Optogenetics is a scientific field, where light responsive proteins are engineered into genetically encoded protein switches, which can be utilized to control cellular signaling and behavior in a time- and space-resolved manner. Thanks to these features, optogenetics enables us to find answers to many biological questions that previously could not be successfully addressed.
OptoBase is a platform on optogenetics, meant for both expert optogeneticists, as well as for any researchers, who are yet inexperienced in optogenetics, but find it inviting as a potential new tool to address their biological questions of interest. Currently it covers the field of molecular optogenetics (so called "not ion-flux based optogenetics"), however, in the future it might expand to include this part as well.
The first main feature of OptoBase is an advanced and comprehensive hand-annotated database of existing optogenetic publications, which provides unique searching and analysis possibilities, thus helping scientists to keep track of the ever-growing number of optogenetic applications and tools. The second main feature is the first database of all available optogenetic switches, which aims to provide an immediate access to comprehensive and well-structured information on them. Last but not least, a set of convenient web tools is available, such as one to find the most suitable optogenetic switch candidates for an upcoming optogenetic project, and the illumination units converter. This tool collection will keep growing with time.
We would like to establish OptoBase as the collaborative optogenetics hub, bringing together the scientists who develop optogenetic tools and the ones who only use them as a means to answer complex biological questions, thus promoting cross-disciplinary science.
Each publication in our database is manually analyzed and assigned a set of tags that allow for advanced filtering and analysis options.
Original publications on optogenetics are assigned the tags that describe which optogenetic switches have been implemented within the work presented in the publication (together with the information on which color of light activates them), in which host organism or cell line was this implementation done, and what kind of biological application(s), if any, were achieved through optogenetic control. Furthermore, in case two or more optogenetic switches were combined within a single optogenetic system, the publication is further tagged as Multichromatic. In addition, if the purpose of a publication was to compare the performance of multiple optogenetic switches, then it has a tag Benchmarking.
Review publications on optogenetics are assigned the tag Review and further tags of all optogenetic switches that the publication discusses. However, since the review publications often address a plethora of optogenetic switches, we display their switch tags only at the level of optogenetic switch classes. Note: Regardless of this display choice, the publication search engine still allows you to search at the precision of single optogenetic switch tags.
switch:"VVD"will give the same set of results as
switch:"vivid", likewise if you search for
host:"mammalian"and hence obtain all the publications matching the child-tags of these latter search options)
host:"rat hippocampal neurons"will give you the results that match this particular host cell line, but
host:"neurons"will be able to find the publications that employ any neuronal type of host)
If you use OptoBase for your optogenetics research work, or would like to mention it in your publication as a valuable resource for optogenetics, please, do not cite it as a website URL, but assign it a proper (measurable) credit by citing the paper within which it was formally presented:
K. Kolar, C. Knobloch, H. Stork, M. Žnidarič, W. Weber: OptoBase: A web platform for molecular optogenetics. ACS Synth. Biol. 2018; 7: 1825–1828. DOI: 10.1021/acssynbio.8b00120.