CONTENTS OF THIS ARTICLE
ACCESS TO TESELAGEN COMMUNITY EDITION
The TeselaGen Community Edition provides a unified interface and a computing infrastructure for you to design DNA constructs, automate the generation of instructions for building DNA assemblies, design primers, and visualize and edit plasmids for free.
To access the TeselaGen Community Edition go to this link. There, you will see the launch screen:
To create a new account click on "Sign up with email" and fill in the required information. If you already have an account, use it to access.
In the next step, add your first & last name and type a secure password for your account. Once done click on Save.
LANDING PAGE
The landing page should look like this:
In the center of the header bar you can find the following tabs:
Molecules: Here you can save, edit, and create libraries with the following data:
DNA Sequences
DNA Parts
Sequence Features
DNA Part Sets
RNA Sequences
RNA Parts
Oligos
Amino Acid Sequences
Amino Acid Parts
Designs: Here you can create, edit, and import designs for your plasmids and vectors or use pre-existing design templates for assemblies.
Reports: Here you can view or import your DNA Assembly reports.
Data: You can manage tags and import collections. The tags are shown as a typical library, where you can see the number of items tagged with each one.
Tools: TeselaGen Community Edition gives you access to the following options:
Create Design from Digest Parts
Create Design from Partition Tool
On the left side of the header menu you can find the following icons:
Notification: The bell-shaped icon will show notifications for your design space.
Theme: Click on the sun/moon icon to switch between the light and dark themes.
Search: Use the search icon to search through your libraries and reports.
WORKING WITH LIBRARIES
Libraries contain information on all your biological data, whether it is a reagent you have in the fridge or a construct you intend to produce with an assembly. You can create new entries or upload them in bulk. The information displayed will change depending on the type of data. A typical library looks like this:
You can create a new entry in your library by clicking on the "New" icon and filling in the required information:
On the other hand, you can click on "Upload" and fill in the required information to add new entries in bulk. Notice that you can upload several file formats, paste the sequence, or directly build the CSV file on the software.
DESIGNS
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.
To add new designs to this library, click on "New Design". You can create your design from scratch by selecting the "Blank Design" option and filling in the required information. However, if you prefer to use a template you can load an example design and choose your assembly method (Gibson or Golden Gate).
A typical design layout looks like this:
You can add bins according to your DNA Design Assembly and personalize them:
Right-click on the bin to open a menu and customize it
Change 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 (direction, specific overlap/overhang position, add or remove a specific number of base pairs, etc.)
Keep in mind that whenever 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.
On TeselaGen Community Edition you can't work with combinatorial designs, since they are only available on the paid version of the TeselaGen software. If you want to either use or explore the feature you can request a demo.
ASSEMBLY 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 the creation of the report
The right panel on the Design Editor
On the report you will 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.