Name: Dr. Karan Kumar
Type: User
Company: RWTH Aachen University
Bio: Postdoc Researcher @iAMB-RWTH-Aachen
I'm a researcher specializing in Computational Biotechnology and Sustainable Biofuel Generation.
Twitter: theSamurai1997
Location: North Rhine-Westphalia, Germany
Blog: https://sites.google.com/view/karaniitg/home
Dr. Karan Kumar's Projects
The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
Open source code for AlphaFold.
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
The BiGG Models website server
Conda recipes for the bioconda channel.
Notebooks to introduce biopython
CMGfunc, functional protein annotation of bacterial proteins (Comparative Microbial Genomics functions)
High-level, high-performance, constraint-based reconstruction and analysis in Julia
Repository of tutorials for The COBRA Toolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
A tool to predict sub-networks from metabolic networks
Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
A Perl script allowing to identify CRISPR arrays and associated Cas proteins from DNA sequences
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
Repository for the HackBio'2021 Internship for Team Drug-Development-A
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
A MATLAB toolbox for exporting publication quality figures
Python implementation of FastSL
MM-PBSA method for GROMACS. For full description, please visit homepage:
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
Data and scripts for evaluations tests
A list of cool features of Git and GitHub.
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
Wish your friend/loved-ones happy birthday in a nerdy way.
iCOMIC is an open source genomic data analysis tool characterized by a user friendly GUI. It integrates many independent core workflows for Whole Genome/Exome Sequencing and RNA-Seq data analysis.
Whole-cell modeling tutorials
A set of graph/networks analysis functions in Octave. This fork focuses on MATLAB compatibility.
MDAnalysis is a Python library to analyze molecular dynamics simulations.