Synthetic Biology:Tools

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Synthetic Biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.

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This page contains a collection of links to online tools that are related to Synthetic Biology. <wikionly>If you are editing this page, please try to keep the tools in alphabetical order, by tool name.</wikionly>

DNA Tools

• BBOCUS by Ferro and Purrello lab
  • BBOCUS (BackTranslation Based On Codon Usage Strategy) is a re-implementation of the algorithm in Graziano Pesole's BACKTR. It's based on cluster analysis (Complete Linkage algorithm), that requires a similarity matrix D containing distance between each pair of sequences of mRNA. After cluster analysis, backtranslation is performed on sequences of homogeneous pool. Unlike in Graziano Pesole's method, where the choose of homogeneous pool was made by a biologist, the choose of cluster in BBOCUS is fully automatic. A Codon Usage Table (CUT) is created through sequences of homogeneuos pool. Generally, to backtranslate an amino acid in a protein the codon chosen it is the one has maximum frequency.

• Benchling by Benchling, Inc.
  • Free online tools for vector editing, restriction analysis, primer search, multi-sequence alignment, and more.
  • Completely browser-based, no installation required. Check out the demo here.
  • Allows for easy collaboration on sequences between colleagues via shared libraries and/or links.
  • Can also generate vector plasmid maps for presentations and publications.
  • Imports from a wide variety of formats including genbank, fasta, ApE, DNA Strider, lasergene, and more.
  • Tracks complete version history of editing and cloning steps.

• Biopolymer calculator by Schepartz lab
  • Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein

• Clipboard by Austin Che
  • Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence

• Cytostudio by Molecula Maxima
  • An integrated development environment and a compiler for a high-level bio-programming language for Synthetic Biology.
  • Based on iGEM conventions. Check out the intro video.
  • Comprehensive debugger and restriction sites map viewer.
  • Autocomplete for the whole iGEM registry.
  • iGEM parts and devices, BioBrick ids, PDB ids, GenBank accession numbers, FASTA format files and codon usage optimizations are part of the language.
  • Visualize plasmid variables (circular view) and strand variables (linear view) as composites of iGEM parts and devices.
  • Proteins Viewer.
  • Use embedded web views to easily search in common databases.
  • Share open source projects as GitHub repositories in a single click.
  • Write plugins with JavaScript or Visual Basic to fit Cytostudio to your needs.

• DNAWorks by Hoover and Lubkowski
  • A web tool for optimizing melting temperature during gene synthesis.

• File format converter by Austin Che
  • Web tool for converting between sequence file formats.

• Geneious by Biomatters
  • Comprehensive suite of tools for molecular biology
  • Drag and drop import a vast range of file formats
  • Simulate Gibson Assembly, TOPO Cloning and other cloning operations in one easy step.
  • Primer design and testing powered by Primer3
  • Built in codon optimization
  • Immediate access to Golden Gate, Biobrick and other important restriction enzymes
  • Automatic plasmid annotation
  • Automatic tracking of cloning operations

• Genome Compiler by Genome Compiler
  • Genome Compiler is the industry's most user friendly genetic engineering design tool. It allows you to manipulate genetic information; from genes to plasmids to whole genomes. You can rapidly access extensive libraries of genetic parts, and easily order your final design from a variety of providers.
  • Some of the key features include: a user-friendly workspace for handling genetic constructs of all sizes, a powerful gene search capability with lightning fast NCBI access, a built-in constructs library that includes a parts registry, vectors-plasmids, complete genomes, as well as seamless collaboration through the Genome Compiler Cloud. Additionally you can drag components between layers and projects (in multiple tabs), design genetic constructs across tightly integrated layers; operon/part level, amino acid, and DNA, perform re-annotation and reverse complement, employ automatic sequence detection to point out restriction enzymes and protein sub-domains.

• GeneDesign by Boeke lab
  • Collection of online (and some command line) tools for codon optimization and shuffling, restriction site editing, and so on.

• GeneDesigner by DNA2.0
  • Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
  • Free to download and works on Mac or PC. User agreement is somewhat restrictive (i.e., does not allow you to sell genes designed on the program without permission).

• GenoCAD
  • GenoCAD is a design tool that uses collections or libraries of genetic parts and explicit design rules describing how these parts should be combined to engineer genetic constructs. Sets of design rules are called grammars. Grammars underpin GenoCAD’s design environment. This design environment is a step-by-step wizard that guides users through the process of designing complex genetic constructs. When a design is completed, its DNA sequence can be exported using standard formats.
  • The theoretical foundations of GenoCAD were published in Bioinformatics.

• NEB Cutter by New England Biolabs, Inc.
  • Tool for finding restriction sites, et cetera.

• Synthetic Gene Designer by Gang Wu
  • A web platform that allows codon optimization to various extent.
  • Compatible with non-standard genetic codes
  • Integrate CUTG
  • Restriction site avoidance
  • Oligo design

• Vector NTI by Informax, Inc.
  • Free-to-academics tool for sequence analysis and data management.

• j5, DeviceEditor, and VectorEditor online tools
  • j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
  • DeviceEditor: a visual DNA design canvas that serves as front-end for j5
  • VectorEditor: a visual DNA editing and annotation tool
  • The j5 and DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.

• Molecular Cloning Designer Simulator by Zhenyu Shi (Latest update 2016-05-13) Published at MEC
  • MCDS aims to set up a standard way for designing, describing and simulating molecular cloning and genetic engineering.
  • MCDS can design primers, simulate restriction enzyme digestion, gel electrophoresis, Gateway cloning, BioBrick assembly, Gibson assembly, yeast assembly, φC31 (or other) site-specific recombination and assembly, lambda red knockout/knockin, homologous recombination, CRISPR digestion. MCDS allows users to customize restriction enzymes, site-specific recombination sites, gRNAs.
  • MCDS can manage and track every molecular cloning and genetic engineering operation in a unique flowchart, which can be printed or exported as emf vector image. The flowchart of MCDS includes all necessary information including PCR primers, product length restriction enzyme sites and even digestion buffers (users can customize support for digestion buffers).
  • MCDS supports GeneBank formats, AB1 formats (and can display sequencing data) and provides embedded access to NCBI and KEGG.
  • Video introduction of the MCDS usage

RNA Tools

• Appendix by Ambion, Inc.
  • Website with many useful nucleic acid parameters.

• mFold by Michael Zuker.
  • This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.

Protein Tools

• Cn3D by NCBI
  • A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.

• DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics
  • Awesome program for viewing and studying protein structure.

• ExPASy Proteomics server by the Swiss Institute of Bioinformatics
  • Collection of links to many pages to calculate parameters of your favorite proteins

• Modeller by Sali Lab
  • For homology or comparative modeling of protein three-dimensional structures.

• Zinc Finger Tools by Barbas Lab
  • Design Zinc Finger DNA binding proteins

CAD Tools

• TinkerCell by Deepak Chandran
  • Construct computational models using biological parts, cells, and modules
  • Plug-in interface allows contributors to add new features and functions (C and Python)
  • Designed to bridge computational and experimental biology

• Metabolic Tinker by Kent McClymont and Orkun Soyer
  • Construct thermodynamically feasible metabolic paths among user-defined compounds
  • Uses all available metabolic data (updated regularly)
  • Source code available for further development

General Tools

• Colibri by Institut Pasteur
  • E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.

• Registry of Standard Biological Parts by MIT
  • Open repository of BioBricks; the place for all your standard biological parts.

• The public instance of the JBEI Registry
  • A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
  • A site where you can explore the various features of the JBEI Registry software, and even get some work done!
  • Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
  • Follow a link to the underlying open-source software source code.

• PaR-PaR Laboratory Automation Platform
  • PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.

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Making life better, one part at a time.