Getting Started

Installation of MaSyMoS Development Environment

Setup workspace

Setup Folder Structure

Note

the 📂 Project folder is represented in this instruction by [ENTER_HERE_YOUR_PROJECT_ROOT]

  • create one single root 📂 Project folder for everything needed for MaSyMoS
  • create the folder structure with subfolders as described below:
    • 📂 Project folder
      • 📁 code
        • all repositories
      • 📁 mvn
        • Maven libraries
      • 📁 eclipse
        • a dedicated Eclipse for MaSyMoS
      • 📁 database-engine
        • the Neo4j database engine with webserver and everything
      • 📁 databases
        • the MaSyMoS-generated databases
      • 📁 raw-data
        • raw data, you’re downloading to work with
      • 📁 workspace
        • your Eclipse workspace

Download/Install needed Software

<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
                              https://maven.apache.org/xsd/settings-1.0.0.xsd">

  <localRepository>[ENTER_HERE_YOUR_PROJECT_ROOT]/mvn/</localRepository>
</settings>

Configure Software

Configure Eclipse

  • start up Eclipse
  • set default workspace to 📁 workspace → restart Eclipse
  • use 📁 mvn as Maven-Path
    • Window → Preferences → Maven → User Settings - Global Settings: [ENTER_HERE_YOUR_PROJECT_ROOT]/mvn/settings.xml

Attention

set default Encoding and line delimiter (most important on Windows!)

  • Window → Preferences → General → Workspace
    • Text file encoding: UTF-8
    • New text file line delimiter: UNIX (\n)

Configure Neo4j

  • edit file 📁 database-engine/neo4j/conf/neo4j.conf
    • ✎ dbms.active_database=model-extraction-sbml
      • the value of this key points to the expected database in this folder: 📁 database-engine/neo4j-enterprise/data/databases/
    • ✎ dbms.security.auth_enabled=false
      • disable security restrictions for authentication

Load Repositories and Projects

Clone Repositories

  • all repositories are stored in 📁 code, you need
    • masymos-cli
    • masymos-core
    • masymos-morre
  • you can do this with Eclipse as well → Git Perspective

Load Eclipse projects

  • Java EE Perspective
  • for all three projects do:
    • File → Import… → Git → Projects from Git
      • existing local repository
    • right-click project → Maven → Update Project…

Work with your first Database

Create Database

-dbPath [ENTER_HERE_YOUR_PROJECT_ROOT]/databases/model-extraction-sbml
-directory [ENTER_HERE_YOUR_PROJECT_ROOT]/raw-data/sbml/curated
-noAnno
-type sbml
-fileMode

Open the Database in Neo4j

  • copy the folder 📁 /databases/model-extraction-sbml to 📁 database-engine/neo4j-enterprise/data/databases/model-extraction-sbml
  • the DB path was already set during Configure Neo4j to:
    • ✎ dbms.active_database=model-extraction-sbml
  • start Neo4j and browse the data
    • go to 📁 database-engine/neo4j
    • ./bin/neo4j console
    • open in Browser: http://localhost:7474
    • simple query: match (m:MODEL)-->(s:SBML_SPECIES) return count(s) as Anzahl, m.NAME order by Anzahl desc