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.

FAQ

We update the database as frequently as possible, but a ground rule is at least once a week.

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.

In addition to the optogenetic publications, our database also contains a set of basic research publications on optogenetic switch proteins. These publications provide further helpful information for optogeneticists, such as the 3D structure of the switch proteins or insights into the proteins’ switching mechanisms; hence the tag Background.
No, our database is actually supported by a rich ontology, which allows one to search for publications in many advanced ways, including
  • synonyms (e.g. switch:"VVD" will give the same set of results as switch:"vivid", likewise if you search for host:"HEK293-T" instead of host:"HEK293T")
  • parent relations (e.g. instead of for a single mouse host cell line or in vivo experiments in mice, one can search for host:"mouse" or host:"mammalian" and hence obtain all the publications matching the child-tags of these latter search options)
  • classes (e.g. 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)
In case something does not function or look as it should, please report it to us by sending a message via our contact form or writing an email to hello@optobase.org. It is in everyone’s interest to make OptoBase as useful and reliable as possible.
Definitely! If you have any suggestions on how to further improve OptoBase, so that it will best serve the scientific community, we would be happy to hear them. Depending on the context and complexity of your suggested feature/tool, we can either arrange to implement it on our own, or set up a collaboration with you (make you a part of our OptoBase team).

The team

Katja Kolar
PhD student,
BIOSS, University of Freiburg
project management
OptoBase conceptualization and development
Hendrik Stork
MSc student, University of Freiburg
analysis of optogenetic publications
coordination of technical support
Christian Knobloch
BSc student, University of Freiburg
lead software engineering
Matej Žnidarič
PhD student, ETH Zurich
design
Prof. Dr. Wilfried Weber
BIOSS, University of Freiburg
project proposal and advisory support
OptoBase is ran on a server maintained by BIOSS, Centre for Biological Signalling Studies, Cluster of Excellence at University of Freiburg, Germany.