol’s collection beside it. Click the collection to open it in the workspace.

• The back arrow returns you to the list with your search, filters and sort as you left them.
• Closing or deleting the protocol also returns you to the list.
• Opened from Protocol runs, the trail starts at Protocol runs instead.
• Opened from a workspace collection, or from a link, search or chat, the trail shows the collection path, as it does for any other item.

The trail appears on a computer. On a phone, protocol pages keep their usual navigation.