Project 1 SRAVANTHI 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/trunk/validation/error-test- files/
To Provide SBGN validation in the Validator Plugin. 13 Earlier the Validator plugin was able to validate onMIMML and GPML format, Hence I have enhanced thefunctionality and provided the validation for SBGN formattoo.● 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).