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
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.
GIMSAN: motif-finder with biologically realistic and reliable statistical significance analysis
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).
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.
ADAPT toolbox for Matlab - Analysis of Dynamic Adaptations in Parameter Trajectories
Variant calling format (vcf) file genomics pipeline for HPC and cloud
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.
A tool to extract mappable reads from various library preparation protocols.
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
Cross-platform GUI desktop application for making biological heatmaps
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
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.
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
10x Genomics Reads Simulator
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