SRAVANTHI SINHA(NRNB STUDENT)MARTIJN VAN IERSEL (MENTOR)

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About the project

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.

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Stoichiometry Plugin

The Plugin is aimed at producing a Stoichiometry Matrix for a standard biological Process Diagram(i.e the causal sequences of molecular processes and their results).

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Features:

● Generate a Stoichiometric Matrix for Process Diagram .

● Can generate an “.txt” file containing Stoichiometry Matrix .

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Improving validation through the PathVisio-Validator Plug-in

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

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Created some of the pass/fail test-cases for Process Diagram, Activity Flow, Entity Relation Languages.

Refer: https://libsbgn.svn.sourceforge.net/svnroot/libsbgn/trunk/validation/error-test-files/

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To Provide SBGN validation in the Validator Plugin.

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

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Feature:

● 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).

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THANK YOU

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