Software Open Access

MitoLink: A Generic Integrated Web-based Workflow System to Evaluate Genotype-Phenotype Correlations in Human Mitochondrial Diseases: Observations from The GenomeAsia Pilot Project

Kumar, Rakesh; Bhardwaj, Anshu

MitoLink is a generic, scalable and modular web-based workflow system developed to study genotype-phenotype correlations in human mitochondrial diseases. MitoLink integrates applications for assessment of genomic variation and currently houses genome-wide datasets from Genome Asia Pilot project, gnomAD, ClinVar and DisGenNet. In this study, a reference list of nearly 3975 proteins (both nuclear and mitochondrial encoded) with mitochondrial function is reported. This protein set is mapped to disease associated variants in the Genome Asia Project and DisGenNet and evaluated for pathogenicity as defined by ClinVar. Observations of shared genetic components in potential comorbidities are discussed from gene-disease network in Asian population, however, the platform is generic and can be applied to any population dataset. MitoLink is a unique customized workflow system that allows for systematic storage, extraction, analysis and visualization of genomic variation to understand genotype-phenotype correlations for mitochondrial diseases. Given the modularity of tool and data integration, MitoLink is a scalable system that can accommodate a diverse set of applications linked via standard data structure within the framework of Galaxy. MitoLink is built on FAIR principles and supports creation of reproducible workflows towards understanding genotype-phenotype correlations across several disease phenotypes globally.

Steps for installing MitoLink VM :-

User need to install VirtualBox (Version 6.1.26 r145957 (Qt5.6.2)) (download link https://www.virtualbox.org/wiki/Downloads) with its extension packs and proceed to import MitoLink Galaxy Virtual Machine (VM) "mitolink_vm".
User can take help from https://www.virtualbox.org/manual/ch01.html#intro-installing or https://www.virtualbox.org/manual/ch02.html to install the VM on their system (Windows, MacOS, Linux).

User should download MitoLink Galaxy VM file "mitolink_vm.ova" file for import VM appliance in VirtualBox. It has file size of ~15.8 GB.
The VM is based on Ubuntu 20.04 x64 with configuration 1 processor, 2 GB RAM, 60 GB HDD disk space, two network (Bridge,NAT), 128MB Video memory and 3D acceleration.
User can take help from https://www.virtualbox.org/manual/ch01.html#ovf-import-appliance or https://www.virtualbox.org/manual/ch08.html#vboxmanage-import to import OVA formatted VM appliance.

MitoLink VM admin username and password are 'mitolink' for login, MySql and Mitolink Galaxy web GUI.
 

Funding from SERB Early Career Research Award (ECR/2017/001077)
Files (16.9 GB)
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mitolink_vm_v1.1.ova
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