MINVAL

Background

Genome-scale metabolic reconstructions are a compilation of stoichiometric reactions that can describe the entire cellular metabolism of an organism. Interrogation of metabolic reconstructions are generally carried through Flux Balance Analysis (FBA), an optimization method in which the biological sense of optimal solution is highly sensitive to thermodynamic unbalance. Research questions resolvable through FBA are dependent on proper reversibility and mass-charge balancing of the reactions. The two most popular implementations of FBA analysis are COBRA (Becker et al., 2007) and RAVEN (Agren et al., 2013) which operate as tools under the commercial MATLAB environment. These two implementations evaluates the proper balance based in the information supplied manually by the user for each metabolite included in the genome-scale metabolic reconstruction.

#Related work Our research group has recently published the minval package for the mass balance validation of stoichiometric reactions. It includes functions to evaluate mass balance and extract all reactants, products, orphan metabolites, metabolite names and compartments for a set of stoichiometric reactions, moreover specific functions to map compound names associated to the Chemical Entities of Biological Interest (ChEBI) database which minimizes the manual introduction of thousands of species in a genome-scale reconstruction. However, do not exist available packages for the evaluation of the load and the reversibility of stoichiometric reactions. This reduces the type of questions to be solved using FBA implementations available in R.

#Details of your coding project We want to empower the minval package including functions to evaluate the charge and reversibility balance of stoichiometric reactions. The main goals of coding project are:

1. Organize the charge and the formation gibbs energy associated for each metabolite in ChEBI database
2. Write and implement functions for charge balance validation
3. Write and implement functions for reversibility validation
4. Write the documentation for the implemented functions

#Expected impact We want minval becomes a fully useful package for the automatic validation of balance of stoichiometric reactions minimizing the manual introduction of thousands of species in a genome-scale reconstruction.

#Mentors Professor Dr. Andrés Pinzon

Bioinformatics and Systems Biology Group Institute for Genetics, National University of Colombia

Professor Dr. Janneth González

Experimental and Computational Biochemistry Javeriana University

#Tests Easy: install minval from CRAN repositories

Medium: extract all mass unbalanced reactions from the ‘glugln’ dataset.

Hard: write a function to compute the formal charge of a compound charge = VE - NE -BE2

#Solutions to Tests

Shrenik Jain

Test 2

Test 3

Additional feature