Update: The exhibition was Highly Commended in Oxford’s The Vice-Chancellor’s Public Engagement with Research Awards 2019! [Link]
As part of outreach efforts, I have been involved with the exhibition “Dimensions: The Mathematics of Symmetry and Space” at the Ashmolean Museum. This exhibition is a great opportunity to explore a selection of the Ashmolean’s impressive collection from a mathematical (but very accessible) point of view.
Continue readingTraceback (most recent call last):
ZeroDivisionError: integer division or modulo by 0We’ve all been there. You’ve written your code, tested it out on some toy data and then when you make the move to the real data, there was something you didn’t expect.
Maybe some samples have been truncated to zero. Maybe the input arrays are the wrong shape. Suddenly your code comes crashing down around you, and you’re left thinking: well how could I have known that was going to happen? I can’t test everything
Continue readingThe idea of bacterial superpowers is perhaps most associated with superbugs: the terrifying, drug-resistant bacterial strains that appear ever more frequently in news reports. While the notion of a world where antibiotics no longer work is chilling, this blog post will focus on a more positive aspect of the bacterial domain.
One of the more “niche” bacterial superpowers is magnetotaxis: the ability of certain bacteria to align their motion to the Earth’s magnetic field. This phenomenon was first reported in 1963 by Salvatore Bellini in the University of Pavia. While observing bog sediment under the microscope, he noticed a set of bacteria orienting themselves in the same direction: towards the Earth’s magnetic North pole. He dubbed these gram-negative bacteria “magnetosensitive”, or “batteri magnetosensibili”, but the discovery went largely unnoticed by the international scientific community [1]. The name “magnetotactic bacteria” (MTB) was introduced about a decade later, when Richard Blakemore reported the same phenomenon for bacteria found in marine sediments [2]. Through transmission electron microscopy, Blakemore was also able to capture the cellular feature that gives MTBs their unusual abilities: a rod-like structure of membrane-bound, iron-rich inorganic crystals, called magnetosomes. Later it was revealed that this structure is supported by a dedicated cytoskeletal system, which keeps it rod-shaped and prevents the aggregation of magnetosomes [4]. Magnetotaxis then results from the combination of the passive alignment of the cell to the Earth’s magnetic field, and flagellar motion. Continue reading
Over the last decade, single-threaded CPU performance has begun to plateau, whilst the number of logical cores has been increasing exponentially.
Like it or loathe it, for the last few years, python has featured as one of the top ten most popular languages [tiobe / PYPL]. That being said however, python has an issue which makes life harder for the user wanting to take advantage of this parallelism windfall. That issue is called the GIL (Global Interpreter Lock). The GIL can be thought of as the conch shell from Lord of the Flies. You have to hold the conch (GIL) for your thread to be computed. With only one conch, no matter how beautifully written and multithreaded your code, there will still only be one thread will be executed at any point in time.
In my new research project, I investigate Non-alcoholic fatty liver disease (NAFLD). This term describes a variety of conditions that are associated with fatty livers. While the early stages of this disease are not harmful, it can lead to cirrhosis (Cirrhosis is the scaring of liver tissue that prevents a liver to function properly). Ultimately, if a liver stops working it can be fatal unless treated, for example, with a liver transplant. NAFLD is the most common liver disease in developed countries and is expected to become the leading cause of liver transplant by 2020 [1].
The disease progresses in four stages: Continue reading
In cheminformatics, there are many possible ways to encode chemical data represented by small molecules and proteins, such as SMILES, fingerprints, chemical descriptors etc. Recently, utilising graph-based methods for machine learning have become more prominent. In this post, we will explore why representing molecules as graphs is a natural and suitable encoding. Continue reading
One of the ways to make your code more robust to unexpected input is to develop with boundary cases in your mind. Test-driven code development begins with writing a set of unit tests for each class. These tests often includes normal and extreme use cases. Thanks to packages like doctest for Python, Mocha and Jasmine for Javascript etc., we can write and test codes with an easy format. In this blog post, I will present a short example of how to get started with doctest in Python. N.B. doctest is best suited for small tests with a few scripts. If you would like to run a system testing, look for some other packages!
Nowadays, biological research science spins around health: Cancer. Neuroscience. Immunology. Pharmacology. And many more health-related areas which are being deeply studied. It seems that everyone is keen to spend their lives looking for the cure of cancer or Alzheimer. What a drag! For this reason (and also to show that research in less popular and less founded sectors can also improve significantly human lives), I have decided to write about something completely different: plant microbiome!
Indeed, I am going to write about bacteria. And no, they are not related to health at all. These bacteria live the soil and infect plants. However, they are not “bad”. Actually, they favour the plant’s growth and development. This is possible thanks to a fascinating process which finishes (ALERT SPOILER!!) with the bacteria transforming the atmospheric nitrogen into ammonia that can be used by the plant (nitrogen fixation).
The process starts with some kind of small talk between Rhizobium (the bacteria) and the legume (the plant): Legumes secrete compounds through their roots that the bacteria living close by can detect. In response to this stimulus, bacteria approach the root hairs of the plant and attach and secrete lipo-chitooligosaccharides known as Nod factors.
It continues with some action: The plants sense the Nod factors, which induce the root hairs curling and trapping the bacteria. The bacteria continue to grow and eventually form an infection thread whose growth allows the bacteria to reach other plant cells.
And it finishes with a happily ever after ending: A structure called a nodule is formed. The bacteria in the nodule form an organelle called the symbiosome, within which the bacteria differentiate to a state called bacteroid. In this stage, the bacteroid fixes nitrogen for the plant.
I know… Everything has happened too fast (the process can take 1 – 2 weeks). And I have not been bothered to explain it in detail so you can enjoy reading this amazing review: https://www.ncbi.nlm.nih.gov/pubmed/23493145
But wait! I almost forget to say why is worth studying this… The point is that plants need nitrogen to grow and they cannot use atmospheric nitrogen. Therefore, the more nitrogen they receive from the bacteria, the more they will grow. Consequently, we may increase the quantity of food available by improving this process.
Vim is great. Despite its steep learning curve , it has many advantages and many loyal Vim followers will tell you that you should force yourself to use it.
Personally I started using Vim when I was ssh-ing into the group servers or into my computer in department. In such scenarios, I could not open the IDEs with the nice GUIs 🙁 However, as time passed, Vim started to grow on me. Now, I can list a few reasons why I think it is great, for example, it requires a small amount of memory to run, has a short start up time and can handle large files pretty well.
Although, I am definitely not a Vim expert, I will tell you about some of the things I have added to my .vimrc. The .vimrc file is very handy for containing all your favourite settings, such as key mappings, custom commands, formatting and syntax highlighting. The file uses vimscript which is a programming language in itself. However, there is a lot of help online that tells you with what lines to add to your .vimrc. I would recommend installing Vundle which is a Vim plugin manager.
Here I will list some cool things that I have discovered you can do with your .vimrc. It has certainly made my life a bit nicer.
.vimrc " Enable folding set foldmethod=indent set foldlevel=99 " Enable folding with the spacebar nnoremap <space> za
Alternatively, you can install the Vim plugin SimpylFold.
" PEP indentation au BufNewFile,BufRead *.py \ set tabstop=4 \ set softtabstop=4 \ set shiftwidth=4 \ set textwidth=79 \ set expandtab \ set autoindent \ set fileformat=unix
You can also install the Vim plugin vim-flake8 which is a static syntax and style checker for Python source code. It shows errors in a quickfix window and lets you jump to their location inside your code.
:set nu .vimrcGenerating low-energy molecular conformers is important for many areas of computational chemistry, molecular modeling and cheminformatics. Many tools have been developed to generate conformers, including BALLOON (1), Confab (2), FROG2 (3), MOE (4), OMEGA (5) and RDKit (6). The search algorithm implemented in these tools can be broadly classified as either systematic or stochastic. These algorithms primarily focus on generating geometrically diverse low-energy conformers. Here, we are interested in finding lowest energy conformation of a molecule instead of achieving geometric diversity and Bayesian optimization is used to find the lowest energy conformation (7). Continue reading