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 description and sharing of designs through libraries.
Provides an open, flexible and fully featured platform for synthetic biology information storage, retrieval and manipulation. JBEI-ICE brings together different synthetic biology software by lowering the barrier of entry and providing a working solution to the part storage problem.
Deduces the "lab-of-origin" of DNA sequence datasets. predict-lab-origin is an application intending to identify signatures which characterize the processing of engineering DNA and extract them to attribute a specific dataset to a given lab. This method leans on the training of a deep Circonvolution Neural Network (CNN) to perform its classification and does not need a hand-selection of features or sequence-function information.
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 Stack functionality. It is available both as a public website to use and as open source software. SynBioHub uses the Synthetic Biology Open Language (SBOL), an open-source standard for representing genetic designs, and also allows sharing design parts from GenBank and FASTA files.
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.
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 consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design.
Generates an all-inclusive report with every possible annotation for a given type of input. dbReport is a web server that provides a visualization of the input values in a chromosome map with the report, if the input values belong to either human or mouse and if a chromosomal location can be found for at least one of these values. The software is part of bioDBnet, a resource that offers interconnected access to several types of biological databases.
Allows users to perform orthologues conversion enabling the transformation of a given identifier into identifier of a different species. dbOrtho is a web application supporting a wide range of databases identifiers including Biocarta, Drugbank or Pfam. Users can submit either similar or different identifiers format. This web server permits the investigation of more than 20 different species such as danio rerio or plasmodium falciparum.
Converts an identifier of interest into a standardized format. dbFind is a web application, part of the bioDBnet project, which allows users to get a normalized identifier among the totality of ID format which are registrated into the platform, including RefSeq or Biocarta. Additionally, users can get an identifier without specifying the actual type of input. The program can also be used with a mixture of database identifiers.
Facilitates database to database conversion. dbWalk provides users with total control of the type of conversion and intermediate databases. This customizable database conversion tool uses data coverage or user’s confidence in the data quality from a particular database to combine preferences into the path followed. This application is a part of the bioDBnet web platform.
Offers a platform dedicated to the annotation of biological identifiers. dbAnnot is a web application, part as the bioDBnet project, that can be interrogated from a taxon ID, an ID list and which can be run to generate six different types of outputs including diseases, Gene Ontology (GO) terms or pathways, both simultaneously or separately.
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 account. It allows the evolution of nucleotide sequences along a tree for user defined systems of neighbourhoods and instantaneous rate matrices. Simulations have shown that SISSI produces sequences under constrained evolution in reasonable time.
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.
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 locally. It can integrate external data sources by making map with the SBOL data model. The database allows user to make complex queries, such as searching for all regulatory interactions for a given coding site.
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.
Helps to discover hidden data properties and detect data quality issues. dim_reduction combines normalized edit distance with Isomap and Laplacian Eigenmaps, to visualized synthetic biology biobricks in two dimensional space. The visualization results illustrate that different types of biobricks could be easily distinguished by applying the proposed method, and some inappropriately labeled biobricks could be determined.
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.
Assists users to perform global optimization with different acquisition functions. GPyOpt is a tool based on GPy, a library for Gaussian process modeling in Python. This program permits the management of large data sets via sparse Gaussian process models. It also includes features to optimize physical experiments (sequentially or in batches) and tune the parameters of machine learning algorithms.
Offers a methodology for understanding how different parameters can affect the data output from gel electrophoresis. Gelbox aids in displaying various ways that gel bands, sample molecules, and the gel itself, interact. This tool supplies multiple dynamic representations of a gel under a wide range of conditions: molecules can vary in size, concentration, shape, or degree of aggregation and degradation.
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 combinatorial design generation (Finch), a recombinase-mediated excision-based boolean circuit design (Loxia), an invertase-based permutation machine design (Permuton) and a protocol automation platform (Puppeteer).
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 user interface (GUI) easy to manipulate such as a command line mode that allows users to personalize the software to make it correspond with their needs.
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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