Synthetic Biology Open Language

Last updated

The Synthetic Biology Open Language (SBOL) [1] is a proposed data standard for exchanging synthetic biology designs between software packages. [2] It has been under development by the SBOL Developers Group [3] since 2008. This group aims to develop the standard in a way that is open and democratic in order to include as many interests as possible and to avoid domination by a single company. The group also aims to develop and improve the design standard over time as the field of synthetic biology reflects this development.

A graphical modeling language called SBOL Visual has also been created to visualize SBOL designs. [4]

Synthetic Biology Open Language (SBOL) standard visual symbols: promoter, primer binding site, cds, restriction site, etc. Synthetic Biology Open Language (SBOL) standard visual symbols.svg
Synthetic Biology Open Language (SBOL) standard visual symbols: promoter, primer binding site, cds, restriction site, etc.

Releases

VersionDate
1.0November 2011
1.1October 2012
2.0July 2015
2.1.0October 2016 [5]
3.0September 2020

Related Research Articles

<span class="mw-page-title-main">Hymenoptera</span> Order of insects comprising sawflies, wasps, bees, and ants

Hymenoptera is a large order of insects, comprising the sawflies, wasps, bees, and ants. Over 150,000 living species of Hymenoptera have been described, in addition to over 2,000 extinct ones. Many of the species are parasitic. Females typically have a special ovipositor for inserting eggs into hosts or places that are otherwise inaccessible. This ovipositor is often modified into a stinger. The young develop through holometabolism —that is, they have a wormlike larval stage and an inactive pupal stage before they mature.

<span class="mw-page-title-main">Jacob Bronowski</span> Polish-born British mathematician and historian (1908–1974)

Jacob Bronowski was a Polish-British mathematician and philosopher. He was known to friends and professional colleagues alike by the nickname Bruno. He is best known for developing a humanistic approach to science, and as the presenter and writer of the thirteen-part 1973 BBC television documentary series, and accompanying book, The Ascent of Man. This endeavour propelled him into the esteemed position of being widely regarded as "one of the most revered intellectuals on the global stage."

<span class="mw-page-title-main">Herbert Spencer</span> English philosopher and political theorist (1820–1903)

Herbert Spencer was an English polymath active as a philosopher, psychologist, biologist, sociologist, and anthropologist. Spencer originated the expression "survival of the fittest", which he coined in Principles of Biology (1864) after reading Charles Darwin's 1859 book On the Origin of Species. The term strongly suggests natural selection, yet Spencer saw evolution as extending into realms of sociology and ethics, so he also supported Lamarckism.

<span class="mw-page-title-main">Beekeeping</span> Human care of honey bees

Beekeeping is the maintenance of bee colonies, commonly in man-made beehives. Honey bees in the genus Apis are the most commonly kept species but other honey producing bees such as Melipona stingless bees are also kept. Beekeepers keep bees to collect honey and other products of the hive: beeswax, propolis, bee pollen, and royal jelly. Other sources of beekeeping income include pollination of crops, raising queens, and production of package bees for sale. Bee hives are kept in an apiary or "bee yard".

Model Driven Architecture (MDA) is a software design approach for the development of software systems. It provides a set of guidelines for the structuring of specifications, which are expressed as models. Model Driven Architecture is a kind of domain engineering, and supports model-driven engineering of software systems. It was launched by the Object Management Group (OMG) in 2001.

<span class="mw-page-title-main">Systems biology</span> Computational and mathematical modeling of complex biological systems

Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach to biological research.

<span class="mw-page-title-main">Synthetic biology</span> Interdisciplinary branch of biology and engineering

Synthetic biology (SynBio) is a multidisciplinary field of science that focuses on living systems and organisms, and it applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature.

Modelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems, to both analyze and visualize the complex connections of these cellular processes.

<span class="mw-page-title-main">Start codon</span> First codon of a messenger RNA translated by a ribosome

The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids.

The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today.

The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.

<span class="mw-page-title-main">BioBrick</span> Standard for components used in DNA synthesis

BioBrick parts are DNA sequences which conform to a restriction-enzyme assembly standard. These building blocks are used to design and assemble larger synthetic biological circuits from individual parts and combinations of parts with defined functions, which would then be incorporated into living cells such as Escherichia coli cells to construct new biological systems. Examples of BioBrick parts include promoters, ribosomal binding sites (RBS), coding sequences and terminators.

Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides de novo. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size.

<span class="mw-page-title-main">Soft science fiction</span> Sub-genre of science fiction emphasizing "soft" sciences or human emotions

Soft science fiction, or soft SF, is a category of science fiction with two different definitions, defined in contrast to hard science fiction. It can refer to science fiction that explores the "soft" sciences, as opposed to hard science fiction, which explores the "hard" sciences. It can also refer to science fiction which prioritizes human emotions over the scientific accuracy or plausibility of hard science fiction.

Natural computing, also called natural computation, is a terminology introduced to encompass three classes of methods: 1) those that take inspiration from nature for the development of novel problem-solving techniques; 2) those that are based on the use of computers to synthesize natural phenomena; and 3) those that employ natural materials to compute. The main fields of research that compose these three branches are artificial neural networks, evolutionary algorithms, swarm intelligence, artificial immune systems, fractal geometry, artificial life, DNA computing, and quantum computing, among others.

During the 2010–11 English football season, Brentford competed in Football League One. The mid-table season was memorable for runs to the final of the Football League Trophy and the fourth round of the League Cup.

GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene networks and other genetic constructs for genetic engineering and is based on the theory of formal languages.

Tal Danino is a synthetic biologist and Associate Professor of Biomedical Engineering at Columbia University.

libRoadRunner is a C/C++ software library that supports simulation of SBML based models.. It uses LLVM to generate extremely high-performance code and is the fastest SBML-based simulator currently available. Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of Python bindings that allow it to be easily used from Python.

References

  1. "The Synthetic Biology Open Language (SBOL)".
  2. Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M (6 June 2014). "The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology". Nature Biotechnology. 32 (6): 545–550. doi: 10.1038/nbt.2891 . PMID   24911500.
  3. "Governance | the Synthetic Biology Open Language (SBOL)". sbolstandard.org. Archived from the original on 2015-12-01.
  4. Quinn, Jacqueline Y.; Cox, Robert Sidney; Adler, Aaron; Beal, Jacob; Bhatia, Swapnil; Cai, Yizhi; Chen, Joanna; Clancy, Kevin; Galdzicki, Michal; Hillson, Nathan J.; Le Novère, Nicolas; Maheshwari, Akshay J.; McLaughlin, James Alastair; Myers, Chris J.; P, Umesh; Pocock, Matthew; Rodriguez, Cesar; Soldatova, Larisa; Stan, Guy-Bart V.; Swainston, Neil; Wipat, Anil; Sauro, Herbert M. (3 December 2015). "SBOL Visual: A Graphical Language for Genetic Designs". PLOS Biology. 13 (12): e1002310. doi: 10.1371/journal.pbio.1002310 . PMC   4669170 . PMID   26633141.
  5. Beal, Jacob; Cox, Robert Sidney; Grünberg, Raik; McLaughlin, James; Nguyen, Tramy; Bartley, Bryan; Bissell, Michael; Choi, Kiri; Clancy, Kevin; MacKlin, Chris; Madsen, Curtis; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Roehner, Nicholas; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H.; Myers, Chris; Sauro, Herbert; Wipat, Anil (2016). "Synthetic Biology Open Language (SBOL) Version 2.1.0". Journal of Integrative Bioinformatics. 13 (3): 291. doi: 10.1515/jib-2016-291 . hdl: 1983/5e0058e9-0cfa-40a5-b0b8-6195f61ff524 . PMID   28187407.