Archive
2024
October
- October 25, 2024 » Plot a phylogenetic tree with bokeh and biopython
June
- June 4, 2024 » Bacterial species identification from WGS using 16S genes
May
- May 31, 2024 » Plot and colour a minimum spanning tree with networkx
- May 30, 2024 » An updated convenience function for ggtree with heatmaps
March
- March 29, 2024 » Calculate PubMLST sequence types using Python
- March 22, 2024 » Two quick ways of building a bacterial species phylogeny
January
- January 28, 2024 » Filtering a QTableView with QSortFilterProxyModel
- January 21, 2024 » Finding genes in a genome or assembly with Python
- January 19, 2024 » Fetch assemblies and associated biosample data using Entrez tools with Biopython
- January 5, 2024 » Excess mortality in Ireland still high in 2023
2023
December
- December 29, 2023 » A Panel app for image-to-image generation
- December 18, 2023 » image-to-image with Stable Diffusion in Python
November
- November 12, 2023 » Speech diarization with OpenAI whisper and pyannote.audio
September
- September 21, 2023 » Condition Stable Diffusion images with ControlNet
- September 19, 2023 » AI art with Stable Diffusion in Python
- September 15, 2023 » SNP clustering and type naming of pathogens from WGS
June
- June 18, 2023 » A phylogenetic tree viewer with PyQt and ToyTree
March
- March 22, 2023 » Simulate land parcels and fragmentation with geopandas
- March 19, 2023 » An individual based model of farm pathogen spread with Python/Mesa
- March 15, 2023 » Make a contact network from a geopandas geodataframe
January
- January 23, 2023 » Make networkx Delaunay graphs from geopandas dataframes
- January 14, 2023 » Using Molecular Nodes in Blender to visualise proteins
2022
December
- December 29, 2022 » Scrape dynamic tables in Python with Playwright
- December 21, 2022 » Can ChatGPT solve bioinformatic problems with Python?
- December 19, 2022 » DALLE-2 and AI generated art.
October
- October 15, 2022 » How to host your podcast with github
September
- September 8, 2022 » Excess mortality in Ireland is still high in 2022
August
- August 13, 2022 » Mapping the historical development of Tallaght
- August 7, 2022 » Plotting gridded quantitative data with geopandas - Irish forestry
- August 4, 2022 » Make regular grids from polygons with geopandas
- August 2, 2022 » Plot phylogenies with annotation in R using ggtree and gheatmap
April
- April 10, 2022 » Parallelize a function in Python that returns a pandas DataFrame
March
- March 28, 2022 » batchfilerename - A simple utility for batch file renaming
- March 20, 2022 » Using IGV inside Jupyter Lab notebooks
February
- February 23, 2022 » Scrape paginated tables in Python with beautifulsoup
January
- January 29, 2022 » Ireland mortality data from RIP.ie, updated for 2021
- January 12, 2022 » Pandemic restrictions have caused misery in low income countries
2021
November
- November 14, 2021 » High vaccination rates don't prevent transmission of SARS-CoV-2
- November 12, 2021 » Seasonality of SARS-CoV-2
October
- October 18, 2021 » Bacterial SNP detection with nanopore vs. illumina sequencing
September
- September 3, 2021 » Natural immunity to SARS-CoV-2
July
June
- June 19, 2021 » wgMLST vs the reference-align-SNP-calling method for M.bovis
- June 15, 2021 » Deaths in Ireland from RIP.ie - another look
- June 10, 2021 » A whole genome MLST (wgMLST) implementation in Python
May
- May 18, 2021 » Viewing the THOR dataset with Bokeh and Panel
- May 15, 2021 » The scale of US bombing in Southeast Asia revealed in the THOR dataset
February
- February 26, 2021 » A phylogenetic tree viewer with Qt and Toytree
- February 16, 2021 » A simple GIS plugin for Tablexplore
January
- January 28, 2021 » Ireland deaths in 2019/2020 compared to previous years
- January 25, 2021 » Daily deaths in Ireland from RIP.ie in 2019 and 2020
- January 20, 2021 » Visualizing Irish girls names since 1970
- January 15, 2021 » M. bovis spoligotyping from WGS reads
- January 11, 2021 » Linux application packaging and universal formats
2020
December
- December 23, 2020 » Detecting polymorphisms in the RD900 region of MTBC species
- December 19, 2020 » Tablexplore - a desktop tool for table analysis
November
- November 29, 2020 » Epidemics, PCR and the dangers of mass testing
- November 28, 2020 » Convert a multi-sample VCF to a pandas DataFrame
- November 15, 2020 » A network agent based infection model with Mesa
- November 10, 2020 » Find PFAM domains in protein sequences with Python
- November 2, 2020 » Covid-19 and T cell immunity
October
- October 28, 2020 » Estimating Irelands tree coverage with QGIS and GeoPandas
- October 18, 2020 » Build an exe using pyinstaller with GitHub Actions
- October 6, 2020 » A simple image gallery in Jekyll without plugins
September
- September 5, 2020 » An MHC-Class I binding predictor with sklearn, part 2
August
- August 18, 2020 » Ireland COVID-19 trend in positive rate
- August 15, 2020 » Predicting cross-reactive T cell epitopes in Sars-CoV-2
- August 6, 2020 » COVID tracking project - tests vs positive rates
July
- July 24, 2020 » Death causes in England and Wales comparison - Winton Centre
- July 21, 2020 » Sequence alignment viewer with Qt/PySide2
- July 11, 2020 » Eurostat deaths from all causes dataset plots
- July 7, 2020 » pathogenie - A desktop application for microbial genome annotation
May
- May 19, 2020 » Fasta alignment from a multi sample VCF - a less terrible method
- May 12, 2020 » SNiPgenie - a tool for SNP site detection from NGS data
April
- April 28, 2020 » Simple MTBC regions of difference analysis with Python
- April 19, 2020 » Finding all amino acid mutations in SARS-CoV-2
- April 14, 2020 » A simple agent based infection model with Mesa and Bokeh
- April 7, 2020 » Create a fasta alignment from a multi sample VCF
- April 1, 2020 » COVID-19 ECDC data dashboard with Panel
March
- March 28, 2020 » COVID-19 ECDC data plots with Bokeh
- March 18, 2020 » Run bcftools mpileup in parallel with Python
- March 11, 2020 » Deploy a Python application with snapcraft
- March 2, 2020 » Model of the SARS-CoV-2 spike protein in Blender
February
- February 28, 2020 » Explore the SARS-CoV-2 spike protein sequences using Python tools
- February 18, 2020 » Updates to a genome annotation on the ENA via Webin-CLI
- February 5, 2020 » Plot fastq file metrics with Python
January
- January 30, 2020 » Compile windows exe files with MSYS2
- January 25, 2020 » A simple genome browser with Qt and dna_features_viewer
- January 6, 2020 » Interactive plots of World development indicators with Panel
- January 3, 2020 » Concurrent processes in PySide2/PyQt5 applications
2019
December
- December 14, 2019 » Genome annotation with BLAST, Prodigal and Biopython
November
- November 29, 2019 » Embed Bokeh plots in Jekyll markdown
- November 28, 2019 » Categorical region plots with geopandas
- November 15, 2019 » Choropleth maps with geopandas, Bokeh and Panel
- November 5, 2019 » Analysis of MTBC regions of difference with NucDiff
October
- October 20, 2019 » Rapid Average Nucleotide Identity calculation with FastANI
- October 13, 2019 » NucDiff for bacterial whole genome comparisons
September
- September 30, 2019 » Plotting global sea ice extent data with four different Python packages
- September 24, 2019 » Interactively view datasets with HoloViews
- September 15, 2019 » Javascript callbacks for linking bokeh plots to panel widgets
August
- August 31, 2019 » Retrieving genome assemblies via Entrez with Python
- August 12, 2019 » Accessing data from the PDB with Python
July
- July 22, 2019 » Bioinformatics on the Raspberry Pi 4
- July 11, 2019 » A sequence alignment viewer with Bokeh and Panel
- July 2, 2019 » Dashboards with PyViz Panel for interactive web apps
May
- May 17, 2019 » Predicting neoantigens
April
- April 4, 2019 » Make protein models with Blender
March
- March 20, 2019 » Sequence, gene and protein databases: are you confused?
February
- February 27, 2019 » Unknown proteins in Mycobacterium tuberculosis
- February 25, 2019 » Reading and writing genbank/embl files with Python
2018
November
- November 25, 2018 » Using epitopepredict for MHC binding prediction in Python
- November 12, 2018 » Create an MHC-Class I binding predictor in Python
October
- October 9, 2018 » Creating a local RefSeq protein blast database
August
- August 14, 2018 » Create a bacterial GFF from a genbank file for BCFtools/csq
2017
July
- July 5, 2017 » DataExplore - grouped plots in version 0.8.0
2015
December
- December 11, 2015 » Example: plotting miRNA abundance data (advanced)
September
- September 15, 2015 » Looking at the Titanic dataset
July
- July 18, 2015 » Zenodo and sharing your software
June
- June 14, 2015 » Educational software for data analysis
- June 11, 2015 » DataExplore Features
May
- May 30, 2015 » DataExplore Introduction