We are happy to introduce OmicsBox Cloud Sync, the asynchronous execution model that powers a growing number of tools in OmicsBox. With Cloud Sync, a demanding bioinformatics analysis can be launched from the desktop, continue running in the cloud after OmicsBox is closed, and deliver its results directly to Cloud Files when it finishes. The full technical reference lives in Cloud Computation and Storage in the user manual.
CloudSync is already available in OmcisBox 4.0 for more than thirty data-intensive tools across every OmicsBox module, and the list keeps growing. This post explains what Cloud Sync is, what changes for the day-to-day workflow, and how to configure a job through the CloudSync Data Handling wizard page.
What is CloudSync?
Cloud Sync decouples OmicsBox from the long-running part of a computation. When a tool runs with Cloud Sync, the job is submitted to OmicsCloud, BioBam’s AWS-based scientific computing platform, and executed entirely in the cloud. The desktop application only needs to be open long enough to configure and submit the task.
From that moment on, four things change compared to a classic local or synchronous cloud run:
- Jobs run independently from the desktop. OmicsBox can be closed, and the local computer can be put to sleep or shut down. The analysis keeps running in the cloud until it completes.
- Results land in Cloud Files. Output files are written to the user’s cloud storage space. The next time OmicsBox is opened, they are there, ready to be loaded or shared.
- Cloud files are valid inputs. A Cloud Sync tool can read directly from Cloud Files, so large datasets or intermediate results from a previous step do not need to be uploaded again.
- Progress is visible in real time. Status, progress, elapsed time, and log messages are streamed to the Cloud Usage view, which makes it easy to monitor long runs without babysitting the application.
The practical outcome is a workflow where assemblies, alignments, annotations, and other heavy steps no longer block the laptop. An overnight Trinity assembly or a multi-sample STAR alignment can be started in the afternoon and reviewed the next morning.
Where Cloud Sync fits in the OmicsBox workflow
Cloud Sync is available for an increasing number of tools in all five OmicsBox modules. It is especially relevant for compute-heavy steps such as genome and transcriptome assembly, read alignment, functional annotation with InterProScan or EggNOG, and metagenomic pipelines. Tools that support Cloud Sync display a dedicated CloudSync Data Handling page in their wizard, so any user can tell at a glance whether a specific pipeline can be offloaded.
The CloudSync Data Handling wizard page
The last step before submitting a Cloud Sync job is the CloudSync Data Handling page. It controls where the input and output of the job live and how the user is notified when it finishes:
- Save local inputs in cloud: uploads local input files to the user’s Cloud Files space before the analysis starts. This is useful for the first run; subsequent analyses can then read the same files straight from the cloud.
- Save results in cloud: stores output files in Cloud Files when the job completes, so they remain accessible from any device signed in with the same OmicsBox account, including OmicsBox Web.
- Cloud Folder: specifies the directory in Cloud Files where input and output files are stored. A simple project-level folder structure makes it easier to find results later.
- Email notification: sends an email once the job finishes, which removes the need to keep checking the Cloud Usage view during long runs.
Monitoring jobs in Cloud Usage
Cloud Sync jobs appear alongside other cloud tasks in the Cloud Usage view, reachable from View > Cloud Usage. The view lists status, submission time, task name, progress, runtime, input and output sizes, and Cloud Units consumed. Each row has quick actions for stopping a running job, opening the real-time Log Viewer, showing detailed algorithm messages, inspecting the full job metadata, or jumping to the output folder in Cloud Files.
Cloud Units and pricing
Cloud Sync uses the same Cloud Units billing as the rest of OmicsCloud. Most tools are included in the standard OmicsBox subscription at no additional charge. Only Alignment and Assembly tools, such as BLAST, InterProScan, ABySS, SPAdes, Flye, BWA, Bowtie, Trinity, STAR, MEGAHIT, and metaSPAdes, consume additional Cloud Units based on CPU time. The Cloud Usage table shows the exact consumption for each job and which part of it is covered by the subscription.
Getting started
Cloud Sync is part of the standard OmicsBox subscription and does not require any extra setup. Users on OmicsBox 4.0 or later will see the CloudSync Data Handling page on any supported tool. The Cloud Computation and Storage section of the manual and the per-tool pages document the exact parameters for each wizard.
About the Author
Dr. Stefan Götz (CEO)Stefan Götz is the founder and CEO of BioBam. Since founding the company in 2011, he has focused on helping researchers simplify genomics and omics data analysis through practical and accessible software solutions. Under his leadership, BioBam has supported scientists and institutions worldwide in advancing research in human health, agriculture, and environmental science. Stefan remains closely involved in product strategy, innovation, and customer-driven development. He holds a Ph.D. in bioinformatics and combines scientific expertise with entrepreneurial leadership to make advanced bioinformatics more accessible to the global research community.
