We are mainly at the stage of testing, debugging and maitenance work. However, new features may still appear and refactorings may still take place. We will be happy, if you would try it out the current version and get back to us by using our Issue Tracker or writing an e-mail to Artsemi Yushkevich.
🎉The first standalone executable release for GPU workstations is available now! 🎉 You may find it on the Releases page.
TomoBEAR is an automated, configurable and customizable full processing pipeline for tomographic cryo-electron microscopy data and subtomogram averaging in the broad field of Cryo-ET based on best practices in the scientific research groups of Misha Kudryashev:
- (previous one) Independent Research Group (Sofja Kovaleskaja) at the Department of Structural Biology at MPIBP (Max Planck Institute of Biophysics) in Frankfurt (Hesse), Germany;
- (current one) In situ Structural Biology Group at the MDCMM (Max Delbrück Center of Molecular Medicine) in Berlin, Germany.
Information on the installation, setup and usage as well as tutorials and example results can be found in the corresponding wiki.
User branches:
main- more or less stable version (in a normal case use this one, please!);develop_live- an experimental (non-stable) version with live data processing functionality (warning! new functionality and bug fixes from main coming here slowly!)
All the other branches are not intended for user usage! They hold non-stable development versions (with new features, bug-fixes and refactorings).
In the future we are planning to introduce wiki versioning as well, stay tuned!
In the following picture you can see a flow chart which visualizes which steps TomoBEAR will and can do for you in an automated and parallel manner. TomoBEAR supports workstations and single interactive nodes with GPUs on the comuting clusters at the moment. We are also working towards enabling the support of computer clusters through a queue manager like SLURM or SGE (Sun Grid Engine).
Note that it is not needed to start from raw data but you can also use already assembled tilt stacks if you provide the angular information.
Orange processing steps in the flow chart are mandatory and must be executed by TomoBEAR. Yellow boxes are optional and can be activated if desired.
In case of any questions or errors do not hesitate to contact one of the provided persons mentioned in the Contacts section below. Alternatively, for bug reports or feature suggestions you may use our Issue Tracker. Please, be polite and precise!
We are grateful to the following organizations:
- Buchmann family and BMLS (Buchmann Institute for Molecular Life Sciences) for supporting this project with their starters stipendia for PhD students;
- DFG (Deutsche Forschungsgesellschaft) for funding the project.
As well we are grateful to the structural biology scientific research group of Werner Kühlbrandt at the MPIBP (Max Planck Institute of Biophysics) and the MPIBP in Frankfurt (Hesse), Germany for support.
Prof. Dr. Misha Kudryashev (Project Leader) - Principal Investigator, head of the In situ Structural Biology Group at the MDCMM (Max Delbrück Center of Molecular Medicine) in Berlin, Germany.
Nikita Balyschew (Developer) - Guest Scientist in the In situ Structural Biology Group at the MDCMM (Max Delbrück Center of Molecular Medicine) in Berlin, Germany; alumni Ph.D. student in the Independent Research Group (Sofja Kovaleskaja) at the Department of Structural Biology at MPIBP (Max Planck Institute of Biophysics) in Frankfurt (Hesse), Germany.
Artsemi Yushkevich (Contributing Developer) - Ph.D. student in the In situ Structural Biology Group at the MDCMM (Max Delbrück Center of Molecular Medicine) in Berlin, Germany.
Vasili Mikirtumov (Application Engineer) - Ph.D. student in the In situ Structural Biology Group at the MDCMM (Max Delbrück Center of Molecular Medicine) in Berlin, Germany.