About SynbioML（synthetic biology module library）
Biological parts repositories serve as an important common resource where synthetic biologists can physically get access to gene samples, which were annotated with crucial properties. So far, there is no modular biological library that focuses on specific products and genetic parts in their biosynthesis pathways. We herein present a modularly designed genetic library, SynbioML, which contains more than 5000 artificial synthetic genes and functional modules for diverse products.
SynbioML covers natural products (terpenes, flavonoid, polyketones, alkaloids, etc), chemical products (steroids, aminoglycosides, polypeptides, etc), nutritions and health care products (fatty acids, vitamins, etc), biofules(bioethanol, aliphatic alcohols, butanediol, etc), environmental biological sensors, products from microbial electrosynthesis and microbial photosynthesis, etc. All these modules are preserved at Tianjin University, China.
These module are obtained primarily through submissions from individual laboratories and batch submissions from national key projects for synthetic biology, including 863 projects and 973 projects. All submissions are prepared with standard format, and SynbioML staff assign accession numbers upon data receipt. SynbioML integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed or Uniprot. BLAST provides sequence similarity searches of SynbioML and other sequence databases.
Users can request any physical modules freely through SynbioML website. The SynbioML is built under MySQL database management system. We also offer an XML schema for standardized data description of genes and modules. Users can get access to the database at http://www.synbioml.org/. Users can search for modules by gene's name, protein name, E.C. number, metabolic pathway, enzyme reaction etc. In addition, users are also able to blast a query sequence.
Contributors and Collaborators: Yuan YJ, Zhou X, Li BZ, Xiao WH, Wang Y, Ding MZ, Tang JJ, Guo F, Li X, Song H, Qi H, Cheng JS, Zhao GR, Zhao XM, Chen T, Li FF, Wen JP, Zhao K, Huang H, Gao F, Li C, Zhu P, Tan TW, Jia XQ, Xi Z, Yang ZY, Wang T, Zhu GP, Lu WY, Zhang WW, Qian JJ
Cooperative organizations: GENEWIZ, Synbio Tech| Genes for life, Genscript, Tianjin University, Nankai University, Institute of Biophysics，Chinese Academy of Sciences, Beijing Institute of Technology