MitoCube

Welcome to the MitoCube respository. MitoCube is a full stack web application to manage proteomics data.

• Protein-centric data visualization
• Dataset-centric analysis and visualization including volcano plots, networks and heatmaps
• Submission management (Submitting samples, state changes, transferring to data visualization parts)

Application

The application is written in ReactJS (frontend)[https://github.com/hnolcol/mitocube-frontend] and Python (FastAPI-based backend)[https://github.com/hnolcol/mitocube-backend].

License

MitoCube is published under the MIT license.

Installation

Requirements

List of requirements to get MitoCube running.

• Sudo rights,
• installed nginx (optional), Python 3.11, NodeJS,
• and an email account set up to send verification codes

Frontend

The frontend is written in ReactJS using Vite. Please clone the repository and call yarn install to install the required packages.

Backend

Please visit the backend installation help. The backend installation requires the input and adjustment of several settings, creation of folders. MitoCube creates a lead account (system admin) upon start, therefore it is fundamental to have an email account.

For a detailed explanation of the required settings please visit the backend installation guide

Attributes/Controlled Vocabulary

MitoCube utilizes controlled vocabulary (attributes) to define metadata. Even though there is a comprehensive set of attributes predefined, you may want to adjust them to your needs. Attributes can have a defined set of attribute values, numeric input (user types in, for example: column length, time), as well as features (by default Proteins). Attributes can be defined for a dataset (e.g. true for all samples) or samples specific. The attributes can be managed via the user interface (ui) or setup in an Excel file. An attribute has a defined set of parameters. An attribute can be defined as mandatory_for_active which means that it must be set for a dataset before it can be published. Published in terms of MitoCube means that it is accessible to all users in the MitoCube, not to the outside world.

class AttributeModel(BaseModel):
    """
    BaseModel for Attributes
    id : int 
        The identifier of the attribute
    tag : str 
        Attribute tag, is validated to be of style ``att_<text>``
    text : str
        Attribute text to be displayed to a user in a ui. 
    priority : int, default 500 
        Priority of the attribute 
    parent_id : int, optional, default None
        The id of the parent attribute. Use for visualization in the ui.  
    parent_tag : str, optional, default None
        Tag tag of the parent attribute. 
    group_tag : str 
        Specifying the type of attribute. 
    mandatory_for_submission : bool, default False
        If true, the attribute must be defined upon submission of a new project.
    mandatory_for_active : bool, default False 
        If true, the attribute must be defined before the data of the dataset can be explored. 
    has_feature_value : bool, default False 
        If true, the attribute_values are the features (proteins) present in the database 
    has_numeric_input : bool, default False 
        If true, the attribute can be defined by a simple numeric value (e.g. attribute_value). 
    min_state : int, default 0
        The minimal state defined in ``SubmissionStates`` the submission must be in to allow the attribute
        to be defined. For example, upon changing the submission to ``MEASURING`` the mass spectrometer should be defined. 
        But this information is not yet available at submission. 
    allow_as_qc : bool, default False
        Allow the attribute for quality control 
    allow_as_filter : bool, default True
        If True, the attribute can be used to filter datasets/submissions. 
    allow_for_dataset : bool, default False 
        If True, the attribute can be used to define a dataset. 
    allow_for_user : bool, default False 
        If true, the attribute can be used to define a user. 
    """
    id : int
    tag : str 
    text : str 
    priority : int = 500  
    parent_id : Optional[int] = None  
    parent_tag : Optional[str] = None  
    group_tag : str  
    mandatory_for_submission : bool = False 
    mandatory_for_active : bool = False  
    has_features_value : bool = False 
    has_numeric_input : bool = False  
    min_state : int = 0  
    allow_as_qc : bool = False 
    allow_as_filter : bool = True  
    allow_for_measurement : bool = True  
    allow_for_genotype : bool = False  
    allow_for_dataset : bool = False  
    allow_for_user : bool = False
    unit : Optional[Literal["length","concentration","weight","time"]] = None # ToDo: define units like this?