Table 2.
Tools that can assist in dealing with challenges posed by big data in cryo-electron microscopy (cryo-EM) and tomography (cryo-ET)
| Big-data challenge | Tool | References | Comment |
|---|---|---|---|
| Data transfer | |||
| File-transfer service | Globus | ||
| rclone | rclone.org | Useful for workflow optimisation | |
| Network performance (baselining and benchmarking) | perfSONAR |
(Hanemann et al. 2005) |
|
| RIPE Atlas | atlas.ripe.net | ||
| SolarWinds | www.solarwinds.com | Commercial solution | |
| Data processing and analysis | |||
| Virtual research environments (VREs) | ScipionCloud | (Cuenca-Alba et al. 2017) | |
| COSMIC2 | (Cianfrocco et al. 2017) | Available in the USA | |
| Electron Microscopy Data-Processing Portal | (van Schyndel 2022) | Available in Australia | |
| Characterisation Virtual Laboratory | imagingtools.au/characterisation-virtual-laboratory | Available in Australia | |
| Virtual Desktop Service | desktop.rc.nectar.org.au | Available in Australia | |
| Australian Research Environment | nci.org.au/our-services/data-services | Available in Australia | |
| Cloud-computing workflow | cryoem-cloud-tools | (Cianfrocco et al. 2018) | Uses Amazon Web Services |
| ZeroCostDL4Mic | (von Chamier et al. 2021) | Uses Google Colab to run deep-learning-based programs (e.g. image segmentation, object detection and denoising) | |
| Artificial-intelligence-based solutions | DeepPicker | (Wang et al. 2016) | Particle picking (cryo-EM) |
| DeepFinder | (Moebel et al. 2021) | Identification of macromolecules (cryo-ET) | |
| Topaz-Denoise | (Bepler et al. 2020) | Image denoising | |
| AD_LTEM | (Zhou et al. 2021) | Enhanced resolution and sensitivity | |
| DoG Picker | (Voss et al. 2009) | Particle picking (cryo-EM) | |
| TiltPicker | (Voss et al. 2009) | Particle picking from image tilt pairs (cryo-EM) | |
| DeepEMhancer | (Sanchez-Garcia et al. 2021) | Post-processing of cryo-EM maps | |
| Data management | |||
| Image data management | OMERO | (Allan et al. 2012; Burel et al. 2015; Li et al. 2016) | |
| Pitschi | (Nguyen 2022) | ||
| NexusLIMS | (Taillon et al. 2021) | ||
| XNAT | (Marcus et al. 2007) | ||
| MyTardis | (Androulakis et al. 2008; Meyer et al. 2014) | ||
| User training | MyScope | myscope.training |