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How useful is Systems Biological Mark Up Language (SBML)?

written by: Finn Orfano • edited by: Leigh A. Zaykoski • updated: 5/6/2008

More and more biology friendly languages are coming on the dock and SBML is one among them. SBML has become highly popular among those who pursue systems biology.

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    More and more biology friendly languages are coming on the dock and SBML is one among them. SBML has become highly popular among those who pursue systems biology.

    The word ‘biological mark up’ with the title gives away the nature of this language!  Biology means the study of living organisms, and mark up, means marking each of the biological structures within the organism which make it.

    Language here refers to the computer software that scientists use in practice to exchange data, databases and information with each other.  Biological research takes place in diverse places, in fact all over the world, given that biological species, including humans, differ in forms, content, certain organisms not present elsewhere.

    And since the study of biology has gone deep down to the elemental level, such as the discovery of the DNA and RNA (which are considered the driving force for organic biology), the level has now reached the genetic code stage. Considerable articles about DNA have now made headlines the world over: the discovery of the DNA, the genetic code cracking which has helped many people to get better drugs and treatment, its helping to reconcile evidences of crime, and also the parentage by comparing the genetic code (more famously known as the DNA test).

    Since these studies are carried out simultaneously everywhere in the world, members of the scientific community were using different types computer software, and thus there was difficulty in obtaining information from other computers which could help other scientists. In the research community, knowledge is not hoarded but shared.

    Thus was born the systems biological markup language (SBML). A meeting was held and It was agreed upon by the researchers, software professionals, and systems analysts who attended. It was decided here that henceforth the databases would be based on this software, using the XML language feature.

    This helped the researchers to reach into other databases. Since SBML was written in open source code, they could incorporate the software within their own software, and make changes in order to make their research jobs easier.

    This software underwent a number of changes, and has now become the industry standard for biology and biomedical informatics professionals. Researchers may borrow or place their own findings in databases using this language feature, thereby giving a considerable push to sharing research across borders. The information can also be shared across various software packages being used by the community.

    The software is continuously updated depending upon the feedback received from the researchers. A team  makes any necessary updates or modifies the language to meet the emerging needs of researchers.