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• Minerva 4 User Manual Transmission

User manual file - location in the directory structure of a MINERVA instance for the user manual file Point and click Max distance for clicking on element (px) - the content visualized by MINERVA is interactive, and clicked elements or interactions are recognized by the vicinity of the click event. View and Download Franke Minerva 4-in-1 Electronic installation and user manual online. 4-in-1 Instant boiling water system. Minerva 4-in-1 Electronic water heater pdf manual download. Minerva We are the Commercial Fire & Security System Experts Throughout the UK. Trusted commercial supplier, installer and maintainer of a wide range of Fire alarm and security systems. We offer a number of services to cater for clients of all sizes - including fire.

You are in administrator's manual » v13.0 ||

Table of contents

• Administrator view
  • PROJECTS
    • Add project
    • Edit project
  • GENOMES

Administrator view refers to the set of functionalities for web-based management of the content and configuration of a MINERVA instance.

Login

Administrator view is accessible via the button with the lock icon in the upper left corner of the main view (see below).

Many projects (maps, networks) can be hosted in parallel on a single MINERVA instance. The users access the projects via direct hyperlinks. To manage these projects, the user with administrator’s rights to at least one of the projects can log as an administrator via lock icon. After successful login, you will have an access to the administrator panel to manage a MINERVA instance (see below).

PROJECTS

This panel allows you to (1) add new projects (2) examine messages generated during the upload of the projects (3) edit and (4) remove them.

Add project

The Add project button invokes a menu allowing you to upload your project and start its generation in the MINERVA platform.

File formats

Files uploaded to create a project on a MINERVA instance can be:

• CellDesigner files (see CellDesigner website)
• SBML files, importantly
  • elements (species) and reactions should be defined by SBOTerms, to match the CellDesigner style (see the list of CellDesigner types matching SBOTerms). If not, all elements will be shown as small molecules and all reactions as state transitions. Find more in example 02 - SBML file modifications.
  • layout package is supported
  • MIRIAM annotations in the <annotation> node are supported
• SBGN files

Single files of these types are uploaded via the Add project button. Advanced project structure can also be uploaded as a compressed file, as described in the Advanced format.

Fields of the Add project window

• Upload file - Choose File invokes a file upload dialog. Available options and configurations of the source file are discussed in section Source file.

• File format - choose a format of an uploading file: CellDesigner, SBGN or SBML.
  Note: Adding CellDesigner file or SBGN-format file automatically changes file format in the window. For an SBML file, the file format must be changed manually.

• Map canvas type - choose Google Maps API or OpenLayers to display the map, if you choose Google Maps API you have to agree on Google Maps API Terms by ticking the checkbox.

• ProjectId - a working name of the uploaded project on the MINERVA platform.

• Project name - the name of the uploaded project displayed in the top left corner of the main view; your official name of the project.

• Project Disease - the disease associated with the project, the code has to be a valid MeSH identifier, e.g.D010300. This is needed for chemical target search, see section chemical target.

• Organism - the taxonomy id of the species, for which the map is primarily developed, e.g. 9606. This is needed to display genetic variants overlays.

• Version - a text field displayed next to the name of your project in the User panel.

• Notify email - e-mail address that should be used for project-related notifications.

• Annotate model automatically - if this checkbox is checked, elements of the uploaded map will be automatically annotated using built in annotators. Behavior of the annotators can be configured by clicking the Advanced button (see section Configure automatic annotation).

• Verify manual annotations - if this checkbox is checked, elements and interactions of the uploaded map will be scanned for existing annotations; if present, these existing annotations will be validated against a set of rules. Verification rules can be configured by clicking the Advanced button (see section Configure automatic verification).

• Cache data - if this checkbox is checked, all hyperlinks in the project resolved by MIRIAM repository (e.g. cross-links to external bioinformatics databases) are resolved and cached.

• Auto margin - if this checkbox is checked, the map will be drawn with equal amount of empty spaces around it.

• Display as SBGN - if this checkbox is checked, the uploaded model will be displayed in SBGN format, instead of the default CellDesigner format.

• Semantic zooming contains multiple overlays - tick the checkbox to display each semantic zoom level as a separate overlay in the General Overlays panel in the map. Find out more about semantic zoom here. This mode is primarily for testing purposes and we advise it should be unchecked by default.

Configure automatic annotation

The Advanced button, next to the Annotate model automatically checkbox under Add project button, invokes a dedicated configuration window (see below).

Clicking on each element type from the tree in the left panel, an annotator can be assigned in the right panel that will attempt to automatically retrieve information from external bioinformatics databases for each relevant element and annotate them.
Copy from button in the right panel copies annotators set from other objects we choose (see above image: GenericProtein will get the same annotators as Gene already has set).
Important note: Settings for lower hierarchy levels are overridden by settings for upper hierarchy levels. For instance, if no Ensembl annotation is selected for GenericProtein, but Protein selects Ensembl, GenericProtein will be automatically annotated with Ensembl as well.

There are a number annotators available, working either by name, or by annotation of an element.
By annotation refers to the MIRIAM identifiers in the <annotation> section of SBML and CellDesigner formats.
These annotators use specific identifiers, mentioned below, to retrieve additional information for elements.For instance, by UniProt annotation means that the annotator needs a valid UniProt identifier in the <annotation> section.
Note: SBGN files can be automatically annotated only by name as they have no <annotation> section.

BRENDA

- By annotation: BRENDA, UniProt.

- Retrieves all BRENDA codes for enzymatic activity of the element.

ChEBI

- By annotation: ChEBI or by name (ChEBI).

- retrieves full name and synonyms in the ChEBI ontology.

ENSEMBL

- by annotation: ENSEMBL.

- Retrieves symbol, full name, HGNC Symbol and identifier, Entrez Gene identifier.

Entrez Gene

- By annotation: Entrez Gene.

- Retrieves full name, symbol, synonyms, description, HGNC identifier and ENSEMBL identifier.

Gene Ontology

- By annotation: Gene Ontology.

- Retrieves full GO definition for this identifier.

HGNC

- By annotation: HGNC and by name (HGNC symbol).

- Retrieves full name, symbol, synonyms and UniProt identifier, RefSeq identifier, ENSEMBL identifier, Entrez Gene identifier.

Protein Data Bank

- By annotation: PDB, UniProt, HGNC, HGNC symbol and by name (HGNC symbol).

- Retrieves all relevant PDB structure identifiers. If HGNC symbol or identifier are used, it will also run the HGNC annotator.

STRING

- By annotation: STRING, UniProt.

- Retrieves all relevant STRING identifiers. If UniProt identifier is used, it will also run the UniProt annotator.

UniProt

- by annotation: UniProt.

- Retrieves HGNC symbol and Enzyme Nomenclature identifier.

Biocompendium

Warning! this annotation service is unstable due to maintenance
- by name, retrieves full name, symbols, description and identifiers:RefSeq, ENSEMBL, Entrez Gene identifier, HGNC symbol, KEGG, Reactome, PubMed and others

Configure automatic verification

The Advanced button, next to the Verify manual annotations checkbox under Add project button, invokes a dedicated configuration window (see below).

Clicking on each element or interaction type in the tree in the left panel, then:

- top right panels

A list of MIRIAM identifiers which are configured as valid. Elements or interactions in the uploaded model annotated with any identifier other than the valid list will raise a warning.

- bottom right panels

A list of MIRIAM identifiers which are configured as mandatory. If checkbox One of these miriam should be required is checked, elements or interactions in the uploaded model annotated without at least one identifier from mandatory list will raise a warning.

Save button: project generation

Clicking Save in the Add project window will start generation of the project.The status of the project in the Projects tab will update during the process. Also, you can use the Refresh button. Any warnings raised during the process will cause an exclamation mark icon to appear next to the project status. The list of warnings is extended gradually when the project upload advances, and you need to wait for the project completion to see the full list. You will receive an email notification after the generation is complete.

It may happen that the project generation will result in a failure. An icon will be displayed, and mouse over itwill display the reason for failure. You will receive an email message with the brief description of the error.

To find out more, check example 1 - CellDesigner file upload and annotation.

Project status

Clicking on the exclamation mark icon (if present) next to the project status description, will displaythe list of warnings raised during the generation of this project (see below).

The list can also be downloaded as a tab-delimited text file. Types and identifiers of the elements and interactions arelisted on the left side of column Content, while the nature of an error is provided on the right.Take a look at the list of possible errors and their explanations.

Edit project

This panel allows you to configure and manage the project. Functionalities are grouped in the following tabs (see below for an illustration):

• General edit information about this project: canvas type, name, version, disease and organism type or notify email address
• Overlays add or configure overlays for this map, both general and user-provided
• Maps configure visuals for the main map and submaps
• Users manage users’ access rights to this map
• Comments manage user-provided comments for this map

Overlays

This tab allows you to add new overlays and edit properties and ownership of existing overlays. You see here overlays that have been:

• uploaded with the project, if it contains overlays already (see sections Add project and Source file)
  Important! Overlays named Pathways and compartments, Network and Empty allow for different ways of displaying the map’s content, and they have no data associated with them.
• uploaded by the users (see section Upload user-provided overlay data)
• uploaded by the administrators by Add overlay button in top left corner

In this tab, besides Name and Description, the following columns are available:

• Public - this checkbox makes the overlay available to any user
• Default - this checkbox sets the default view of the map
• Owner - the user having the access right to a given overlay. Dropdown menu allows to choose from existing users
  Important!
  Choosing the owner to be ‘N/A’ (top of the list) and checking the Public checkbox makes this overlay a General overlay, accessible for all users
• Data - action buttons to download the associated dataset
• Update - action buttons to save any changes in the configuration of the corresponding overlay
• Remove - action buttons to remove the corresponding overlay

Maps

This tab lists all available maps (the main map and submaps) in the project, and allows to change default displaying options of the maps, see below.

The following columns are available:

• Default center x and y sets the default center point of the (sub)map
• Default zoom level set the default zoom level for this (sub)map
• Update to save the changes

Users (of this map)

This tab lists all users of a MINERVA instance and allows to configure their access rights to this particular map.It contains the following columns of checkboxes:

• Manage comments
• Manage overlays
• View project
• Update button, to save changesTicking a checkbox in a respective column for a given user assigns the corresponding privilege to them. Each change needs to be saved with the Update privileges button.

General users privileges are discussed in detail in the following section USERS.

This panel allows you to manage comments provided by users to the particular map (see section User manual - Comments).

The field Title is a hyperlink to a given comment in the map. In the following columns there are author of the comment, his email and the content. Pinned informs if the comment’s icon is visible on the map.
Users logged in as administrators have a possibility to delete a comment by pressing press the Remove button. The removed comment will no longer be visible among the pinned comments on the map, and its status will be updated in the Removed panel with comment in the brackets (see image below).

USERS

Registered users can be allowed to upload data overlays to maps hosted on a MINERVA instance, and to manage it.This panel allows you to Add (1) users, Configure LDAP authentication (2) and Edit (3) their privileges, or Remove(4) them. See image below:

Clicking on the Add user button invokes the window (see below) allowing to set login, password and personal details of a new user.
The panel to Edit allows to modify user data except the login field. Remove button removes this registered user from a MINERVA instance.

The two next tabs in the window allow to configure the access rights and privileges of the user.

• Global privileges concern all projects on a MINERVA instance.
  • Add project if checked, permits the user to add new projects (Add project button becomes visible).
  • Custom overlays field defines how many overlays can be created by a given user across all projects.
  • Manage configuration if checked, grants the access right to Configuration tab and permits to configure the parameters of MINERVA platform.
  • Manage genomes if checked, grants the right to access Genomes tab and manage a reference genomes for MINERVA.
  • Map management if checked, grants the right to access Map manager tab and manage existing projects.
  • User management if checked, grants the right to access the User manager tab and to manage users.
• Project-specific privileges concern only the project, for which they are configured
  • Top row: Default privilege for a new project checkboxes - set up default privileges assigned to this user for any new project.
  • The list of available projects on a MINERVA instance, contains four columns:
    • ProjectId name of the project.
    • Manage comments if checked, grants access to the comments tab in Edit project and allows them to manage comments for this project.
    • Manage overlays if checked, grants the right to manage overlays of all users for this project.
    • View project if checked, grants the right to open the URL of this project, and makes it visible in the PROJECTS tab.Important for non-administrators, only this box should be selected.
      Important unchecking this box for the user anonymous makes this map inaccessible without login. Only registered users with proper privileges will be able to open the URL of this map.

CONFIGURATION

Configuration tab allows privileged users to configure global parameters of a MINERVA instance. Particular categories of configuration items are grouped in separate tabs (see image below).

Global MINERVA configuration category are:

• Email notification details
  • E-mail address - e-mail address used for sending notifications about the activity of a MINERVA instance - project uploads, comments, etc.
  • Email settings for requesting an account - the Info and Overlay tabs in the user interface allow to a Request for an account action, which will auto-compose an email with the message defined in Email content used for requesting an account to addressed to the e-mail, or e-mails (separated by a semicolon) provided in the field Email used for requesting an account.
  • E-mail server login, E-mail server password, IMAP server, SMTP port and SMTP server - configuration of your mail server for notification sending
• Server configuration
  • Issue tracker - a tool to submit MINERVA issues.
  • Default project Id - the project that will be displayed by default under the root address of the platform (your.url/MapViewer/)
  • Domain allowed to connect via x-frame technology - the address of a website allowed to embed a MINERVA instance via x-frame technology
  • Google Analytics tracking ID used for statistics - provide here a valid Google Analytics ID to track user activity of a MINERVA instance
    • Max session inactivity time (in seconds) set the time after inactive session is expired
  • Path to store big files - location in the directory structure of a MINERVA instance to store big files
• Legend and logo
  • Legend 1-4 image file - path in the directory structure of a MINERVA instance for displayed legend images
  • Logo description - the popup text that will be displayed upon mouse over your logo
  • Logo icon - the filename of your logo icon, displayed in the bottom-left corner of the main view; path in the directory or URL
  • Logo link (after click) - the website to which you will be redirected after clicking on the logo
  • Show reaction type when browsing map checkbox
  • URL of platform Terms of Use file
  • User manual file - location in the directory structure of a MINERVA instance for the user manual file
• Point and click
  • Max distance for clicking on element (px) - the content visualized by MINERVA is interactive, and clicked elements or interactions are recognized by the vicinity of the click event. This parameter controls how close to an element or interaction, in pixels, you need to click to select them
  • Max number of results - sets the max number of search results, (similar elements are grouped into a single search result)
  • Max number of map zoom levels - sets the max size (of canvas) of the map, that can be uploaded to MINERVA.
• Overlays
  • Opacity used when drawing data overlays (value between 0.0-1.0)
  • Overlay color for negative/positive values - sets the colors should be used for positive and negative values in basic overlays. Values close to zero have the lowest color saturation, values close to -1/1 have the highest color saturation
  • Overlay color for value=0
  • Overlay color when no values are defined - sets the color to use for coloring list of elements overlays
    • see section User manual - Upload user-provided overlay data

• Default user privilegesSets default user privileges to manage comments, overlays and view projects for any project on a MINERVA instance.

• Search panel optionsDefines which search results in the left panel will be expandable via plus/minus icon.

• LDAP configuration
  • LDAP address - address of the machine where LDAP server is located
  • LDAP port - port on which LDAP is listening (by default it’s 389, for SSL connections usually it’s 636)
  • LDAP uses SSL - check to use SSL for LDAP connection
  • LDAP bind DN - Distinguished Name of the user account that should be used for LDAP connection (this user should be able to search/list accounts on LDAP server)
  • LDAP password - password for the LDAP bind DN
  • LDAP base DN - definition of the point from where a server will search for users
  • LDAP filter objectClass - this parameter allows to filter by objectClass type of LDAP entry; * value skips the filtering
  • LDAP first name attribute - which attribute in LDAP directory corresponds to “First name” of the user
  • LDAP last name attribute - which attribute in LDAP directory corresponds to “Last name” of the user
  • LDAP email attribute - which attribute in LDAP directory corresponds to the user email address
  • LDAP filter - when there are many accounts in LDAP administrators create groups of users that have access to specific systems, this filter allows to define LDAP filter that will limit set of accounts that can access minerva, empty string disable filtering
  • LDAP login (user id)

GENOMES

In this section an administrator can set up a reference genome for displaying genetic variant overlays and a genome browser in the map. Currently, MINERVA supports human genomes data from UCSC Genomics Institute. Available fields (see also image below):

• Type informs about type of data, currently MINERVA supports UCSC format
• Organism identifier of the organism of the added reference genome (e.g. 9606)
• Version version of the added reference genome (e.g. hg19)
• Progress of the upload
• Source - url address of the genome data; sets up automatically after selecting Version, or user can paste own url addressNote: the file must be in .2bit format
• Edit/Remove buttons allows to edit the gene mapping and remove the genome from the instance

Important note:
The Taxonomy id (e.g. 9606) for Organism must be provided for the project, and reference genomes uploaded on a MINERVA instance must include its type. If Organism for the project is missing, the genome browser is not displayed in the overlay’s popup window.

Add new genomes

In top left corner choose ADD GENOME button; the window pops up, as shown below:

The window contains two tabs:

• DETAILS - select new genome parameters as described above
• GENE MAPPING - information about the gene loci in the genome, which are visualized on the blue axis in the genome browser. In the dialog window, provide the name of the data set and its url address. The name will be displayed in the genome browser (here: gene ref), see User manual - Overlays. The data must be provided in .bb format file. More details how to create .bb file.

PLUGINS

The plugin tab allows the administrator to add a public plugin to a MINERVA instance. These plugins will be displayed if in the Plugins menu in the map.
The Plugin tab is shown on the image below, it contains:

• Name of the plugin
• Version of the plugin
• URL of the plugin
• Remove the plugin from a MINERVA instance

To add a new plugin, click Add plugin button, and paste the plugin url into the URL field and click Validate (see image below). The name and version fields are usually filled automatically from the plugin content. Click Save to add the plugin to a MINERVA instance.

Note: The administrator cannot add the same plugin twice to the MINERVA in the Administrator panel (the notification is displayed). But a user can upload an already exiting plugin via Plugins menu in the user’s view of a map.

You are in user's manual » v13.0 ||

Table of contents

• MAIN VIEW
  • Basic exploration tools
• FUNCTIONAL AREA
  • Search tab
  • Overlays tab
    • Upload user-provided overlay data
  • Info tab
• INFORMATION BAR

User view refers to the visualization and functionalities accessed by users of the content hosted by your MINERVA instance.

You can also see the brief summary of this page in the MINERVA Quick Reference Guide or you can followthe guide.

The main view of the MINERVA platform is summarized in the figure below.

Main components of this view are:

(1) Display area where the contents of the projects are visualized.
(2) Functional area allowing for advanced interaction with explored content.
(3) Information bar containing additional overlay functions.
(4) Plugins / Administrator login allowing an administrator on login and a user on upload of own plugin.
Note: To login as a user go to Overlays or Info tab.

Accessing the project

Your instance of MINERVA platform can host many projects, which are uploaded by the administrators (see add project). Every project project can be accessed by a dedicated web address.

Exploring the display area

MINERVA platform displays molecular interaction diagrams, their annotations and links to databases. MINERVA uses externally curated content in one of the two: SBGN-compliant format or SBML format. In case of SBML format, it is important to customize the file before the upload to MINERVA. Read more about the content curation here.

The content is visualized using Google Maps API or Open Layers Library (chosen on project upload), and allows for similar pan-and-zoom functionalities. The content is interactive, the user can click on an element or an interaction to examine additional details, displayed in the left panel (functional area). More exploration tools are available via right click on the map.
The map content is by default displayed in semantic zoom mode, which enhances map’s clarity. In that view, the compartments and the pathways areas are displayed in a particular order, regulated by the zoom level.

Semantic zoom

Semantic zoom is a default view of the map. It makes the compartments and the areas cover underlying elements on higher levels of zoom. This view is generated procedurally, directly from the uploaded content(compartments of SBML/SBGN and layers of CellDesigner). MINERVA calculates which areas cover others, and assigns them to the appropriate zoom levels.
Note: In the left panel (functional area), in the tab Overlays tab semantic zoom is activated via Pathways and compartments overlay. You can turn it off by changing the view on Network or Empty.
Find out more here: procedural generation of the semantic zoom.

Basic exploration tools

Right-click in the display area invokes a contextual menu, see image below. It allows to add a comment on a map, to download the map or its selected area, and to visualize the structures of proteins.

Add comment

This functionality allows to comment on contents in the display area. Clicking on Add comment invokes a form that can be filled out by the user and sent to the administrators of the project (see below left). Type field is a drop-down menu, listing elements nearby to the click location. This allows to choose and attach the comment to a particular element or interaction (see below middle). If particular type is selected, its name is displayed (see below right).
The field Pinned controls, whether the comment will be visible in the map.

After sending, if the Pinned box was ticked, the comment bubble becomes visible in the display area (see below left). Note that the checkbox Comments located in Information bar must be ticked to make the comments visible at all.

Clicking on the comment bubble displays annotated element and the text of the comment (see above right). Name and email are not disclosed, they will be accessible only to project and platform administrators (see Administrator’s manual - Comments).

Select mode

Clicking the Select mode enables the functionality supported by Google Maps API and Open Layers Library. It allows to select an arbitrary shape in the display area.
To select the area: choose Select mode and click on the map, it is your start point. Draw all of your polygon’s points. To close the polygon choose the end point of the polygon the same as the start point, or double click on the end point.
Right click on the selected area allows to remove the selection or download it in various formats, either as a map or an image.

• Export as image produces a rectangular image containing the selection. Export to vector and raster graphics is supported, allowing to modify and enhance the downloaded image.

• Export as map produces a file acceptable by either CellDesigner, pure SBGN or SBML editors, containing the editable fragment of the selected display area, together with its contents and layout. Importantly, in the case of CellDesigner or SBML export, all additional annotations provided by MINERVA platform are downloaded as well.

Export as image

This option creates an image of the part of map on your display area. Export to vector graphics is supported, allowing to modify and enhance the downloaded image.

Export as map

This option allows to produces a file acceptable by either CellDesigner, pure SBGN or SBML editors containing the editable fragment of the selected display area, together with its contents and layout. Importantly, in the case of CellDesigner or SBML export, all additional annotations provided by MINERVA platform are downloaded as well.

Open MolArt

This option is active only for the protein annotated with UniProt ID (see image below). MolArt (MOLeculAR structure annoTator) is a JavaScript tool and library. It visualizes sequence-related annotations over available experimental or predicted structures (click here for MolArt documentation).

MolArt opens a new window, which displays in the left panel the molecule’s sequence, relevant annotations (including variation data) and the list of available structures (either experimental or predicted) for a given molecule. The right panel of MolArt window shows selected 3D structure over which any of the sequence annotations can be color-overlaid. See image below:

Functional area (the panel to the left from the display area) displays additional information about selected elements and interactions, allows to query the content, generate custom overlays and browse the submaps.

Search tab

Search tab allows to search for a particular elements or interactions in the displayed map. Also, under this tab, the panel displays the detailed information on selected elements or interactions, such as: element’s compartment and full name, symbols, annotations and their source (automatic or manual by curator), see below:

There are four subtabs available in the Search tab, offering different scopes:

• GENERIC for regular search
• DRUG for drug target search
• CHEMICAL for chemical target search
• MiRNA for miRNA target search

GENERIC

The generic scope works as follows:

• Search field: Type your search query here, separating multiple elements with a semicolon ‘;’. Searches for separate terms will be visible in separate tabs. Search will look for similar names and synonyms of elements in the map.
  You can also search for an identifier of a reaction (visible in the left panel after clicking on a particular reaction). To do this, you need to add reaction: prefix to the searched term, e.g. for a reaction with id “re944” you will search for a term “reaction:re944” (see below).

The reaction kinetics, if available, is displayed after clicking on chosen reaction in the display area.

Search pins indicate hits in the display area. Similar search results are merged (marked with the same number) and the left panel contains information about size of that group of x elements. If search pin is be blank (no number), it would mean that aggregated search results exceed 100.For multiple elements search, the results have icons of different color and shape (see image below) which are clickable and show information in the popup window. When searching for different targets (e.g. generic target and drug target) common targets are highlighted with a special icon. The same icon indicates search results that are found in a submap. See more in Submaps tab.

• Perfect match tick box: If this box is ticked, only terms exactly matching the query will be returned. For large networks or broad queries the search results may be capped to ensure the performance of the system. The limit of displaying search results can be configured by the administrator (see Administrator’s manual - Configuration).

Direct link to the elements in the display area is possible, as the search query can be provided within the web address ofthe displayed project. An address has to be manually constructed, directly into web browser, as below:

is a link executing the search for a given search query in the default project of your MINERVA instance. For example, an address

will directly point to an interaction with id xyz123. Referring to a given project on your MINERVA instance requiresadditionally to pass the project identifier in the address, as shown below. Identifiers of projects are accessible using the Admin view.

DRUG (target)

The Drug scope works as follows. Drug subtab under the the Search tab allows to look for known drugs or their brand names and display their targets in the map. The pins have specific shape, different than the results of other search scopes.

• Search field: type your search query here, separating multiple drug names or their brand names with a semicolon ‘;’. DrugBank (click) and ChEMBL (click) will be queried for known targets to be displayed in the map.
• Drug description, synonyms and all known targets will be displayed in the left panel.

CHEMICAL (target)

The Chemical scope works as follows. Chemical subtab under the the Search tab allows to look for known chemicals or their synonyms and display their targets in the map. The pins have specific shape, different than the results of other search scopes.

• Search field: type your search query here, separating multiple chemical names or their synonyms with a semicolon ‘;’. Clinical Toxicogenomics Database (click) will be queried for known targets to be displayed in the map.
• Drug description, synonyms and all known targets will be displayed in the left panel.

MiRNA (target)

The microRNA scope works as follows. MiRNA subtab under the the Search tab allows to look for miRNAs and display their targets in the map. The pins have specific shape, different than the results of other search scopes.

• Search field: type your search query here, separating multiple miRNAs with a semicolon ‘;’. miRTarBase (click) will be queried for known targets to be displayed in the map. Use only mature sequence IDs according to miRBase (click) (e.g. hsa-miR-125a-3p)
• Known targets will be displayed in the left panel.

Overlays tab

Overlays tab allows to display or generate custom coloring of elements and interactions in the map. It is composed of two sections - general overlays and user-provided overlays (which becomes visible upon login).

General Overlays

The table located in the top of the left panel (see image below), it contains:

• View column allows to change the viewing mode and display default multiple overlays:
  • Viewing mode is changed by clicking on the magnifying glass icon, allows to switch between:
    • Pathways and compartments (hierarchically masked content)
    • Network (only colored network structure shown)
    • Empty (only network structure, no coloring, recommended for data display)
  • Display multiple overlays (tick chosen boxes) - choosing that option automatically turns the viewing mode to Empty to emphasize the overlay’s colors.
• Data column contains buttons, where applicable, allowing to download the dataset used to generate the overlay.
  

Overlays provide additional information about elements and interactions. Hover over the overlay name/view/data to display a short description of the dataset, if provided on upload.
Overlays are also visible in the popup window, displayed after clicking on the element’s pin, showing the value and the sign marked on the horizontal color bars. The popup contains information about Interacting drugs, chemicals and MicroRNA with selected element, available after ticking check box Show all.

In the figure above:

• General overlays are overlays accessible for every user viewing the content
• User-provided overlays menu becomes available upon login

User-provided overlays

User-provided overlays are the overlays uploaded by and visible to the currently logged user. Available overlays can be reordered by name or number. Hover over any of them display short description, if one was provided on the upload.
Adding a new overlay is available via Add overlay button (see below image on the left side), which opens the dialog window (see below image on the right side):

There are two types of overlays the user can provide: generic and genetic variant.

• Generic overlay displays a coloring on the map according to data set of indicated molecules (e.g. differentially expressed genes).
• Genetic variant overlay displays a coloring for the genes, for which the variants are present. It also enables the genome browser popup, displaying the position of a variant in the sequence of the corresponding gene. To upload and correctly display the genomics information your instance must contain reference genomes, uploaded by the administrator. Also, the Organism id (e.g. 9606) must be provided for the project, and reference genomes uploaded on MINERVA instance must include its type.

The list of user-provided overlays contains columns (image above):

• No number of the overlay
• Name of the overlay
• View column with boxes enabling switching between User-provided overlays
• Data column with buttons allowing the user to download the dataset used to generate the overlay. The users have access only to their respective datasets.

• Edit column with buttons allowing the user to edit the description to the uploaded datasets

• Add overlay button invoking the dialog window with the following components
  • Name field for the new overlay
  • Description of the dataset
  • Type field, which depends on the header of uploaded file - TYPE field
    After choosing a file, the dropdown list TYPE switches automatically between GENERIC/GENETIC_VARIANT as Minerva recognizes file’s header. This happens because genetic variant overlays need to have a specific header field
  • Upload file - Choose file button to select a file with overlay data
  • List of elements field - instead of providing an overlay file, the user can provide a list of named elements to highlight in the map (e.g. list of genes). Choose TYPE corresponding to the content of your list: GENERIC for named elements; GENETIC_VARIANT for variants
  • Upload button to generate the user-define
  • (Optional) if a map is displayed using Google Maps API engine, Google Maps API Terms of Use checkbox will appear
• Refresh allows to refresh the overlays list. It is necessary in case an overlay is added via API during viewing a map in a browser

The user-provided overlays are displayed identically as default general overlays. The genetic variant overlays additionally contain the genome browser in the popup window (see below):

The genome browser allows to view the position of a variant in the sequence of the corresponding gene. In Gene variants section (see image above) user can choose the location in chromosome, zoom the scale in/out by clicking on +/- buttons and swipe the base pairs axis. The popup window contain following:

• Reference genome contains reference genomes uploaded into the instance by admin (e.g. hg19, hg38)
• Scale of base pairs displayed, changed by +/- buttons
• Location indicates current position in genome
• Genes ref display the reference genes locus provided to the instance by admin, see more in add new genomes
• User-provided overlay displays the variants from uploaded file

Upload user-provided overlay data

Here, we describe how the data overlays files should look like, so MINERVA can handle them and color the map as needed. To learn more about uploading data sets go to example 3 - Custom data upload.

Generic format: basics

The file in a basic format is a two-column, tab-separated text file, with the columns Name and Value. Please note that the basic format does not have a header.

• Name column contains the names of elements to be colored
• Value column contains the values normalized to [-1, 1] range

Basic format will match names of the elements provided in the Name column among the names of elements in a given network and for the matching ones will assign them colors: blue for negative values, red for positive values, with the saturation proportional to the value. The color range for the data upload is customizable in the admin panel.

Click here for an example of basic format overlay.

Generic format: advanced

The advanced format allows for by identifier matching, custom color assignment and coloring of interactions.The uploaded dataset has two sections - the header and the body.

The header lines start with ‘#’ and can contain the following elements:

• Version# VERSION=xyz - a version of this overlay file
• Name# NAME=xyz - a name that will be automatically assigned upon upload
• Description# DESCRIPTION=xyz - a description that will be automatically assigned upon upload

The body is a table with a following set of allowed columns:

• Name, Value - same as in basic overlay
• Compartment - name of a compartment in which coloring should take place
  Warning! Coloring compartments works ONLY for separate (not nested) compartments. Setting a color for elements in a compartment that encloses other compartments sets the color in the nested compartments as well.
• ChEBI - ChEBI identifiers of elements to be colored
• Entrez gene - Entrez identifiers of elements to be colored
• Gene ontology - Gene Ontology identifiers of elements to be colored
• Ensembl - Ensembl identifiers of elements to be colored
• HGNC symbol - HGNC symbols of elements to be colored
• UniProt - UniProt identifiers of elements to be colored
• ReactionIdentifier - ID of interaction to be colored (interactions coloring only)
• LineWidth - lineWidth of the colored interaction (interactions coloring only)
• Color - color of the colored element, in the hex format, e.g. #00CCFF

The dataset for upload may be integrated and sparse, i.e. a document may contain all columns at once, and, where irrelevant, their content may be left blank. In other words, you can color interactions and elements in the same dataset, leaving blank fields in ReactionIdentifier and LineWidth for elements, and leaving blank fields in Name for interactions.
Click here to view an example of generic advanced overlay.

Genetic variant format

It is a particular type of advanced format, it contains the header and the body, see below:

• Type - #TYPE=GENETIC_VARIANT
• Genome type - #GENOME_TYPE=UCSC - type of reference genome being used (e.g. UCSC)
• Genome version - #GENOME_VERSION=xyz - version of reference genome being used (e.g. hg19)

The body is a table with a following set of allowed columns:

• Position - the location of the variant in the genome
• Original_DNA - the reference DNA
• Alternative_DNA - the variant of the DNA
• Name of the gene with the variant
• Contig number of the chromosome
• Allele_frequency - relative frequency of this variant; it will be visualized by the height of the bar in the genome browser popup

Click here to view an example of genetic variant overlay, to have an insight on the file’s content.

UploadChoose the dataset to upload and press the Upload button. You will be notified by email when your overlay is ready. The email will also contain the list of elements in your dataset and the number of elements they colored in the map.

Minerva Instructions

Important reminder:

• The number of available overlays is configured in the Administrator’s manual - Users.
• The number of available overlays is common for all projects hosted on your MINERVA instance. If a user is registered in a number of projects and uploads custom datasets in all of them, the global number of available custom overlays will be reduced with each uploaded overlay.

Submaps tab

The Submaps tab summarizes all the submaps linked to the main map of this project hosted by your MINERVA instance. See Administrator’s manual - Source file to learn how to upload the submaps together with the main file.
The tab Submaps is visible in the left panel only if the map contains at least one submap. The tab contains names of the submaps and the buttons to display them.

The submaps show as a pop-up window on top of the main map, and are synchronized with respect to search queries and displaying data overlays.This means that search results and search pins will be visible in the main map and the active submaps. Similarly, overlays are mirrored in the submaps. Also, on the main map there is an icon informing that search results hit submap. See figures below:

Info tab

The Info tab has two components, displaying Project info and User data (for registered and logged users).

Project info

Displays name, version and description of the map.

The Data section features four links to:

• browse the publications supporting the map. The Publication list dialogue allows to search for articles by title or author names and contains links to interactions supported by particular articles.
• download the source files
• export the contents of the map (see below)
• open the manual

Export

The Export page contains three tabs (Elements, Network and Graphics), allowing to download the map contents in different formats.

• Elements tab allows to download the list of elements in the map as a text file. Available filters include:
  • Type - filters elements by the element type (e.g. Protein, RNA)
  • Column - selects particular columns, including:
    • Id - identifier of the element in the MINERVA system
    • Name - name of the element
    • Model - identifier of the (sub)network containing this element
    • Type - type of element
    • Complex - if applicable, id of the complex containing this element
    • Compartment - the smallest compartment/pathway containing the element
    • Element external id - corresponding source file e.g. CellDesigner ID
  • Annotations - filters the annotations of elements in the downloaded file; by default all annotation types are considered. Fields highlighted in green are non-empty annotation sources
  • Included/excluded compartment/pathways - filters the elements by compartments/pathways they are in; by default all compartments are considered as “included”, none as “excluded”
• Network tab allows to narrow down and download the interactions in the map. The exported network file is not a fixed-column table. As interactions are in fact hyper-edges, each line may contain different number of reactants, products and identifiers. Available filters include:
  • Element type - filters the nodes of exported interactions by the element type
  • Reaction type - filters interactions by type
  • Column - selects particular columns, including:
    • Elements - information about reactants, products and reaction modifiers
    • Reaction external id - reaction identifier from the source file e.g. CellDesigner ID
    • Map id - identifier of the (sub)network containing this element
  • Annotations - filters the annotations of elements and interactions in the downloaded file; by default all annotation types are considered. Green highlighted fields are non empty annotation sources
  • Included/excluded compartment/pathways - filters the elements by compartments they are in; by default all compartments are considered as “included”, none as “excluded”
• Graphics tab allows to download graphics of the (Sub)map in one of the Format: PNG image, PDF and SVG image

User data

If registered, users can login here, or request for an account from the administrators of this MINERVA instance.Platform administrators can register new users (see Administrator’s manual - General USERS) and configure Request an account functionality(see Administrator’s manual - Configuration)

After login, this panel displays information about the user. After the successful login the user gains the possibility to upload custom overlays (see Overlays).

Information bar is the topmost part of the user view, containing the Show overview button, Comment and Legend checkboxesand Clear button. The Clear button clears all search results currently shown in the display area. The remaining functionalitiesare detailed below.

Show overview

This button invokes a static image associated with the displayed content. It may be a graphics helping to understandthe underlying map, or any other visual cue that the content curator decided to present. The initial image displayed with theShow overview button can be linked to:

• another static image to be displayed next
• a defined area in the displayed content
• a set of elements or interactions.

Detailed information on how to configure Show overview images display is provided in Administrator’s manual - Source file.

If this checkbox is checked, the comments provided by users with Pinned option set to Yes will become visible in the display area (see Add comment).

Legend

Minerva 4 User Manual Download

If this checkbox is checked, the legend describing element and interaction types will be displayed.

Plugins allow for creating client-side custom visualizations, independent from the core functionalities of MINERVA. After clicking on the plugin icon a popup window becomes available (see images below).
The user can choose any of the plugins that are available on the MINERVA platform, uploaded on the instance by the admin. Also, in the URL field one can supply a URL to the plugin, written in JavaScript. To learn how to write your own plugins, visit the “Plugin starter kit” repository.

Example plugin: you can upload below URL into the plugin dialog to find out more:
https://raw.githubusercontent.com/davidhoksza/minerva-plugins-starter-kit/master/dist/plugin.js

Afterwards, a plugin panel becomes available on the right (see image below). To close that panel, click the plugin icon to open the window and click Unload button.

Please find below the list of available plugins. Click at the plugin name to find more information about it.

Minerva 4 User Manual Transmission

The options available in the top left corner of the map. The padlock shape icon allows the administrator to login or request an account. To login as user go to Overlays or Info tab.