Team:METU-BIN Ankara/NextVersion

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Revision as of 15:43, 21 September 2011

METU-BIN iGEM Software TeamProject: Mining for BioBricks

Next Version: Future Plans

NEW FEATURES TO BE INCLUDED in M4B by 2012

Features we would like to introduce in the next version of “Mining for BioBricks” can be listed under two categories.

  • Improvements on our code that we couldn’t add this year due to limited time for the development of the software.
    • Offering search options for multiple input and output parameters.
    • Including all possible biobrick categories in search algorithm, such as DNA, linker etc. Current vesion of M4B is limited to basic parts, which are promoter, RBS, gene, and terminator.
    • Providing link-outs for gene products to external databases such as NCBI, ENSEMBL.
  • Improvements to the Parts Registry that are needed so new information provided can be utilized by our software.
    • In the next version of M4B we are planning to integrate with SBOL. This year we have tried to demonstrate SBOL symbols at least in a limited way, but we faced difficulty in assigning the right categories. For example iGEM classifies biobricks as terminators but in SBOL there are three different subclasses for a terminator and no symbol for a general terminator. Therefore, we suggest that biobricks in the Parts Registry needs to be characterized according to SBOL first, then we can utilize this information to provide SBOL codes to present and share the composite device results choices M4B suggests.
    • We would like to add safety warnings for the composite devices that contain subparts with potential threats. In order to integrate this into M4B, Classification of bioparts in the Parts Registry with gene products that are pathogenic, infective or toxic with potential threats to researchers, public health and environment, is needed. When this information is available, the subparts can be tagged within the composite devices presented in query results to warn the users. By this way, users of the Parts Registry will be aware of the potential dangers of any bioparts they are planning to use in their devices.

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