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

• Download the newest "Eclipse IDE Enterprise for Java Developers" and extract it to 📁 eclipse
• Download Neo4j v3.5 end extract it to 📁 database-engine
• install Java 11 JDK (apt install openjdk-11-jre)
• create a file settings.xml in 📁 mvn and paste the following content (please replace [ENTER_HERE_YOUR_PROJECT_ROOT]):

<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

• get SBML Models from https://www.ebi.ac.uk/biomodels/

  • i.e. ftp://ftp.ebi.ac.uk/pub/databases/biomodels/releases/2017-06-26/
  • extract to 📁 raw-data

• create a Java Application runner model-extraction-sbml for class /masymos-cli/src/de/unirostock/sems/masymos/main/MainExtractor.java with the following parameters

-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