https://happykhan.com Personal website of Nabil-Fareed Alikhan. Bioinformatician. Microbial genomics. https://happykhan.com/posts/qc-read-classification https://happykhan.com/posts/qc-read-classification Mon, 11 Nov 2024 00:00:00 GMT One of the things to help us understand what's in our data is to classify the reads using Kraken2. We can use Kraken2 to classify reads against a database of known sequences. This is a quick way to get an idea of what is in our data. We can then visualise the results in another tools like Krona or Pavian. https://happykhan.com/posts/five-lazy-grant-tips https://happykhan.com/posts/five-lazy-grant-tips Thu, 17 Aug 2023 00:00:00 GMT I've been meaning to write a comprehensive guide to grant writing but it's a tall ask. Here's a lazy "5 tips for better grant writing". https://happykhan.com/posts/intro-mlst-ecoli https://happykhan.com/posts/intro-mlst-ecoli Sun, 04 Jun 2023 00:00:00 GMT Multi-locus sequence typing (MLST) is a molecular typing method used to characterize bacterial strains, including E. coli. It involves sequencing multiple housekeeping genes and assigning unique allele numbers to variations in these genes. By comparing the allelic profiles, known as sequence types (STs), it becomes possible to infer the genetic relatedness and population structure of E. coli isolates. MLST has been instrumental in understanding the epidemiology, transmission dynamics, and evolut https://happykhan.com/posts/one-health-many-definitions https://happykhan.com/posts/one-health-many-definitions Mon, 13 Mar 2023 00:00:00 GMT After reading too many publications and proposals I do not understand the relationship between one health, and antimicrobial resistance and microbial genomics. I write this as an exercise for myself, hoping to clarify these concepts and their interdependence. This may be of interest to you too. https://happykhan.com/posts/mj3-vs-mj4 https://happykhan.com/posts/mj3-vs-mj4 Sun, 13 Nov 2022 00:00:00 GMT Midjourney is a proprietary artificial intelligence program that creates images from textual descriptions. You interact with the Midjourney bot on Discord. There is a free trial, but ultimately Midjourney is a paid service. There is a choice of plans to choose from. There are alternative software such as the free Craiyon (formerly DALL-E Mini), and freemium DALL-E and DALL-E 2. There is also the open source (and free) Stable diffusion that you can run on your own hardware. https://happykhan.com/posts/binfie-guide-serovar https://happykhan.com/posts/binfie-guide-serovar Mon, 31 Oct 2022 00:00:00 GMT A practical guide for bioinformaticians to understand Salmonella serovars, antigenic formulae, and serotyping methods. https://happykhan.com/posts/what-is-mastodon https://happykhan.com/posts/what-is-mastodon Fri, 28 Oct 2022 00:00:00 GMT (Skip ahead if you know how the internet works) https://happykhan.com/posts/rmlst-in-acinetobacter https://happykhan.com/posts/rmlst-in-acinetobacter Sun, 09 Oct 2022 00:00:00 GMT In the previous post, I describe rMLST (Jolley et al. 2012) as a ready and able alternative for species without existing MLST schemes. https://happykhan.com/posts/supp-methods-for-rmlst-acineto https://happykhan.com/posts/supp-methods-for-rmlst-acineto Fri, 07 Oct 2022 00:00:00 GMT These are some notes for how to install software and fetch the data required for the rMLST comparison in Acintobacter. https://happykhan.com/posts/support_for_rmlst https://happykhan.com/posts/support_for_rmlst Sat, 01 Oct 2022 00:00:00 GMT There is a follow up post where I dive into the usage of rMLST and apply it futher to Acinetobacter. https://happykhan.com/posts/drawing-phylogenetic-trees-with-microreact https://happykhan.com/posts/drawing-phylogenetic-trees-with-microreact Tue, 30 Aug 2022 00:00:00 GMT I make a lot of phylogenetic trees, and I have used a lot of different programs. In this post, I want to show you how to get the most out of the online visualization tool, Microreact, so you can draw publication ready figures. We will make a figure like this: https://happykhan.com/posts/the-process-of-transforming-data https://happykhan.com/posts/the-process-of-transforming-data Thu, 25 Aug 2022 00:00:00 GMT Continuing from last time, what is bioinformatics, we are discussing which topics we need to know to understand bioinformatics. As per our definition, https://happykhan.com/posts/text-to-image-with-stable-diffusion https://happykhan.com/posts/text-to-image-with-stable-diffusion Tue, 23 Aug 2022 00:00:00 GMT Stability.ai has just publicly released an open source text to image AI that you can download and run on your local consumer GPU. From the github: https://happykhan.com/posts/abstraction-in-computer-science https://happykhan.com/posts/abstraction-in-computer-science Mon, 22 Aug 2022 00:00:00 GMT You might have heard that the language of computers is binary (zeros and ones). You may have then wondered why when you using any of your devices there is nary a zero or one in sight. How do these devices that take our words and do anything useful? After all, a computer is a machine and has no understanding of anything. https://happykhan.com/posts/what-is-bioinformatics https://happykhan.com/posts/what-is-bioinformatics Sun, 21 Aug 2022 00:00:00 GMT I work in the field of microbial genomics; we are interested in the genome of microbes. I specialise in using computers to analyse genomes. They call me a bioinformatician. These days, these skills are in demand. Sometimes people ask me what they would need to know to do what I do. I find it difficult to explain, because I did not do a degree in Bioinformatics. The field changes quickly, so it is difficult to give a firm answer. https://happykhan.com/posts/phd-tips https://happykhan.com/posts/phd-tips Tue, 05 Jul 2022 00:00:00 GMT When I was a doctoral student, I actively asked anyone I could for advice about academia and being a scientist. It has been seven years since my doctorate was awarded and thinking back, these were the five single most useful quotable pieces of advice I received. These were either advice given directly given to me by my professors, or recounted by fellow students. Many of these topics are very complex. I will touch on them only briefly here. https://happykhan.com/posts/my-wishlist-of-conferences https://happykhan.com/posts/my-wishlist-of-conferences Sat, 02 Jul 2022 00:00:00 GMT These are meetings that apply to my area of microbiology, genomics and bioinformatics. These include meetings I have attended in the past, and recommend. Or other meetings that I have heard that are good. https://happykhan.com/posts/ggtree-start https://happykhan.com/posts/ggtree-start Mon, 27 Jun 2022 00:00:00 GMT Here are some notes on how to use R (specifically the ggtree package) to draw phylogenetic trees. In this first section, I will show: https://happykhan.com/posts/self-sabotage https://happykhan.com/posts/self-sabotage Fri, 24 Jun 2022 00:00:00 GMT I saw an interesting video recently talking about Self Sabotage. It was talking about creative work generally, but I see a lot of scientists with these habits. They even tell me these are good habits! Without realizing that they are following the guidebook for "How to Self Sabotage". https://happykhan.com/posts/dark-secret-about-containers https://happykhan.com/posts/dark-secret-about-containers Thu, 23 Jun 2022 00:00:00 GMT If you talk to your friendly neighbourhood bioinformatician (Binfie) these days, you might hear them mention "containers", "docker", and "singularity". They'll talk about these as if these are the greatest things since PCR. I am not different; we've talked about containers at length on the Micro Binfie Podcast https://happykhan.com/posts/map-projections-in-r https://happykhan.com/posts/map-projections-in-r Fri, 20 May 2022 00:00:00 GMT In this example we will: https://happykhan.com/posts/advanced-map-making-in-r https://happykhan.com/posts/advanced-map-making-in-r Wed, 18 May 2022 00:00:00 GMT In this example we will: https://happykhan.com/posts/making-a-map-in-r https://happykhan.com/posts/making-a-map-in-r Sun, 15 May 2022 00:00:00 GMT I recently made a map in R showing our SARS-CoV-2 collaborations. I thought that it came out really well and maybe other people might want to make a map (about anything). Here I will show you how to make a map in R that shows which countries have a monarchy, as a simple illustrative example. https://happykhan.com/posts/what-is-mamba https://happykhan.com/posts/what-is-mamba Sun, 10 Apr 2022 00:00:00 GMT If you use conda, you should use mamba. What is mamba then? The website describes it as: https://happykhan.com/posts/conda-install-r https://happykhan.com/posts/conda-install-r Fri, 25 Mar 2022 00:00:00 GMT Installing and controlling R and jupyter notebooks through conda is a much easier than installing it natively. I give a full explanation at the end as to why I do this way, but here's the method to start with. https://happykhan.com/posts/digital-platforms-for-reseacher https://happykhan.com/posts/digital-platforms-for-reseacher Sun, 13 Feb 2022 00:00:00 GMT Building an online presence can sound all very daunting, and you may think this means that you need to write a website, and start blogging, do social media, and spend lots of time on your digital persona. You do not. As scientists, we are lucky that there are a number of existing platforms that help us present the information I described (in the last post) as part of a digital introduction. I will outline the resources I feel are the most useful. They might require some effort to set-up but once https://happykhan.com/posts/better-online-presence-for-researchers https://happykhan.com/posts/better-online-presence-for-researchers Wed, 02 Feb 2022 00:00:00 GMT Over the years I have attended a number of seminars and courses that talk about online marketing, networking and personal branding. I have so far found that although these methods are effective, they are based on a presumption - There is an ultimate transaction that occurs between you and your audience/client/customer. This can be to buy something, refer us to someone else, endorse us, love us, “like-comment-subscribe.” This is at odds with how scientists interact. https://happykhan.com/posts/fasta-quick-cat https://happykhan.com/posts/fasta-quick-cat Sat, 24 Jul 2021 00:00:00 GMT Here is a Dirty python script to look in a directory, find fasta files (ext. ".fa"), and modify the header and merge them into a single fasta file. This will only look one directory down. It is not recursive. It won't even check if the directory records are directories, so it is pretty fragile. https://happykhan.com/posts/zip-on-hpc https://happykhan.com/posts/zip-on-hpc Thu, 16 Jul 2020 00:00:00 GMT The problem is to find all fastq files, and submit each one, one by one as a job to be gzipped. https://happykhan.com/posts/build-no-space https://happykhan.com/posts/build-no-space Wed, 23 Oct 2019 00:00:00 GMT You see an error message like this: https://happykhan.com/posts/timed-phylo-with-bactdating https://happykhan.com/posts/timed-phylo-with-bactdating Fri, 16 Aug 2019 00:00:00 GMT You want to calculate the time to most recent common ancestor (tMRCA) and dates for internal splits for a given phylogeny. BactDating is an R package available at: https://github.com/xavierdidelot/BactDating https://happykhan.com/posts/shortest-passwordless-ssh-tutorial https://happykhan.com/posts/shortest-passwordless-ssh-tutorial Fri, 23 Aug 2013 00:00:00 GMT I've used this thrice in three days, so I'm just keeping a copy for myself. https://happykhan.com/posts/brig-in-action https://happykhan.com/posts/brig-in-action Tue, 23 Aug 2011 00:00:00 GMT These are some of my favourite BRIG figures from recent Open Access publications. They are all really amazing and go far beyond what I thought was possible with the tool. I did not make these figures; all credit (and kudos) belong to the respective authors. https://happykhan.com/posts/getting-trnascan-to-work-on-linux https://happykhan.com/posts/getting-trnascan-to-work-on-linux Sun, 21 Aug 2011 00:00:00 GMT A friend/collaborator was having problems getting tRNAscan-SE to work on his Debian machine (I think it was Debian). We came up with a fix for it that I'd like to share.