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Administration

The "Administration" page block is accessible only to the Program administrator. It includes the "Configurations", "Users", "Organizations", "Active tasks", and "Tariffs" pages.

Configurations#

The page contains configuration settings that can be transferred to new users when they register in the System.

To add a configuration to the System, click . In the Add Configuration dialog, enter the configuration name and, optionally, a description. Then add the settings preset, report template, and/or demo sample that you want to provide to the new user as part of the configuration.

Settings Presets#

To add a settings preset to the configuration, click the corresponding search field and select a preset from the settings presets available in your System. Then click .

One of the added presets must be designated as the default preset. To change the default preset, click next to the desired preset.

To remove a preset from the configuration, click .

Report Templates#

To add a report template to the configuration, click the corresponding search field and select a template from the report templates available in your System. Then click .

To remove a report template from the configuration, click .

Demo samples#

Demo samples are demonstration samples that can be provided to a new user when they register in the System. They are intended to help users become familiar with the Program. Using these samples, users can explore the Program's main features without having to search for and upload suitable samples themselves.

To add demo samples to a configuration, locate the desired samples among those you have uploaded to the System. You can use the search box and the navigation controls to find them.

The table of available samples displays the sample name and either the patient ID or the name of the run to which the sample belongs. A non-tumor sample is marked with , and a tumor sample is marked with .

Only samples that belong to a patient or a run that is not archived are available for inclusion in a configuration.

Select the required samples by checking the corresponding boxes. The message below the "Demo samples" section heading will change from "No samples selected" to "Demo files selected:" followed by the number of selected samples.

After you add at least one settings preset, at least one report template, or at least one demo sample to the configuration, the button becomes active. Click it to add the configuration to the System.

To edit a configuration, click its row in the table, make the necessary changes, and then click .

The configurations added to the System are displayed in a table with the following columns:

  1. CONFIGURATION – the configuration name.
  2. DESCRIPTION – the configuration description.
  3. REGISTRATION LINK – the link used to register new users in the System with this configuration. To copy the link to the clipboard, click .
  4. MODIFIED – the date the configuration was last modified, in the format M/d/yyyy.

The table is sorted by configuration name.

When you hover over a configuration row, the button appears, allowing you to delete the configuration.

Users#

The page displays all users who have registered in the System or have been invited to it, and allows administrators to invite new users.

For Administrators, all users are displayed. Organization administrators see only the users who belong to their organization.

Registered and invited users are displayed in a table with the following columns:

  1. LOGIN - the user's login name specified during registration. Users who have been invited to the System but have not yet completed registration are labeled "Pending invitation".
  2. EMAIL - the user's email address, either specified during registration or entered in the invitation form.
  3. ORGANIZATION - the organization to which the user belongs. Organizations are groups of users created to facilitate collaboration. Administrators and Organization administrators can configure settings that apply to all users within an organization on the Organizations page. This column is available only to Administrators, who can assign users to organizations. Administrators can also filter the user list by organization using the Organization filter above the table.
  4. ROLE - the user's role in the System. Administrators can change the roles of other users by clicking the current role and selecting a new one. Organization administrators can change the roles of all users except those with the Administrator role.
  • Administrator - has full administrative privileges and can manage other users. Administrators have access to all pages in the Administration section, including the Tariffs page.
  • Organization administrator - can manage users who belong to the same organization. Compared with an Administrator, the following restrictions apply:
    • on the Users page, only users from the same organization are displayed, and the organization search field and Organization column are not displayed;
    • cannot manage Administrators (cannot change their role, sign in to their accounts, or remove them from the System);
    • on the Organizations page, only the Organization administrator's own organization is displayed. They cannot delete the organization, change its maximum number of processed samples, or create new organizations;
    • on the Active tasks page, only sample and group analysis processing tasks belonging to users from the same organization are displayed;
    • the Tariffs page is not available, including when selecting another user on the Users page.
  • User - has full access to the System except for user administration (the Administration section is unavailable).
  • Fixed settings - has the same permissions as a User, with the following restrictions:
    • cannot access the Settings page;
    • cannot change analysis settings or the sequencing type when uploading samples. The default analysis settings designated by the administrator are always used, and the sequencing type is determined by those settings;
    • cannot modify analysis parameters (the Parameters tab is disabled);
    • cannot restart sample processing from scratch or from any analysis stage.
  • Read only - can browse the Program but cannot perform any actions.
  1. SAMPLES VISIBILITY - determines which samples are visible in the user's account:
  • Owned only - the user can access only the samples they uploaded (demo samples may also be available).
  • All in organization - the user can access samples uploaded by all users in their organization. This option is available only if the user belongs to an organization.
  • Selected in organization - the user can access samples belonging to specific patients uploaded by other users in the same organization. This option is available only if the user belongs to an organization. When this option is selected, a dialog opens where you can choose the patients whose samples will be available to the selected user.

The list contains all patients in the organization. The username of the user who added each patient to the System is shown in parentheses. Select the required patients by checking the corresponding boxes, then click anywhere outside the list within the dialog to close it.

The selected patients are displayed in the Selected Patients section:

To confirm your selection, click . The number of patients whose samples are available to the user is displayed in the Samples Visibility column:

If you need to change the selection later, click the displayed value, modify the list of selected patients, and confirm your changes.

  1. SAMPLES QUOTAS - displays information about the number of samples processed by the user during their entire time using the Program, as well as any processing limits. The value is displayed in the format "N of M", where N is the number of samples processed by the user in Genomenal, and M is the maximum number of samples the user is allowed to process (configured using the "Max number of processed samples" parameter). The value in parentheses, if present, indicates the maximum sample size that the user is allowed to process (configured using the "Max sample size, GB" parameter).

To edit these limits for a user, click the current value in the Samples Quotas column, enter the desired values in the dialog that opens, and confirm the changes by clicking :

If both fields are left empty, no sample processing limits are applied, allowing the user to process an unlimited number of samples of any size. If the maximum number of processed samples is set to 0, the user will not be able to process any samples.

  1. OMIM DATA - determines whether the user has access to the OMIM database. Users with OMIM access can view the OMIM Gene-Phenotype Relationships section and use the OMIM Phenotype filter in SNV Viewer. To grant access, select the corresponding checkbox in the column.
  2. LAST LOGIN AT - the date (in M/d/yyyy format) and time (in HH:mm:ss format) of the user's most recent login to the System (that is, when they authenticated using their login and password).

By default, the table is sorted by user login. It can also be sorted in ascending or descending order by the "Login", "Email", "Organization", "Role", and "Last Login At" columns. To sort the table, click a column header once for ascending order or twice for descending order. An ascending () or descending () sort indicator is displayed next to the column name. To clear the sorting, refresh the browser page. "Login" and "Email" columns are sorted alphabetically. Sorting by the "Organization" column groups users by organization. "Role" column is sorted in the following order: User, Read only, Administrator, Fixed settings, Organization administrator. "Last Login At" column is sorted chronologically, from the earliest to the latest login time or vice versa. Users who have been invited but have not yet completed registration are always displayed at the top of the table, regardless of the selected sort order.

By clicking the row of a registered user, an Administrator can open that user's Payments page. This functionality is not available to Organization administrator.

When you hover over another user's row, the following actions become available:

  • - sign in to that user's account.
  • – for users who have been invited but have not yet registered, copy the invitation link to the clipboard.
  • – for users who have been invited but have not yet registered, delete the invitation. After clicking the button, confirm the action in the dialog that appears:

  • – for registered users, delete the user's account from the System. After clicking the button, confirm the action in the dialog that appears:

Only inactive user accounts can be deleted from the System. A user is considered inactive if they have no patients, runs, group analyses, uploaded capture kits, or custom annotations in the System. If you are unable to delete a user even after removing all of these items from their account, contact technical support. The database may still contain archived SNVs/Indels associated with the user that cannot be removed through the Program interface.

Inviting a New User#

To invite a new user to the System, click . In the dialog that opens, enter the email address of the user you want to invite:

You can also configure a number of settings for the invited user:

  1. Configuration. Select a configuration containing settings presets, report templates, and/or demo samples that will be added to the user's account after registration. For information on creating configurations, see above.
  2. Role. Select one of the following roles for the invited user:
  • Administrator – has full administrative privileges and can manage other users. Administrators have access to all pages in the Administration section, including the Tariffs page. This role can only be assigned by an Administrator, not by an Organization administrator.
  • Organization administrator - can manage users who belong to the same organization. Compared with an Administrator, the following restrictions apply:
    • on the Users page, only users from the same organization are displayed, and the organization search field and Organization column are not displayed;
    • cannot manage Administrators (cannot change their role, sign in to their accounts, or remove them from the System);
    • on the Organizations page, only the Organization administrator's own organization is displayed. They cannot delete the organization, change its maximum number of processed samples, or create new organizations;
    • on the Active tasks page, only sample and group analysis processing tasks belonging to users from the same organization are displayed;
    • the Tariffs page is not available, including when selecting another user on the Users page.
  • User - has full access to the System except for user administration (the Administration section is unavailable).
  • Fixed settings - has the same permissions as a User, with the following restrictions:
    • cannot access the Settings page;
    • cannot change analysis settings or the sequencing type when uploading samples. The default analysis settings designated by the administrator are always used, and the sequencing type is determined by those settings;
    • cannot modify analysis parameters (the Parameters tab is disabled);
    • cannot restart sample processing from scratch or from any analysis stage.
  • Read only - can browse the Program but cannot perform any actions.
  1. Samples Visibility:
  • Owned only - the user can access only the samples they uploaded (demo samples may also be available).
  • All in organization - the user can access samples uploaded by all users in the organization to which the inviting administrator belongs (and to which the invited user will belong). This option is available only if the inviting administrator belongs to an organization.
  • Selected in organization - the user can access selected samples uploaded by other users in the inviting administrator's organization. The specific samples can be selected later using the Samples Visibility column on the Users page. This option is available only if the inviting administrator belongs to an organization.
  1. OMIM Data. Grants the user access to the OMIM database. Users with OMIM access can view the OMIM Gene-Phenotype Relationships section and use the OMIM Phenotype filter in SNV Viewer.
  2. Max number of processed samples. Specifies the maximum number of samples the user is allowed to process. If the field is left empty, the user can process an unlimited number of samples. If the value is set to 0, the user will not be able to process any samples.
  3. Max sample size, GB. Specifies the maximum sample size (in GB) that the user is allowed to upload. If the field is left empty, no file size limit is applied.

After completing the required fields, click . A registration link will be sent to the specified email address and copied to your clipboard, allowing you to send it directly to the invited user if needed.

User Page#

The User page is used to manage billing for the Genomenal platform. It is available only to Administrators and is not accessible to Organization administrators.

To open the page, click the corresponding user's row on the Users page.

The page contains the Payments, Usage Details, and Pricing tabs.

At the top of the page, the following switches are available:

  1. "Enable billing" – controls whether billing information is available to the user. When enabled, the following information becomes available on the Profile settings page:
  • completed and upcoming payments;
  • usage details;
  • pricing.
  1. "Allow file downloads" - controls whether the user is allowed to download and export files from their account. When disabled, the user cannot:
  • download original sample files from the Workflow details tab;
  • download result files generated during sample analysis from the Main and Workflow details tabs;
  • export SNVs/Indels from SNV Viewer;
  • export gene coverage information from the Coverage Analysis tab;
  • export interpreted SNVs/Indels statistics from the Profile page.

The following actions remain available:

  • export reports in PDF format;
  • download attachments from the Patient Info section;
  • export report templates in JSON format;
  • download capture kits;
  • download custom annotations.

For users whose file download permission is disabled, the restriction is displayed as follows:

1. Payments#

The Payments tab displays information about the user's completed and upcoming payments for using Genomenal.

At the top of the tab, the amount due (in RUB) as of the beginning of the current month is displayed. This amount is updated automatically as information about received payments is added.

Completed payments are displayed in a table with the following columns:

  • Payment amount - the payment amount in RUB;
  • Payment date - the date the payment was made;
  • Comments - additional information about the payment.

To add a payment, click . In the dialog that opens, specify the payment amount and payment date (the current date is selected by default). Optionally, enter a comment.

After filling in the required fields, click .

To delete a payment record, hover over the corresponding row in the table and click . In the confirmation dialog, click to confirm the deletion:

2. Usage Details#

The Usage Details tab displays information about the user's usage of Genomenal products and the calculated cost for the selected time period.

At the top of the tab, you can select the time period for which usage details are displayed. By default, the period spans from the first day of the current month to the current date.

Usage details for the selected period are presented in a table with the following columns:

  1. Product - the name of the service provided. Expanding a row displays the samples or group analyses for which the service was provided.

The expanded entries are displayed in the following formats:

  • Patient samples: patient ID / sample name
  • Run samples: run name / sample name
  • Patient samples in a run: run name / patient ID / sample name
  • Group analyses: group analysis name (Samples: number of samples included in the analysis)

If a sample has been deleted after processing, (deleted) is appended to its name.

  1. Usage - represents the amount of resources consumed or the number of services provided during the selected period.
  • For Processing, Annotation, and Group analysis services, the value represents the number of completed operations.
  • For the Analysis support service, the value represents the total size of stored sample files, expressed in GB*day (1 GB of data stored for 1 day).
  • For the SNV viewer support service, the value represents the total number of stored genetic variants (SNVs/Indels), expressed in 100K SNV*day (100,000 variants stored for 1 day). The displayed value is rounded.

Actual usage is calculated as: Usage − Added. The added amount is excluded from billing because storage is provided free of charge for the first 30 days after sample processing.

For Processing, Annotation, and Group analysis services, detailed usage information is available in the expanded rows.

  1. Cost - the cost of the service for the selected period (in RUB).

The general formula is: Cost = Actual Usage × Unit Price / 30 days

Prices are available on the Pricing tab.

  • The cost of Processing, Annotation, and Group analysis services depends on the number of processed samples or completed group analyses during the selected period.
  • The cost of Analysis support depends on the total size of the stored sample files.
  • The cost of SNV viewer support depends on the number of stored SNVs/Indels.

For Processing, Annotation, and Group analysis services, detailed cost information is available in the expanded rows.

The bottom row of the table (Total for the period) displays the total cost of all services during the selected period.

  1. Details - contains additional information for each service.

Details for Processing, Annotation, and Group analysis:

  • Processed at – the date and time when the sample or group analysis was processed.

Details for Analysis support:

  • GB*day on period start - the storage usage carried over to the beginning of the selected period. This value is always 0, because each reporting period is calculated independently and accumulated usage is not carried over.
  • GB*day added for the period - the amount of newly stored data during the selected period that is excluded from billing. This value is recalculated for the full 30-day free storage period according to the formula: Storage Size (GB) × 30 days.
  • GB*day used for the period - the actual storage usage during the selected period, calculated as: Storage Size (GB) × Actual Storage Time (days).
  • GB*day on period end - the storage usage at the end of the selected period. This value is always 0, because each reporting period is calculated independently.

Expanded row details for Analysis support:

  • Sample files size - the size of a single sample file, or the combined size of the primary and mate files for paired-end sequencing.
  • Period - the time interval selected at the top of the Usage Details tab. Usage is calculated in whole days within the selected period according to the System time zone.
  • GB*day added for the period - see above.
  • GB*day used for the period - see above.

Details for SNV viewer support:

  • 100K SNV*day on period start - the number of SNVs/Indels counted at the beginning of the selected period. Always 0, because each reporting period is calculated independently.
  • 100K SNV*day added for the period - the number of SNVs/Indels added during the selected period and excluded from billing. This value is recalculated for the full 30-day free storage period according to the formula: Stored Variants (100K SNV) × 30 days.
  • 100K SNV*day used for the period - the actual usage during the selected period, calculated as: Stored Variants (100K SNV) × Actual Storage Time (days).
  • 100K SNV*day on period end - the number of SNVs/Indels counted at the end of the selected period. Always 0, because each reporting period is calculated independently.

Expanded row details for SNV viewer support:

  • SNV count for sample - the total number of variants stored in the sample's SNV Viewer. If both somatic and germline variants are present, their counts are added together.
  • Period - the time interval selected at the top of the Usage Details tab. Usage is calculated in whole days within the selected period according to the System time zone.
  • 100K SNV*day added for the period - see above.
  • 100K SNV*day used for the period - see above.

Total for the period row at the bottom of the table displays:

  • Debt on period start - the unpaid balance at the beginning of the selected period (RUB).
  • Period payments - the total amount of payments received during the selected period (RUB).
  • Cost of usage for the period - the total cost of all services during the selected period (RUB).
  • Debt on period end - the amount due for the selected period (RUB), calculated as: (Debt on period start) + (Cost of usage for the period) − (Period payments).

3. Pricing#

The Pricing tab displays the current prices for Genomenal products available to the user.

The available prices are displayed in a table with the following columns:

  1. Product - the name of the Genomenal service:
  • FASTQ/BAM gene panel processing;
  • FASTQ/BAM whole-exome processing;
  • FASTQ/BAM whole-genome processing;
  • FASTQ/BAM low-pass whole-genome processing;
  • VCF gene panel annotation;
  • VCF whole-exome annotation;
  • VCF whole-genome annotation;
  • VCF Structural variations annotation;
  • Analysis support, 1GB per 30 days (the first 30 days after sample processing are free of charge);
  • Group analysis of FASTQ/BAM gene panels, per sample (price depends on the number of samples in the analysis);
  • Group analysis of FASTQ/BAM whole-exome samples, per sample (price depends on the number of samples in the analysis);
  • Group analysis of FASTQ/BAM whole-genome samples, per sample (price depends on the number of samples in the analysis);
  • SNV viewer support, 100000 variants per 30 days (the first 30 days after sample processing are free of charge).
  1. Price - the price of the product (in RUB). A personal price is indicated by the icon.
  2. Valid from - the date from which the price becomes effective.

To assign a personal price for a specific product, hover over the corresponding row in the table and click . In the dialog that opens, specify the price (in RUB) and the date from which the price should become valid. The current date is selected by default.

After filling in the required fields, click .

To delete a personal price, hover over the corresponding row in the table and click . In the confirmation dialog, click to confirm the deletion.

Organizations#

The Organizations page displays the organizations added to the System. An organization is a group of users united by a common characteristic. Organizations are typically created to facilitate collaboration between users.

Only the Administrator has access to all organizations in the System. An Organization administrator can access only the organization to which they belong. In addition, unlike the Administrator, the Organization administrator cannot delete an organization, change the organization's maximum number of processed samples, or create new organizations.

Organizations are displayed as individual cards. The blue header at the top of each card contains the organization name. It also includes:

  • - edits the organization. The edit dialog contains the same fields as the Add organization dialog (see below), except for the "Personal Interpretation Results" option. The "Max number of processed samples" field is also unavailable to the Organization administrator.
  • - deletes the organization. This button is not available to the Organization administrator.

Each organization card contains the following sections:

  • Quotas usage - displays the total number of samples processed by users in the organization throughout their use of the System, as well as the maximum number of samples that users in the organization are allowed to process (configured by the "Max number of processed samples" parameter).
  • Personal Interpretation Results - displays "Yes" or "No", depending on whether this option was enabled when the organization was created.
  • Default parameters for new users - displays the default user role, samples count quota, and size quota in GB assigned to new users invited to the organization. These settings can be modified either for the entire organization or for individual users in the invitation dialog.
  • Custom logo - displays the organization's logo, if one has been uploaded. The logo is used throughout the interface in place of the Genomenal logo (for example, in the navigation sidebar).
  • Demo files - displays "No demo files selected" if no demo files have been configured for newly invited users, or "Demo files selected:" followed by the number of selected files.
  • Work actions - stages used to track the progress of sample interpretation. Work actions are intended to support collaborative interpretation by multiple users within an organization. If work actions are configured for an organization, all users in that organization will see the Work actions tab on the sample page. From this tab, users can add actions defined for the organization and assign responsible users to complete them. To add a work action:
  1. Click .
  2. In the dialog that opens, enter the action name.

  1. The first word of the action name is automatically used as the action's short name. This short name is displayed in the Interpretation actions column on the Samples page. If necessary, edit it.
  2. Select the action type:
  • Interpretation - actions related to sample interpretation.
  • Administration - actions intended for reviewing or supervising other users' work.
  1. Select the visibility:
  • All organization users - the action is available to all users in the organization.
  • Administrators only - the action is available only to the Administrator and Organization administrator.
  1. Click .

The list of work actions can be managed as follows:

  • move an action up by clicking ;
  • move an action down by clicking ;
  • edit an action by clicking , then save your changes by clicking ;
  • delete an action by clicking .

Add organization#

To add a new organization to the System, click . This button is available only to the Administrator and is not available to the Organization administrator.

In the dialog that opens, complete the following fields:

  1. Organization name.
  2. Custom logo. Optionally, upload your organization's logo. It will be displayed throughout the interface in place of the Genomenal logo (for example, in the navigation sidebar). To upload a logo, drag and drop an image into the upload area or click the area to open the file browser. The logo must be an SVG image no larger than 100 KB with an aspect ratio of 8:1 (for example, 200 × 25 pixels).
  3. Max number of processed samples - the total number of samples that users belonging to this organization are allowed to process. If the field is left empty, no limit is applied. If the value is set to 0, users in the organization will not be able to process samples.
  4. Personal Interpretation Results. If this option is enabled, users who share samples within the organization can interpret them independently. Changes made by other users (such as variant interpretations, pinned variants, report inclusion, hidden variants, pathogenicity classifications, and similar modifications) will not be visible. If this option is disabled, users sharing samples within the organization will see one another's changes, enabling collaborative variant interpretation. Note that this option cannot be changed after the organization has been created.
  5. User role - the default role assigned to users invited to the organization. This value can be changed later in the invitation dialog. Available roles are:
  • User - has full access to the System except for user administration (the Administration section is unavailable).
  • Fixed settings - has the same permissions as a User, with the following restrictions:
    • cannot access the Settings page;
    • cannot change analysis settings or the sequencing type when uploading samples. The default analysis settings designated by the administrator are always used, and the sequencing type is determined by those settings;
    • cannot modify analysis parameters (the Parameters tab is disabled);
    • cannot restart sample processing from scratch or from any analysis stage.
  • Read only - can browse the Program but cannot perform any actions.
  1. Samples count quota - the default maximum number of samples that users invited to the organization are allowed to process. If the field is left empty, no limit is applied. If the value is set to 0, invited users will not be able to process samples. This value can be changed later in the user invitation dialog.
  2. Size quota in GB - the default maximum sample size (in GB) that users invited to the organization are allowed to process. If the field is left empty, no size limit is applied. This value can be changed later in the user invitation dialog.
  3. Demo samples - demonstration samples that are automatically added to the accounts of all new users invited to the organization. They help users become familiar with the System by allowing them to explore its main features without having to find and upload their own sample data. Instructions for adding demo samples are provided above.

Active tasks#

The Active tasks page displays the sample processing and group analysis tasks that are currently scheduled or running in the System. An Organization administrator can view only the active tasks of users belonging to their organization.

The page displays a table with the following columns:

  1. PATIENT/RUN - the patient and/or run to which the processed sample assigned.
  2. SAMPLE/ANALYSIS - the name of the sample or group analysis currently being processed.
  3. STATUS - the name of the scheduled analysis task and its progress.
  4. SCHEDULED AT - the date (MM/dd/yyyy) and time (HH:mm:ss) when the task was scheduled.
  5. STARTED AT - the date (MM/dd/yyyy) and time (HH:mm:ss) when task execution began.

Tasks are grouped by the user who owns the processed samples.

To cancel an active task, click in the corresponding table row.

Tariffs#

The Tariffs page displays the prices of the services provided by Genomenal. This page is available only to the Administrator.

To change the price of a service for all users in the System, hover over the corresponding row in the table and click . In the dialog that opens, specify the price (in RUB) and the date from which the new price should become valid. The current date is selected by default.

After filling in the required fields, click .

To delete a price entry, hover over the corresponding row in the table and click .

In the confirmation dialog, click to confirm the deletion.