Difference between revisions of "Resources/Software Tools"

 
(10 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 +
 
{{Main2019}}
 
{{Main2019}}
 
<html>
 
<html>
 
<div class="column full_size">
 
<div class="column full_size">
 
<h1>Software Tools</h1>
 
<h1>Software Tools</h1>
−
<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><span class="on_page"></span>
−
<br>
+
<B>On this page</B> you will find:
−
<br>
+
<a href="#design">Design Tools</a>,
−
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>
+
<a href="#modeling">Modeling Tools</a>, and
−
<!--
+
<a href="#visualization">Visualization Tools</a>.
−
<p><b>Mathworks Sponsorship Offer</b>
+
</p>
 +
 
 +
 
 +
<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>
 +
 
 +
<div class="highlight post_item gray">
 +
<div class="details">
 +
<span class="icon notice"></span>
 +
<div class="title">Resources</div>
 +
</div>
 +
<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>
 +
</div>
 
<br><br>
 
<br><br>
−
All iGEM teams are welcome and invited to sign up for the Mathworks Partner Sponsorship Offer (details can be found <a href="https://2019.igem.org/Sponsors/Special_Offers/Mathworks">here</a>)! As an iGEM Partner, MathWorks will provide complimentary software and technical support to all iGEM 2019 teams for use in the competition.​ ​</p>-->
+
 
 +
<h2>Sponsorship offers</h2>
 
</div>
 
</div>
 +
 +
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2018/f/fe/New-mathworks_logo.jpg">
 +
</div>
 +
<div class="column two_thirds_size">
 +
<h3>MathWorks</h3>
 +
<p>
 +
iGEM Partner MathWorks is offering complimentary MATLAB software, including Simbiology and Simulink, and technical support to all iGEM 2019 teams for use in the competition.​All iGEM teams are invited to sign up for the Mathworks Partner Sponsorship Offer (details can be found <a href="https://2019.igem.org/Sponsors/Special_Offers/Mathworks">here</a>)!</p>
 +
</div>
 +
 +
<div class="clear"></div>
 +
 +
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/4/40/Benchling_500x200.png">
 +
</div>
 +
<div class="column two_thirds_size">
 +
<h3>Benchling</h3>
 +
<p>
 +
Benchling is partnering with iGEM for the first time to help iGEM teams accelerate their work! In 2019, all iGEM teams can sign up for free Benchling accounts, with special access to an enterprise feature, Benchling Sync, and 10 GB of extra space. Learn more <a href="https://2019.igem.org/Sponsors/Special_Offers/Benchling">here</a>.</p>
 +
</div>
 +
 +
  
 
<div class="clear extra_space"></div>
 
<div class="clear extra_space"></div>
 
<div class="line_divider"></div>
 
<div class="line_divider"></div>
−
<div class="clear extra_space"></div>
+
<div class="clear extra_space" id="design"></div>
  
 
<div class="column full_size">
 
<div class="column full_size">
Line 22: Line 57:
  
 
<div class="column third_size">
 
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/8/85/Seqviz-brand.png">
 +
</div>
 +
 +
<div class="column two_thirds_size">
 +
<h3>Seqviz</h3>
 +
<p>
 +
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.
 +
</p>
 +
<div class="button">
 +
<a href="https://tools.latticeautomation.com/seqviz/">
 +
Seqviz ⇗
 +
</a>
 +
</div>
 +
</div>
 +
 +
<div class="clear extra_space"></div>
 +
 +
 +
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/e/ee/Resources_synbiohub.jpg">
 +
</div>
 +
 +
<div class="column two_thirds_size">
 
<h3>SynBioHub</h3>
 
<h3>SynBioHub</h3>
 
<p>
 
<p>
Line 28: Line 86:
 
<div class="button">
 
<div class="button">
 
<a href="http://synbiohub.org">
 
<a href="http://synbiohub.org">
−
SynBioHub
+
SynBioHub ⇗
 
</a>
 
</a>
 
</div>
 
</div>
 
</div>
 
</div>
 +
 +
<div class="clear extra_space"></div>
  
  
 
<div class="column third_size">
 
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/d/d8/Resources_SBOLDesigner.jpg">
 +
</div>
 +
 +
<div class="column two_thirds_size">
  
 
<h3>SBOLDesigner</h3>  
 
<h3>SBOLDesigner</h3>  
Line 42: Line 106:
 
<div class="button">
 
<div class="button">
 
<a href="https://sboldesigner.github.io">
 
<a href="https://sboldesigner.github.io">
−
SBOL Designer
+
SBOL Designer ⇗
 
</a>
 
</a>
 
</div>
 
</div>
  
 
</div>
 
</div>
 +
 +
 +
 +
 +
<div class="clear extra_space"></div>
 +
  
 
<div class="column third_size">
 
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/e/eb/Resources_benchling.jpg">
 +
</div>
  
 +
<div class="column two_thirds_size">
 
<h3>Benchling</h3>
 
<h3>Benchling</h3>
−
<p>
+
<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.
−
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.
+
 
<br><br>
 
<br><br>
 
Benchling is also an iGEM startup!
 
Benchling is also an iGEM startup!
Line 59: Line 131:
 
<div class="button">
 
<div class="button">
 
<a href="https://benchling.com/academic">
 
<a href="https://benchling.com/academic">
−
Benchling
+
Benchling ⇗
 
</a>
 
</a>
 
</div>
 
</div>
Line 68: Line 140:
  
  
−
<div class="column half_size">
+
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/0/01/Resources_eugene.jpg">
 +
</div>
 +
 
 +
<div class="column two_thirds_size">
 
<h3>Eugene</h3>
 
<h3>Eugene</h3>
−
<p>
+
<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>
−
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>
+
 
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>).
 
</p>
 
</p>
  
 
<div class="button">
 
<div class="button">
−
<a href="http://eugene.cidarlab.org/">
+
<a href="http://cidarlab.org/eugene/">
−
Eugene
+
Eugene ⇗
 
</a>
 
</a>
 
</div>
 
</div>
 
</div>
 
</div>
  
−
<div class="column half_size">
+
 
 +
<div class="clear extra_space"></div>
 +
 
 +
 
 +
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/d/db/Resources_cello.jpg">
 +
</div>
 +
 
 +
<div class="column two_thirds_size">
 +
 
 
<h3>Cello</h3>
 
<h3>Cello</h3>
−
<p>
+
<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.
−
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.
+
 
<br>
 
<br>
 
<br>
 
<br>
−
Cello is maintained by Nona Research Foundation (<a href="https://nonasoftware.org/">https://nonasoftware.org/</a>)..
+
Cello is maintained by Nona Research Foundation (<a href="https://nonasoftware.org/">https://nonasoftware.org/</a>).
 
</p>
 
</p>
  
 
<div class="button">
 
<div class="button">
 
<a href="http://cellocad.org/">
 
<a href="http://cellocad.org/">
−
Cello
+
Cello ⇗
 
</a>
 
</a>
 
</div>
 
</div>
Line 107: Line 188:
 
<div class="column full_size">
 
<div class="column full_size">
 
<h2>Modeling Tools</h2>
 
<h2>Modeling Tools</h2>
−
<br><br>
+
</div>
  
  
 +
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/b/b3/Resources_ibiosim.jpg">
 +
</div>
 +
 +
<div class="column two_thirds_size">
 
<h3>iBioSim</h3>
 
<h3>iBioSim</h3>
  
−
<p>
+
<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.  
−
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.  
+
 
</p>
 
</p>
 
<div class="button">
 
<div class="button">
 
<a href="http://www.async.ece.utah.edu/ibiosim">
 
<a href="http://www.async.ece.utah.edu/ibiosim">
−
iBioSim
+
iBioSim ⇗
 
</a>
 
</a>
 
</div>
 
</div>
Line 125: Line 210:
 
<div class="clear extra_space"></div>
 
<div class="clear extra_space"></div>
 
<div class="line_divider"></div>
 
<div class="line_divider"></div>
−
<div class="clear extra_space"></div>
+
<div class="clear extra_space" id="visualization"></div>
  
 
<div class="column full_size">
 
<div class="column full_size">
 
<h2>Visualization Tools</h2>
 
<h2>Visualization Tools</h2>
 +
</div>
 +
 +
 +
 +
<div class="column third_size">
 +
<img src="https://static.igem.org/mediawiki/2019/6/66/Resources_pidgeon.jpg">
 +
</div>
  
 +
<div class="column two_thirds_size">
 +
 
<h3>Pigeon</h3>  
 
<h3>Pigeon</h3>  
 
<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.  
Line 140: Line 234:
 
<div class="button">
 
<div class="button">
 
<a href="http://pigeon.synbiotools.org/">
 
<a href="http://pigeon.synbiotools.org/">
−
Pigeon
+
Pigeon ⇗
 
</a>
 
</a>
 
</div>
 
</div>
Line 147: Line 241:
  
  
−
 
+
</div>
 +
</div>
 
</html>
 
</html>
 +
{{Footer2019}}

Latest revision as of 17:50, 27 August 2019

Loading...

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.



Sponsorship offers

MathWorks

iGEM Partner MathWorks is offering complimentary MATLAB software, including Simbiology and Simulink, and technical support to all iGEM 2019 teams for use in the competition.​All iGEM teams are invited to sign up for the Mathworks Partner Sponsorship Offer (details can be found here)!

Benchling

Benchling is partnering with iGEM for the first time to help iGEM teams accelerate their work! In 2019, all iGEM teams can sign up for free Benchling accounts, with special access to an enterprise feature, Benchling Sync, and 10 GB of extra space. Learn more here.

Design Tools

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.

Seqviz ⇗

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