Making engaging conference presentations is a core part of research. For the recent Models of Consciousness 2025 Conference
I tried using the wonderful manim
software to create rich web-compatible animations as part of my presentation
.
This post describes how to generate similar slides using these tools.
updated 2025-10-14
If the hype is anything to go by, we’re entering a bright future where “Artificial Intelligence” will revolutionize medicine. This post provides some counterpoints to that hype, focusing on three issues:
- image (1024x1024) generated using Stable Diffusion
v2.0 (Linux, NVIDIA RTX 3090, 24GB)
prompt:
creepy humanoid AI doctor looking at medical files, Steps: 20, Sampler: Euler a, CFG scale: 7, Seed: 403319539, Size: 512x512, Model hash: de2f2560, Batch size: 4, Batch pos: 0
Document editing and report creation are key parts of any researcher’s workflow.
Thankfully, the tools to edit research documents have improved greatly over the last few years. While I used to write most documents with $ \LaTeX $, I’d now recommend that researchers use R Markdown
.
R Markdown allows the use of R code in a Markdown format and is also easily extended with features. For example, there is the excellent bookdown package which allows easy use of book formatting, bibliographies and cross-references with Markdown.
Setting up wireless networking can be a frustrating experience. Available commercial routers vary greatly in their implementation and standards compliance, meaning that compatability between brands of router can be problematic. There are also significant security issues in implementing WiFi netowrks, compounded by the fact that manufacturers rarely update their firmwares and dump support for routers after only a few updates.
Thankfully, there are now some great options for installing open-source software on routers so that it’s easier to have cross-compatibility and maintain up-to-date security patches. The two main open-source software stacks for WiFi routers are: OpenWRT and DD-WRT . In fact, they are related to each other, with OpenWRT providing a lot of code for DD-WRT. They also serve slightly different interests, OpenWRT is focused on providing an open and modular architecture, ideally allowing low-level access to the nuts and bolts of router features, while DD-WRT aims for simplicity of use with a consisten user interface. There are also other open firmwares with narrower scopes, for example Xwrt-Vortex , Tomato , Advanced Tomato and Gargoyle which provide enhanced features for a smaller subset of routers (generally based on the Broadcom chipsets).
this post was previously published on my old website, there’ll be a few of those older but useful posts that I’ll be migrating over in the next little while…
Molecules are beautiful things, intricate and infinitely variable. As part of research publications it can be useful to catch them from their best angles. This short post gives some tips on how to present molecules in publications.
Our model for today is Prostaglandin-F2α
Scientific computing increasingly involves handling large amounts of raw data. This is particularly the case for neuroimaging. With increases in processing speed outpacing storage speed, disk i/o has become a limiting factor in many computing applications, especially in multi-user systems.
For my consulting work with GreenAnt Networks , I was asked to build a high-speed disk array for scientific computing and virtual machine storage. This is a brief build log and performance test of the outcome.
Scientific publishing is undergoing a transition from corporate-controlled, for-profit publishing to more open models. While “Open-Access”, is part of this, there are a number of considerations important in true “Open Publishing”:
This post will focus on item (6) from above. While the choice of software tools is rarely considered as part of the Open Publishing ecosystem, it is of key importance. The economics of publishing are highly dependent on software. Open-source software enables the creation of open journals. This post will be followed-up with some discussion in the frture about how Open Publishing systems can be structured with incentives aligned to the best interests of the progress of science.
Sharing MRI data with colleagues can be a time-consuming exercise. The files are often large and data-sets need to be viewable in a flexible fashion. Rich features assist the communication of results, including:
While there are many software packages for running on the desktop, there’s nothing better than being able to point to a simple HTML link and open the scan data in a prepared format. Therefore, I went digging for an open-source package or library to display MRI renders and slices.
Below is the poster I will be presenting at the conference, it’s a metaphysical take on consciousness theory, which hopefully will trigger some debate.
please be patient while it loads, it’s a big SVG image!
LaTeX is a fantastic way to create and display print-ready scientific documents. There are a number of different ways to edit and produce LaTeX documents, which we’ll revist in a future post. In this post, I want to deal with one of the major issues that people find difficult with LaTeX: tables.
LaTeX can certainly produce any type of table you’d like to create, but it does so in a way that can be very difficult to follow visually.
