Infobiotics v1.0.3 – Modelling platform for Systems and Synthetic Biology

Infobiotics v1.0.3

:: DESCRIPTION

The Infobiotics Workbench is a executable biology framework implementing multi-compartmental stochastic and deterministic simulation, formal model analysis and structural/parameter model optimisation for computational systems and synthetic biology.

::DEVELOPER

Infobiotics team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX

:: DOWNLOAD

Infobiotics

:: MORE INFORMATION

Citation:

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology.
Blakes J, Twycross J, Romero-Campero FJ, Krasnogor N.
Bioinformatics. 2011 Dec 1;27(23):3323-4. doi: 10.1093/bioinformatics/btr571

SYNMOD 2.0.3 – Synthetic Biology Game

SYNMOD 2.0.3

:: DESCRIPTION

Synthetic Biology is the re-design of existing, natural biological systems for useful purposes. And SYNMOD is based on a real scientific project that uses synthetic biology to design new antibiotics.

::DEVELOPER

BIOFACTION

:: SCREENSHOTS

:: REQUIREMENTS

iPhone/iPad/ Android

:: DOWNLOAD

for Android

:: MORE INFORMATION

BioPartsBuilder – Synthetic Biology tool for Combinatorial Assembly of Biological Parts

BioPartsBuilder

:: DESCRIPTION

BioPartsBuilder is a web design tool for the design of biological parts for combinatorial assembly. The software is designed to assist synthetic biologists in retrieving biological sequences, design and optimize biological parts for Golden-Gate.

::DEVELOPER

BioPartsBuilder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BioPartsBuilder

:: MORE INFORMATION

Citation

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.
Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS.
Bioinformatics. 2016 Mar 15;32(6):937-9. doi: 10.1093/bioinformatics/btv664

SYNBADm 20160206 – Toolbox for Automatic Optimal Design in Synthetic Biology

SYNBADm 20160206

:: DESCRIPTION

SYNBADm is a Matlab-based toolbox for the automatic design of gene circuits with targeted functions from libraries of components.

::DEVELOPER

(Bio)Process Engineering Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
MacOsX

:: DOWNLOAD

SYNBADm

:: MORE INFORMATION

Citation:

SYNBADm: a tool for Optimization-based Automated Design of Synthetic Gene Circuits.
Otero-Muras I, Henriques D, Banga JR.
Bioinformatics. 2016 Jul 8. pii: btw415.

BioPartsDB – DNA Synthesis Workflow System for Synthetic Biology

BioPartsDB

:: DESCRIPTION

BioPartsDB is an open-source, modular tool for DNA synthesis workflow and parts registration, ready to be used in most scenarios, such as molecular biology laboratories or iGem teams.

::DEVELOPER

BioPartsDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BioPartsDB

:: MORE INFORMATION

Citation

BioPartsDB: a synthetic biology workflow web-application for education and research.
Stracquadanio G, Yang K, Boeke JD, Bader JS.
Bioinformatics. 2016 Jul 13. pii: btw394.

CloneStudio – Visualization for Synthetic Biology Quality Control

CloneStudio

:: DESCRIPTION

Synthetic biology projects require generation of error- free DNA molecules. A significant current bottleneck is assuring that DNA is error-free at the first point when it moves from an in vitro biochemical system to an in vivo cell-based host. CloneStudio helps eliminate this bottleneck by providing a visual interface to compare a desired sequence with sequence traces, basecalls for individual clones, and positions where the synthetic and desired sequences may differ.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

::REQUIREMENTS

Linux / Windows / MacOsX
JRE

:: DOWNLOAD

CloneStudio

:: MORE INFORMATION

TinkerCell 20120703 – CAD Software for Synthetic Biology

TinkerCell 20120703

:: DESCRIPTION

TinkerCell is a CAD software for synthetic biology. The visual interface allows users to design networks using various biological “parts”. Models can include modules and multiple cells.

::DEVELOPER

Deepak Chandran

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

TinkerCell

:: MORE INFORMATION

Citation:

Deepak Chandran, Frank T Bergmann and Herbert M Sauro.
“TinkerCell: modular CAD tool for synthetic biology”
Journal of Biological Engineering 2009, 3:19 DOI: 10.1186/1754-1611-3-19

Deepak Chandran, Frank T. Bergmann and Herbert M. Sauro.
“Computer-aided design of biological circuits using TinkerCell”
Bioengineering Bugs 2010, 1:4 Pages 276 – 283 DOI: 10.4161/bbug.1.4.12506

Athena r4 – Modular CAD/CAM software for Synthetic Biology

Athena r4

:: DESCRIPTION

Athena is a software that allows biological models to be constructed as modules. Modules can be connected to one another without altering the modules themselves. In addition, Athena houses various tools useful for designing synthetic networks including tools to perform simulations, automatically derive transcription rate expressions, and view and edit synthetic DNA sequences. New tools can be incorporated into Athena without modifying existing program via a plugin interface, IronPython scripts, Systems Biology Workbench interfacing and the R statistical language.

::DEVELOPER

Frank T. Bergmann (fbergman@u.washington.edu)

:: SCREENSHOTS

:: REQUIREMENTS

Windows
r package
SBW

:: DOWNLOAD

Athena

:: MORE INFORMATION

Citation

Athena: Modular CAM/CAD Software for Synthetic Biology
Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro