Apps Collections for Synthetic Biology

 

Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization [1]. Here are bio-apps collections for you. Personally Tinkercell and UNAFold are mostly used.

Circuit design and simulation
 Biojadehttp://web.mit.edu/jagoler/www/biojade/
 Tinkercellhttp://www.tinkercell.com/Home
 Asmpartshttp://soft.synth-bio.org/asmparts.html
 ProMoThttp://www.mpimagdeburg.mpg.de/projects/promot
 GenoCADhttp://www.genocad.org/genocad/
 GEChttp://research.microsoft.com/gec
 TABASCOhttp://openwetware.org/wiki/TABASCO#TabascoSimulator
 Hy3Shttp://hysss.sourceforge.net/index.shtml
Circuit optimization
 Genetdeshttp://soft.synth-bio.org/genetdes.html
 RoVerGeNehttp://iasi.bu.edu/∼batt/rovergene/rovergene.htm
DNA and RNA design
 Gene Designerhttps://www.dna20.com/index.php?pageID=220
 GeneDesignhttp://www.genedesign.org
 UNAFoldhttp://www.bioinfo.rpi.edu/applications/hybrid/download.php
 mfoldhttp://mfold.bioinfo.rpi.edu/download/
 DINAMelthttp://dinamelt.bioinfo.rpi.edu/
 Vienna RNA packagehttp://www.tbi.univie.ac.at/∼ivo/RNA/
 Vienna RNA web servershttp://rna.tbi.univie.ac.at/
 Zinc Finger Toolshttp://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
Protein design
 Rosettahttp://www.rosettacommons.org/main.html
 RAPTORhttp://www.bioinformaticssolutions.com/products/raptor/index.php
 HHpredhttp://toolkit.lmb.uni-muenchen.de/hhpred
 Modelerhttp://salilab.org/modeller/
 PFPhttp://dragon.bio.purdue.edu/pfp/
 Autodock 4.2http://autodock.scripps.edu/
 HEX 5.1http://webloria.loria.fr/∼ritchied/hex/
Integrated workflows
 SynBioSShttp://synbioss.sourceforge.net/
 Clothohttp://biocad-server.eecs.berkeley.edu/wiki/index.php/Tools
 Biskithttp://biskit.sf.net

 

Suggested pages listing useful bio-apps maybe you will like in synthetic biology research:

  1. WikiGenes Toolbox ( http://www.wikigenes.org/e/art/e/187.html). As a free on-line tutorial edited by people all around the world, WikiGenes has spirits of Linux: open-source, sharing, interest, so is WikiGenes-Synthetic-Biology page. It enables you fast-learn what is synthetic life.
  2. OpenWetWare (http://openwetware.org/wiki/Computational_Tools).
  3. JCVI (http://www.jcvi.org/cms/research/software/#c614). This page is from J. Craig Venter Institute.

 

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[1] Marchisio, M. A., & Stelling, J. (2009). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 20(4), 479-485. Retrieved from http://www.sciencedirect.com/science/article/pii/S0958166909001001

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