tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

Unclassified tools | Synthetic biology

SBOL
Format

SBOL Synthetic Biology Open Language

Allows to exchange designs within the synthetic biology community. SBOL is a…

Allows to exchange designs within the synthetic biology community. SBOL is a data exchange standard for descriptions of genetic parts, devices, modules, and systems. It encourages and facilitates the…

SGAtools
Web

SGAtools

Allows to design genetic screens. SGAtools helps the user to quantify colony…

Allows to design genetic screens. SGAtools helps the user to quantify colony sizes from images of agar plates, correct for systematic biases in the observations and calculate a fitness score relative…

SBOL…
Web
Desktop

SBOL validator/converter

Provides a validation and conversion utility for the Synthetic Biology Open…

Provides a validation and conversion utility for the Synthetic Biology Open Language (SBOL). SBOL validator/converter can be accessed directly in software using the libSBOLj library, through a web…

SBOLme
Dataset

SBOLme

Hosts a repository of SBOL 2.0-compliant metabolic parts for metabolic…

Hosts a repository of SBOL 2.0-compliant metabolic parts for metabolic engineering. The SBOLme parts are divided into four different types: chemical compound, reaction, EC number, and protein. SBOLme…

SBOL Stack
Dataset

SBOL Stack

Permits to store, integrate, and publish Synthetic Biology Open Language (SBOL)…

Permits to store, integrate, and publish Synthetic Biology Open Language (SBOL) data. SBOL Stack allows the definition of a library of synthetic parts and the storage of designs of biological systems…

SynBioHub
Web
Desktop

SynBioHub

Allows users to upload new SBOL biological designs, download SBOL documents,…

Allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. SynBioHub is a design repository for synthetic biology, built on the SBOL…

SBOL Visual
Dataset

SBOL Visual Synthetic Biology Open Language Visual

Provides an open-source graphical notation that uses schematic “glyphs” to…

Provides an open-source graphical notation that uses schematic “glyphs” to specify genetic parts, devices, modules, and systems. SBOL Visual is a graphical standard for genetic engineering. It…

gitter
Desktop

gitter

Processes robust and accurate analysis of images from colony-based screens.…

Processes robust and accurate analysis of images from colony-based screens. gitter finds the grid of colonies from a preprocessed image and then locates the bounds of each colony separately. It is…

ClusterCAD
Dataset

ClusterCAD

Provides a polyketide synthases (PKSs) database that specifically targets…

Provides a polyketide synthases (PKSs) database that specifically targets engineering applications. ClusterCAD is a web-based toolkit that offers substantial improvements over existing databases. It…

SISSI
Desktop

SISSI Simulating Site-Specific Interactions

Simulates evolution of a nucleotide sequence along a phylogenetic tree…

Simulates evolution of a nucleotide sequence along a phylogenetic tree incorporating user defined site-specific interactions. SISSI is a general framework to take site-specific interactions into…

GENtle
Desktop

GENtle

Allows to edit DNA and amino acid, manage database, map plasmid, etc. GENtle…

Allows to edit DNA and amino acid, manage database, map plasmid, etc. GENtle permits to explore and manipulate DNA, protein, PCR and primer design, sequencing and alignments. It offers a graphical…

libSBOLj
Desktop

libSBOLj

Provides a native Java implementation of the SBOL 2.0 data model, enriched with…

Provides a native Java implementation of the SBOL 2.0 data model, enriched with an application programming interface (API) to instantiate data objects and to define their relations compliant with the…

GenBank…
Web

GenBank Converter

A webapp which converts Genbank format sequence files to and from SBOL XML…

A webapp which converts Genbank format sequence files to and from SBOL XML format files.

REACT
Desktop

REACT

Contains a novel network inference algorithm within the algebraic framework of…

Contains a novel network inference algorithm within the algebraic framework of Boolean polynomial dynamical system (BPDS). The algorithm considers time series data, including that of perturbation…

Automated…
Desktop

Automated design of genomic Southern blot probes

Automatically identifies a probe sequence that is unique within the genome for…

Automatically identifies a probe sequence that is unique within the genome for gene or locus of interest. Southern blot is applicable to region of a genome which contains little or no repetitive DNA…

SBPkb
Desktop

SBPkb Standard Biological Parts knowledgebase

A publically accessible semantic web resource for synthetic biology. The SBPkb…

A publically accessible semantic web resource for synthetic biology. The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology.

Eugene
Desktop

Eugene

An ecosystem of human- and machine-readable languages developed to speed up and…

An ecosystem of human- and machine-readable languages developed to speed up and innovate the design of novel biological DNA Sequences, Parts, Devices, and Systems.

Seq-Gen
Desktop

Seq-Gen Sequence Generator

Simulates the evolution of nucleotide sequences along a phylogeny, using common…

Simulates the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. Seq-Gen has been designed to be a general purpose simulator that incorporates most…

Finch
Web

Finch

A web app for combinatorial genetic design space generation. Finch needs…

A web app for combinatorial genetic design space generation. Finch needs inscription to the web platform Synbiotools to be accessible.

Synbiotools
Web

Synbiotools

A workflow for synthetic biology. Synbiotools contains a tool for design…

A workflow for synthetic biology. Synbiotools contains a tool for design visualization (Pigeon) without inscription needed. After inscription to this platform, it also contains a tool for…

GoSynthetic
Web

GoSynthetic

Provides a simple and fast way to analyse biological processes applying a…

Provides a simple and fast way to analyse biological processes applying a hierarchical database. Four different search modes are implemented. Furthermore, protein interaction data, cross-links to…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.