Difference between revisions of "Resources/Software Tools"

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<h1>Software Tools</h1>
 
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<p>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.
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<B>On this page</B> you will find:
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<a href="#design">Design Tools</a>,
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If you know of any other useful, free tools that should be included, please send an email to Traci at <i>traci AT igem DOT org</i> and she will evaluate the tool for inclusion on this page.</p>
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<a href="#modeling">Modeling Tools</a>, and
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<a href="#visualization">Visualization Tools</a>.
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<p>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.</p>
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<p>If you know of any other useful, free tools that should be included, please send an email to Traci at <i>traci AT igem DOT org</i> and she will evaluate the tool for inclusion on this page.</p>
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<h3>Benchling</h3>
 
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<p>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.
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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.
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Benchling is also an iGEM startup!
 
Benchling is also an iGEM startup!
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<h3>Eugene</h3>
 
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<p>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.<br><br>
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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.
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Eugene is maintained by Nona Research Foundation (<a href="https://nonasoftware.org/">https://nonasoftware.org/</a>).
 
Eugene is maintained by Nona Research Foundation (<a href="https://nonasoftware.org/">https://nonasoftware.org/</a>).
 
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<h3>Cello</h3>
 
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<p>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.
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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.
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<p>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.  
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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.  
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<p>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.  
 
<p>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.  
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Revision as of 17:04, 31 January 2019

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Software Tools

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

SynBioHub

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.

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!

Benchling

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/).

Eugene

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/).

Cello

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.

iBioSim

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/).


Pigeon

iGEM Foundation

The International Genetically Engineered Machine (iGEM) Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open community and collaboration. Visit us at igem.org


hq AT igem DOT org


27 Drydock Avenue
Suite 27E-230
Boston, MA 02210


+1.617.500.3106