Manual Oniro

Chapter 1. Overview

Oniro is a web container that encapsulates a number of Molecular Discovery solutions for structure elucidation, in-silico predictions, spectral database, search and reporting that could be used in multiple fields. The platform is distributed together with the WebMetabase 4.1, Compound Library 2.0, WebChembase 1.0 and WebQuant 2.0 applications and it is way to manage user, settings, import exported files and access to the applications it self.

Oniro Platform

The Oniro and its applications are accessible from a web browser, after you type the URL of the application, typically https://MDServer/WebMetabase (the URL would depend in the user installation, please refer to your IT to know the correct URL) the user will be prompted to login the user and password . Ask to you Oniro manager to get the login and password. If it is the first time that no one is accessing to the system, you may use the admin login and the default password would be admin, you will need to modify the password after you have logged into the system.

Login window.

After login the system window will be shown . The buttons to access the multiple sections will be shown in a new window.

Oniro Platform

Chapter 2. Oniro utilities

There are a number of utilities that are accessible from the Oniro level. The window is divided in 3 areas . On the upper part, it shows the module in the Oniro where we are, the different sections can be accessed by clicking in this part. On the left part there are the Oniro accessible function like settings and the logout button, this area could be hidden by clicking the icon on the right of the section bar. The buttons to access the WebMetabase, WebQuant, WebChembase and Compound Library sections as well as the three main functionalities buttons are shown in the middle part of the third area.

Manage users

Oniro use a login system that recognize the user authenticated and show the appropriate functions and experiments for the user roles and work group/s. The definition of the users properties is done in the Users Management area accessible by pressing the Users button in the main Oniro window and then selecting the tab Users. The Work groups are defined at the Work groups tab. There it is possible to define new work groups and assign to them existing users.

Users

In the Users tab it is possible to create new users, assign to each user a set of levels that will define the functions the user has access to. Only users with User management level assigned can create/modify/remove user conditions levels for the user with administrative role has some parameters that affects to all Oniro users, and also the work groups to which the user is assigned to.

Users management

Authentication

In this section the user manager can set up the name of the user, or use the LDAP system it has been associated. Also the password can be set in this section, he user manage can force to the user to change the password the next time he or she login into the system by activating the check box Change password at next login. Also the user can be in active mode or inactivate mode depending if the check box User active is checked or not respectively.

Modules

Oniro is a container of multiple modules. The access of the users to the different modules can be customized.

  • WebMetabase (small molecule)

  • WebMetabase (macro molecule)

  • Compound Library (small molecule)

  • Compound Library (macro molecule)

  • WebQuant

  • WebChembase

Functions

The different roles would depend on the module under consideration:

  • WebMetabase (Small Molecule)

    • Result visualization:

      • Experiment type: Definition of the tabs

        • Pending: Access to the Pending tab.

        • Approved: Access to the Approved tab.

        • Calibration: Access to the calibration tab

      • Access:

        • In any work group: Access to experiments that belong to any work group

        • Unowned experiments: Access to experiments that do not have any owner

    • Experiment panel visualization: definition for the tabs accessible from Pending and/or Approved

      • Chromatography: Access to the Chromatogram tab.

      • Metabolites: Access to the Compounds tab.

      • Chemical results: : Access to the "Chemical Results" tab.

      • Analysis Tools:: Access to the Analysis tools tab.

      • Notebook: Access to visualize the Notebook where all the saved actions are recorded.

      • Settings: Access to the user settings.

      • Attachments: Access to the attachment tab.

    • Definitions: Access to the tools that define different aspects of the protocol.

      • Units: Access to define Units.

      • Properties: Access to define property names.

      • Properties values: Access to define the values for the properties.

      • Metabolic groups: Access to define metabolite group names.

      • Experimental flags: Access to define experimental flags state and names.

      • Protocol labels: Access to define protocol labels.

      • Macros: Access to define macro actions, values and names.

      • Protocols: Access to define protocol values and names.

      • Templates: Access to define templates.

    • Experiment management: Access to the functions that affect the experiments

      • Create Experiment: Access to upload an experiment.

      • Manual upload: Access to manually upload an experiment.

      • Delete files: Access to remove all the files loaded for an existing experiment.

      • Delete Experiment: Access to remove the entire experiment.

      • Edit again: Access to bring an approved experiment back to pending state.

      • Group Edition: Access to modify the groups the experiment belongs to.

      • Folder management: Access to rename, move, remove, copy folders.

      • Chromatogram raw data management: Access to import or move raw data files in sms format.

      • Data import: Enables the user to import external data from another WebMetabase installation, that has to be from the same version.

      • Data export: This option enables the user to export the data.

      • Change owner: This options controls if the user can change the owner of a particular experiment.

      • Manage Attachment: Access to upload, remove, make public or private the attachment connected to an experiment.

    • Tools: Access to the experimental analysis tools

      • SMRT: Access to the Structure Metabolism Relationship Tables analysis tool to compare different compound with the same protocol definition.

      • Cluster View: Access to the Cluster View tool to compare same compound with different experimental conditions, limited to the Unique Met ID identifiers.

      • Comparator: Access to the Comparator View tool to compare same compound with different experimental conditions.

      • Fragment analysis: Access to the Fragment analysis, in order to analysis the fragments that suffer different metabolic reactions.

      • Experimental analysis tools: Access to the kinetic and computation tools.

      • Report writer: Access to write reports in agreement to a report template

    • Maintenance:

      • Users and groups: Access to create/modify/remove Users and Work groups

      • Unlock experiments: Access to the option to unlock experiments when they have been locked by a user that open it to edit the results-

      • License management: Access to the option to add/change/remove the license for the system

      • Global settings: Access to the settings that affect every user

      • DB management: Access to the DB management tools

      • Analysis tools data:

        • Report Templates: Access to import the template for reporting.

        • MetaDesign Databases: Access to import the databases for the MetaDesign analysis tool.

        • Model definition: Access to define a user model.

        • MassMetaSite Settings: Access to introduce new MassMetaSite settings.

  • WebMetabase (Macro Molecule)

    • Result visualization:

      • Experiment type: Definition of the tabs

        • Pending: Access to the Pending tab.

        • Approved: Access to the Approved tab.

        • Calibration: Access to the calibration tab

      • Access:

        • In any work group: Access to experiments that belong to any work group

        • Unowned experiments: Access to experiments that do not have any owner

    • Experiment panel visualization: definition for the tabs accessible from Pending and/or Approved

      • Chromatography: Access to the Chromatogram tab.

      • Metabolites: Access to the Compounds tab.

      • Chemical results: : Access to the "Chemical Results" tab.

      • Analysis Tools:: Access to the Analysis tools tab.

      • Notebook: Access to visualize the Notebook where all the saved actions are recorded.

      • Settings: Access to the user settings.

      • Attachments: Access to the attachment tab.

    • Definitions: Access to the tools that define different aspects of the protocol.

      • Units: Access to define Units.

      • Properties: Access to define property names.

      • Properties values: Access to define the values for the properties.

      • Metabolic groups: Access to define metabolite group names.

      • Experimental flags: Access to define experimental flags state and names.

      • Protocol labels: Access to define protocol labels.

      • Macros: Access to define macro actions, values and names.

      • Protocols: Access to define protocol values and names.

      • Templates: Access to define templates.

      • Monomer management: Access to the monomers in the macromolecule mode.

    • Experiment management: Access to the functions that affect the experiments

      • Create Experiment: Access to upload an experiment.

      • Manual upload: Access to manually upload an experiment.

      • Delete files: Access to remove all the files loaded for an existing experiment.

      • Delete Experiment: Access to remove the entire experiment.

      • Edit again: Access to bring an approved experiment back to pending state.

      • Group Edition: Access to modify the groups the experiment belongs to.

      • Folder management: Access to rename, move, remove, copy folders.

      • Chromatogram raw data management: Access to import or move raw data files in sms format.

      • Data import: Enables the user to import external data from another WebMetabase installation, that has to be from the same version.

      • Data export: This option enables the user to export the data.

      • Change owner: This options controls if the user can change the owner of a particular experiment.

      • Manage Attachment: Access to upload, remove, make public or private the attachment connected to an experiment.

    • Tools: Access to the experimental analysis tools

      • SMRT: Access to the Structure Metabolism Relationship Tables analysis tool to compare different compound with the same protocol definition.

      • Cluster View: Access to the Cluster View tool to compare same compound with different experimental conditions, limited to the Unique Met ID identifiers.

      • Comparator: Access to the Comparator View tool to compare same compound with different experimental conditions.

      • Fragment analysis: Access to the Fragment analysis, in order to analysis the fragments that suffer different metabolic reactions.

      • In silico: Access to the Site of Metabolism (SoM) prediction tool.

      • Experimental analysis tools: Access to the kinetic and computation tools.

      • Report writer: Access to write reports in agreement to a report template

    • Maintenance:

      • Users and groups: Access to create/modify/remove Users and Work groups

      • Unlock experiments: Access to the option to unlock experiments when they have been locked by a user that open it to edit the results-

      • License management: Access to the option to add/change/remove the license for the system

      • Global settings: Access to the settings that affect every user

      • DB management: Access to the DB management tools

      • Analysis tools data:

        • Report Templates: Access to import the template for reporting.

        • MetaDesign Databases: Access to import the databases for the MetaDesign analysis tool.

        • Model definition: Access to define a user model.

        • MassMetaSite Settings: Access to introduce new MassMetaSite settings.

  • Compound Library (Small Molecule)

    • Definitions: Access to the tools that define different aspects of the properties.

      • Units: Access to define Units.

      • Properties: Access to define property names.

      • Properties values: Access to define the values for the properties.

    • Compound management: Access to the functions that affect the compounds

      • Create Compound: Access to upload a compound.

      • Delete Compound: Access to remove the compound.

      • SDF upload: Access to upload a sdf file with multiple compounds.

      • Folder management: Access to rename, move, remove, copy folders.

    • Tools: Access to the experimental analysis tools

      • Cluster View: Access to the Cluster View tool to compare same compound with different experimental conditions, limited to the Unique Met ID identifiers.

      • Comparator: Access to the Comparator View tool to compare same compound with different experimental conditions.

      • Compound analysis/in-silico tools: Access to the MetaSite, descriptor calculation, Pka and logD prediction and ADME prediction.

      • Report writer: Access to write reports in agreement to a report template

    • Maintenance:

      • Users and groups: Access to create/modify/remove Users and Work groups

      • License management: Access to the option to add/change/remove the license for the system

      • Global settings: Access to the settings that affect every user

      • DB management: Access to the DB management tools

  • Compound Library (Macro Molecule)

    • Definitions: Access to the tools that define different aspects of the properties.

      • Units: Access to define Units.

      • Properties: Access to define property names.

      • Properties values: Access to define the values for the properties.

      • Protocols; Access to define the protocols to importa properties from a csv file

      • Modeling: Access to the modeling module

    • Compound management: Access to the functions that affect the compounds

      • Create Compound: Access to upload a compound.

      • Delete Compound: Access to remove the compound.

      • SDF upload: Access to upload a sdf file with multiple compounds.

      • Folder management: Access to rename, move, remove, copy folders.

    • Tools: Access to the experimental analysis tools

      • Cluster View: Access to the Cluster View tool to compare same compound with different experimental conditions, limited to the Unique Met ID identifiers.

      • Comparator: Access to the Comparator View tool to compare same compound with different experimental conditions.

      • Compound analysis/in-silico tools: Access to the MetaSite, descriptor calculation, Pka and logD prediction and ADME prediction.

      • Report writer: Access to write reports in agreement to a report template

      • Modeling management: Access to manage the models build within the application.

      • Prediction tool: Access to the to to use the models built to predict new compounds.

    • Maintenance:

      • Users and groups: Access to create/modify/remove Users and Work groups

      • License management: Access to the option to add/change/remove the license for the system

      • Global settings: Access to the settings that affect every user

      • DB management: Access to the DB management tools

      • Analysis tools:

        • Insilico Settings: Access to the tool to define the settings for the multiple in-silico tools.

  • WebQuant

    • Result visualization:

      • Experiment type: Definition of the tabs

        • Pending: Access to the Pending tab.

        • Approved: Access to the Approved tab.

      • Access:

        • In any work group: Access to experiments that belong to any work group

        • Unowned experiments: Access to experiments that do not have any owner

    • Definitions: Access to the tools that define different aspects of the protocol.

      • Units: Access to define Units.

      • Properties: Access to define property names.

      • Properties values: Access to define the values for the properties.

      • Metabolic groups: Access to define metabolite group names.

      • Experimental flags: Access to define experimental flags state and names.

      • Protocol labels: Access to define protocol labels.

      • Macros: Access to define macro actions, values and names.

      • Protocols: Access to define protocol values and names.

      • Templates: Access to define templates.

    • Experiment management: Access to the functions that affect the experiments

      • Create Experiment: Access to upload an experiment.

      • Manual upload: Access to manually upload an experiment.

      • Delete files: Access to remove all the files loaded for an existing experiment.

      • Delete Experiment: Access to remove the entire experiment.

      • Edit again: Access to bring an approved experiment back to pending state.

      • Group Edition: Access to modify the groups the experiment belongs to.

      • Folder management: Access to rename, move, remove, copy folders.

      • Chromatogram raw data management: Access to import or move raw data files in sms format.

      • Data import: Enables the user to import external data from another WebMetabase installation, that has to be from the same version.

      • Data export: This option enables the user to export the data.

      • Change owner: This options controls if the user can change the owner of a particular experiment.

    • Tools: Access to the experimental analysis tools

      • Report writer: Access to write reports in agreement to a report template

    • Maintenance:

      • Users and groups: Access to create/modify/remove Users and Work groups

      • Unlock experiments: Access to the option to unlock experiments when they have been locked by a user that open it to edit the results-

      • License management: Access to the option to add/change/remove the license for the system

      • Global settings: Access to the settings that affect every user

      • DB management: Access to the DB management tools

      • Analysis tools data:

        • Report Templates: Access to import the template for reporting.

        • MetaDesign Databases: Access to import the databases for the MetaDesign analysis tool.

        • Model definition: Access to define a user model.

        • MassMetaSite Settings: Access to introduce new MassMetaSite settings.

        • Rapiflex Settings: Access to introduce the New LipostarMSI Settings.

  • WebChembase

    • Result visualization:

      • Experiment type: Definition of the tabs

        • Pending: Access to the Pending tab.

        • Approved: Access to the Approved tab.

        • Calibration: Access to the calibration tab

      • Access:

        • In any work group: Access to experiments that belong to any work group

        • Unowned experiments: Access to experiments that do not have any owner

    • Experiment panel visualization: definition for the tabs accessible from Pending and/or Approved

      • Chromatography: Access to the Chromatogram tab.

      • Metabolites: Access to the Compounds tab.

      • Chemical results: : Access to the "Chemical Results" tab.

      • Analysis Tools:: Access to the Analysis tools tab.

      • Notebook: Access to visualize the Notebook where all the saved actions are recorded.

      • Settings: Access to the user settings.

      • Attachments: Access to the attachment tab.

    • Definitions: Access to the tools that define different aspects of the protocol.

      • Units: Access to define Units.

      • Properties: Access to define property names.

      • Properties values: Access to define the values for the properties.

      • Metabolic groups: Access to define metabolite group names.

      • Experimental flags: Access to define experimental flags state and names.

      • Protocol labels: Access to define protocol labels.

      • Macros: Access to define macro actions, values and names.

      • Protocols: Access to define protocol values and names.

      • Templates: Access to define templates.

    • Experiment management: Access to the functions that affect the experiments

      • Create Experiment: Access to upload an experiment.

      • Manual upload: Access to manually upload an experiment.

      • Delete files: Access to remove all the files loaded for an existing experiment.

      • Delete Experiment: Access to remove the entire experiment.

      • Edit again: Access to bring an approved experiment back to pending state.

      • Group Edition: Access to modify the groups the experiment belongs to.

      • Folder management: Access to rename, move, remove, copy folders.

      • Chromatogram raw data management: Access to import or move raw data files in sms format.

      • Data import: Enables the user to import external data from another WebMetabase installation, that has to be from the same version.

      • Data export: This option enables the user to export the data.

      • Change owner: This options controls if the user can change the owner of a particular experiment.

      • Manage Attachment: Access to upload, remove, make public or private the attachment connected to an experiment.

    • Tools: Access to the experimental analysis tools

      • SMRT: Access to the Structure Metabolism Relationship Tables analysis tool to compare different compound with the same protocol definition.

      • Cluster View: Access to the Cluster View tool to compare same compound with different experimental conditions, limited to the Unique Met ID identifiers.

      • Comparator: Access to the Comparator View tool to compare same compound with different experimental conditions.

      • Fragment analysis: Access to the Fragment analysis, in order to analysis the fragments that suffer different metabolic reactions.

      • Experimental analysis tools: Access to the kinetic and computation tools.

      • Report writer: Access to write reports in agreement to a report template

    • Maintenance:

      • Users and groups: Access to create/modify/remove Users and Work groups

      • Unlock experiments: Access to the option to unlock experiments when they have been locked by a user that open it to edit the results-

      • License management: Access to the option to add/change/remove the license for the system

      • Global settings: Access to the settings that affect every user

      • DB management: Access to the DB management tools

      • Analysis tools data:

        • Report Templates: Access to import the template for reporting.

        • MetaDesign Databases: Access to import the databases for the MetaDesign analysis tool.

        • Model definition: Access to define a user model.

        • MassMetaSite Settings: Access to introduce new MassMetaSite settings.

The are a number of options that are available by right clicking in this area:

Oniro offers six pre-defined user levels that have the roles already pre-defined, that are accessed by right clicking in the role area and would depend on the module analysed:

  • WebMetabase (small molecule):

    • admin: The default administrator has the roles assigned for protocol definition and user management.

    • Met ID expert: A Metabolite Identification Expert has the Analysis tools, Database browsing, Experiment review and approval, Group-project management, manual Experiment upload, result visualization, rule definition and Sample list generation activated.

    • Chemist: The default chemist user has the analysis tools, the database browsing and the result visualization activated

    • Met ID lab: A Met ID lab category has the Manual Experiment upload and a sample list generation active.

    • Computational Chemist: The users in this level can access only approved experiments, and the analysis tools

    • IT Maintenance: In this level the user can access the Users & groups, the licence management and the global settings.

  • WebMetabase (Macro molecule):

    • admin: The default administrator has the roles assigned for protocol definition and user management.

    • Met ID expert: A Metabolite Identification Expert has the Analysis tools, Database browsing, Experiment review and approval, Group-project management, manual Experiment upload, result visualization, rule definition and Sample list generation activated.

    • Chemist: The default chemist user has the analysis tools, the database browsing and the result visualization activated

    • Met ID lab: A Met ID lab category has the Manual Experiment upload and a sample list generation active.

    • Computational Chemist: The users in this level can access only approved experiments, and the analysis tools

    • IT Maintenance: In this level the user can access the Users & groups, the licence management and the global settings.

  • Compound Library (Small Molecule)

    • Admin: The default administrator has the roles assigned for protocol definition and user management.

    • Scientist: A scientist can view the data, perform calculations, but it is not allowed to remove compounds from the database

    • IT Maintenance: In this level the user can access the Users & groups, the licence management and the global settings.

  • Compound Library (Macro Molecule)

    • Admin: The default administrator has the roles assigned for protocol definition and user management.

    • Scientist: A scientist can view the data, perform calculations, but it is not allowed to remove compounds from the database

    • IT Maintenance: In this level the user can access the Users & groups, the licence management and the global settings.

  • WebQuant:

    • admin: The default administrator has the roles assigned for protocol definition and user management.

    • Met ID expert: A Metabolite Identification Expert has the Analysis tools, Database browsing, Experiment review and approval, Group-project management, manual Experiment upload, result visualization, rule definition and Sample list generation activated.

    • Chemist: The default chemist user has the analysis tools, the database browsing and the result visualization activated

    • Met ID lab: A Met ID lab category has the Manual Experiment upload and a sample list generation active.

    • Computational Chemist: The users in this level can access only approved experiments, and the analysis tools

    • IT Maintenance: In this level the user can access the Users & groups, the licence management and the global settings.

  • WebChembase:

    • admin: The default administrator has the roles assigned for protocol definition and user management.

    • Met ID expert: A Metabolite Identification Expert has the Analysis tools, Database browsing, Experiment review and approval, Group-project management, manual Experiment upload, result visualization, rule definition and Sample list generation activated.

    • Chemist: The default chemist user has the analysis tools, the database browsing and the result visualization activated

    • Met ID lab: A Met ID lab category has the Manual Experiment upload and a sample list generation active.

    • Computational Chemist: The users in this level can access only approved experiments, and the analysis tools

    • IT Maintenance: In this level the user can access the Users & groups, the licence management and the global settings.

User Work groups

The User Work groups utility is designed to allow the Oniro experiments to be available only to certain users inside a work group.

When a protocol instance (experiment) is prepared, it can be assigned to any of the work groups the user that is preparing belongs to, or leave it without any work group assignment. In the later case, the experiment will be available to all the WebMetabase users to access to unowned experiments when it is approved, and only to the users in the work group in the first case.

The use of work groups is applied to tools like Déjà vu function if an experiment is assign to a work group only the experiments assigned to that work group will be available for this function, unless in the global settings of admin area the "Use whole db for data process (ignore groups) is checked, that will make that all experiments are available for all functions within Oniro.

Right click on this area give you access to Add, Rename or remove a work group.

Work groups

In this tab the user manager can create new work-flows and assign the different users to the different work groups.

Work group management

This tab is composed of 3 areas. The list on the left is the list of available work groups, the middle one is the different users available and the one in the right is the user assigned to the selected work group. The arrows in between the 2nd and 3rd area are useful to move the users in or out a certain work group. Right clicking on the left area one can access to generate New, Remove or copy a work group.

Actions

There are a number of actions that can be done in the user management section:

  • New: Generate a new user. In order to create a User the Name and Password have to be introduced (the password has to be repeated in the next field).

  • Copy: Copy the User configuration of an existing user to a new one. Click a user on the left panel and click Copy

  • Delete: Remove a User.

  • Save: Save the settings done for a new user

  • Close: This will close the User Management window.

Settings

In order to access the user setting you have to be login into Oniro. In the web browser go to the http://serverName:8080/WebMetabase. (Server Name is replaced by the name of the computer that is used as server). The login window will be shown unless you already have logged before into the system and indicated that you would like to be remembered by clicking the Remember me check box in the login window.

After you are logged into Oniro (Figure 2.3) click in the Settings button to access the user settings. The number of tabs that will be shown would depend on the role assigned to the user.

User

User Settings: User

  • Authentication

    • Token: Token to be user by the user for authentication.

    • Password:

    • Confirm: Same password as in the line before.

    • Name: Name of the user that is logged into Oniro.

  • Global settings:

    • Open search results in: The result from a search into WebMetabase can be open in three modes: Chemistry View, Protocol List, Review Tool. The user can define the default view he/she prefers.

    • Default signal: This is the default signal that will be used in the chart plots. The user could choose between: MS Area, MS Area/Internal Standard, UV Area, UV Area/Internal Standard, Scaled value, concentration.

    • Depiction zoom level: This is related to the default size of the molecule depiction it could be from 0.5 to 5.

    • Font size: This is the size of the font to be used in the report system.

  • Active work groups

    • Display only experiments of active groups: It only shows a to experiments that work groups are in active mode. Select the work groups to be active

Experimental data

User Setting: Experimental data
  • Tolerance:

    • MZ tolerance: m/z mass tolerance that is considered to compare peaks of similar retention time across different chromatograms, by default this value is 25 mDa

    • RT tolerance: retention time tolerance when two peaks of the same mass are compared across chromatograms. The default value is 0.2 min

    • Calibration RT: This is the tolerance to be applied to the retention time for the peak that is used in a calibration experiment. The default value is 0.6 min.

  • Compounds:

    • Show hidden mets in chart: In the case of hiding peaks by using the two previous options and having this option unchecked, will mean that the chromatographic peaks will not only be removed from the chromatography table but also from the chromatogram charts.

    • Most important metabolites: This is the default number of metabolites shown in the Chem Results tab

    • Remove empty compound when approved an experiment check box: If the check box is activated, the metabolites that do not have any interpretation or no structure is selected will be removed from the experiment.

  • Labels:

    • Group labels (applicable for protocols with ONLY ONE non numeric property): This is to group the values obtained for different labels for the Metabolic pathway definition.

    • Default data for labels: This is the default values that are represented in the Metabolic pathway. The options are: MS Area, MS Area/Internal Standard, UV Area, UV Area/Internal Standard, Scaled value, concentration and no signal.

    • Default format for labels: This is setting the default format of the labels in the Metabolic Pathway. The options are: Value range (min and max), Max value, Average value and All values (comma separated).

  • Peptide:

    • Show peptide in monomer notationn: Check this option in order to visualize the macromolecule as a sequence of building blocks

    • Bond breaking rules: These are the chemical rules apply to a peptide in order to find the monomer structures.

      • All amide bonds: Break the amide bond (the bond between the carbonyl and the nitrogen atom) from the following pattern. R group is any atom.

        Peptide. Bond breaking rules, All amide bonds.
      • Alpha amide bond:Break the amide bond (the bond between the carbonyl and the nitrogen atom) from the following pattern. R group is any atom.

        Peptide. Bond breaking rules, Alpha amide bonds.
      • Beta amide bond:Break the amide bond (the bond between the carbonyl and the nitrogen atom) from the following pattern. R group is any atom.

        Peptide. Bond breaking rules, Beta amide bonds.
      • Gamma amide bond:Break the amide bond (the bond between the carbonyl and the nitrogen atom) from the following pattern. R group is any atom.

        Peptide. Bond breaking rules, Gamma amide bonds.
      • Disulphide bridge:Break the disulphide bond from the following pattern. R group is any atom.

        Peptide. Bond breaking rules, All amide bonds.
    • Apply on:

      • Only new experiments: The selected rule(s) are applied only for the newly parsed experiments.

      • All experiments: The selected rules are applied to all the peptide experiments in the database.

  • Custom columns:

UNIFI Servers

This section covers the settings that are saved for UNIFI connections.

User Settings Unifi servers

  • UNIFI servers:

    Client the user right click in this are, 2 actions are available:

    • New: Generate a new UNIFI connection parameter.

    • Delete: Remove an existing UNIFI connection parameter.

  • Parameters:

    • Name: Name for the unifi connection to the server.

    • Active: Indicates if the connection is active or not.

    • Auth URL: http://<ComputerID>:50333/identity/connect/authorize

    • Valida button: Click this button to check if the connection is well established.

    • Client ID: mms

    • Secret: abc

    • Scope: unifi

    • API URL: http://<ComputerID>:50034/unifi/v1

    • Username: user name for the unifi user.

    • Password: password for the unifi user.

Analysis Tools

User Setting: Analysis tools
  • MetaDesign Database:

    • Default: If the user selects one database of the drop down list this will be the one proposed by default in MetaDesign runs.

  • CLint Calculation:

    • Variable to be used as a Concentration: This is the variable to be used in the calculation it will be the variable with a number type.

    • Concentration value to use: This is the default protein concentration used for the Clearance calculation

    • Units use as concentration: This is the default units to compute the clearance.

  • Global Settings:

    • Scale MS chromatography throughout the experiment: This is to report the scale of the Y axis equal in all the chromatographic charts

Admin

User Setting. Admin

The following options are available:

  • General Settings:

    • Remove "new" experiment mark when: Every time a new experiment is shown in Oniro it gets a blue dot indicating that it has not be opened. By marking this options the system will remove this mark when it is:

      • opened for the first time

      • saved for the first time

    • Use whole db for data process (ignore groups): Oniro can use all the database data for some data mining functions such as UniqueMetId's or Déjà Vu functions, or only the data in the work groups of the corresponding experiment and the public data.

    • Keep original data files in the DB: Oniro keeps a copy of the files used to import if this option is activated.

    • Use Markush system for depiction: Oniro can use two depiction frame-works: in the case of having this option checked it will plot the multiple structures resulting from a structure elucidation task as a single Markush plot, but if this option is off it will depict the individual structures without Markush. The second option is faster, since the system does not need to compute the Markush, but also the results could be confusing if there are a great number of potential metabolite structures.

    • Max number of structures: bis is the maximum number of structures per experiment that can be uploaded automatically

    • Metabolites name prefix: This is the default prefix given to the chromatographic peaks identify in a LC-MS approach. The default value is M

    • Unique Metabolite Identification System MZ tolerance: This is the tolerance value for the m/z in the unique metabolite identification system used in the Déjà Vu functions in amu. The default value is 0.025

    • Date format: There are 3 options for the data format: yyyy-mm-dd, dd-mm-yyyy and mm-dd-yyyy.

    • Server for report rendering: Name of the server where the rendering of the images for the report is done. Since this is a time consuming process, the user may want to use another server to perform this task and therefore free the installation server for other operations.

    • MassMetaSite Server: Name of the server where the MassMetaSite computation is done. The server has to be in Windows operating system. Since this is a time consuming process, the user may want to use another server to perform this task and therefore free the installation server for other operations.

  • Node configuration:

    • Storage Path: It is the folder where the temporary files will be saved

    • Maxima executable file location: This is the location for the maxima (http://maxima.sourceforge.net/) executable (bat file in windows). This external program is used of the kinetic evaluation of the metabolic path.

    • licenses: In this are the user should paste the license provided by Molecular Discovery (http://www.moldiscovery.com/) to access the different modules. The user can access the Oniro even is the license is expired, but it can not import any new information. If a license (expired or not) is not shown in here the button to access the module will not be visible.

    • Licenses for external tools: In this are the user should paste the license provided by Molecular Discovery (http://www.moldiscovery.com/) to access the different external programs like MSITE, MASS_MSITE, MOKA or VOLSURF+

  • Prediction count limits: Sometime the predictions that are coming from MassMetaSite or MassChemSite could be too many and may cause the system to parse those files slowly. These options gives the possibility to warn the user about this or to stop the paring by given an error.

    • Warning: This value is used to warn the user that a compound as too many predictions

    • Error: The error stop the parsing if we receive a met with more than that value predictions.

  • System

    • Lock System: when checked the Oniro application will block all the running processes and sends a message to all the users in it's screen (you can write that message in the next to the Lock System check box). This allows to assure that all processes are stopped in the moment of doing important administrative maintenance operations such as a consistent backup or database consolidation.

    • RestFull Interface: This option enable/disable the API that allows to access Oniro functions as a web service and that is needed in order to run the batch processor from Mass-MetaSite/MassChemSite. It has 3 different levels:

      • Off: The access to Oniro web services and data is disable.

      • Open: The access to Oniro web services and data is enable without restriction.

      • Require user login: The access to Oniro web services and data is enable restricted to a login into the system.

    • NMR prediction URL (Charming): The system call an independent software called Charming to perform the NMR prediction. This software can be downloaded from the Lead Molecular Design web page (http://www.leadmolecualr.com/)

  • LDAP:

    • Use LDAP system to authenticate users: This check box activate the capability of use a LDAP server to authenticate the users.

      • LDAP uri server: This is the URL for the LDAP system.

      • LDAP uid pattern: This is the uid pattern used to retrieve the information from the LDAP system

      • SSL: Active this check box if you want to use a secure connection between the Oniro and LDAP servers.

      • Use only LDAP system to authenticate users: If activated this will be the only way to have users within the MD Platform system.

MetaDesign DB

User Setting: MetadesgnDB Management

This tab controls the databases that are used in the MetaDesign tool. The screen is divided in two parts;

  • MetaDesign databases: In this list appears the list of database that have been uploaded into Oniro. The information in the right panel would depend if a database from this list is selected or not:

    • If no database is selected:

      • Information:

        • Name: This area contains the list of names for the databases that are saved in the Oniro.

        • File:

          • Upload File: It would be deactivated

          • Database file(zip or gzip): By clicking the Browse button the user can navigate the local folder system to find the MetaDesign DB. The DB file with the set of molecular fragments could be generated using the application that is found in http://www.moldiscovery.com/software/webmetabase/#metadesign.

    • If the database is selected:

      • Information:

        • Name: This area will be the name of the database that is saved in the Oniro.

        • File:

          • Upload File: It would be activated. If you check in here the user can upload a new MetaDesign DB to replace the existing one.

          • Database file(zip or gzip): By clicking the Browse button the user can navigate the local folder system to find the MetaDesign DB. The DB file with the set of molecular fragments could be generated using the application that is found in http://www.moldiscovery.com/software/webmetabase/#metadesign

Report Templates

User Setting: Report Templates

This tool enables the user to upload into Oniro different Report Templates.

The reporting system in Oniro is based in Jasper Reports Reporting system, and report templates can be built using the program Jaspersoft iReport Designer from Jaspersoft Corporation (https://www.jaspersoft.com).

The window is divided in two parts:

  • Report templates: This contains the list of names for the report templates that are saved in the Oniro.

  • If a report template is NOT selected:

    • Information:

      • Name: Type a new report template. This will be the name that will be shown in later in the report analysis tools.

      • Report Type: There are three options:

        • Experiment report: The target of the temple is a single experiment from the WebMetabase module.

        • Multiple experiment report: The target of the temple is a set of experiments from the WebMetabase module.

        • Compound Library report. The target of the temple is a compound from the compound Library module.

      • Upload report templates: This is deactivated when no template report has been selected.

      • Report template file (.zip): By clicking the Browse button the user can navigate the local folder system to find the compressed template files.

  • If a report template is selected.

    • Information:

      • Name: It shows the name of the report template.

      • Report Type: It shows the type of the report template selected.

      • Upload report templates: If checked the suer can upload a new report template compress file to replace the existing one

      • Report template file (.zip):By clicking the Browse button the user can navigate the local folder system to find the compressed template files. It is only active if it is Upload report templates is activated.

      • Main file: The report is usually composed of multiple components and one of them is the main one. This is the jasper file that is shown as main.

      • Extra files: In this list it is shown the rest of jasper files that are complementary to the main one.

Models

User Setting: Model Management

The Oniro can use an external software in order to do prediction in selected compounds. The expected results from the calculation is a value (string or number) in a tab separated result that would be parsed following the conditions specify in the model management. This tab section controls the Model management. The window is divided in two different areas:

  • Models: This area contains the list of names for the databases that are saved in the Oniro.

    • If a model is NOT selected: As an example an external prediction with the program VolSurf (http://www.moldiscovery.com/software/vsplus/)in order to predict the Blood Brain Barrier. will be shown

      • Information:

        • Name: This is the name of the model that will be shown to the Oniro users. In this example Blood Brain Barrier

        • File: This is the name of the model file

        • Model Active: This should be checked in order to have the model available for prediction to the end users.

        • Model file: This is the VolSurf file that contains the model

        • Command line: In this area one have to type the command line that will be used to run the model. In the case of VolSurf model it will be: C:\Program Files (x86)\Molecular Discovery Ltd\VolSurf+ 1.0.7.l\vsplus-cli.exe <COMMAND_FILE>. As it is shown the command line has to contain the full path to the executable. In addition VolSurf needs a command_file where the options for the calculation are set. These options are set in the Command line text area.

        • Command line text: In this area the calculation options for VolSurf have to be specified. Any other software my have a different set of options or may do not have any options and can be run directly from the command line.

          set FIELD_PARAM = STATIC;

          set GRID_SPACING = 0.5;

          set PROTONATION = NEUTRALIZE;

          set GRUB_PATH = "C:\Program Files (x86)\Molecular Discovery Ltd\VolSurf+ 1.0.7.l\grub.dat";

          set VOLSURF_LIBRARY = <MODELS_LIBRARY>;

          new attribute "HIA";

          import SDF <COMPOUNDS_FILE> name by MOL_NAME;

          project on library model "PLS Model BBB";

          export "PLS Model BBB" predicted activities as CSV <RESULTS_FILE> using separator ",";

        • Column in results file to import: This is the header of the result file created by the external program that will need to be parsed.

        • Added labels: The user can add labels that could be use to transform the numerical values from the prediction to categories

        • Classification levels: The suer can provide numeric values to set up the classification levels to classify the results from the prediction.

    • If a model is selected: If a model is selected on the right information panel it will show the corresponding formation of the selected model.

MassMetaSite setting

User Settings: MassMetaSite Settings

This Section enables the option to set up the MassMetaSite calculation. In the left panel there is the list for the MassMetaSite Settings that have been saved. In the middle part are the settings organized by multiple tabs:

  • General data:

    • Information:

      • Name: This field set up the name for the setting.

    • MS Acquisition: MassMetaSite works with two ways of acquisition:

      • Data Driven MS/MS(DD-MS/MS): IN this case the MSMS is acquired using an input m/z that is selected by the acquisition software base on multiple and diver rules.

      • Two Energy of Collision (TEC): In this case the high energy trace of the MSMS is done without preselecting the ion to be fragmented.

    • WMB Calibration:

      • Calibration setting: Use this settings if only the compound of the parent has to be selected.

    • CYPS: The user can select among the metabolic mechanism phase I produced in multiple organs. The prediction of the SoM is don by the combination of the cytochromes that are present in each tissue or the user can select an specific CYP from the list.

  • Import: The User may change the protonation policy to apply to the imported structures and also the conformational sampling. It is recommended to keep the default (neutralize) protonation policy to get the highest prediction efficiency. 2D->3D conversion may be skipped if the Macromolecule mode is selected, this will increase the quality of the 2D depictions. Since no 3D conformation has been generated, no SoM prediction will be performed later on.

    User Settings: MassMetaSite - Import
  • Metabolite generation: This tab controls the metabolic mechanisms to be applied to generate the structure of the metabolites.

    User Settings: MassMetaSite- Metabolite generation

    There are different sections in this tab:

    • Minimum mass: Metabolites with a mass below the assigned value are discarded. A null threshold value disables this filtering mechanism.

    • Ignore metabolite stereo chemistry: When this option is set, stereoisomers are treated as the same compound

    • Ignore redundant metabolites: When a reaction implies bond cleavage (e.g. dealkylation) more than one single metabolite is often produced from the same reaction pathway and the smaller ones are not associated with any additional information.

    • MIM %: When the previous option is set, metabolites with a mass percentage (relative to the parent substrate) below the given threshold are considered to be redundant and discarded.

    • Reaction mechanism: the user can select the reaction mechanism by clicking on each of them or using the Shift + Click in order to select a group of mechanism. Also the buttons: Recombinant, Microsomes and Hepatocytes can be used to pre-select some of the mechanisms.

  • Mass: the Mass settings is further organize in multiple tabs:

    • Experiment:

      User Settings: MassMetaSite- Mass - Experiment

      The user can select multiple options that affect the MassMetaSite calculation:

      • Global:

        • User retention time range (min): The usr can define the retention time window from the chromatography that can be used to do the analysis. The Min value indicates the start of the analysis and the Max value the end of the chromatographic time.

        • Mode: MassMetaSite can work in three different modes that affect the way molecules are fragmented and signal are analyzed.

          • Standard: All bonds are fragmented in order to get potential fragments. Only aromatic bonds between atoms of the same type are not broken.

          • GSH: All bonds are fragmented in order to get potential fragments. Only aromatic bonds between atoms of the same type are not broken. The system looks for the neutral lost and fragment ions typical for a GSH adduct.

            • Advanced: In this mode the user can select the fragment ions and neutral losses to be used to identify the GSH adduct. depending if charge (z) is 1 or 2. The neutral losses or Fragments ions classified as Triggers are the ones that should be found in order to mark the mark the name of the metabolite with and * or a ! respectively. The Extras and the Neutral looses or Fragment ions that re used to at a * or ! mark in the name of the metabolite. One of the marks for each new value found.

              User Settings: MassMetaSite- Mass - Experiment - Mode: GSH Advanced button
          • Peptide: In the case of the peptide mode only the bonds between atoms of different type or hybridation are broken in order to generate potential fragments.

      • UV:

        • Use UV peal area. Threshold(%): If this option is marked, the user can set the area in percentage to be used to exclude potential peaks. Any peak with and area lower than the indicated one will be removed from the analysis independently of the MS area.

        • Use preset UV wavelength (nm): In order to compute the area the data that is needed is the Diode array data and the user can select the wavelength to be used to do the area calculation.

        • Wavelength selection method: In case that the user does not select a wavelength, it can be automatically pre-selected.

          • Area ratio:

          • Local maxima:

      • Radio Labeled:

        • Use Radio peak area. Threshold (%): If this option is marked, the user can set the area in percentage to be used to exclude potential peaks. Any peak with and area lower than the indicated one will be removed from the analysis independently of the MS area.

        • Radio Peak detection smoothing: In the case of this type of signal the peaks can be smoothed and there are several levels to perform this: Very High, High, Medium, Low and None.

      • Fluorescence:

        • Use Fluorescence peak area. Threshold (%): If this option is marked, the user can set the area in percentage to be used to exclude potential peaks. Any peak with and area lower than the indicated one will be removed from the analysis independently of the MS area.

        • Fluorescence Peak detection smoothing: In the case of this type of signal the peaks can be smoothed and there are several levels to perform this: Very High, High, Medium, Low and None.

      • Internal Standard:

        • Name: This is the name of the internal standard.

        • Retention time(min): The expected retention time in minutes for the internal standard

        • Tolerance(min): This is the tolerance for the internal standard retention time. If the user does not have an idea of the expected retention time, it can have a retention time, the half of the overall chromatographic time and the has a tolerance of the same value.

        • m/z (amu): This is the expected m/z for the internal standard

        • UV wavelength (nm): This is the wavelength to compute the area.

    • MS Peaks:

      User Settings: MassMetaSite- Mass - MS Peaks
      • Global:

        • Use maximum count Limit: When this option is selected the number of metabolites are used to report only those peaks with the highest area.

        • Area threshold:

          • (%): Metabolites with a total area in percentage higher than the indicated value are selected

          • absolute: Metabolite with an absolute area higher than the specified values are selected.

        • Peak detection smoothing: The system allows the possibility to perform some smoothing in the chromatographic peak detected.

        • Advanced: This option control the m/z used to compute the areas that used for each peak. By default the areas of the multiple charges are always added.

          • Sum Areas:

            • Positive Adduct area: Add the area of the positive adducts to the area of the m/z under consideration.

            • Negative Adduct area: Add the area of the negative adducts to the area of the m/z under consideration.

            • Neutral Adduct area: Add the area of the neutral adducts to the area of the m/z under consideration.

            • Dimer area: Add the area of the dimers to the area of the m/z under consideration.

            • neutral Loss area: Add the area of the neutral losses to the area of the m/z under consideration.

          • Sum Chromatogram Signals: Add all the areas for all the signals

      • Expected Metabolites:

        • Split computed DRM peaks: If there are two m/z that correspond to two known metabolites that are co-eluting and if they have the same peak shape, if this option is ON, the system will show 2 different metabolites. If this option is OFF, the system will select the one with the highest m/z as the metabolite and the other m/z will be treated as a fragment.

        • Rescue computed DRM peaks: If this option is ON, even if a metabolite with a fragment uncommon or shifted compared to the parent has an area lower than the indicated Area threshold, the metabolite will be selected. If this option is OFF, only the metabolites that full fill the previous filter will be shown.

      • Isotopes:

        • Skip: No isotope criteria related to the expected isotope intensity will be used in peak selected.

        • Filtering: The expected isotope intensity from the calculated formulae will be used to filer potential peaks with the tolerance in percentage indicated in the Pattern filtering Tolerance setting.

      • Adducts: If this option is on the system will look not only for the expected m/z generated by the application of the metabolic mechanisms to the compounds but also to the selected adduct. If there is a m/z detected that correspond to the m/z of the adduct, but there is no m/z detected for the parent molecule a light blue peak will be shown.

      • Neutral Losses: Similar to the previous option but for dimeric ions-

      • Dimeric Losses: Similar to the previous option but with the dimer losses.

      • Multiple-Charge Ions: This option sets the maximum charge to be applied when looking a matching between the observed and calculated m/z.

      • Unexpected metabolites: This option is used to find peaks that the m/z does not correspond to the an known m/z generated by the application of the metabolic reactions to the parent molecule.

      • Advanced:

        • Fragment Ions: One of the filters used to accept a peak as a potential metabolite is the analysis that it should have one m/z in common or shifted compared to the parent. If this option is marked as OFF, this criteria is not used for peak filtering.

        • Sum Areas:

          • Retention time filtering: Those peaks that are not related to any metabolic mechanism, and the retention time is higher than 20% of the retention time observed for the parent, are filtered out. IN the case of having this option OFF, the filtering is not applied and the "unknown" may have any retention time.

        • Selection:

          • Split unexpected from expected metabolites: As explained in the Split option if two m/z that correspond to known metabolites are co-eluting, they will be assigned as 2 different peaks. If this option is marked as ON, two m/z where one corresponds to a known metabolite and the other one to an unknown m/z, both will be shown as two potential peaks.

          • Split modified from expected metabolites: Same as before but for one of those m/z it would correspond not to an unknown but to a adduct, dimer or neutral lost.

    • Met ID:

      User Settings: MassMetaSite- Mass - Met Id
      • Metabolite generation:

        • Number of metabolite generations: This is the number of metabolic mechanism steps are applied. Phase II metabolism mechanism are only apply one time.

      • Compound Fragmenting:

        • Substrate bond breaking limit: MassMetaSite generate a list of fragments by breaking bonds in the molecule. If the bond is not in a ring when the action of braking a bond will generate 2 fragments, each of these fragments them is broken another time and this is done the number of times it is indicated in this setting. In case of cyclic peptide and macromolecule it is recommended to use 2, for small molecule 3 or 4 it typically used.

        • Break Metabolites: In the original MassMetaSite process only fragments that are comparable to the parent where considered. But if this option is on, the system will generate fragments from the structure of the metabolites by applying the number of bond creaking cycles indicated. It is recommended to use 1, since it is a time and memory consuming process.

        • Exclude fragments having an absolute m/z diff above: It is possible to exclude fragments from the interpretation with a ppm values higher than the indicated value.

        • Break 6-memberred heteroaromatic rings: See figure for the structural description of the fragmentation.

        • Bond breaking reorganizations: In order to perform the structural elucidation, hypothetical fragments are generated by breaking each bond with the exception of 6-membered ring aromatic bonds, triple bonds, some double bonds involving hetero-atoms and bonds to hydrogen atoms. 5-membered ring aromatic bonds are broken when involving at least one hereroatom. 6-membered ring heteroaromatic cycles are broken if the proper option is activated. In the generated fragments, a maximum of four bonds have been broken. Moreover, in the fragmentation process some basic reorganizations are allowed. Although protonated and deprotonated molecules almost always fragment into even-electron ions, some known odd-electron fragmentations have been allowed.

          User Settings: MassMetaSite- Mass - Met Id - Bond breaking reorganizations
          • Even Electron: See figure for the structural description of the fragmentation.

          • Odd Electron:See figure for the structural description of the fragmentation.

          • N-Oxide:See figure for the structural description of the fragmentation.

        • Bond breaking experimental reorganizations:

          User Settings: MassMetaSite- Mass - Met Id - Bond breaking experimental reorganizations
          • Benzyk Alcohol: See figure for the structural description of the fragmentation.

          • Amide Water Loss: See figure for the structural description of the fragmentation.

          • Alkyl Sulphate: See figure for the structural description of the fragmentation.

          • Aryl Methoxy: See figure for the structural description of the fragmentation.

    • DD-MS/MS:

      User Settings: MassMetaSite- Mass - Data Dependent MS/MS
      • Mass Spectrometer: A set of radio buttons allow to select the current Mass Spectrometer and its associated parameter. Select the instrument from the list.

      • Algorithms Thresholds:

        • Same peak tolerance (amu): Defines the tolerance used to accept if a calculated mass and a observed mass are equivalent or not. Used also to test if a substrate and a metabolite peak are equivalents or shifted by a known mass. The optimal value for this parameter depends strongly on the mass spectrometer technology used.

        • Chromatogram automatic filtering threshold: Parameter modifying the chromatogram peak recognition. Smaller, close to noise, peaks are accepted if the parameter value is increased. Increasing too much the parameter value promotes the formation of wide peaks with long irrelevant tails while decreasing too much the value may cause the loss of minor metabolite peaks.

        • MS automatic filtering threshold: Parameter modifying the MS spectra noise filtering. More noisy MS spectra are generated if the threshold is increased. The value also affect metabolite peak finding. A low value will increase speed because less MS peaks will be considered as potential metabolite peak candidates, however a high value will increase the chance of finding less abundant or poorly ionized metabolites.

        • MS/MS automatic filtering threshold: Parameter modifying the MS/MS spectra noise filtering. More noisy MS spectra are generated if the threshold is increased. Too low values will produce clean spectra but potentially missing some relevant peaks. Too High values will produce more noisy spectra that may confuse the Substrate/Metabolite peak matching.

      • Ionization Mode: The user may choose to have positive or negative ionization mode. If there 2 ionization modes in the same acquisition (polarity switching), the system will analysis only the ionization mode indicated in this setting.

      • Spectra comparisons:

        • Maximum MS/MS level: By selecting the Maximum MS/MS level the user defines how many levels of MS/MS data will be used for metabolite structure identification. For example a level of 3 means that MS, MS/MS and MS/MS/MS data will be used, if possible.

        • collapse MS/MS levels: MSn spectra may be merged into a single 'pseudo' MS2 spectrum (Collapse MS/MS levels check box) which may simplify the fragment interpretation in some cases.

      • Signal Filtering: This option specifies how much of the raw spectrum data will be considered as noise and discarded.

        • Automatic: The noise level is computed by the system.

        • Signal Threshold: The user may specify a noise level manually.

      • Scan Filtering: Mass-MetaSite may be set up to reduce the number of scan/min. in order to save processing time when dealing with very fast MS scanning device

        • Automatic: The system chooses the number of scan per minute to analyze.

        • Max scan ration (scan/min): The user chooses the number of scan per minute to analyze.

    • TEC:

      User Settings: MassMetaSite- Mass - TEC
      • Mass Spectrometer: A set of radio buttons allow to select the current Mass Spectrometer and its associated parameter. Select the instrument from the list.

      • Algorithms Thresholds:

        • Same peak tolerance (amu): Defines the tolerance used to accept if a calculated mass and a observed mass are equivalent or not. Used also to test if a substrate and a metabolite peak are equivalents or shifted by a known mass. The optimal value for this parameter depends strongly on the mass spectrometer technology used.

        • Chromatogram automatic filtering threshold: Parameter modifying the chromatogram peak recognition. Smaller, close to noise, peaks are accepted if the parameter value is increased. Increasing too much the parameter value promotes the formation of wide peaks with long irrelevant tails while decreasing too much the value may cause the loss of minor metabolite peaks.

        • MS automatic filtering threshold: Parameter modifying the MS spectra noise filtering. More noisy MS spectra are generated if the threshold is increased. The value also affect metabolite peak finding. A low value will increase speed because less MS peaks will be considered as potential metabolite peak candidates, however a high value will increase the chance of finding less abundant or poorly ionized metabolites.

        • MS/MS automatic filtering threshold: Parameter modifying the MS/MS spectra noise filtering. More noisy MS spectra are generated if the threshold is increased. Too low values will produce clean spectra but potentially missing some relevant peaks. Too High values will produce more noisy spectra that may confuse the Substrate/Metabolite peak matching.

      • Ionization Mode: The user may choose to have positive or negative ionization mode. If there 2 ionization modes in the same acquisition (polarity switching), the system will analysis only the ionization mode indicated in this setting.

      • Spectra comparisons:

        • Merge MS/MS from multiple charge states: By selection this options: for Sciex SWATH or Waters HDDA data, it might be useful to merge the MS/MS spectra coming from different charge states

      • Signal Filtering: This option specifies how much of the raw spectrum data will be considered as noise and discarded.

        • Automatic: The noise level is computed by the system.

        • Signal Threshold: The user may specify a noise level manually.

      • Scan Filtering: Mass-MetaSite may be set up to reduce the number of scan/min. in order to save processing time when dealing with very fast MS scanning device

        • Automatic: The system chooses the number of scan per minute to analyze.

        • Max scan ration (scan/min): The user chooses the number of scan per minute to analyze.

    • Results:

      User Settings: MassMetaSite- Mass - Results
      • Predictions:

        • Auto select structures: This option makes it possible to automatically discard complex structures for the display of the Markush representation solutions, if more simple solutions are available. If the "Auto Select structures" is checked, only the most plausible structures, from a mechanism complexity point of view, will be chosen. Otherwise all the structures having the best mass score will be selected.

        • Discard predictions with score below: This option will remove predictions below the specified threshold. By Default this value is equal to 0.0. It means that any predicted structure is discarded if its mass score is below 0.0. Consequently, if all the predictions have a negative score, no structure will be shown. This option is activated by default since it can considerably reduce the size of the MetaSite files, as well as the parsing time by WebMetabase.

      • Filters:

        • Exclude metabolites without formula: This option will remove unexpected compounds for which MassMetaSite did not find a proper formula.

        • Exclude metabolites having an absolute m/z diff(ppm) above: This option allows to filter out metabolites based on their ppm error. For historical reasons, MassMetaSite works internally using absolute amu errors. This filter allows to exclude peaks that are inside the range of the amu tolerance but not the ppm one.

DatabaseUUID

User Settings: Database UUID

This tool allows the user to manage database Universal Unique Identifier (UUID).

Oniro databases have an unique identify like "3a9f24f1-aaf7-4497-998d-c949e2e714ef" and this tool allows the user to manage a mapping from this UUID string to a "Name" string that easily identifies the database. It is also possible to add a "Prefix" string that can have a maximum of five characters.

The "Allow automatic mapping for not mapped objects" check is an information that will be used during the automatic import of experiments. This flag allows the system to automatically assign a name to an experiment to import in the case of a conflict name and to automatically map a not previous mapped part of an experiment to import, letting the system to create a new part for it.

When the flag is checked, in the case of a conflict name, the new name will be the "Prefix" followed by the original name of the object to import. For example, the first time we import a property named"Time" from "Italy database" and we already have a property "Time" in the destination database, the system will create a new property named "IT_01 Time". When the flag is no checked, if the system during the import process finds one part of an experiment not previous mapped or when there is a conflict name, the automatic mapping fails and the user has to manually do the mapping.

The button for the "Database UUID Management" is present only for users that have assigned the "Data import" function, that is a member of "Experiment management" functions, or for the "Admin" user.

Substructure sets

User Settings: Sub-structure sets

Users can create their own set of fragments, and use them in analysis of substrate fragments from this panel. The window is divided in 2 different areas:

  • Substrate sets:

    • In the list are the user will find all the substructures sets that have been defined or they can by right clicking in this area:

      • New: Create a new set of fragment. this option will remove all the content in the right area.

      • Delete: This option will remove the selected existing substructure set.

      • Copy: it will copy the selected substructure set with a new name for further modification.

    • Upload SDF: This button enable the import of new data sets of sub structures of fragments that are in the sdf. By clicking this option a new window will pop up:

      User Setting. Substructure sets. Upload SDF
      • Name: This is the name of the substrate set that will be shown to the user in the Fragment analysis tool.

      • Description: This is a brief description of the set.

      • SDF file: Click on the Browse button to find the sdf file with the chemical structures.

      • Structure name: Each substructure should have a name. The name can be on:

        • first line

        • SDF tag

      • SDF tag: If in the previous radio selection the user selected SDF tag, the name of this tag has to be specified in here

      • Action buttons:

        • OK: The file will be processed and the substructures will be shown in the panel on the right

        • Close: This will cancel the import of the set

      After the set has been imported the new window will be shown like this:

      User setting. Substructure sets uploaded
  • Information: In this area there is the information for the selected substrate set or for the newly manually input one.

    • Name: This is the name of the substrate set that will be shown to the user in the Fragment analysis tool.

    • Created by: The user that has created the user set.

    • Description: This is a brief description of the set.

    • Saved on: The date the user set was saved

    • Substructure set enabled: The substructure set should be enabled in order to be shown as an option to the user in the fragment analysis tool.

    • List of structure: The representation of the structures with their names that composes the substructure set.

    • Right Click on the area to Add manually a new substructure

MetaSite Settings

User Settings. MetaSite

The user need a specific license line to active this option.

The user can select and save the seetings for a MetaSite computation:

  • MetaSite settings: This section contains the name of the saved settings.

  • Information:

    • Name: The user can add the name of the setting used.

    • SoM: This option will compute the Site Of Metabolism.

    • Met ID: This option will compute the virtual metabolite structures and will rank them in agreement to the SoM for the atom in the parent that has reacted to create the metabolite.

  • Protonation policy:

    • As is: The algorithm would use the structure of the compounds as input by the user.

    • neutralize: The protonation state of the molecule will be modified to get the neutral form.

    • normalize pH: The protomer that will be used in the computation will be the most abundant at the pH indicated.

  • Conformation sampling:

    • Maximum number of conformers: During the MetaSite computation the interaction between the parent compound and the enzyme is evaluated by optimizing the position of the compound into the enzyme cavity, in order to do this optimization a number of conformers of the compound is used.

  • Site Of Metabolism prediction:

    • Enzymes:

      • LIVER: The SoM is computed for multiple cytochrom enzymes in the proporsion they are found in the Liver.

      • SKIN: The SoM is computed for multiple cytochrom enzymes in the proporsion they are found in the Skin.

      • BRAIN: The SoM is computed for multiple cytochrom enzymes in the proporsion they are found in the Brain.

      • Scpecific CYP: The SoM is computed using the selected structures from the list

        • CYP1A1,CYP1A2,…....

      • Others: The SoM is computed using the selected structures from the list

        • AOX1

        • FMO3

Moka Settings

User Settings: Moka

The user need a specific license line to active this option.

This section controls the settings to be used in a Moka computation:

  • Moka Settings: This section contains the name of the saved settings.

  • Information:

    • Name: The user can add the name of the setting used.

    • Ony Pka calculation: Select to only compute the PKa of the molecule.

  • Show predictions for: Select the maximum number of acidic and basic pKas to output by using the Show predictions for pane.

    • Acid center(s): For example, when you only want one acidic pKa, select 1 acid center. Only the lowest pKa is exported when more than one acidic pKa is present.

    • Basic center(s): Similarly, in allowing for a maximum of n basic centers, only the stronger bases (higher pKa) are exported.

    • Min. Abundance: Indicates the minimum abundance of the protomer to be selected

  • Additional output: QP and SD will be added to the main result line while LogP and LogD values will be added as new SD attributes.

    • SD Values: The standard deviation (SD).

    • QP Values: The quality parameter (QP).

    • logD in pH Range: The predicted LogD values at specified pH

    • log P Value: The predicted LogP value

  • Acid cut off values: Select the desired cutoff filters in the dialog box that appears.

    • Upper limit:, Lower limit.

  • Basic cut off values: Select the desired cutoff filters in the dialog box that appears.

    • Upper limit:, Lower limit.

  • QP cut off values: Select the desired cutoff filters in the dialog box that appears.

    • QP cut off.

VolSurf+ Settings

User Seetings: VolSurf

The user need a specific license line to active this option.

This section controls the settings to be used in a VolSurf computation:

  • VolSurf Settings: This section contains the name of the saved settings.

  • Information:

    • Name: The user can add the name of the setting used.

    • ADME prediction: Select to only compute the ADME values from VolSurf computation.

      • Blood-Brain Barrier permeation model (LogBB): To be effective as therapeutic agents, centrally acting drugs must cross the Blood-Brain Barrier (BBB), and entry into the brain is a complex phenomenon which that depends on a multiplicity of factors. Nevertheless, the basic assumption used in this model is passive permeation.

        The VolSurf+ model for BBB permeation is a quantitative model containing about 500 related, but chemically diverse, compounds extracted from the literature and in house data which are either brain-penetrating (Exp. logBB > 0.5), have moderate permeation (LogBB between 0 and 0.5), possess little ability to cross the blood-brain barrier (Exp. logBB greater than -0.3) or demonstrate very little permeation (LogBB less than -0.3).

        In order to rank the BB behavior of external compounds, the model can be used to project external compounds in the chemical space represented by the model.

      • Thermodynamic solubility model (SOLY): Aqueous solubility has long been recognized as a key molecular property in pharmaceutical science. Drug distribution, delivery and transport depend on solubility. Many groups have discussed the correlation between solubility and molecular properties.

        The SOLY model is a quantitative model for thermodynamic solubility containing more than 1100 different chemical structures. The structures were checked in the literature and extracted to form the dataset, and the dataset was also completed using in-house produced solubility data. The solubility values are the log[Soly] where Soly is expressed in Mol/litre at 25°C. A three components PLS model was used to correlate chemical structures and solubility values.

        The average error in the external prediction is about ±0.7 log unit. While this range is not suitable for predicting the solubility values of external compounds, it is still sufficient to rank compounds in different categories and to use this ranking to filter compounds in virtual databases. Overall, it seems to be unlikely that this model can be improved upon, and all attempts made to do so resulted in dangerous overfitting. Many factors can play a role in solubility, and most of these are virtually impossible to control.

      • Caco2 permeation model (CACO2): The use of Caco2 cell monolayers as an in vivo human absorption surrogate has increased. However, due to the mechanisms involved, Caco2 cell permeability measurements exhibit certain limitations. Both passive and active pathways exist. Unstirred water can significantly modify the penetration coefficient. Intervariability between laboratories ia also a common problem.

        Quantitative comparison and modelling are almost impossible for all these problems. In order to avoid inconsistencies in the data, the Caco2 permeability values are transformed according the following schema:

        • Papp. < 4*10-6 cm/s ==> score -1

        • Papp. > 8*10-6 cm/s ==> score +1

        However, different assumptions were made in special cases, when the experimental protocols were different or no internal standard compounds were used. A basic assumption used in the model is passive permeation.

        The CACO2 model is a qualitative model containing a thousand related, but chemically diverse, compounds collected from the literature or experimentally measured in laboratories connected with our group. Data are either penetrating (score 1), or have little if any ability to penetrate the epithelial cells (score -1). PLS discriminant analysis was used to build the statistical model and two significant latent variables emerged from the cross validated PLS model.

        The model can be used to project external compounds in the chemical space represented by the model in order to rank the Caco2 behavior of external compounds.

      • Protein Binding model (PB): "In silico" quantitative models to predict binding affinity to Human Serum Albumin (HSA) are often useful in the pharmaceutical industry as they provide pharmacokinetic properties in an early phase of drug discovery. As HSA is the principal biological carrier of many drugs, it facilitates their transport through the circulatory system to the target tissues. Determining the probability of a molecule binding with a protein depends on the type of analysis used (dialysis, ultra-centrifugation, ultra-filtration, NMR, UV, HPLC and other chromatographic methods), the instruments used (type of dialysis membrane, type of spectrometer, type of chromatographic equipment) and the experimental conditions chosen in different laboratories (type of albumin, its concentration, temperature and the duration of the analysis). The variation of these parameters not only dramatically affects the final results but also the experimental errors. Such huge variability of experimental conditions produces noise and makes interpretation of the data more difficult.

        The Protein_Binding model is a qualitative model containing 500 related, but chemically different compounds partially collected from the literature or experimentally measured in laboratories connected with our group. The data mainly report albumin protein binding values between 10% and 100% obtained using spectroscopic techniques. The average experimental error reported was 8%. Therefore, the model is not able to discriminate between protein binding values ranging from 95% to 100%.

        The model can be used to project external compounds in the chemical space represented by the model in order to rank the protein binding profile of external compounds.

      • Volume of Distribution model (VD): The volume of distribution (VD) for a drug is the volume that accounts for the total dose administration based on the observed plasma concentration. The plasma volume of the average adult is approximately 3 litres. Therefore, apparent volume of distribution larger than the plasma compartment (i.e. greater than 3 litres) indicates that the drug is also present in tissue or fluid outside the plasma compartment. Volume of distribution represents a complex combination of multiple chemical and biochemical phenomena. It also measures the relative partitioning of drug between plasma and the tissues. Although the volume of distribution cannot be used to determinate the actual site of distribution of a drug in the body, it is of extreme importance in estimating the loading dose necessary to rapidly achieve a desired plasma concentration.

        The Volume_Distribution model was obtained by collecting more than 600 compounds from the literature. The VD data (Litre/Kg) were converted into -Log[VD] values. Low VD values mean low distribution into tissues while high VD values mean high distribution into tissues.

      • CYP3A4 Metabolic Stability model (MetStab): Metabolic stability in human CYP3A4 cDNA-expressed microsomal preparation offers a suitable approach to predicting the metabolic stability of external compounds. VolSurf+ provides a model to estimate the metabolic stability of drug incubated at a fixed concentration for 60 min with a fixed concentration of protein at 37°C. Compounds with a final concentration greater than or equal to 50% of the corresponding control sample were defined as stable, whereas compounds with final concentrations of less than 50% of the corresponding control were defined as unstable.

        The model can use the 3D structure of drug candidate to evaluate its metabolic stability prior to experimental measurements.

    • Descriptor computed:

      • Size and shape descriptors:

        • Molecular volume (V). represents the water-excluded volume (in Å3), i.e. the volume enclosed by the water-accessible surface computed at a repulsive value of +0.2 kcal/mol.

        • Molecular surface (S). represents the accessible surface (in Å2) traced out by a water probe interacting at +0.2 kcal/mol when a water molecule rolls over the target molecule.

        • Rugosity (R). is a measure of molecular wrinkled surface; it represents the ratio of volume/surface. The smaller the ratio, the larger the rugosity.

        • Molecular globularity (G). is defined as S/Sequiv with Sequiv = surface area of a sphere of volume V, where S and V are the molecular surface and volume described above, respectively. Globularity is 1.0 for perfect spherical molecules. It assumes values greater than 1.0 for real spheroidal molecules. Globularity is also related to molecular flexibility.

        • Flexibility parameters (Flex, Flex_RB). represents the maximum flexibility of a molecule. For each molecule 50 conformers (random) are produced, and Flex represents the Log averaged (on atom i) result of the differences between the maximum and minimum distances of atom 'i' in a selected conformer with the atom 'i' in all the other conformers. Flex_RB descriptor is the ratio between Flex and the number of rotable bonds.

      • Descriptors of hydrophilic regions:

        • Hydrophilic volumes (W1 - W8). describes the molecular envelope which is accessible to and attractively interacts with water molecules. The volume of this envelope varies with the level of interaction energies. Hydrophilic descriptors computed from molecular fields of -0.2 to -1.0 kcal/mol (W1 - W3) account for polarizability and dispersion forces; descriptors from molecular fields of -2.0 to -6.0 kcal/mol (W4 - W8) account for polar and strong H-bond donor-acceptor regions.

        • Capacity factors (CW1 - CW8)). represent the ratio of the hydrophilic volume over the total molecular surface. In other words, it is the hydrophilic volume per surface unit. Capacity factors are calculated at eight different energy levels, the same levels used to compute the hydrophilic volumes.

      • Descriptors of hydrophobic regions:

        • Hydrophobic volumes (D1 - D8). GRID uses a probe called DRY to generate 3D lipophilic fields. In analogy to hydrophilic regions, hydrophobic regions may be defined as the molecular envelope generating attractive hydrophobic interactions. VolSurf+ computes hydrophobic descriptors at eight different energy levels adapted to the usual energy range of hydrophobic interactions (from -0.2 to -1.6 kcal/mol).

        • Capacity factors (CD1 - CD8). represent the ratio of the hydrophobic volume over the total molecular surface. In other words, it is the hydrophobic volume per surface unit. Capacity factors are calculated at eight different energy levels, the same levels used to compute the hydrophobic volumes.

        • Differences of the Hydrophobic volumes (DD1 - DD8). the difference between the maximum hydrophobic volumes (obtained upon variation of ligand conformation) and the hydrophobic volumes (D1 - D8) of the the imported 3D structure calculated at the 8 levels of energy.

      • INTEraction enerGY (= INTEGY) moments:

        • INTEGY moments (IW1 - IW4, ID1 - ID4). express the unbalance between the centre of mass of a molecule and the barycenter of its hydrophilic or hydrophobic regions.

          When referring to hydrophilic regions, integy moments (IW1-IW4) are vectors pointing from the centre of mass to the centre of the hydrophilic regions: high integy moments indicate a clear concentration of hydrated regions in only one part of the molecular surface, low ones indicate that the polar moieties are either close to the centre of mass or they balance at opposite ends of the molecule, so that their resulting barycenter is close to the centre of the molecule.

          When referring to hydrophobic regions, integy moments measure the unbalance between the centre of mass of a molecule and the barycenter of the hydrophobic regions.

      • Descriptors of H-bond donor / acceptor regions:

        • H-bond donor volumes (WO1 - WO6). GRID uses a probe called O (carbonylic oxygen) to generate 3D H-bond ligand donor fields. In analogy to hydrophilic regions, H-bond donor regions may be defined as the molecular envelope generating attractive H-donor interactions. VolSurf computes H-bond donor descriptors at six different energy levels adapted to the usual energy range of interactions (from -1 to -6 kcal/mol).

        • H-bond acceptor volumes (WN1 - WN6). GRID uses a probe called N1 (amide nitrogen) to generate 3D H-bond ligand acceptor fields. In analogy to H-bond donor regions, H-bond acceptor volumes may be defined as the molecular envelope generating attractive H-bond acceptor interactions. VolSurf+ computes H-bond acceptor descriptors at six different energy levels adapted to the usual energy range of interactions (from -1 to -6 kcal/mol).

      • Mixed descriptors:

        • Hydrophilic-Lipophilic balance (HL1, HL2). represents the ratio between the hydrophilic regions measured at -3 and -4 kcal/mol and the hydrophobic regions measured at -0.6 and -0.8 kcal/mol. The balance describes which effect dominates in the molecule, or if they are roughly equal balanced.

        • Amphiphilic moments (A). is defined as a vector pointing from the centre of the hydrophobic domain to the centre of the hydrophilic domain. The vector length is proportional to the strength of the amphiphilic moment, and it may determine the ability of a compound to permeate a membrane.

        • Critical packing parameter (CP). defines a ratio between the hydrophilic and lipophilic part of a molecule. In contrast to the hydrophilic-lipophilic balance, critical packing refers just to molecular shape. It is defined as: volume(lipophilic part)/[(surface(hydrophilic part)*(length of lipophilic part)].

          Lipophilic and hydrophilic calculations are performed at -0.6 and -3.0 kcal/mol, respectively. Critical packing is a good parameter to predict molecular packing such as in micelle formation, and may be relevant in solubility studies in which the melting point plays an important role.

        • Polarizability (POL). is an estimation of the average molecular polarizability. This method is based on the structure of the compounds (and not any molecular field) and is therefore independent of the number and type of probes used. The correlation between the experimental molecular polarizability and the polarizability calculated with VolSurf+ for more than 300 chemicals is very good (r = 0.99).

        • Diffusivity (DIFF). computed using a modified Stokes-Einstein equation, controls the dispersion of chemical in water fluid at 25°C.

        • Molecular Weight (MW). is simply computed by summing the atomic weights.

        • LogP octanol/water (LOGP n-Oct). the logarithm of the partition coefficient between 1-octanol and water is computed via a linear equation derived by fitting GRID-derived atom type to experimental data on n-octanol/water partition coefficients.

        • LogP cyclohexane/water (LOGP c-Hex). the logarithm of the partition coefficient between cyclohexane and water is computed via a linear equation derived by fitting GRID-derived atom types to experimental data on cyclohexane/water partition coefficients.

        • LogD (LgD5 - LgD10). the logarithm of the partition coefficient between 1-octanol and water is computed via the sum of the logP and the fraction of every species at pH 5, 6, 7, 7.5, 8, 9 and 10.

        • Polar and Hydrophobic Surface Areas (PSA, HSA, PSAR, PHSAR). the Polar Surface Area (PSA) is calculated via the sum of polar region contributions, while the Hydrophobic Surface Area (HSA) is calculated via the sum of hydrophobic region contributions. PSAR is the ratio between the polar surface area (PSA) and the Surface (S), while PHSAR is the ratio between the polar surface area (PSA) and the hydrophobic surface area (HSA).

      • Charge State descriptors:

        • Number of Charged Centers (NCC). reports the number of the charged centers present in the imported molecule, according to its charge state at the chosen pH.

        • Available Uncharged Species (AUS7.4). represents the available uncharged species at pH 7.4 and it is calculated as the logarithm of the percentage of the unionised species at pH 7.4 + 2 (AUS7.4 = Log(% unionised) + 2).

        • % unionised species (%FU4 - %FU10). the percentage of unionised species is calculated at pH 4, 5, 6, 7, 8, 9 and 10.

      • 3D pharmacophoric descriptors:

        • Dry, H-bond donor, H-bond acceptor and mixed Dry, H-bond donor and acceptor 3D triplets pharmacophoric areas (DRDRDR, DRDRAC, DRDRDO, DRACAC, DRACDO, DRDODO, ACACAC, ACACDO, ACDODO, DODODO). these parameters represent 3D pharmacophoric descriptors based on the Triplets Of Pharmacophoric Points descriptors. At first the atoms (points) of a structure are classified as Dry, H-bond donor and H-bond acceptor, then all possible triplet of distances between these atoms are generated. The derived descriptors are the maximum area (over all possible conformers) of the triangles derived from every following class of pharmacophoric triplets:

          • DRDRDR refers to the Dry-Dry-Dry triplet

          • DRDRAC refers to the Dry-Dry-Acceptor triplet

          • DRDRDO refers to the Dry-Dry-Donor triplet

          • DRACAC refers to the Dry-Acceptor-Acceptor triplet

          • DRACDO refers to the Dry-Acceptor-Donor triplet

          • DRDODO refers to the Dry-Donor-Donor triplet

          • ACACAC refers to the Acceptor-Acceptor-Acceptor triplet

          • ACACDO refers to the Acceptor-Acceptor-Donor triplet

          • ACDODO refers to the Acceptor-Donor-Donor triplet

          • DODODO refers to the Donor-Donor-Donor triplet

  • Protonation policy:

  • As is: The algorithm would use the structure of the compounds as input by the user.

  • neutralize: The protonation state of the molecule will be modified to get the neutral form.

  • normalize pH: The protomer that will be used in the computation will be the most abundant at the pH indicated.

  • Geometry optimization:

    • Search for intramolecular hydrogen bonds: Check this option if the conformation to be used in the descriptor computation is one that looks for internal hydorgen bonds

  • GRID directives:

    • GRID field parmetrization:

      • Static/Dynamic: The energy of the interaction can be computed considering the target molecule rigid or flexible. IN case of using static the molecule will be considered as a rigid body

      • GRID spacing: This is the space between the grid points

Action buttons

There are a collection of action buttons that are activated or deactivated depending on the tab and the status of the different tabs. These actions are:

  • Copy: This is to copy the selected setting, it is typically copied with the same name adding _Copy

  • New: This button set the options in the selected tab to enable writing a new stetting.

  • Save: Save the setting into the database after modifications has been done.

  • Delete: Remove the selected setting.

  • Download: This option is available when it is possible to download some content of the setting.

Import

Click in this button to access the functionalities to import experiment exported from other Oniro installations. This functionality enables the possibility to share experiment between different Oniro installations. The Oniro only accepts experiments that have been exported from the Oniro and not from previous WebMetabase versions.

Import

The new window has 2 main areas:

  • Import settings: In this area is where the user can select the options and the files to be imported. The options are:

    • Automatic import: If this option is activated the experiment will be automatic upload using the saved mapping into the new database. If the system would not find a existing mapping for any element it will stop the import.

    • Import SMS files: If this option is activated the sms files (Molecular Discovery raw data files for MS) from the import file will be added to the database. This is only possible if the experiment has been exported with this information, otherwise this would not be considered.

    • Import attachments: If this option is activated the attached files to the experiment from the import file will be added to the database. This is only possible if the experiment has been exported with this information, otherwise this would not be considered.

    • Use default folder to put incoming experiments: If this option is activated the experiments can be imported to the same folder tree that they were originally from. Otherwise, the experiment will go to the base folder specify in the next option.

    • Base folder: If the Use default folder to put incoming experiments is not activated the user can specified the folder where the experiments will be imported to.

    • File(.zip): Click on the Browse button to get to the file to be imported. This file has to be generated with Oniro.

    • Action buttons:

      • Upload: After the file has been specified, the user can upload it to the system by clicking in this button.

        Import. Upload. Click OK to continue
      • Cancel: Click this button to start the process and put all option in default

  • Experiment import: In this area it is shown the experiments that have been uploaded as well as those ones that have been already imported.

    Import. File already uploaded

    Right click or select the button to continue.

    • Refresh: This option refresh the information in the table. Specially interesting when there are multiple experiments imported at different phases.

    • Show: It is show the result of an already mapped experiment.

    • Map: In order to import the experiment into the database the different parts of the experiment: units, properties, property values, users, work group, protocol, experiment need to map with the results in the database. When clicking the Map button the mapping process start the Experiment mapping window is show:

      Import. Mapping Step 1

      Click in confirm to move to the next one, or modify if needed. At the end of the process a summary of the entire mapping process will be shown. Click OK to continue

      Import. Mapping data reviewing
    • Delete: This option remove the import information line from the table list