MINERVA v12.2
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=“700px”}

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.

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=“800px”}

File formats#

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

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#

Configure automatic annotation#

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

Configuration window{:width=“900px”}

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).

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. You see here overlays that have been:

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

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

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.

Edit projects - tab maps{:width=“900px”} The following columns are available:

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:

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 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).

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 Add (1) users, Configure LDAP authentication (2) and Edit (3) their privileges, or Remove(4) them. See image below:

USERS{:width=“900px”}

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.

Add new user{:width=“900px”}

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

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”}

Global MINERVA configuration category are:

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 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:

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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