MINERVA v14.0
Manual

MINERVA configuration: Administrator’s manual#

Administrator view#

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).

Login view{:width=“400px”}

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).

Successful login{:width=“900px”}

PROJECTS#

This panel allows you to:

Projects view{:width=“900px”}

Add project#

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

Add project{:width=“900px”}

File formats#

You can upload to MINERVA a single file or zip-compressed file (advanced upload).

Fields of the Add project window#

Configure automatic annotation#

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

Configuration window{:width=“900px”}

Clicking on the object in the left panel, displays available annotators that can be assigned for it. Selected annotators will attempt to automatically retrieve information from external bioinformatics databases for each relevant element and annotate them. Copy from button allows to copy the annotators set from other objects we choose (see above image: GenericProtein will get the same annotators as AntisenceRna already has set). Bottom part of the window presents information than MINERVA provides for the selected annotators. These boxes can be checked depending to user’s preferences.

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.

List of provided information by MINERVA (these can be found in the bottom panel of Configure automatic annotation, see image above):
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, synonyms, 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, HGNC Symbol and 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, Enzyme Nomenclature identifier and Entrez Gene identifier.

Configure automatic verification#

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

Configuration window{:width=“900px”}

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 it will 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 display the list of warnings raised during the generation of this project (see below).

Warnings list{:width=“900px”}

The list can also be downloaded as a tab-delimited text file. Types and identifiers of the elements and interactions are listed 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):

Edit project - tab general{:width=“900px”}

Overlays#

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

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.

Edit project - tab overlays{:width=“900px”}

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

Important note: choosing the owner undefined (- - -) from the top of the list and checking the Public checkbox makes this overlay a General overlay, accessible for all users.

Maps#

This tab lists all available (sub)maps in the project. Also, it allows to personalise the default displaying options for the (sub)maps, see image below.

Edit projects - tab maps{:width=“900px”}

The available display parameters are described below:

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:

Ticking a checkbox in a respective column for a given user assigns the corresponding privilege to them. General users privileges are discussed in detail in the following section USERS.

Comments#

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 or curators have a possibility to delete a comment by pressing press the Remove button. The users can remove only their own comments. 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).

Edit project - tab comments{:width=“900px”}

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 (see image below):

USERS{:width=“900px”}

Add user#

Add user window is presented below. The first tab Details allows to provide user details and set his role. The role describes the user’s access rights - Admin, Curator or User. The second tab Project privileges is concerned on user’s privileges for a particular projects (View project, Modify project). Note that users can not be granted only with Modify project, as View project is necessary to see the project on the projects list, see images below.

Add new user{:width=“900px”}

Add user second tab{:width=“900px”}

The project’s privileges are listed below:

Roles are listed below. More detailed specification is presented in the following table.

Role if View if View & Modify
Admin N/A - full access N/A - full access
Curator add/view the project; view only the project details (in Edit); add overlay; remove own comments add/remove/view the project; full access to manage the project (in Edit)
User can create overlay view the project; add/remove overlay (in User View) view/manage the project’s general details & maps; remove own comments; add/remove overlay (in User View)
User view the project view the project; manage the project’s general details & maps; remove own comments

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).

Configuration tab{:width=“900px”}

General configuration#

MINERVA configuration categories are listed below:

LDAP configuration#

LDAP allows to log in to MINERVA with user’s global credentials. Note that: A user can log in to MINERVA via LDAP authentication without creating account on MINERVA instance. Such users is granted with Default user privileges (see section above). To set non-default privileges for a user (who have not logged in yet) it is necessary to create MINERVA account for him. Then set the custom privileges and choose LDAP authentication in USERS section.

Please find below description and examples of LDAP configuration for MINERVA:

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):

Important note: The Taxonomy id (e.g. 9606) for Organism must be provided for the project, and the 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.

Genomes main view{:width=“900px”}

Add new genomes#

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

Genomes add new{:width=“900px”}

The window contains two tabs:

The second tab is inactive unless you choose a genome in Details and SAVE it.

Gene mapping inactive{:width=“900px”}

After saving the genome, open Edit for it and add a gene mapping. Genomes gene mapping{:width=“900px”}

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:

Plugins main view{:width=“900px”}

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. Add new plugin{:width=“900px”}

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.

This documentation does not correspond to the latest official release of MINERVA (v19.0).
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