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Web application of metabolics pathway visualisation, for the Gencovery business (https://gencovery.com/), created during the PDP project during the M1 of the Master of Bioinformatics, in Bordeaux.

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Metabolic Mapping

Web application to visualise metabolic pathways in a 3-dimensional space. Uses 3D Force Graph and ThreeJS libraries.

example screenshot

Install

Repository import

git clone https://gitlab.gencovery.com/dev/internships/2020/m1-ubordeaux/testclass.git

Node server installation & set up

Node installation :
sudo apt install npm
Server installation, with the http-server package :
sudo npm install -g http-server

Usage

To run the web application, browser use is required. Only Chrome and Firefox browser are guaranteed. Local node server is required (See below).

cd testclass/
http-server

Open the first link to open the browser (http://127.0.0.1:8080).

Authors

Students of the Bioinformatics Master of the University of Bordeaux.

Marine ALVES DE BARROS - [email protected]
Mathieu BOLTEAU - [email protected]
Mélanie CARRIAT - [email protected]
Solweig HENNECHART - [email protected]

Programs versions used

  • Google Chrome 79.0.3945.117
  • Firefox 72.0.1
  • Node 6.13.4

Architecture

Classes implemented are organised like this diagram :

UML

API

Table of Contents

stringToJSON()

Transforms each JSON file data as string from the list to JSON object

parseJSON()Map

Parses the JSON object and instanciates the objects

putElementToPreviousElementCompound(pathway, idCompoundToSearch, idElementToAdd)

Adds the id of the reaction to the PreviousElement list of metabolites

putElementToNextElementCompound(patwhay, idCompoundToSearch, idElementToAdd)

Add the id of the reaction to the NextElement list of the metabolite

initCofact(list, pathway)Object

Creates Cofactors list for duplication

getObjectById(list, id)Element | boolean

Gets an element corresponding to an id if it's found else, returns false

duplicreate3dForceObject(map, cofact_list)Object

Creates the 3D-Force object required to display the graph with the 3D-Force Graph library with duplication possibility

create3dForceObject(map)Object

Creates the 3D-Force object required to display the graph with 3D-Force Graph library

jsonFileToGraph()

Reads and parses JSON file, to display the graph

arrowlink(graph3D)

Sets links to arrows with chosen characteristics

particuleLink(graph3D)

Adds directional particles to links

formNode(value, sizeproportion)Object

Allows the choice of the node geometry between TorusKnot, Sphere and Box.

displayGraph(object, map)

Displays graphs and loads elements information on click

graphChange()

Applies custom changes

loadFileAsText()

Loads files selected by the user and calls conversion function

get3dForceObject()Object

Gets and returns currently displayed graph

saveGraphToJSON()

Calls functions to save displayed graph as a new JSON file

createNewFile(SAVE_GRAPH_EXTENSION)

Creates JSON file(s) with modifications from the graph

modifyJSONObject(object3dForce)

Modifies the coordinates in the JSON object with the coordinates of the graph

getCofactList()Object

Return cofactors' id in list with user selection on interface


stringToJSON()

Transforms each JSON file data as string from the list to JSON object

Kind: global function

parseJSON() ⇒ Map

Parses the JSON object and instanciates the objects

Kind: global function
Returns: Map - Map object which contains the elements

putElementToPreviousElementCompound(pathway, idCompoundToSearch, idElementToAdd)

Adds the id of the reaction to the PreviousElement list of metabolites

Kind: global function

Param Type Description
pathway Pathway Pathway object which is created during the parsing
idCompoundToSearch String Id of the compound where the reaction id will be added in PreviousElements list
idElementToAdd String Id of the reaction to add

putElementToNextElementCompound(patwhay, idCompoundToSearch, idElementToAdd)

Add the id of the reaction to the NextElement list of the metabolite

Kind: global function

Param Type Description
patwhay Pathway Pathway object which is created during the parsing
idCompoundToSearch String Id of the compound where the reaction id will be added in next elements
idElementToAdd String Id of the reaction to add

initCofact(list, pathway) ⇒ Object

Creates Cofactors list for duplication

Kind: global function
Returns: Object - list of Cofactor objects

Param Type Description
list Object array containing id of certain elements
pathway Pathway object which is created during the parsing

getObjectById(list, id) ⇒ Element | boolean

Gets an element corresponding to an id if it's found else, returns false

Kind: global function
Returns: Element | boolean - Element object or "false"(boolean)

Param Type Description
list Object List containing objects
id String String corresponding to an element's id

duplicreate3dForceObject(map, cofact_list) ⇒ Object

Creates the 3D-Force object required to display the graph with the 3D-Force Graph library with duplication possibility

Kind: global function
Returns: Object - 3D-Force object which contains nodes and links data

Param Type Description
map Map Map object which contains the pathways
cofact_list Object list of cofactor ids to duplicate

create3dForceObject(map) ⇒ Object

Creates the 3D-Force object required to display the graph with 3D-Force Graph library

Kind: global function
Returns: Object - 3D-Force object which contains nodes and links data

Param Type Description
map Map Map object which contains the pathways

jsonFileToGraph()

Reads and parses JSON file, to display the graph

Kind: global function

arrowlink(graph3D)

Sets links to arrows with chosen characteristics

Kind: global function

Param Type Description
graph3D Object 3D-Force graph object

particuleLink(graph3D)

Adds directional particles to links

Kind: global function

Param Type Description
graph3D Object 3D-Force graph object

formNode(value, sizeproportion) ⇒ Object

Allows the choice of the node geometry between TorusKnot, Sphere and Box.

Kind: global function
Returns: Object - 3D Force Graph Icon

Param Type Description
value String corresponds to the choice of geometry we want to apply to our nodes
sizeproportion Number is useful in order to display bigger reaction nodes compared to the metabolites ones

displayGraph(object, map)

Displays graphs and loads elements information on click

Kind: global function

Param Type Description
object Object 3D-Force object which contains nodes and links data
map Map Map object which contains the pathways data

graphChange()

Applies custom changes

Kind: global function

loadFileAsText()

Loads files selected by the user and calls conversion function

Kind: global function

get3dForceObject() ⇒ Object

Gets and returns currently displayed graph

Kind: global function
Returns: Object - ForceObject 3D Force Graph object which contains data

saveGraphToJSON()

Calls functions to save displayed graph as a new JSON file

Kind: global function

createNewFile(SAVE_GRAPH_EXTENSION)

Creates JSON file(s) with modifications from the graph

Kind: global function

Param Type Description
SAVE_GRAPH_EXTENSION String new file name extension

modifyJSONObject(object3dForce)

Modifies the coordinates in the JSON object with the coordinates of the graph

Kind: global function

Param Type Description
object3dForce Object 3D Force Graph object

getCofactList() ⇒ Object

Return cofactors' id in list with user selection on interface

Kind: global function
Returns: Object - Cofactors List

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Web application of metabolics pathway visualisation, for the Gencovery business (https://gencovery.com/), created during the PDP project during the M1 of the Master of Bioinformatics, in Bordeaux.

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