Resources/Software Tools

Software Tools

On this page you will find: Design Tools, Modeling Tools, Collaboration Tools,and Visualization Tools.

Below, you will find various software tools that are free to use and may be of some help in your iGEM project. Many of these are web-based tools but a few will require you to install them on your computer. Instructions for installation will be provided for those tools.

Resources

If you know of any other useful, free tools that should be included, please send an email to the Software Committee at software AT igem DOT org and they will evaluate the tool for inclusion on this page.



Design Tools

BOOST

The Build-Optimization Software Tools (BOOST), which enable optimizing sequences for synthesis and expression. Specifically:

  • reverse-translation of protein sequences into DNA sequences
  • codon-optimization of protein coding DNA sequences,
  • verification and modification of DNA sequences against synthesis limitations (e.g., %GC, repeats) using APIs of commercial DNA synthesis vendors (e.g., Twist, IDT),
  • partitioning of long sequences into synthesizable building blocks including assembly instructions

Seqviz

SeqViz, by Lattice Automation, is a framework agnostic DNA viewer for sequences or files (gb, fasta, etc) with auto-feature annotation. This web tool is customized for use with iGEM parts and is powered by a free, open source JavaScript library of the same name under the hood. You can find links to the library’s source code and documentation from the application.

SynBioHub

SynBioHub is a web-based design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources. It includes the parts from the iGEM Registry.

SBOLDesigner

SBOLDesigner is a tool for creating and manipulating the sequences of genetic constructs. Create and edit genetic designs with a simple drag-and-drop graphical interface, using either your own parts or parts and designs imported from genetic repositories (including the iGEM Registry). Designs can be exported in SBOL, GenBank, or FASTA.

Benchling

Benchling is an integrated software solution for experiment design, note-taking, and molecular biology. It is a free, intelligent research platform with tools for note-taking, molecular biology, and sample tracking. Benchling includes an electronic lab notebook, a molecular biology suite for design and analysis, and a bioregistry to track inventory.

Eugene

Eugene is a human- and machine-readable language developed to aid in the design of novel biological devices. It provides facilities to specify biological parts and devices, which can be composed according to user-defined rules. This allows users to generate biological device designs based on customizable constraints, such as the maximum number of included genetic parts, the directionality of specific components, or the total sequence length of the output device.

Eugene is maintained by Nona Research Foundation (https://nonasoftware.org/).

Cello

Cello is a framework that describes what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering.

Cello is maintained by Nona Research Foundation (https://nonasoftware.org/).

Modeling Tools

iBioSim

iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well.

Collaboration Tools

JOGL

JOGL is a platform where users can launch their projects and collaborate with other iGEM teams to solve problems that address the UN Sustainable Development Goals (SDGs) by pushing the boundaries of synthetic biology. The goals are 1) to foster efficient and transparent collaboration across and within iGEM teams and enhance collective intelligence to address the same goals, 2) to provide iGEM teams accessibility to skills and resources that they lack within their teams, and 3) to contribute to and develop solutions to the Sustainable Development Goals (SDGs).


Visualization Tools

Pigeon

Pigeon is a web-based tool that translates a textual description of a synthetic biology design into an image. It allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be connected to other software tools for visualizing their output.

Pigeon is maintained by SynBioTools (http://synbiotools.org/).