Dedicated VIDEO TUTORIALS for each module are appropriately placed in various sections of this documentation. They can be accessed by clicking on   icon on the right extreme of titles of various sections. All these video tutorials alongwith more module specific videos are also available on each of the module's execution page itself. We hope that this documentation coupled with the module specific video tutorials will act as a suitable guide to your experience with iVikodak.

A manual of standard operating procedures for choosing appropriate modules of iVikodak may be downloaded HERE

A major limitation of the current methods for function prediction is the inability to account for the constituents of a metabolic pathway. In other words, a metabolic pathway might be effected by the joint expression of over 30 genes/enzymes, but mere expression/presence of 1-5 genes/enzymes might not effect the expression of the associated pathway. It is thus crucial to define a parameter for filtration of pathways based upon the proportion of various pathway associated genes/enzymes expressed by the microbiota.

Considering the need for such a parameter, Pathway Exclusion Cut-off (PEC) value has been defined in both algorithms of Global Mapper. PEC value is defined as the minimum percentage of genes/enzymes belonging to any metabolic pathway, that must be expressed by a given microbiota for tagging that pathway as being expressed by the microbiome. For example, a PEC value of 30 would mean that a given microbe/microbiota must express atleast 30% of genes/enzymes belonging to any metabolic pathway for considering that pathway as being expressed by that microbe/microbiome.

Both algorithms of Global Mapper have been developed in such a way that apart from providing the raw hits (where raw hits refer to the most inclusive criteria wherein even the expression of single enzyme/gene is considered for presence of a metabolic pathway) they provide the KEGG pathway (all three level) expression profiles for the microbial abundance data at various PEC values (50-90) as well.

Global Mapper is the heart of iVikodak. It is Global Mapper that infers the functional profiles for microbial environments using 16S microbiome datasets. Given that a set of microbes in an environment can either exist as a consortium (i.e. with co-metabolic associations) or they might thrive independently, Global Mapper module provides to end-users the choice of two distinct algorithmic work-flows for functional inferences viz. 'Co-metabolism' and 'Independent Contributions'.
In addition to functional inference, Global Mapper has been upgraded to perform Ordination, Network analysis, Top function analysis, Core-functional analysis, Differentiating function analysis in an integrated fashion.

It is worth noting that the functional inferences are no longer limited to KEGG database, but have been extended to KEGG, PFAM, TIGRFAM, COG, and inferences for KOs and Modules are planned as well.

To further strengthen the utility of iVikodak, there is no limit on the amount of metadata that can be supplied to Global Mapper (functional inferences and related analyses will be performed for all environments corresponding to the metadata).

And we understand the importance of good and interpretable graphics and visualizations, so an honest attempt has been made to generate high quality graphic visualizations for all results.

ISFA - ISFA module of iVikodak is developed to enable comparative metagenomics using the inferred function profiles (generated using Global Mapper module). ISFA uses wilcoxon and (or) kruskal wallis tests on a pair of or multiple environments supplied by the user (through metadata). Based on the differentiating functional profiles obtained using the statistical tests so performed, ISFA provides the end users with various analytical insights:

PEC Profiles

Heatmap of functions that are observed to be differentiating at all PEC thresholds

Cladogram

A cladogram (visualized using Sankey plot), highlighting the hierarachical view of differentiating functions (at all levels)

Contributors Profile

A filtrable, sortable and exportable tabulated view of microbes that contribute towards the differentiating functions, alongwith their median contributions towards the functions in each individual environment

and more..

Local Mapper - Local Mapper module of iVikodak is a logical extention to Global Mapper and ISFA. Using Local Mapper, end users can zero-in to some specific function of interest (like a Core Function from Global Mapper or some important differentiating function from ISFA) and deeply probe that particular function for various environments available in the data. Local Mapper is specifically designed to enable 'individual function' level analytics for all samples/ classes available in an metagenomic environment. Following are some key insights obtained using Local Mapper:

Enzyme Profiles

Enzyme abundance profile, of the enzymes constituting the given function, are generated for all samples of all environments, and visualized as heatmaps as well

Dendrobars

Dendrobar plots, highlighting the key contributing microbes (and their taxonomic lineage) towards the specific function in each environment of the data. Corresponding textual files (tables) are also generated

KEGG Maps

Special KEGG-Map files are generated for visulaizing the pathway of interest as 3D KEGG diagram or colored KEGG diagram

and more..

Recreator - Recreator module of iVikodak enables permanent retention, portability, and sharability of the personal Dashboards.

iVikodak follows a unique 10-character alphanumeric JOB ID driven job handling and performs all analyses without seeking any personal information. Coupled to that, each JOB ID is subsequently tagged to a personal Dashboard, which packages and presents all visualizations and results. All the dashboards, corresponding to user-specific job IDs, can be downloaded as unique '.dash files' which can be retained and shared by the end-users for future re-explorations. The 'dash files' can be uploaded to the specifically developed 'Recreator' module of iVikodak, which recreates an entire dashboard using the unique dash file.