Resources/Software Tools
Software 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.
If you know of any other useful, free tools that should be included, please send an email to Traci at traci AT igem DOT org and she will evaluate the tool for inclusion on this page.
Design Tools
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.
To learn more aout SBOLDesigner, click here.
Installation requirements: Make sure you have an updated version of Java.
Installation instructions:
- Download the jar file from the tool's Github page here: SBOL Designer Github
- Double-click on the jar file to install SBOL Designer
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.
Benchling is also an iGEM startup!
Pinecone
Pinecone is a web-based application that helps scientists explore, design and manage synthetic protein constructs. Users can efficiently design single proteins, combinatorial protein sets or mutation sets based on functional protein parts. Those designs can then be submitted for manufacture by a DNA synthesizer in order to get double stranded or plasmid DNA delivered to your bench. Pinecone also enables groups to efficiently organize and manage the functional biological relationships between various protein constructs.
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.
To learn more about Eugene, click here.
Eugene is maintained by Nona Research Foundation (http://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.
To learn more about Cello, click here.
Cello is maintained by Nona Research Foundation (http://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.
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.
To learn more about Pigeon, click here.
Pigeon is maintained by SynBioTools (http://synbiotools.org/).
