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Unclassified software tools | Synthetic biology

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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 to a control experiment. It aims to quantify relatively small-scale screens. The tool comprises three independent methods: (i) produces colony size measurements, (ii) produces a measure of genetic interaction strength and (iii) permits to visualize interactively and test results for Gene Ontology (GO) term enrichment.
SBOL validator/converter
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 interface, or using a web service via RESTful API calls. The validator checks all required and best practice rules set forth in the SBOL specification document, and it reports back to the user the location within the document of any errors found. The converter is capable of translating from/to SBOL 1, GenBank, and FASTA formats to/from SBOL 2. The SBOL Validator/Converter utility is released freely and open source under the Apache 2.0 license.
Automated design of genomic Southern blot probes
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 sequence. It can design polymerase chain reaction (PCR) primers to facilitate the recovery of probes from cellular DNA for subsequent Southern blotting. This tool uses a brute-force search approach to significantly improve the chances of finding the best probe for loci of interest.
Seq-Gen / Sequence Generator
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 of the commonly used (and computationally tractable) models of DNA sequence evolution. It also allows the repetitive simulation of DNA sequences under most of the models of nucleotide substitution that are commonly used for the reconstruction of phylogenies. Seq-Gen provides a flexible and efficient source of such simulations under a wide range of models of substitution, and may be a useful tool for researchers studying the phylogenetic relationships and molecular evolution of DNA sequences.
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 SBOL 2.0 data model. That is, libSBOLj enables software tools to use its API to construct objects to store data. In addition, the library distribution includes detailed documentation of the class definitions and the methods provided by the API. In particular, libSBOLj organizes all SBOL data within an SBOLDocument object. The SBOLDocument includes a collection of each type of TopLevel object (i.e., Collection, ModuleDefinition, ComponentDefinition, Sequence, Model, or GenericTopLevel). Every object has a uniform resource identifier (URI) and consists of properties that may refer to other objects, including nonTopLevel objects, such as SequenceConstraint and Interaction objects. libSBOLj organizes the URI collections to enable efficient access, and validation of uniqueness. The libSBOLj library provides methods to create, access, update, and delete all of the data objects and properties in SBOL 2.0.
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 able to produce same colony sizes to other tools in simple cases but outperforms them by handling a wider variety of screens and more accurately quantify colony sizes from difficult images. The tool contains several methods which can be used for autorotation of plates, noise removal, contrast adjustment and image resizing.
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 organism-specific databases (17 organisms including six model organisms and their interactions), COG/KOG, GO and IntAct are warehoused. The built in connection to technical and engineering terms enables a simple switching between biological concepts and concepts from engineering, electronics and synthetic biology.
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 experiments such as knock-out mutants and RNAi experiments. To infer the network topology and dynamic models, it allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS.
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