Unclassified tools | Synthetic biology
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…

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…

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.

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
Data

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…

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…

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…

SBOLme
Data

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…

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…

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.

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…

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.

SBOL
Format

SBOL Synthetic Biology Open Language

A data exchange standard for descriptions of genetic parts, devices, modules,…

A data exchange standard for descriptions of genetic parts, devices, modules, and systems. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between…

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…

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