Repositories list

• emevo

  Public
  Simluate Embodied Evolution of Agents

  Jupyter Notebook

  •

  Apache License 2.0

  •0•2•0•0•Updated Apr 4, 2025Apr 4, 2025

• smartphone-robot-cad

  Public
  All 3D CAD and PCB design files for smartphone-robot project.

  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated Apr 4, 2025Apr 4, 2025

• BioinfoUgrp

  Public
  OIST Bioinfo user group

  hpcoistbioinformatics

  Shell

  •2•7•1•0•Updated Apr 4, 2025Apr 4, 2025

• NEXTNet

  Public
  C++ implementation of the NEXT-Net algorithm for efficient simulation of epidemics on complex networks

  C++

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Apr 3, 2025Apr 3, 2025

• BioinfoUgrp_UnixGoodies_Images

  Public
  Singularity images with cool Unix tools to be exported as modules in HPC clusters

  Dockerfile

  •0•3•3•0•Updated Apr 3, 2025Apr 3, 2025

• NEXTNetR

  Public
  C++

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

• optinist

  Public
  calcium imaging pipeline tool

  neurosciencecalcium-imaging

  TypeScript

  •

  GNU General Public License v3.0

  •13•39•50•9•Updated Apr 2, 2025Apr 2, 2025

• iSciComp

  Public
  JupyterBook: Introduction to Scientific Computation

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

• LuscombeU_CodingTheTreeofLife

  Public
  Python

  •1•0•0•0•Updated Mar 28, 2025Mar 28, 2025

• Physics-of-Behavior-Tutorials

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Mar 28, 2025Mar 28, 2025

• nf-core_configs

  Public
  Config files used to define parameters specific to compute environments at different Institutions

  Nextflow

  •

  MIT License

  •299•0•0•1•Updated Mar 27, 2025Mar 27, 2025

• smartphone-robot-android

  Public
  Android development for smartphone-robot

  Java

  •1•0•3•0•Updated Mar 24, 2025Mar 24, 2025

• LuscombeU_Oikopleura_genome_assemblies

  Public
  List of github links for Oikopleura genome assemblies

  0•1•0•0•Updated Mar 19, 2025Mar 19, 2025

• VisualStimulation

  Public
  matlab gui for vstim with psychophysics toolbox

  Jupyter Notebook

  •0•2•0•0•Updated Mar 17, 2025Mar 17, 2025

• LuscombeU_nfcore_pairgenomealign_fork

  Public
  Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

  Nextflow

  •

  MIT License

  •4•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• LuscombeU_BAR12_assembly

  Public
  0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

• LuscombeU_OSKA2016_rescaffolding

  Public
  Rescaffolding of the OSKA2016 genome assembly

  Shell

  •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

• TER-MT-DB

  Public
  The Termite Mitogenome Database. Centralization of termite mitogenomes and assignation of unique identification code.

  Other

  •1•0•0•0•Updated Mar 1, 2025Mar 1, 2025

• NEXTNetPy

  Public
  Python wrapper for the NEXTNet library for efficient simulation of epidemics on complex networks

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• LuscombeU_fork_of_FASTGA

  Public
  Local fork of https://github.com/thegenemyers/FASTGA – Pairwise whole genome aligner

  C

  •

  Other

  •8•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• plessy_nf_GenomicBreaks

  Public
  Draft Nextflow pipeline to convert alignment files and extract basic stats.

  Nextflow

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• Oikopleuradioica_genomeannotation

  Public
  Genome annotation of Oikopleura dioica from different geographical locations

  Shell

  •0•1•1•0•Updated Feb 8, 2025Feb 8, 2025

• SallanU_impressiontray

  Public
  Dental impression tray for animals (Wibisana et al., 2024)

  MIT License

  •0•1•0•0•Updated Jan 6, 2025Jan 6, 2025

• LaTeX-template-lab-rotation-proposal

  Public
  LaTeX Template for the OIST Lab Rotation Proposal

  TeX

  •

  MIT License

  •2•0•0•0•Updated Dec 23, 2024Dec 23, 2024

• LaTeX-template-lab-rotation-report

  Public
  LaTeX Template for the OIST Lab Rotation Report

  TeX

  •

  MIT License

  •3•0•0•0•Updated Dec 23, 2024Dec 23, 2024

• plessy_pairwiseGenomeComparison

  Public
  Draft workflow for pairwise genome comparison. We recommend you use the new nf-core version instead: https://nf-cor.e/pairgenomealign

  bioinformaticsgenomicsnextflow+ 2comparative-genomicswhole-genome-alignment

  Nextflow

  •3•5•2•0•Updated Dec 18, 2024Dec 18, 2024

• LuscombeU_stlpreprocess

  Public
  Download and pre-process genomes for the Scrambling in the Tree of Life project

  genomedownloadfilter+ 2scramblingoist

  Nextflow

  •

  MIT License

  •0•0•2•0•Updated Dec 18, 2024Dec 18, 2024

• TER-UCE-DB

  Public
  The Termite UCE Database. Centralization of termite UCE data and assignation of unique identification code.

  Other

  •2•3•0•0•Updated Dec 12, 2024Dec 12, 2024

• FastAndExactSimulationsOfStochasticEpidemicsOnStaticAndTemporalNetworks_arxivSI

  Public
  Supplemental information for "Fast and exact simulations of stochastic epidemics on static and temporal networks" on the arXiv

  0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• iridophore-automeasure

  Public
  Python code for automated measuring of iridophore crystals from TEM images

  Python

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024