Overview:
This article provides initial orientation and information for users transitioning from Byos to Byopshere and for users new to Byosphere. Key concepts of Byosphere and differences from Byos relevant to the typical user are discussed.
For deeper review of the topics discussed, please see the Byosphere User Manuals, Tutorial Videos, and linked Knowledgebase articles. Always feel free to reach out to support@proteinmetrics.com for support and guidance.
Introduction:
Executing MS data analysis and reporting in Byosphere is very similar to Byos. The same data processing algorithms, user interfaces, project investigation visualizations and tools, and reporting capabilities in Byos are also used in Byosphere. The same Byos workflows, projects, reports, and analysis approaches are easily transferred to Byosphere.
The concepts listed below are unique to Byosphere and are useful to understand. Each concept is briefly discussed in the following sections.
- Byosphere ENT Server
- Data Upload to Byosphere
- Analysis Server and Job Queue
- Byosphere Web Client
- Bysophere Desktop/Virtual Client (Equivalent to Byos)
- Metadata
- Searching and Querying
- Deep Query Dashboards
- Autoprocessing
- Upgrading Byosphere
- Web Analysis
1. Byosphere ENT Server:
In Byos, files are accessed from and saved to any directory the desktop has access to. Byosphere is an enterprise solution where raw MS datafiles, project files, and other file types are centralized for the entire organization on a Byosphere ENT Server (Cloud or On-Prem). There are significant advantages of centralizing an organization's data. For example, files are better organized, information is easily searchable, and powerful capabilities requiring centralized data are uniquely available to Byosphere.
2. Data Upload to Byosphere:
Raw MS datafiles must be uploaded to the Byosphere ENT Server for storage and analysis. Other file types may also be uploaded to Byosphere, including old Byos project files, workflows, report templates, CSV files, etc. During Byosphere deployment, Protein Metrics will work with your team leaders and IT to set up a data upload configuration and approach. Protein Metrics and your internal team members coordinating the Byosphere deployment will explain data uploading for your team's specific Byosphere deployment.
NOTE: When raw MS datafiles are imported into Byosphere, they are compressed to the .paqc format, which can be directly processed and analyzed in Byosphere.
2a. Data Uploader:
Usually a Data Uploader is configured to upload raw MS datafiles to the Byosphere ENT Server. The Data Uploader monitors a defined staging folder and automatically uploads raw MS datafiles from the staging folder to the Byosphere ENT Server.
Additional Data Uploader information relevant to the typical user:
- Data Uploader is the recommended approach for importing raw MS datafiles into Byosphere.
- The Data Uploader automatically duplicates the staging folder subdirectories in Byosphere. For a folder to appear in Byosphere, at least one raw MS datafile must be uploaded from that folder.
- The Data Uploader can be configured to automatically populate Metadata for imported raw datafiles, usually based on the raw datafile name or file path in the staging folder. See Section 6 for more information on Metadata.
- Usually it takes 5-60 minutes for raw MS datafiles to upload from the staging folder to Byosphere. This will depend on the size of MS datafiles and other factors.
- The Data Uploader can be configured to delete raw MS datafiles from the staging folder after data upload. This is optional, but is usually recommended for efficiency.
- It is common for Byosphere Customers to configure additional backend data management and transfer strategies independent of Protein Metrics. For example, automatic transfer of datafiles from MS acquisition computers to the Data Uploader staging folder.
When getting started, we suggest checking with your team to ensure you understand the unique Byosphere Data Uploader configuration deployed for your team. You can always reach out support@proteinmetrics.com if further explanation or support is needed.
2b. Byosphere Desktop Client Upload:
The Byosphere Desktop Client application (see Section 5) can also upload raw MS datafiles and other file types to Byosphere by clicking File>Upload.
Additional Byosphere Desktop Client data upload information relevant to the typical user:
- While the Byosphere Desktop Client can be used to upload raw MS datafiles to Byosphere, it is not usually the recommended approach. The Data Uploader (see Section 2a above) is usually the recommended approach for raw MS datafiles upload for several reasons. To give one example, unlike the Data Uploader, Metadata is not automatically populated for raw MS datafiles uploaded using the Byosphere Desktop Client.
- As of Byosphere v5.7, the Byosphere Desktop Client is usually the best tool for importing other files besides raw MS datafiles. For example, the Byosphere Desktop Client should be used to import old Byos project files into Byosphere.
- One file or one folder can be uploaded at a time with the Byosphere Desktop Client. When a folder is uploaded, all files and subfolders contained within the selected folder are uploaded to Byosphere at once.
2c. Web Client Data Upload:
Finally, the Byosphere Web Client (see Section 4) allows users to upload files directly to a specific Byosphere folder.
Additional Byosphere Web Client data upload information relevant to the typical user:
- The Byosphere Web Client is usually recommended for quickly uploading one or a few files.
- It is not well designed or recommended for batch upload of many files at once. Files must be added for upload one by one.
- While the Byosphere Web Client can upload raw MS datafiles, it is usually not recommended for upload of raw MS datafiles, especially for uploading >1 MS raw datafile. Users are almost always better off uploading raw MS datafiles using the Data Uploader (see Section 2a above), and in some cases the Byosphere Desktop Client.
3. Analysis Server and Job Queue:
When a project is created with Byos, processing is completed locally on the Desktop. Project creation speed is dependent on the local computer. All Byosphere project creation processing is submitted to a shared Analysis Server and Job Queue.
Project processing and other jobs are monitored on the Analysis Server Job Queue, which can be viewed from the Byosphere Virtual/Desktop Clients (Section 5) and the Byosphere Web Client (Section 4).
Additional Byosphere Analysis Server and Job Queue information relevant to the typical user:
- Byosphere is usually deployed with a single Analysis Server always ready for job processing and Autoscaling, which spins up additional analysis server instances when the job queue fills up allowing for simultaneous job processing. With Autoscaling, multiple jobs can be completed efficiently in parallel.
- The Job Queue status does not update real time. Note the Job queue refresh behavior shown in the figures above for the Byosphere Web Client and Byosphere Virtual/Desktop Client.
4. Byosphere Web Client:
The Byosphere Web Client is a web based application critical for many Byosphere user functions, some of which are highlighted in the figure below.
The Bysophere Web Client is accessed with a URL specific to an organization's Byosphere deployment, where users will log in with their account email and password. On deployment, users receive an email to set up their Byosphere account, which includes the Byosphere Web Client URL.
NOTE: Byosphere log in can be configured to use third party Single Sign-On (SSO).
Following Byopshere deployment, Protein Metrics will provide End User Training to cover many of the Byosphere Web Client basics. The Byosphere Web Client User Manual is also a great resource.
5. Byopshere Desktop/Virtual Clients:
The Byosphere Desktop and Virtual Clients look and operate like Byos. They are tools for analysts to create projects, review/edit/interpret results, create reports, and more. For the most part, they are equivalent to Byos. However, unlike Byos, both the Byopshere Desktop and Virtual Client access the Byosphere server and submit jobs to the Analysis Server and Job Queue for project creation.
Additional Byosphere Virtual/Desktop Byos Client information relevant to the the typical user:
- Review the Opening, Editing, and Saving Byosphere Projects KB article.
- See Byosphere Virtual and Desktop Clients for information and discussion regarding similarities, differences, and advantages of Virtual vs. Desktop Byos Client.
- When opening the Byosphere Virtual Client for the first time in a day or working session, it can take about a minute to start up, similar to starting up a computer. This is because a user's Virtual Client AWS instance shuts down when not in use to avoid wasting resources. After initial startup, the Byosphere Virtual Client only takes a couple seconds to open for the rest of the working session, until the instance shutdowns again after a time out period.
- At the end of a working session using the Byosphere Virtual Client (or end of the day), we recommend closing all projects in the Byosphere Virtual Client, saving any desired project changes to the Byosphere Server (see Opening, Editing, and Saving Byosphere Projects for details), and signing out of the Byosphere Web Client (see figure below).
6. Metadata:
Metadata is information describing data and allows users to:
- Better organize and track information on the Byosphere Server
- Quickly search for relevant information (Section 8)
- And create Dashboards summarizing results across many projects, updated real time (Section 9)
Any file in Byosphere can be annotated with Metadata. A simple example of Metadata for a raw MS datafile is shown in the figure below.
The Metadata fields available in Byosphere can be customized by Byosphere Administrators. Users should coordinate with their team leads and Byosphere Administrators to ensure needed and appropriate Metadata fields are configured, available, and up to date.
There are many ways to populate and edit Metadata for files in Byosphere. Users can view and edit Metadata using the Byosphere Web Client, as shown in the figure below.
The Data Uploader (Section 2a) can be configured to automatically populate Metadata for uploaded raw MS datafiles. Your team will work with Protein Metrics to set up automatic Metadata population rules, usually guided by the raw datafile name and/or file path. This powerful approach provides automatic and consistent Metadata population for raw MS datafiles.
Finally, when creating projects, users can define Metadata for the resulting project file (.blgc, .ntms, .bmap, .olms, etc.). Metadata can be entered manually, or the user can directly copy Metadata from one of the raw MS datafiles being processed.
NOTE: The Autoprocessor (Section 8) can be configured to automatically populate Metadata of resulting project files.
For more information on Metadata, see the Knowledgebase article Using Metadata and Deep Queries in Byosphere®.
7. Byosphere Searching/Querying:
Easy file searching across an organization is a major benefit and advantage of Byosphere, powered by centralization of data on the Byosphere ENT server (Section 1) and Metadata annotation (Section 6).
The Byosphere Web Client includes a file searching tool supporting basic and advanced searches. The figure below highlights capabilities and features of the Byosphere Web Client Search tab. See the Byosphere Web Client User Manual for more information.
The Byosphere Desktop/Virtual Client file browsers also include a basic keyword search tool that matches the text in the search to filenames and/or associated Metadata. This can help analysts find relevant raw MS datafiles, Byos Project files, Workflows, Report Templates, and other file types when using the Byosphere Desktop/Virtual Client.
8. Autoprocessor:
As the name implies, Autoprocessor automatically processes raw MS datafiles uploaded to Byosphere, populating and launching appropriate workflows to create Projects. Autoprocessing can save expert users time and boost efficiency, especially for routine data processing/analysis tasks. This feature is unique to Byosphere. The Autoprocessor is configured by Protein Metrics in coordination with your team. To learn more about Autoprocessor capabilities, reach out to support@proteinmetrics.com.
When getting started with Byosphere, we suggest checking with your team for information on any unique Autoprocessor configurations and capabilities available to your organization's Byosphere Deployment.
9. Deep Query Dashboards:
Dashboards are a powerful tool unique to Byosphere. A Dashboard is a collection of visualizations, tables, and calculations summarizing key results of mass spectrometry analyses. Dashboards can be configured for various types of mass spectrometry analyses and purposes. Importantly, Dashboards Query the centralized Byosphere ENT Server and leverage Metadata to generate real time updated outputs and summarize key results across many Projects at once. A few key features of Dashboards are listed below.
1. Users can use the Byosphere Web Client to create custom Dashboards with visualizations, tables, and calculations to meet the team's specific needs. Users can also start with one of the many prebuilt Dashboards included in Byosphere.
2. Query all analyzed Project data saved to the Byosphere ENT Server using defined global and visualization specific filters to automatically populate Dashboards real time, updating results as new data is analyzed in Byosphere.
3. Leverage Metadata to configure, filter and annotate Dashboards.
4. Create custom derived fields to perform advanced calculations.
5. Configure Background Alerts to automatically notify users when certain conditions have been met for data within a Dashboard. For example, an Out of Spec warning for a System Suitability Dashboard.
6. Copy links and export Dashboards to easily share information within your organization.
7. Viewers can apply filters and interact with Dashboard visuals and tables to focus on key results contained within the Dashboard.
8. Analysts can easily open specific Byosphere Projects directly from the Dashboard view to inspect and analyze data in detail using the Byosphere Virtual Client.
For more information on Dashboards, see the Byosphere Deep Query Manual and Byosphere Deep Query Quick Start Manual.
We strongly recommend working with the Protein Metrics Support Team to configure and take full advantage of Dashboards in Byosphere, especially if you are new to Dashboards. Reach out to support@proteinmetrics.com for guidance and to schedule working sessions with the Protein Metrics Support Team.
10. Upgrading Byosphere:
Upgrading Byosphere is not completed by the individual user. Instead, the Byosphere server is upgraded by Protein Metrics in coordination with your team's leadership and internal IT. Like Byos, new Byosphere versions are typically released every quarter. Because upgrading enterprise software is more resource intensive than upgrading a desktop application, users can generally expect Byosphere to be upgraded 1-2 times per year, depending on customer needs. This means lag time between the release of Byosphere versions/features and upgrade of your organization's Byosphere deployment is usually expected.
While upgrade of the Byosphere Web Client (and associated Byosphere Virtual Client) is handled by Protein Metrics, individual users will need to download and install new versions of the Byosphere Desktop Client, similar to the download and install process for Byos. Reach out to support@proteinmetrics.com if you need the link and password to download and install a new version of the Byosphere Desktop Client.
NOTE: The Byosphere Desktop Client version must match your team's currently deployed Byosphere version.
11. Web Analysis:
Byosphere Web Analysis is a web application providing users with the ability to perform mass spectrometry data analysis and reporting directly within the Byosphere Web Client. Web Analysis provides an interface embedded within the Byosphere enterprise server that can improve customer experience by enabling interactive and iterative computations, providing platform independence, and avoiding upload and download issues inherent to the Byosphere Virtual/Desktop Client. As of Byosphere v5.7, Web Analysis workflows exist for Peptide and Intact analysis.
NOTE: As of Byosphere v5.7, significant Web Analysis development and improvement is still underway. At this time we generally do not recommend starting with Web Analysis when getting started with Byosphere. Future versions of Byosphere will feature more refined and powerful Web Analysis workflows in Byosphere.
For more information on Byosphere Web Analysis, see the Byosphere Web Analysis Manual, Byosphere Intact Web Analysis Quick Start Manual, and Byosphere Peptide Web Analysis Quick Start Manual.