pdf of the nrnb project

1. Project
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SRAVANTHI SINHA(NRNB STUDENT)
MARTIJN VAN IERSEL (MENTOR)

2. About the project
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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.

3. Stoichiometry Plugin
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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).

4. Features:
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● Generate a Stoichiometric Matrix for Process
Diagram .
● Can generate an “.txt” file containing Stoichiometry
Matrix .

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11. Improving validation through the PathVisio-
Validator Plug-in
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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/

13. To Provide SBGN validation in the Validator Plugin.
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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

14. Feature:
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● 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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18. THANK YOU
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