Bioinformatics and other bits -
Background The increased price of RAM since 2025 has led to the rise in cost of many computer hardware components including graphics cards (GPUs) that rely heavily on VRAM for performance in both AI workloads and gaming. The R9700 Pro is a professional level GPU designed for use specifically for local AI inference, large language model (LLM) development, and content creation (i.e. 3D rendering).…
Background Bokeh can be used to make a wide variety of interactive plots. Here we use it to plot an interactive phylogenetic tree. We skip the more complicated part of tree drawing by using the Biopython Phylo module to read a newick tree and then get the tip coordinates from the tree object. From here it’s a simple matter of connecting the tips with the branches and adding labels and so on. This…
Background The 16S rRNA gene is present in all bacteria and contains both highly conserved and hypervariable regions. The conserved regions allow for the design of universal primers that can amplify the gene across a wide range of bacteria and archaea. The hypervariable regions (e.g., V1-V9) provide species-specific sequences that can be used to distinguish between different taxa. This is a widely…
Background A Minimum Spanning Tree (MST) is a concept from graph theory. Given a connected, undirected graph with weighted edges, an MST is a subset of the edges that connects all vertices together, without any cycles, and with the minimum possible total edge weight. While MSTs and phylogenetic trees both deal with the concept of connecting nodes in a graph, their purposes are different.…
Background Previously we looked at a convenience function for drawing and colouring phylogenetic trees with ggtree . This post contains an updated version of this function with some improvements. Recall that the appropriate meta data is provided as a data.frame object with row names matching tip names of the tree. The first column in cols is used for the tip colors. You also need to provide…
Background PubMLST, or Public databases for Molecular Typing and Microbial Genome Diversity, is a web-based platform that provides access to databases of microbial genetic sequences. It is primarily used for microbial typing, strain comparison, and epidemiological studies. The primary purpose of PubMLST is to facilitate the standardization and sharing of microbial sequence data. The databases…
Background Performing phylogenetic analysis with whole or core genome sequences maximizes the information used to estimate phylogenies and the resolution of closely related species. Usually sequences are aligned with a reference species or strain. However genome alignment is a process that does not scale well computationally. Even for small numbers of genomes it can be time consuming. Here are two…
Background Qt is a popular GUI toolkit for writing desktop applications. It has bindings for Python using either PySide2 or PyQt5 (which use essentially identical syntax). QTableView is the default class for table representations. It uses a QAbstractTableModel as the data source class. These can be sub classed to use whatever data backend you want. Here is some code using a pandas DataFrame as the…
Background There are lots of tools for finding specific genes inside genome sequences. The well established technique is to blast the query gene sequence to your own (the target). You generally need to use some threshold of percentage identity and coverage of the sequence to filter results. Here is a method in Python that uses blast to search a genome sequence in a fasta file. The sequence can be…
Background This is a somewhat altered version of code from an old post for downloading assemblies. GenBank provides access to information on all it’s assembled genomes via the assembly database. You have several options: download assemblies individually or in bulk via the website or the Entrez database search system using command line tools without the website. The later is good for large…
Background Previously we have looked at potential excess deaths in Ireland using data retrieved from RIP.ie. These represent quite accurate real-time all-cause mortality estimates that are an alternative to the official GRO data which lag behind by many months. It appears that the unusually high mortality signal present since around the start of 2021 continues to the present (December 2023). Below…
Background Previously we saw how to implement the Stable Diffusion image-to-image model using the Python diffusers library. There are plenty of websites now that offer AI image generation since it has become so popular. This post simply shows how you can make your own basic web dashboard with Panel that does something similar. The app allows someone to upload an image and generate new ones with a…
Background Previously we saw how to implement the Stable Diffusion text-to-image model using the Python Diffusers library, which is a library for state-of-the-art pre-trained diffusion models. It is hosted by huggingface. You can also use the image-to-image pipeline to make text guided image to image generations. This is essentially using one image as a template to make another. This would be…
Background OpenAIs whisper library is an effective and free means of doing speech-to-text analysis. It’s easy to use once installed and will output a set of files with timestamps for each sentence spoken. This is ideal for things like subtitling videos. It does not identify individual speakers however, so won’t group the conversation into passages according to who is speaking. This process is…
Background This is another aspect of the Stable Diffusion AI art library, covered previously . With ControlNet, users can ‘condition’ the generation of an image with a spatial context such as a segmentation map or a scribble. That is, you can weight the model to produce images that are constrained to the form of another. We can turn a cartoon drawing into a realistic photo for example, or place…
Background Stable Diffusion is a text-to-image model trained on 512x512 images from a subset of the LAION-5B dataset. You can implement this model on your own computer using the Python Diffusers library, which is a library for state-of-the-art pre-trained diffusion models for generating images, audio, and 3D structures. It is hosted by huggingface. The workings of the library are beyond the scope…
Background Whole genome sequencing (WGS) has emerged as a powerful tool in the field of public health, specifically in the context of pathogen strain typing. In order to categorize strains they are traditionally ‘typed’ using molecular methods like spoligotyping, MIRU-VNTR, RFLP or MLST. With WGS this can be accomplished at a superior resolution. WGS provides a detailed blueprint of virtually the…
Background Toyplot is a Python toolkit for plotting using HTML, SVG, and Javascript to create embeddable graphs. Toytree is based on toyplot and provides the ability to plot tree structures. It is a fairly minimalist package but can create useful tree plots that are better than some alternatives in Python. There are relatively few packages in Python that support rendering of phylogenetic trees…
Background Land fragmentation is the division of land holdings into discrete parcels that may be dispersed over a wide area. It is common in an agricultural context where a single farmer can own multiple parcels of contiguous (separated by roads, hedgerows or fencing) or non-contiguous land. For cattle farming this means animals could spend their time in different portions of land at different…
Background Computer-based disease spread models are frequently used in veterinary science to simulate disease spread. So called Agent based (ABM) or individual based models simulate each ‘agent’ in a network of contacts. Each agent could be an animal or other entity like a herd with certain behaviours. For example the agents can randomly contact each other and transmit disease. Running such a…