HeRBi: Helmholtz Repository of Bioparts

Advances in molecular and cell biology rely on the availability of well-characterized tools that can be used to sense or manipulate biological processes. Many of these tools are genetically encoded parts, that is, proteins or protein domains from various organismal sources that can be combined to produce new biological systems with desired functionality. We established the Helmholtz Repository of BioParts (HeRBi; www.herbi.kit.edu) as part of the Helmholtz Association's Synthetic Biology Initiative. HeRBi relies on voluntarily contributed parts and distributes these on a nonprofit basis to the research community.

The HeRBi repository linked to the European Zebrafish Resource Centre (EZRC; www.ezrc.kit.edu/) places currently a focus on zebrafish-related bioparts, including transgenes and cDNAs. Our stocks comprise 2500 cDNAs of mostly transcription regulators and transgenes. It is planned for the future to place also zebrafish-relevant transcription activator-like effectors derivatives and Crispr guide DNAs in the HeRBi repository. The EZRC maintains several databases that list additional information, including an in situ expression atlas of more than 1200 genes in the healthy and injured adult brain (http://cory.itg.kit.edu/agetaz/index.php).^1,2 A second database summarizes the expression patterns of around 1700 genes encoding mostly transcription regulators in the zebrafish embryo (http://itg-cory.itg.kit.edu/ffdb/index.php). ³ The databases provide information on clone identity, patterns of expression, RNAseq data, etc. (Fig. 1).

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FIG. 1.

Screenshots of FishFactor database providing additional information on the parts stored in Helmholtz Repository of BioParts (HeRBi) at the European Zebrafish Resource Centre (EZRC). Color images available online at www.liebertpub.com/zeb

HeRBi is only as good as its content. We rely on the submission of bioparts by the community. Maintaining such a repository only makes sense if the community uses it.