Getting Started with Gnomesh

1. Create an account and log in

1. Open Register. Enter a Username, your Email, a Password and the same password again under Confirm Password. First and last name are optional. Press Register.
2. If the server can send email, Gnomesh emails you a link to confirm your address. You can log in before you confirm it, but other people can only share a project with you by email once your address is confirmed.
3. Log in at Login with your username or email and your password. If you forget either, the login page has Forgot password? and Forgot your username? links.

An administrator can turn off new registrations. If the Register page says registration is disabled, ask the site administrator for an account.

2. Create a project

A project holds your data files, one workflow, and the people you share it with.

1. Open the Projects menu in the site header and choose New Project (or press New Project on the My Projects page).
2. Give the project a Project Name (required) and, if you like, a Description. Press Create Project.
3. Gnomesh opens the new project's page.

3. Meet the workflow canvas

Below the project details is the Workflow Pipeline section with a toolbar and a canvas. A workflow is a set of nodes, each of which does one job, joined by connections that carry data from one node's output to the next node's input. Inputs are the dots on a node's left edge; outputs are on its right edge.

If the pipeline card says Hidden in the basic view, you are in the Simple view, which shows only the workflow's inputs, the Run controls and the results. Press Show pipeline, or the Advanced View button in the Collaborators row, to see the canvas; Gnomesh remembers the choice. Advanced is the default for new accounts.

An empty canvas says This workflow is empty. To add a node, right-click anywhere on the canvas, or press Ctrl + Space. A menu opens with a search box and the list of node types; the ? button beside the search box shows what the highlighted node does.

4. Add a File node and choose your data

1. Open the node menu, type File, and press Enter (or click File). The node appears on the canvas.
2. Click the node to select it. The inspector panel opens with the node's settings.
3. Under File Selection, press Choose…. The Add data window opens. It has two panes: On this computer and In this project.
4. In On this computer, press Choose folder… and pick the folder your data is in. Browse into subfolders by clicking them. Tick the files you want. A Bruker .d acquisition folder is shown as a single item that you tick as a whole.
5. Press Add selected. Gnomesh copies the data into the project. Each item appears in In this project, dimmed while it is being copied, with a progress bar in the window's footer. When the copy finishes, the item is selected for you.
6. Press Use for this node. The File node now shows the item's name.

Instead of the window, you can drag a file or a folder from your computer onto the File node or onto the inspector's drop area. A single file, or a single acquisition folder that Gnomesh can read, is added and assigned to the node at once; anything more opens the Add data window with what you dropped already ticked.

Files Gnomesh can read include CSV and other delimited text, Thermo .raw, mzML, mzXML, and Bruker .d folders in TDF or BAF format. The full list, and the limits, are in the manual's Supported data section.

5. Add a Parse node and connect it

The File node only hands on the raw bytes. The Parse node reads them: a delimited text file becomes columns, and a mass-spectrometry file becomes a run of spectra.

1. Add a Parse node from the node menu.
2. Drag from the File node's output dot (right edge) to the Parse node's input dot (left edge). A connection is drawn between them. If you drag onto empty canvas instead, the node menu opens showing only the nodes that can take that connection, and the one you pick is connected for you.

Gnomesh checks each connection: if the receiving node cannot accept that kind of data, it says so and does not connect them.

6. Add a Mass Spec or Plot node

• Mass-spectrometry data: add a Mass Spec node and connect the Parse node's output to its first (upper) input. The Mass Spec node opens the interactive MS Explorer and turns the run's detected chromatogram peaks into views you can plot.
• Tabular data (CSV and similar): add a Plot node and connect the Parse node to it.

7. Run the workflow

Press Execute Workflow (the play button at the left of the toolbar). Each node runs once its inputs are ready. Many nodes' inspectors then show a summary of their last result. If a node needs something from you, such as a file or a setting, it stops and the message tells you what is missing.

The workflow is saved with the project automatically while Auto-Save is on (it is on by default; see Workflow Settings, the gear at the right of the toolbar). The Save Workflow button saves it at once.

8. Explore the run

After the run, select the Mass Spec node and press Open MS Explorer in its inspector, or double-click the node. The explorer shows the Total Ion Chromatogram at the top and the Mass Spectrum below it.

• Detected chromatogram peaks are drawn as shaded ranges. Click inside a range to see its combined spectrum, or use ← and → to step from one range to the next.
• The Sensitivity slider runs from 0 (no peaks) to 100 (every candidate): more peaks to the right, fewer to the left, with 50 as the default.
• The mouse wheel zooms, a right-drag pans, and a double-click resets the view.
• Press Esc or the close button to leave the explorer. Your detection settings are saved on the node.

Changing the explorer's settings marks the Mass Spec node and everything after it as out of date; run the workflow again to update the nodes downstream.

9. Plot the result

1. Add a Plot node and connect the Mass Spec node's output to it, then run the workflow again.
2. Select the Plot node and press Open plot editor…, or double-click the node.
3. From a Mass Spec node, the editor has one tab per view: the chromatogram, and one spectrum for each detected range. From a Parse node with columns, choose the X column and a Y column in the Data panel, then press Run.
4. Set the title, axis labels, plot type, colors and more from the sections on the left. Changes are saved as you make them; there is no separate save step. Press Esc or the close button when you are done.

10. Export

1. Add an Export node and connect the Plot node to it.
2. In its inspector, type a Filename and choose a Format (PNG or JPEG for plots).
3. Run the workflow. Under Last Export, press Download. A Plot node with several plots gives one image per plot; five or more files download together as one .zip.

For a single plot, the Plot node's own Download PNG button, and the plot editor's PNG button, are quicker.

11. Where to go next

• The User Manual describes every node, its inputs, outputs and settings, the explorers, the plot editor, sharing and keyboard shortcuts.
• To share the project, use + Add Collaborator on the project page (owners only); see Sharing and permissions.