1. Byosphere® Web Client Manual
1.1. Overview
Protein Metrics Byosphere® is a server repository where Protein Metrics projects and related files can be generated, viewed, and managed. Byosphere Web Client is a web-based portal to load, view and manage files, folders, and jobs. Byosphere Web Client is currently supported on Google Chrome.
1.2. Introduction
The Byosphere Web Client consists of nine pages or work areas: Home page, Deep Query Dashboards, Web Analysis, Browse, Upload, Search, Jobs, Notifications, and Resources. These areas are accessed by the icons found in the navigation panel on the left side of the page:
Figure 1.1 Byosphere navigation panel
Each Byosphere Web page represents a set of related functions:
- In the Home
page, users can view the eight most recent files that they have interacted with, as well as all associated actions for these files. The page names on the navigation panel appear in full from the homepage.
- In the Deep Query Dashboards
page, users can access the Deep Query application, which allows a user to collate data from multiple Byosphere Byos projects and/or Web Analyses into a Dashboard to provide aggregate information. The user can develop multiple outputs from data, including Dashboards, status indicators, listings, and statistical analyses. For more information, see the Byosphere Deep Query Dashboards Manual.
- In the Web Analysis
page, users can access Web Analysis, an application embedded within the Byosphere enterprise server that improves customer experience by enabling interactive and iterative computations and the creation of analyses directly within Byosphere. For more information, see the Byosphere Intact Web Analysis Manual and the Byosphere Peptide Web Analysis Manual.
- In the Browse
page, users can access and manage files and folders. Designated users can create folders, upload, or download files and edit, move, and delete files and or folders. Other designated users can view and download these files and folders. Under File History, older versions can be viewed and downloaded. Reports can be generated from project files.
- In the Upload
page, users can upload standard files as well as MS files by clicking the dropzone, which will launch the File Explorer, or dragging MS files and folders (.d and .raw) from the File Explorer and dropping them directly into the zone.
- In the Search
page, users search for files and folders, according to their assigned privileges, and filter by metadata. Users can access or edit records from the search results list directly.
- In the Jobs
page, users can view information about Analysis Server jobs that they or other users submitted, according to their assigned privileges. Users can view job status and open job log files. Note that Web Analysis tasks are not included in the Jobs page.
- In the Luma™
page, users can navigate to the main page of the Dotmatics Luma Platform.
- In the Notifications
page, users can view notifications of their completed jobs with links to the job results.
- In the Virtual Client
page (Note: only visible for users who have the Virtual Client configured), users can open a hosted instance of Byosphere Byos in the Web Client for very fast large project and sample downloads. Byosphere Virtual Client needs to be configured on the Byosphere server to enable this feature. For more information, see the Virtual Client section of this manual or the Byosphere Virtual Client Configuration Manual.
- In the Resources
page, the user has access to useful links that provide more information about tutorials, Protein Metrics resources, and the Knowledge Base.
In addition to Byosphere Web Client, Byosphere Byos Client allows designated users to submit Analyses to be processed on an Analysis Server. These users can load sample files into the Byos workflow from the Byosphere server, load local support files, set parameters, and generate Protein Metrics project documents that are saved to the Byosphere server. For more information on running analyses, see the Byosphere 02 Byos Client Manual.
1.3. Deep Query Dashboards
Byosphere Deep Query allows the user to collate data from multiple Byosphere Byos projects and Web Analyses into a Dashboard to provide detailed information. The user can develop multiple outputs from data, including Dashboards, status indicators, listings, and statistical analyses.
Dashboards are a collection of Visualizations supporting data viewing across multiple projects. They provide a dynamic view of data that can be used to monitor processes, assess changes over time, or to create descriptive models of data for business intelligence purposes. A Visualization is a chart, table, or other kind of visual component that renders data.
For more information, see the Byosphere Deep Query Dashboards Manual and the Byosphere Deep Query Quick Start Manual.
1.4. Web Analysis
Byosphere® Web Analysis is a new native web application that provides users with the ability to perform Intact and Peptide protein analyses directly within the Byosphere Web Client. Web Analysis provides an interface embedded within the Byosphere enterprise server that improves customer experience by enabling interactive and iterative computations, provides platform independence, and avoids upload and download issues that are inherent to the desktop client.
For more information, see the Byosphere Web Analysis Manual, Byosphere Intact Web Analysis Quick Start Manual, and the Byosphere Peptide Web Analysis Quick Start Manual.
1.5. User Group Privileges
Users can be assigned to User Groups by an Administrator. There are four kinds of privileges that User Groups can be assigned that are associated at the folder level and that enable access to folders, files, and their functions. These privileges are independent of each other and often must be assigned together, as detailed below.
- Viewer - User Groups given only Viewer privileges to a folder can view and download files in that folder and view reports for Protein Metrics project files. Viewers cannot edit, delete, or move files or folders.
- File Editor - User Groups given File Editor privileges to a folder can add, edit, move, download, and delete any files in that folder. They cannot manage the assigned folder or sub-folders. File Editors must also be given Viewer privileges to the same folder so they can view the files they manage.
- Folder Editor - User Groups given Folder Editor privileges to a folder can edit, move, and delete that folder, as well as add sub-folders under it. They cannot manage files in the folders unless they are also given File Editor privileges. Folder Editors must also be given Viewer privileges to the same folder so they can view the folders they manage.
- Analyst – User Groups given Analyst privileges to a folder can process, or analyze, sample files in the folder to create Protein Metrics projects through the Byosphere Byos Client. Analysts must also be given Viewer and File Editor privileges to the same folder so they can view and manage the source sample files and resulting project files.
Note that a special category of users called Super Users automatically have all the above privileges for all files and folders. Super User privileges are assigned to users by a Byosphere Administrator.
Users with specific privileges are assigned to User Groups created by an Administrator in the Byosphere Admin Web Client. User Groups are then assigned to folders in the Byosphere Web Client by Folder Editors. To assign the same User to separate folders with different privileges, that User must be in multiple User Groups with the different privileges. Then, the different User Groups are assigned to the separate folders by Folder Editors.
Privileges are not assigned to files directly. Users in a User Group assigned to a folder have uniform privileges to all files in the folder. To separate access privileges among files, place them in different folders with different User Group assignments.
User Group privileges are enabled or disabled by the Byosphere license. Users are assigned entitlements from this license by an administrator. Product entitlements are needed to use Analyst privileges, and role entitlements are needed for any privileges beyond Viewer privileges. Users who cannot exercise their assigned User Groups privileges should contact the Byosphere administrator to ensure that they have the correct role entitlement. Users must logout and login again to enable changes made by the administrator to their license entitlements.
The Users and privileges in a User Group are not inherited by the folders below a parent folder. Sub-folders are assigned User Groups independently. When a new sub-folder is created, the User Groups assigned to the parent folder are checked by default to simplify propagating users and privileges among sub-folders. However, when the User Groups of a folder are edited, the User Groups of sub-folders are not affected.
1.6. First Login
When a new User is created by an administrator, an email is sent to that User containing a link to access the Byosphere Web Client in the default web browser. When login accounts are managed by the Byosphere server, the link opens a welcome screen in the Byosphere Web Client:
Figure 1.2 The emailed link prompts the user to set a password
To set a password, enter the same string in both cells with a minimum of six characters and click Submit. The user is then prompted to login.
Figure 1.3 Byosphere Web login dialog
If the User forgets the password, click Forgot Password? on the login dialog. A message is then sent to the User’s email with a link to change the password.
1.6.1. Single Sign-On Login
The Byosphere system may be configured for Single Sign-On (SSO) logins. When this is enabled, user credentials are not managed by Byosphere but by a third-party identity provider such as Active Directory. The account email used by the identity provider must match an existing Byosphere email account. Users would then login with these email accounts but instead with their passwords from their identity provider service, not with the passwords managed by Byosphere.
When SSO is enabled, entry of the Byosphere server URL brings up a link to begin the login:
Figure 1.4 SSO-enabled login
Click Sign In. The login screens that follow depend on the identify provider. The examples below use Active Directory, which manages Microsoft Windows accounts:
Figure 1.5 Enter the Byosphere email account
Enter the email address shared by Byosphere and the account managed by the identity provider. In this example, click Next to move to the Password screen:
Figure 1.6 Enter the identity provider (not Byosphere) account password
Enter the password for the account managed by the identity provider, not the password managed by the Byosphere account. In this example, click Sign In:
Figure 1.7 For Microsoft Windows, choose whether to remain logged in
In this example, the user can choose to click Yes to remain signed in when closing and reopening Byosphere Web Client, or to click No to log out when closing the web browser.
1.7. Home Page
Upon logging in, users are immediately greeted with the Home page.
Figure 1.8 Byosphere Web Client Home page
From the Home page, the user can view and perform actions on their eight most recently accessed files. Files are sorted in descending order based upon their modification date.
The left navigation panel within the Home page lists out all pages available within Byosphere.
Figure 1.9 Byosphere pages
1.8. Upload Page
Figure 1.10 Upload Page
The Upload page features a dropzone which allows for the upload of standard files as well as MS files by clicking the dropzone, which will launch the File Explorer, or dragging MS files and folders (.d and .raw) from the File Explorer and dropping them directly into the zone.
Note: Self-contained MS data files behave differently than MS data folders. Individual files and folders can be dragged directly from the File Explorer into the dropzone, but only individual files can be opened from the File Explorer dialog; otherwise, the entire folder cannot be selected.
1.9. Web Analysis Page
From the Web Analysis page, users can create a new web analysis by clicking on a Web Analysis Project Template, as shown below. Templates are prepopulated with Modifications and custom Presets so that users can easily start their analysis.
Figure 1.11 Web Analysis Project Templates
An empty analysis can also be created from the Byosphere Home page by clicking the box that reads “New Web Analysis”.
1.10. Deep Query Dashboards Page
From the Deep Query Dashboards page, users can create a Deep Query Dashboard from scratch by clicking New Dashboard or from a system template by clicking one of the System Dashboards.
Figure 1.12 Deep Query System Dashboards
Users can also view their 10 most recently accessed Dashboards from the Deep Query page under Recent Dashboards.
Figure 1.13 New Dashboard and Recent Dashboards
To return to the Home page from the other pages, click the 
1.11. Browse Page
The Browse page shows the User a list of all folders and files they have been granted access to.
Figure 1.14 Browse page
In the left panel of the Browse page, all folders that the User has access to are displayed in a tree structure. That is, all the folders that folder editors have assigned User Groups that include that User. To expand a collapsed folder, click the right arrow button before the name. To collapse an expanded folder, click the down arrow before the name. In the main panel, all files within the selected folder are visible; there is no pre-filtering of files in folders. Details about the files are displayed in a table. The Files table (see Figure above) includes the following columns.
- Actions show icons associated with the actions that the user can perform on the files of this folder. These actions are described in the Managing Files section.
- ID is the unique identifier for that file. Duplicate names and file names are allowed in a folder. The IDs distinguish among such duplicates.
- File Alias defaults to the file name without an extension. Alias can be edited by the user.
- File Name is the name of the file that was uploaded. File name cannot be edited by the user.
- Created By is the User with File Editor privileges who uploaded the file to the server.
- Created On is the date and time the file was uploaded to the server.
- Signature State (Regulatory mode only) shows whether a Protein Metrics project has been signed or approved.
To navigate among folders, click the right arrow to expand a folder and the down arrow to collapse a folder. Click the folder name to select it; the file contents are displayed in the main panel. If a sub-folder is selected and a parent of this folder is collapsed, the parent folder becomes selected and files for the parent folder are displayed.
The buttons above the folders in the left pane (see Figure above) are folder actions available to Users who are Folder Editors. The buttons above the file table (and the 
Figure 1.15 File actions
Users can access a Dashboard by clicking on the View Dashboard 
Users can access a Web Analysis by clicking the View Analysis 
For more information about the 
1.11.1. Root-Level Folders
Before a User can view and manage files and folders, a Super User must add folders at the root level (with or without sub-folders) and assign User Groups to those folders that contain User Groups and their privileges. To avoid folder clutter, Folder Editors cannot create folders at the root level. The Super User defines the workspace with folder hierarchies and their User Group access in advance. Adding folders is described below.
1.11.2. Managing Folders
As previously stated, only Super Users and Users with Folder Editor privileges can add, edit, move or delete folders. Note: Folder additions and edits are not automatically updated in the Browse pages of other users already logged into the Byosphere server. To see new or edited folders, other users should collapse and expand the parent folder to the changed folders. To see new root-level folders, other users will need to logout and log back in again.
1.11.2.1. Add Folders
To add a folder, click the 
Figure 1.16 Add Folder dialog
Enter a unique value for Name. Note: Folder names have an 80-character limit. The dropdown to the right of the label In is the name of the parent folder that contains the new folder. The current folder is selected by default. A Super User will see every folder on the server in this dropdown, as well as <root>, which represents adding a folder at the root level. A User will see only those folders with User Groups that contain them along with Folder Editor privileges. Users who are not Super Users cannot add or move folders to the root level.
Clicking on the user groups dropdown shows a list of available User Group appears. Select a User Group name to add it to the folder. Alternatively, type the first letters of a User Group name to filter by that name and then select it. Multiple User Groups can be added. Click the x after a name in the User Groups cell to remove that User Group. Super Users see all available User Groups. Users see only those User Groups that include them. At least one User Group must be added.
Signatures can be enabled or disabled. See the Signatures section for details about signing projects. When a folder is enabled for signatures, an asterisk (*) appears after the folder name.
Click Add to create the folder. An add confirmation message is displayed, and the folder tree is updated for the new folder in the left pane.
1.11.2.2. Edit Folders
To edit the selected folder, click the 
Figure 1.17 Edit Folder dialog
Edit the name, select a new parent folder, add or remove User Groups, and/or enable or disable Signatures. Click Save. An edit confirmation message is displayed, and the folder tree is updated in the left pane for moved or renamed folders.
The Subfolders option allows users to propagate changes to User Groups and Signatures to all subfolders. Note that user group changes are appended to previous user group selections and in order to remove user group(s) from a subfolder they must be removed manually from each subfolder.
1.11.2.3. Delete Folders
To delete a folder, click the 
Figure 1.18 Delete Folder dialog opened from Edit Folder
Click Delete to remove the folder and its file contents. A delete confirmation message is displayed, and the folder tree is updated in the left pane. Note that the folder is not completely deleted; the server Administrator can restore the deleted folder in the Byosphere Admin Web Client. Likewise, the Administrator can permanently delete the user-deleted folder.
1.11.3. Folder History
Users can see the Folder History for any folder for which they are a Folder Editor (Super Users can see the Folder History for all folders). To view a Folder History, select the folder in the left pane and click the 
Figure 1.19 Folder History
Version lists the count of each folder save. Name, Parent, User Groups and Signatures are described above. Changed By and Changed On display the User who made each change and the date and time of the change. Change lists the kind of folder change. Changes include Add, Edit, Delete, Restore, Create Content, Edit Content, or Upload. To return to the Files table, click the 
1.11.4. Folder Links
The link icon 
1.11.5. Managing Files
As previously stated, only Super Users and Users with File Editor privileges can add, edit, move, download, or delete files. Note: file additions and edits are not automatically updated in the Browse pages of other users already logged into the Byosphere server. To see new or edited files, other users should refresh the web browser.
1.11.5.1. Adding MS Files and Folders
The following MS file types are supported for uploading into Byosphere and converting into *.pacq format: *.raw, *.wiff, *.wiff2, *.lcd, *mbi, *.mzxml, *.mfaux2, and *.byspec2.
The following folder types are supported for uploading into Byosphere and converting into *.pacq format, assuming all content in the folder is mass spec content: .d and .raw
To add a file, click the Add button above the Files table. The Add File dialog opens:
Figure 1.20 Add File dialog
Clicking on the file dropzone will launch the file selection dialog. Any file can be uploaded, but beginning with Byosphere 5.0, MS files are properly compressed into *.pacq format, making them immediately available for Byosphere projects. For a single mass spec file, e.g., *.byspec2, the user can select the file in the file chooser dialog and click Open. The File box will populate with the name and size of the file selected, additionally noting that it will be uploaded as mass spec content. The Alias box will populate with the name of the file sans extensions.
Figure 1.21 Add file with local file name and alias
The file name is not editable. The Alias field is editable. For example, very long names can be shortened to a more reasonable length. Note: Alias values longer than 255 characters will be truncated.
For *.wiff or *.wiff2 content, the user should do a multi-select of all the output files in the file choose dialog and click Open. The files will then be displayed in the dropzone, additionally noting that it will be uploaded as mass spec content, and the file alias will be populated based on the *.wiff or *.wiff2 file name.
Figure 1.22 Add *.wiff file(s) with local file name and alias
Note: *.wiff uploads require multiple files. If not all necessary *.wiff files are included in a file upload, the User will be prompted with the following error message:
Figure 1.23 Invalid .wiff input
Duplicate names are allowed for files in the same folder. Files are identified by their IDs, which are also displayed in the Files table (See Figure 11 and 12).
MS folders are uploaded (.d or .raw) by dragging and dropping the folder into the (note that clicking Open in the file chooser will simply open the folder, so the user must drag and drop those folders). Once dropped, the folder name will be displayed in the dropzone and the Alias will be updated based on the folder name. Non-MS folders cannot be uploaded in the Web Client, but they can be uploaded in Byosphere Byos.
Figure 1.24 Folders must be dragged and dropped into the dropzone for upload
An entry in the Comment box is optional. Click Add to begin the file/folder upload. A status bar displays the progress of the upload above the Files table. If there are multiple files (e.g., a folder upload) a number next to the current upload will show how many files are still pending upload within the batch.
Figure 1.25 File upload status bar
Very large files can take several minutes to complete. A confirmation message is displayed when the upload is complete, and the Files table is updated with the new file.
Once files are uploaded, they are placed in queue to be converted into *.pacq format.
1.11.5.2. Jobs Page for Pacq type
The user can check on the progress of their MS file uploads on the Jobs page. For MS file/folder uploads, the Type will be listed as “Pacq”, with the Name showing up as the file name that will be converted into *.pacq format. Before files are converted to *.pacq format, they are temporarily saved as .zip files, hence the .zip extension following the original name of the file. Canceling a Pacq job will result in the associated MS file being deleted.
Figure 1.26 Submitted File Uploads on Jobs page
1.11.5.3. Protein Metrics Project and Sample Files
Certain files should be loaded to the Byosphere server using the Byosphere Byos Client instead of the Byosphere Web Client.
Byosphere Byos Client should be used to perform uploads for the following cases:
- Protein Metrics project files with reports – In order to make reports available on the Byosphere Web Client, Protein Metrics project files need to be uploaded via the Byosphere Byos Client. Byos uploads include the option to generate a report for the project. Since large uploads can tie up Byos for long periods, users can continue working in another instance of Byos.
- Non-MS folders
The Byosphere Web Client is recommended to perform uploads for the following cases:
- Very large files not in the list above – Very large file uploads on ordinary connections (such as home networks) can take hours. Any network interruption will cause the upload to fail. Web browsers tend to be more resilient to brief network interruptions.
- Multiple files not in the list above – The Byosphere Web Client creates a queue of file uploads. Several files can be added to the Add file queue from different folders, and then work can continue in another Byosphere Web Client tab or in Byosphere Byos Client. On the other hand, Byosphere Byos Client can only upload one file at a time, requiring a manual upload for each file, one after the other. Alternatively, target files can be moved into a single folder and uploaded in Byos as a folder.
1.11.5.4. Edit Files
To edit an existing file, click the 
Figure 1.27 Edit File dialog
To replace the existing file with a file with the same name (file names must match), click the dropzone to launch the file selection dialog, select the desired file, and click Open.
Optionally, the user can edit the Alias of the selected file and/or add a comment or Metadata. Comments are helpful to distinguish new versions of files. Click Save. An edit confirmation message is displayed, and the Files table is updated with any changes to Name or File Name.
1.11.5.5. Metadata
Metadata is information associated with a particular file, such as the instrument used to obtain the data, digestions used, batch numbers, or other important process characteristics. Metadata fields are defined by the Byosphere Administrator. To include Metadata when adding a file in the File table, click Add and in the Add File dialog, click the right arrow after Metadata. The arrow changes to a down arrow, and exposes the available Metadata fields:
Figure 1.28 Some of the available Metadata fields from the File uploader
Metadata can also be added to an existing file from the Edit File dialog.
To prevent any issues, the user should add the metadata columns of interest within the file folder view and inspect the existing metadata before editing metadata so that existing metadata does not get overwritten.
Figure 1.29 Metadata column options under Toggle columns
1.11.5.6. Delete Files
To delete one or more files, check the boxes before the file records to delete (to check all files, check the box in the header row) and click the Delete button above the Files table. The Delete Files confirmation appears:
Figure 1.30 Delete Files confirmation
Click Delete. A delete confirmation message is displayed, and the files are removed from the Files table.
Note that the file is not completely deleted-- the server Administrator can restore the deleted file in the Byosphere Admin Web Client. Likewise, the administrator can permanently delete the User-deleted file.
1.11.5.7. Move Files
To move one or more files, check the boxes before the file records to move (to check all files, check to box in the header row) and click the Move button above the Files table. The Move Files dialog appears:
Figure 1.31 Move Files dialog
Click the drop-down arrow after Move To, select the new folder and click Move. A move confirmation message is displayed, and the file is removed from the current Files table.
1.11.5.8. Download Files
To download a file, click the 
Figure 1.32 Download status in browser status
1.11.5.9. Display Common Files
Many common file types that are stored on the Byosphere server can be displayed directly in the Byosphere Web Client window from the Browser Files table and Search Results table.
These file types include text files (*.csv, *.log, *.txt), *.json, *.pdf, image, video and audio files. If the file type is supported for opening in the Web Client, the file name displays a blue web link:
Figure 1.33 Files that can be displayed in the Web Client show web links in blue
Click the blue file name and the contents are displayed in an embedded window in the Web Client:
Figure 1.34 Server *.txt file displayed in the Web Client
Click the 
Properly formatted *.csv, *pi, and .arw files can be plotted as spectra/traces. To do so, click the blue file name of the *.csv file to display it as a text file. Then, check View as spectrum or View as Trace at top right to plot the data:
Figure 1.35 Server *.csv file displayed as a plot in the Web Client
Note: CORS must be enabled on the server storage to enable this feature. Refer to the platform-specific Byosphere Admin Manual for instructions to enable CORS.
1.11.6. File History
Users can see the File History for any file in a folder they have privileges to view. To view a File History, click the
Figure 1.36 File History
Action shows available actions. The 
Figure 1.37 Analysis project File References table
The File References table includes the sample raw files used in the analysis, the assigned report template (if no report template is listed, the default report was used) and the workflow. Click the 
Other File History header fields include Version, which lists the count of each file save. Folder, Name and File Name are described above. Changed By and Changed On display the user who made each change and the date and time of the change. Change lists the kind of change. Changes include Add, Edit, Delete, Restore, Create Content, Edit Content, or Upload . To return to the Files table, click the
Every Byosphere Document has a file history showing the file-level changes that have happened to that document. The File history page now allows the User to download the file history of a desired document as a text file and to select a version in the file by clicking the Download File History Report icon.
Figure 1.38 Download File History Report
Clicking the download icon for the File History Report for a legacy project will trigger an AuditLog job to generate the Byos Audit Trail for that project. After the job has completed, click the download icon again to download the File History Report.
Figure 1.39 Example File History Report
1.11.7. Signatures
When the Regulatory mode is enabled on the Byosphere system, Protein Metrics project files containing reports can be signed. Folders must have Signatures enabled for projects to be signed. Folders that are signature-enabled cannot be deleted or moved. Projects can only be signed by a user with File Editor privileges. Signing requires a login independent from the system login. Signed projects can often be moved to another state (by default, Approved) or returned to a previous or unsigned state (by default, Rejected). Some signature states (by default, Approved) cannot be reversed. Projects that have a signature state typically cannot be edited, moved, deleted, or updated with new versions.
To enable signatures for an added or edited folder, set Signatures to Enabled:
Figure 1.40 Enabling Signatures for a folder
Click Add or Save to enable Signatures for the added or edited folder. The name of the folder is identified as Signature-enabled by an asterisk ( *) appended to the name:
Figure 1.41 Names of folders that are Signature-enabled are marked with ( *)
Signature-enabled folders can be edited or moved but not deleted. Once Signatures are enabled, project files containing reports can be signed by Users with File Editor privileges to that folder.
Initially, Byosphere with Regulatory mode enabled is configured with three signature states: unsigned, Signed and Approved. The initial configuration allows transitions between unsigned to Signed, Signed to unsigned, and Signed to Approved, but not Approved to Signed or unsigned. Byosphere administrators can edit the signature configuration to add or remove signature states and/or transitions. Likewise, administrators can edit states to allow signed documents to be edited, moved, or deleted. What follows is a description of the behavior of the initial signature configuration.
To sign a project with a report (which displays the 
Figure 1.42 The Sign icon appears at top right of the Edit dialog
Click the 
Figure 1.43 Sign File dialog
Enter the Byosphere Password, add a Comment as needed and click Sign.
Note: if SSO is enabled, the signature username and password will be managed by the identify provider.
The project will be identified as Signed in the Signature State in the Files table:
Figure 1.44 Signed projects are identified in the Signature State column
The signed project cannot be edited, moved, deleted, or updated with a new version.
The signed file can set back to the unsigned state through the Reject action. To reject a signed file, click the 
Figure 1.45 Rejecting (un-signing) a signed project
Enter the Byosphere password, add a required Comment and click Sign. The Signature State for the project will be blank. The file can be modified as an ordinary file.
Signed projects can also be approved. Like signed projects, approved projects cannot be edited, moved, deleted, or updated with a new version. Unlike signed projects, approved projects cannot be reverted to another signature state.
To approve a signed file, click the
Figure 1.46 Approving a signed project
Enter the Byosphere password, add an optional Comment and click Sign. The project will be identified as Approved in the Signature State in the Files table:
Figure 1.47 Approved projects are identified in the Signature State column
1.11.8. File Links
The link icons 
1.12. Web Reports
Web reports closely resemble Protein Metrics project reports generated on the desktop. Web reports are generated for server project files created on Byosphere Byos Client. They can be generated in three ways: when creating a Byosphere server analysis, when rerunning a report job, or when uploading a Protein Metrics project file with Generate Report checked. For instructions on generating web reports, see Byosphere 02 Byos Client Manual.pdf. Web reports are viewed for project files in the Byosphere Web Client in the Browser page Files table and File History table, and in the Search page Results table. All users who can view project files can also view web reports for those files.
To view the web report for a project file, click the 
Figure 1.48 Protein Metrics project with web report icon highlighted
The View Report dialog opens:
Figure 1.49 View Report dialog
Select as Report Type HTML Report or PDF Report and click View, and the web report opens in an embedded window:
Figure 1.50 Example web HTML report
The web page that displays the report contains sub-tabs corresponding to the report template (*.rptc file) assigned to the workflow when the project was generated or uploaded through the Byosphere Byos Client. If no report template was assigned to the analysis workflow, the default report associated with the workflow is used. To close the embedded report, click the X at top right and the Web Client returns to the original window.
To display the fields available for the project, select Show Configuration above the tabs:
Figure 1.51 Web HTML report with Show Configuration selected
When Show Configuration is enabled, pivot table displays can be edited and filtered as they are in Byos desktop reports. To edit a pivot table display, drag unused fields from the first column into the center column to create new row headers or to the top of the table to create new column headers. To filter content by field values, click the down arrow for a row header, column header or unused field, and select or unselect the available field values.
A PDF version of a report can be viewed in the web window or downloaded as a *.pdf file (see the next section). To view a PDF report in the Web Client, click the 
Figure 1.52 Example web PDF report
To download the inserted PDF report, click the
Reports viewed from a project in the File table are from the last version of that project. To view reports for previous versions of that project, open the File History.
Figure 1.53 Reports are available for previous project versions
Web reports are available for server analysis reports and for all subsequent versions uploaded from Byosphere Byos Client with the Generate a report option checked. Web reports are not available for project versions resulting Byosphere Byos Client from web edits, file moves or restores from deletion because the project content, and web report, have not changed. The last available web report is valid for those project versions.
To copy the web report URL to send to another Byosphere user, click the 
Figure 1.54 Copy Link for a report
1.12.1. Web Report Downloads
To download a web report, click the
Figure 1.55 Download Report dialog
Select report type and click Download to export the report to the default download directory. The CSV Report option downloads a zipped file containing a *.csv file for each table tab and a *.csv file for the flat table for the primary table (for example, Elution peaks or Peptides).
Figure 1.56 Contents of an example CSV Report zip file
The PDF Report option downloads a single, multi-page pdf file for the entire report:
Figure 1.57 PDF report
To return from the Download Report dialog to the View Report dialog, click the 
*.zip) do not download as *.csv files or *.pdf reports.
JSON Reports are added for all projects starting in Byosphere v5.0 (example *.ntms):
Figure 1.58 Available Reports
*.bmap and *.blgc projects created in 5.0:
Figure 1.59 *bmap and .blgc projects
5.0 Preview project ( *.zip ) download options:
Figure 1.60 *.zip download options
1.13. Search Page
The Search page filters all files and folders that the user has privileges to view using entered search strings.
Figure 1.61 Search page
The Search page opens in the Basic Search mode with a search entry box, and additional options to open a saved search query, save a search query, clear the search query, or switch to Advanced Search mode:
Figure 1.62 Search options
1.13.1. Basic Search
In a Basic Search, the entered text string is searched across all the available fields in the File and Folder tables. To search for a text string, enter the string in the box and click the Search button at left. The file results appear below the search entry box along with optional Metadata filters to the left:
Figure 1.63 Search results of all records containing the entered string in any field
If the search string matches a folder name, all the fields under that folder are included in the search results.
To filter the search results by available Metadata field values, check all values below the fields that apply. Only those records that match each of the conditions are displayed in the table:
Figure 1.64 Metadata options to filter on are based upon available metadata in initial search results
The Clear button above the Metadata fields unchecks the values to show all records that contain the search string. To clear the entire query to begin again, click Clear above the entry box and click Clear again to confirm the action.
To search by file ID, enter the text “file:” before the ID number:
Figure 1.65 Search by File ID
The Edit Batch checkbox, when checked, filters search results to only files which the user has edit access for.
Figure 1.66 Edit Batch
When Edit Batch is checked, the user will see the following options within the Search Page:
Figure 1.67 Edit Batch options
These options will be grayed out until the user checks at least one row from the search results. The Delete and Move options behave in the same way as the corresponding buttons for the Files table in the File Browser. The Edit Metadata option, if clicked, allows the user to check multiple files and edit the associated Metadata in a batch rather than one at a time.
Figure 1.68 Edit Metadata
1.13.2. Advanced Search
The Advanced Search mode allow users to search values by specific fields using a variety of operators, as well as the use of Boolean logic between search query lines. Unlike a Basic Search, which searches all fields for a given textual term, an Advanced Search searches specific fields for specific terms in query combinations. To do an Advanced Search, click Switch to Advanced above the query line. A query builder opens:
Figure 1.69 Advanced Search query builder
The Boolean options And or Or applies between subsequent query lines. Click +Rule to add a new query line then click the dropdown to select the field to search:
Figure 1.70 Click +Rule to add a query line and choose a field
In the second dropdown, select the desired query operator:
Figure 1.71 Choose a query operator
Finally, add the field value to search in the last column. If the query is complete, click Search. To search across multiple fields, choose the Boolean operator And or Or, click +Rule and populate the new query line:
Figure 1.72 Advanced Search with multiple query lines
Advanced Searches can also include nested query lines with the +Group button:
Figure 1.73 Advanced Search using query groups
1.13.3. Save Search Query
Both Basic Search and Advanced Search queries can be saved for future use. To save a search query, click Save at the top. The Save Query dialog opens:
Figure 1.74 Save query
Enter a unique query name and select a query folder. The My Queries folder is only visible to that User. The other query folders are created by the Administrator and their queries are visible to all users who have privileges to that folder. Add an optional description and click Save to save the query.
1.13.4. Open Search Query
After Basic Search and Advanced Search queries are saved, they can be opened for searching in later sessions. To access a saved query, click Open. A table of the queries available to that user is displayed:
Figure 1.75 Click Open to view saved queries
Click the 
1.13.5. Search Result Actions
The checkbox and icons in the Actions column allow the User to perform a number of actions on search result files that would otherwise be performed in the Browser page:
- To delete one or more result files, check the boxes for those file rows, click Delete and click Delete again to confirm the action.
- To move one or more result files, check the boxes for those file rows, click Move, choose the destination folder for the move, and click Move.
- To edit a file, click
for the file record, make the desired file changes and click Save.
- To view the File History of a result file, click
to open the File History table.
- To view the file in the context of other files in the same folder, click
to open the file’s folder in the Browser page.
- To download a file, click
for the file record.
- To view a web report for the result file, click
to open the web report in a new tab.
The
1.14. Jobs Page
The Jobs page displays the status of the server analysis and web report Job queue.
Figure 1.76 Jobs page
Users can view all Jobs they have submitted, all Jobs in the Running or Queued state that all Users have submitted, and all Jobs in folders they have privileges to view:
By viewing all queued Jobs and the current running Job, users have a sense of when their Job may begin.
Job types include Analysis for projects submitted for creation on the server, Report for a report generated for a project that already has an analysis completed, Conversion for jobs that parse project files to load project data into tables for Deep Query dashboard searching, AuditLog for jobs that generate Byos Audit trails as part of File History Reports for projects, and Pacq for MS files and folders uploaded through the Web Client. Preview jobs and multi-doc analyses, using special Preview and Multi-doc workflows, are also supported.
Figure 1.77 Various job status types
Jobs are ordered by Status and then by ID. The Status of current running Jobs are colored yellow. Queued Jobs (colored white) run after the current Job in the order they were submitted unless an Administrator increases the priority of a later Job. Jobs that completed successfully are colored green and those that failed are colored red. Canceled Jobs are colored gray.
Completed, failed, and canceled running Jobs generate log files named for the Job ID. These job logs can be downloaded by a click on the 
Figure 1.78 File name link to view the Job log
The link (identified by the blue font) opens the job log for the project in the Web Client window:
Click
Users can cancel running and queued Jobs they have created. Super users can cancel Jobs generated by any user. To cancel a running and queued job, click the 
Figure 1.79 Users can cancel their queued and running jobs by clicking the x button
Users can access the project from a completed Analysis or Report Job using the 
Figure 1.80 The eye button accesses the completed project file
When
Figure 1.81 The project from the completed job as a search result
From the search result, the project report can be viewed or the folder containing the project can be opened.
At the top of the Jobs page, the total Job count is shown on the top left and the number of Jobs displayed per page can be set on the top right:
Figure 1.82 Job counts and counts displayed per page
To page through lists of earlier Jobs, click the page numbers at bottom right:
Figure 1.83 Click Jobs page numbers to view earlier jobs
The 
Figure 1.84 Job History
The
1.15. Notifications Page
The Notifications page displays a table of the user’s notifications, such as completed or pending jobs.
Figure 1.85 Notifications page
The table will be blank if the user has no new notifications. When the user has a new notification, the icon changes to display the notification count:
Figure 1.86 Notifications page icon with notification
Click the Notifications page icon to display a table of new notifications:
Figure 1.87 Notification of a completed job
To see the job run results, click the blue link here at the end of the notification. For a completed job, the Search page will open with the completed project as a search result.
The Notification for a failed job contains a different link:
Figure 1.88 Notification of a failed job
The link from a failed job opens the Jobs page. From there, the user can click the 
1.16. Virtual Client Page
The Byosphere Web Client supports the hosting of Byosphere Virtual Client remote instances of Byosphere Byos for extremely fast performance when opening large projects with large sample files. The Virtual Client instances reside on the Byosphere server host, enabling direct contact over a very fast network. The instances automatically shut down upon logout or timeout to save hosting costs. Each user account is assigned an instance, which persists from their last session when they login again.
After Byosphere Virtual Client is configured on the server and activated by a Byosphere Administrator, a Virtual Client page icon is displayed in the navigation panel:
Figure 1.89 Virtual Client icon to open a hosted image of Byosphere Byos
When the Virtual Client icon page is opened, a hosted Virtual Client instance of Byosphere Byos opens in the Web Client window:
Figure 1.90 Byosphere Byos image hosted on the server but available in the Web Client
In addition, project files in the Files tables in the Browser or Search pages can be opened directly into the Virtual Client window by clicking the 
Figure 1.91 Virtual Client icon to open project files directly in the Virtual Client window
The project is opened in the Virtual Client window, optionally with the downloaded sample files:
Figure 1.92 Server project opened in the Virtual Client window1
The download performance will reflect the network speed and proximity of the Byosphere host machine (where the image is located) to the Byosphere server.
Note: The remote Virtual Client does not currently allow access to local desktop files. Therefore, functions that involve local file access, such as Upload and Download, have been removed:
Figure 1.93 File menus for Virtual Client do not include local file access
The Virtual Client feature is best suited for downloading projects with their sample files, modifying the projects, and saving them again to the server, all with greatly enhanced performance.
Note: Work on projects that is not saved is persisted between sessions. However, if an administrator replaces the Virtual Client image for any updates, the working image will be replaced with a new one, and all unsaved work will be lost. Be sure to save any critical work to the server between sessions.
1.17. Managing Tables
The Files table, File History table, Folder History table, Search Results table and Jobs table can all be sorted and filtered by column. Individual table columns can be hidden or restored. The behavior for all tables is the same.
1.17.1. Sort by Column
Tables can be sorted by each column, descending or ascending. To sort a column descending, click the pair of arrows behind the column header. The down arrow is displayed in black, and the table is sorted by those column values in descending order:
Figure 1.94 Files table sorted by ID, descending
To sort ascending, click the column header a second time. The up arrow is displayed in black and the table is sorted by those column values in ascending order.
1.17.2. Filter by Column
Tables can be filtered by each column for entered text. To filter the values in a column, click the
Figure 1.95 Files table filtered by “Name contains Intact”
To filter by additional column values, enter those values in the appropriate entry boxes. The rows that contain all the filter strings in their corresponding columns are displayed. To display all rows again, delete all filter strings. To remove the filter entry boxes, click the
1.17.3. Show and Hide Columns
Desired but hidden columns (such as File Size and Metadata fields) can be shown and unwanted columns can be hidden. To change which columns are displayed, click the
Figure 1.96 Hide table Columns
To hide columns, click the
1.18. Username Menus
The dropdown arrow after the User’s name at top right exposes a menu:
Figure 1.97 Username menus
Reset Password is self-explanatory.
Figure 1.98 Reset Passwords
Enter the password in the two boxes. Passwords must contain at least six characters. Click Reset. Note: This menu is only available for non-SSO logins. For SSO, password resets are managed by the identity provider.
About shows the Byosphere version:
Figure 1.99 About box
Help downloads a compiled pdf version of all Web Client manuals to the browser. The user can select which manual they wish to look at from the first page.
Sign Out signs the User off the server. Users are automatically logged off after a long period of activity.
Branch: release/2025.09
Compile Date: 2025-Oct-03
Compile Time: 12:00:53