Uploading Files

This lesson is for intermediate Antha users who wish to customise their Antha experience with edited files for upload.

About this tutorial

This lesson is an overview of the different ways in which you can download templates for, edit, and upload custom files which modify your laboratory workflow. For worked examples of how to edit these files, check out the Case Studies section of the documentation.

Things you'll need

Before you get started you will need an Antha license so that you have access to Antha OS. It may also be helpful if you download a copy of Gene Designer.

What you'll learn

  1. How to upload design files
  2. How to upload plate layout files
  3. How to upload bundle files

Design files

If you want to construct an assembly de novo, you must first provide a digital representation of your genetic design, which is to say, a file which contains the DNA base pairs that make up your new assembly. In the Antha OS environment, you can upload your design as a Gene Designer file (.gdx)

Download the template

The templates for all of the files compatible with the Antha OS environment can be found in the Type IIS Construct Assembly Protocol card.

To access the Type IIS Construct Assembly Protocol card, select the "Protocol" tab at the top of the app and choose the "Type IIS Construct Assembly" card.

Uploading files

Within the protocol card there is a link for downloading a .zip of template files. Click on the yellow "Download the template files" text to download this .zip archive.

Uploading files

Once the file has downloaded, unzip the archive to access the files.

Uploading files

Within the unzipped folder you will find three template files: A sample .json bundle file, a sample .gdx design file, and a sample .csv plate file.

Uploading files

Open the .gdx design file in Gene Designer to begin editing.

Edit the file

Instructions for using Gene Designer can be found here (pdf link).

Upload the file

Once you have finished editing the design file, you can upload it in one of two places.

Uploading the file in card view

If you are looking to assemble your construct with the Type IIS Construct Assembly Protocol Card, you can upload the design file in the same place where you downloaded the template files. Drag the file onto the uploader area indicated by the dashed line, or manually select the file using your file explorer.

Uploading files

Once your file is uploaded, click the "Run Simulation" button to test whether your assembly is valid.

Uploading files

Uploading the file in the Workflow Editor

If you are looking to use your design in a custom workflow using the workflow editor, you must find an element which uses a design file as an input. One such element is "ParseDesign"

Uploading files

To upload the design file to such an element, click on the element's name in the Parameters section of the Workflow Properties sidebar. Find the parameter for the design file and click the upload icon to upload your new .gdx file.

Uploading files

Uploading files

Plate Layout File

The Plate Layout file is available for when you need to manually specify a custom plate.

Download the template

There are three places where you can download the plate layout file: The Type IIS Construct Assembly Protocol card, the Workflow Information Sidebar (which is shared between the Job Queue and the Dashboard) or within the Plate Prep task of an existing job.

Getting the template files through the Type IIS Construct Assembly Protocol card

The templates for all of the files compatible with the Antha OS environment can be found in the Type IIS Construct Assembly Protocol card.

To access the Type IIS Construct Assembly Protocol card, select the "Protocol" tab at the top of the app and choose the "Type IIS Construct Assembly" card.

Uploading files

Within the protocol card there is a link for downloading a .zip of template files. Click on the yellow text reading "Download the template files" to download this .zip archive.

Uploading files

Once the file has downloaded, unzip the archive to access the files.

Uploading files

Within the unzipped folder you will find three template files: A sample bundle file, a sample .gdx design file, and a sample .csv plate file.

Uploading files

Open the .csv plate file to begin editing.

Getting an existing plate layout file from the Dashboard or the Job Queue

You can modify the input plate in the Dashboard or the Job Queue by downloading the auto-generated input plate, editing it, and re-uploading it.

Scroll down on the Workflow Details sidebar until you see "Plate files." Click on the input plate (the one with the blue icon).

Uploading files

Open the downloaded file and save to a memorable location

Uploading files

Getting the template file in the Plate Prep task of your workflow

You can also modify the input plate in the Plate Prep Task View by downloading the auto-generated input plate, editing it, and re-uploading it.

From the Dashboard of a selected Job, click on the Plate Prep task.

Uploading files

Choose a plate for which you would like to download the plate layout file. Click the word "Download" above the plate image.

Uploading files

Your plate layout will be downloaded as a .csv file which you can edit and upload elsewhere.

Uploading files

Edit and upload the file

To learn more about editing and uploading the plate template file, see the Editing plate layout lesson.

Bundle File

The bundle file is a document which combines the workflow and parameters parts of a job and is written in JSON format.

Download the template

The templates for all of the files compatible with the Antha OS environment can be found in the Type IIS Construct Assembly Protocol card.

To access the Type IIS Construct Assembly Protocol card, select the "Protocol" tab at the top of the app and choose the "Type IIS Construct Assembly" card.

Uploading files

Within the protocol card there is a link for downloading a .zip of template files. Click on the yellow text reading "Download the template files" to download this .zip archive.

Uploading files

Once the file has downloaded, unzip the archive to access the files.

Uploading files

Within the unzipped folder you will find three template files: A sample .json bundle file, a sample .gdx design file, and a sample .csv plate file.

Uploading files

Open the bundle file to begin editing.

Download an exported bundle file

Sometimes when you have created and configured a custom workflow, you can to save it in text form for upload later. To do this, click the download icon from the import/export section of the Workflow Properties sidebar. A bundle file will be downloaded to your machine.

Uploading files

Edit the file

To edit the bundle file, simply open in in the text editor or IDE of your choice. However, doing so can be risky and prone to error, so it is recommended that any editing of the bundle file happen in the Workflow Editor.

Upload the file

Once you have edited your bundle file (or you wish to upload it for editing) navigate to the Workflow Editor by clicking the "Editor" tab in the top navigation bar. Click on the upload icon in the Workflow Properties sidebar to bring up an upload window, and select the bundle file of your choosing.

Uploading files