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2path

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Introduction

Installation of 2path core and system

Configuration of 2path system

Performing Metabolic Reconstruction

What is 2path?

2path core is a terpenoid metabolic network modelled using a graph database (in this version: OrientDB).

2path also provides a Python program to reconstruct the terpenoid network of a plant organism of interest from genomic data.

You can either use the database and explore the terpenoid metabolic network or reconstruct the terpenoid metabolic network of a target organism from protein or nucleotide sequences.

I want to install the database and the metabolic reconstruction system

Installation of 2path core and system

I just want to explore the 2path terpenoid database

In this case, you just need to import the 2path into your OrientDB

How to access the OrientDB to perform queries?

After starting your OrientDB, you have four options:

  • web interface in your browser:
http://0.0.0.0:2480
  • console:
$ ./PATH_TO_ORIENTDB/bin/console.sh

More detail here

  • gremlin language:
$ ./PATH_TO_ORIENTDB/bin/console.sh
orientdb> gremlin

More details here

  • using a programming language: More details here

Next features

  • SBML generator for a 2path metabolic network
  • Export metabolic path as a figure
  • FBA input file for a 2path metabolic network
  • Sesquiterpenoids predictor

Updated