LibSBMLSim mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
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Updated
Dec 14, 2021 - C
LibSBMLSim mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
In this project, I studied how the life time of chimera states increase due to plastic rule.
Sequential and Parallel Implementation of the Hodgkin-Huxley Neuron model.
Variant calling format (vcf) file genomics pipeline for HPC and cloud
A tool to extract mappable reads from various library preparation protocols.
GIMSAN: motif-finder with biologically realistic and reliable statistical significance analysis
semi-automated regular-unit counting using photos
A numerical study on the phenomenon of sympatric speciation in both sexual and asexual species, within a static habitat with intra-species competition.
A short repo of some C implementation of Computational Biology programs
Bio::PhyloXS - Core Bio::Phylo modules implemented in C
Chiang, S., Shinohara, H., Huang, J. H., Tsai, H. K. & Okada, M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. (2020).
MICA-aligner is a new short-read aligner that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core.
All UCSC Genome Browser source code that is under an open source license, mostly file format converters, command line tools and C libraries. A subset of the "kent" repo, updated every three weeks.
An improved compression tool for DNA sequences
ADAPT toolbox for Matlab - Analysis of Dynamic Adaptations in Parameter Trajectories
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.
Cross-platform GUI desktop application for making biological heatmaps
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka et al. (2018) J. Computer-Aided Molec. Design
10x Genomics Reads Simulator
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