bioAF helps researchers organize genomic data and run computational pipelines. It keeps track of your biological samples and the steps taken to process them. This tool ensures your experiments remain consistent and repeatable. You can manage metadata, handle experimental logs, and trigger compute tasks from one dashboard.

Follow these steps to get bioAF on your computer.

1. Visit the official releases page to find the latest version.
2. Look for the section labeled Assets.
3. Select the file ending in .exe for Windows.
4. Save the file to your desktop or downloads folder.
5. Double-click the file to start the installation.
6. Follow the prompts on your screen to complete the setup process.

Your computer needs specific components to run bioAF effectively. Ensure your current Windows machine meets these standards.

• Operating System: Windows 10 or Windows 11.
• Memory: At least 8 gigabytes of RAM.
• Storage: 2 gigabytes of free disk space for the program files.
• Processor: Dual-core 2.0 gigahertz processor or faster.
• Internet Connection: A stable connection for downloading pipeline components.

Once the installation finishes, you must initialize the platform to connect your data storage.

1. Open the bioAF shortcut on your desktop.
2. On the welcome screen, provide a path to a local folder where the software should store your experimental metadata.
3. If you connect to cloud services like Google Cloud Platform, enter your credentials in the Settings menu under the Cloud Auth tab.
4. Verify that the software detects your system resources. The dashboard lists the status of your compute nodes and storage endpoints.

A pipeline serves as a set of instructions for analyzing biological data. bioAF manages these instructions so you do not have to.

1. Select the New Project button from the main sidebar.
2. Enter a unique name and a brief description for your research study.
3. Add your raw data files by dragging them into the File Manager window.
4. Choose a workflow template from the library. Templates include common tasks such as sequence alignment or variant calling.
5. Map your input files to the workflow parameters by following the on-screen prompts.
6. Click Run to start the calculation.

The dashboard provides a real-time view of your active tasks. Each task generates a unique record. This ensures you know exactly which data produced each result.

• Progress bars indicate the status of each step in your pipeline.
• Color codes show whether a step completed successfully or encountered an error.
• The logs tab displays text outputs for each process. Use this if a step stops unexpectedly.
• You can pause, stop, or restart tasks at any time using the control buttons located near the task name.

Good research requires tracking how you obtained each result. bioAF creates a record for every operation performed within the software.

• Metadata: The software stores details about the sample type, the date of the experiment, and the researcher who ran the task.
• Provenance: You can trace the lineage of any final data file back to its source. Right-click any file in the Results section and select View Lineage.
• Export: You can export these records as reports to share with your team. This makes your work easy to review.

Check for updates frequently to keep your bioinformatics tools current. The software alerts you when a new version becomes available.

1. Navigate to the Help menu.
2. Click Check for Updates.
3. If a new version exists, the software prompts you to download and apply the patch.
4. You do not need to delete your existing projects to update the software. Your metadata and data remain safe during the process.

Most issues arise from file permissions or network interruptions. Review these steps before seeking further help.

• Permission Denied: Ensure you run bioAF with user permissions that allow it to write to your selected storage folder.
• Network Timeout: If you use a cloud-based compute node, verify your internet connection. Refresh the page if the dashboard stops updating.
• Missing Files: Ensure you did not move or rename files while an active task was running. The software requires consistent file paths to maintain the pipeline.
• Logs: If software behaves strangely, open the Logs folder. The most recent log file contains specific error codes that help identify problems.

The software comes with built-in templates for common genomics tasks. These templates act as pre-configured pipelines.

• Alignment: Matches sequencing reads against a reference genome.
• Quality Control: Checks raw files for contamination or errors before you perform analysis.
• Variant Calling: Identifies differences between sample sequences and reference sequences.

To use a template, select it from the template library under the Pipelines menu. You only need to provide the raw data files. The software handles the complex software configurations for you.

Community support makes the platform better for everyone. If you find a bug, create a new issue on the repository tracking page. Include the steps you took to reproduce the problem and the error logs generated by the system.

For questions about standard use, look through the existing issues to see if others have faced similar situations. Calm and clear descriptions of your problem help the team find a solution faster. This project relies on clear communication to keep workflows running smooth and stable across all research environments.