Project 1SRAVANTHI SINHA (NRNB STUDENT) MARTIJN VAN IERSEL (MENTOR)
About the project 2 The Objectives of the project is to :• Develop a Stoichiometry Plugin for Pathvisio.• Improving validation through the PathVisio- Validator plug-in.• To Provide SBGN validation in the Validator -Plugin and to update SBGN Plugin – to deal with ‘Auxiliary Units’ issues.
Stoichiometry Plugin 3 The Plugin is aimed at producing aStoichiometry Matrix for a standard biologicalProcess Diagram(i.e the causal sequences ofmolecular processes and their results).
Features: 4• Generate a Stoichiometric Matrix for Process Diagram .• Can generate an “.txt” file containing Stoichiometry Matrix .
Improving validation through the PathVisio- Validator Plug-in 11 Created some new validation rules in schematron to check valdations like:• a logic arc should always connect to a logic gate, such as "OR" or "AND“• process nodes should have at least one input and at least one ouput pointing to the arcs• Whether a certain Glyph is allowed in PD,ER,AF languages
12 Created some of the pass/fail test-cases for Process Diagram, Activity Flow, Entity Relation Languages.Refer: https://libsbgn.svn.sourceforge.net/svnroot/libsbgn/tru
To Provide SBGN validation in the Validator Plugin. 13 Earlier the Validator plugin was able to validate on MIMML and GPML format, Hence I have enhanced the functionality and provided the validation for SBGN format too.• Now theValidator Plugin automatically selects the ruleset based on the format. Possible formats: GPML, MIMML, SBGN-PD,ER,AF
Feature: 14• we can simply choose to validate it, the plugin can understand which format it is and validates accordingly based on the format. (or)• We can explicitly validate the pathway against any of the Ruleset (choosing Ruleset manually).