In the following tutorial/guide you'll be introduced to the TeselaGen Community Edition and how you can use it to for DNA Design and more.

The topics covered include:

  1. Access

  2. Creating An Account

  3. Molecules & Sequences

  4. Design

  5. Reports

We have also created specific articles on the following topics which you can access by clicking on them:

  • How To Create An Account on TeselaGen Community Edition

  • Creating and Importing Sequences on the TeselaGen Community Edition

  • DNA Design on TeselaGen Community Edition

Let's Get Started!

The TeselaGen Community Edition provides a unified interface and a compute infrastructure for you to design DNA constructs, automate generation of instructions for building DNA assemblies, design primers, and visualize and edit plasmids for free.

Access:

You can access the TeselaGen Community Edition:

  1. TeselaGen Website: teselagen.com/community-edition/

  2. Direct Link: https://community.teselagen.com/design/client/login

Creating an Account:

Once you're on the launch screen, click on select "Sign up with email" and check the box for agreement policies. On the same screen you can also customize the cookie policies for your account.

Now enter the email address you want to use your TeselaGen Community Edition account and click Next.

In the next step, add your first & last name and type a secure password for your account. Once done click on Save.

Once you've finished Sign Up you will be prompted to the landing page of the TeselaGen Community Edition (the DESIGN module) as seen below:

On the center of the header bar you can find 3 tabs:

  1. Molecules: Here you can save, edit, and create libraries

    1. DNA Sequences

    2. DNA Parts (Read this article to know more about DNA Parts and how to use them)

    3. Sequence Features

    4. DNA Part Sets

    5. RNA Sequences

    6. RNA Parts

    7. Oligos

    8. Amino Acid Sequences

    9. Amino Acid Parts

  2. Designs: Here you can create, edit, import designs for your plasmids & vectors or use pre-existing design templates for assemblies.

    1. Design

    2. Codon Maps

  3. Reports: Here you can view or import your DNA Assembly reports.

One to the left of the header menu you can find 4 icons:

  • Notification: The bell shaped icon will show notifications for your design space.

Once you click on the icon. a toast notification pop-up will show you all your notifications. You can also click on the filter icon to personalize your notification settings:

  • Theme: Click on the moon icon to switch to Dark Theme. The icon will change to Sun and you can click on it to shift to the Light Theme.

  • Search: Use the search icon to search through your libraries and reports.

Sequences

Sequences represent any piece of DNA/RNA, whether it is a plasmid you have in the fridge or a construct you intend to produce with an assembly. You can create a new sequence from scratch or upload them in bulk.

On the TeselaGen Community Edition you can both create new sequences or upload them.

Creating a New Sequence

To create a new sequence you click on the "New Sequence" button which gives you the option to start with a completely empty sequence. This will pop up a "Create New Sequence" window where you will be asked to enter a sequence name, description, and tags (such as published, unpublished, IP Status) that can be customized select the checkbox if you want it to be circular and click Save. You will be taken to the Vector Editor tab where you can start creating your sequence.

Importing/Uploading Sequences

To import sequences, click the "Upload Sequences" button. This opens the Upload Sequences dialog. Browse for sequences on your computer to import them. You can select and open or simply drag and drop a folder or file to the dashed area of the window.

Supported Formats: .zip, .ab1, .dna, .fasta, .fas, .fa, .fna, .ffn, .csv, .gb, .gp, .gbk, .gp, .txt, .xml, .xlsx, .rdf

Design

From the header, click on “Designs” and choose the submenu “Designs”. This opens the Design Library which is a repository of designs that you have created or imported.

A design is a schematic representation of a DNA assembly process in which users specify the biological parts and the order they appear in the final assembled construct.

On the TeselaGen Community Edition you can:

Create your own Designs

To create a design, click on the “New Design” button and select "Blank Design". At the “Create New Design” page you have the following options: create a new design, upload an existing design, or load an example design.

Give your design a name (this is required), you can add a description and you have the option to select a Design Layout Type i.e. either combinatorial or add the design to a Project, then just click Save. This will take you to the Design editor.

You can add bins according to your DNA Design Assembly and personalize them accordingly:

  1. Right click on the bin and this will open up a pop-up menu through which you can personalize your bin.

  2. You can also personalize the bin icon according to SBOL standards by left clicking on the icon in the Bin Details section. Moreover, you can also add and select additional information for your part such as its:

    1. Direction

    2. Set specific overlap/overhang position between assembly pieces at junctions that occur at the 3' end of the highlighted bin.

    3. Add or remove a specific number of base pairs from the 5' side of the Gibson/SLIC/CPEC overlap for the junction that would occur on the 5' side of this bin.

    4. Add or remove a specific number of base pairs from the 5' side of the Gibson/SLIC/CPEC overlap for the junction that would occur on the 5' side of this bin.

Loading Example Designs

There are two ways to access our provided example designs:

  1. When creating a new design

  2. When inside the design editor

When creating a new design, you are given an option to create a Blank Design or Load Example Design.

Hover over the Load Example Design and select one of the five example Designs available:

  1. Golden Gate

  2. Gibson

  3. Combinatorial Golden Gate*

  4. Combinatorial Gibson*

  5. Gateway

(You can read more about these assembly methods in this article.) Give your design a name and click submit. You will be directed to the Design Editor, which will be loaded with DNA parts that are defined in the selected example design. When you load up an example design, the parts associated with these designs will be automatically saved in the DNA Parts Library, which can be reused in other designs.

The image below is an example of a Combinatorial Golden Gate* design.

*The Combinatorial Designs are available on the paid version of the TeselaGen software. If you want to either use or explore the feature you can request for a demo here and our team will reach back to you.

Another way to access our example designs and data is to click on the Help tab within the design editor, hover over Load Example Design and select the example design of interest.

Reports
With the TeselaGen Community Edition you can auto-generate reports and protocols for your assembly. Once you've created your design, click on Submit for Assembly. This will run the j5 algorithm which will power the automatic protocol generation step.

You can now view your report from the Reports from:

  • The Reports window by clicking on Reports at the header bar.

  • A notification for creation of report will appear from where you can also access it

    • or you can directly access it from the side information tab in the design editor.

Here you can find:

  • Prebuilt Constructs: Desired sequences that have already been built and are available in your library.

  • Assembled Constructs: Desired sequences to be built in a j5 run.

  • Input Sequences: Sequences that contain the input parts.

  • Input Parts: Segments of a sequence that are being used in a j5 run.

  • Assembly Oligos: List of oligos that need to be directly synthesized.

  • Synthon Sequences: List of DNA pieces that need to be directly synthesized.

  • PCRs: PCR reactions that need to be run to generate the assembly pieces. The software will automatically develop primers and will also provide you the Mean Tm, Delta Tm, Mean Tm3', Delta Tm3'

  • Assembly Pieces: Pieces of DNA that will be put together in a final assembly reaction to give the desired constructs.

  • Assemblies: Assembly pieces that need to be combined to create each reaction.

Did this answer your question?