https://timingliu.org/post/ Recent content in Posts on Timing Liu Hugo -- gohugo.io en-us Copyright © Timing Liu {year}. All Rights Reserved. Please contact me for any errors Fri, 29 Aug 2025 00:00:00 +0000 https://timingliu.org/post/2025-08-29-part-ii-i-won-t-write-happy-poems/ Fri, 29 Aug 2025 00:00:00 +0000 https://timingliu.org/post/2025-08-29-part-ii-i-won-t-write-happy-poems/ https://timingliu.org/post/2025-08-29-part-i-white-stone/ Fri, 22 Aug 2025 00:00:00 +0000 https://timingliu.org/post/2025-08-29-part-i-white-stone/ https://timingliu.org/post/2025-08-10-goodbye/ Sun, 10 Aug 2025 00:00:00 +0000 https://timingliu.org/post/2025-08-10-goodbye/ Thoughts on palliatative care https://timingliu.org/post/2025-08-30-may/ Sun, 01 Jun 2025 00:00:00 +0000 https://timingliu.org/post/2025-08-30-may/ https://timingliu.org/post/2023-07-09-service-sunday/ Sun, 09 Jul 2023 00:00:00 +0000 https://timingliu.org/post/2023-07-09-service-sunday/ TL;DR: Let me know if I can be of any help. If my skills could be useful to you, drop me an email at timingliu[at]outlook[dot]com with the subject: Service Sunday (symbols translated to English to avoid spammers). I will build a running to-do list and help as much as I can. Undone tasks will be attended to in the subsequent weeks. If you are here because you messaged me via other means, rest assured that your request will be taken care of, too. https://timingliu.org/post/2023-04-15-conference-at-new-orleans-arvo-2023/ Sat, 15 Apr 2023 00:00:00 +0000 https://timingliu.org/post/2023-04-15-conference-at-new-orleans-arvo-2023/ Association for Research in Vision and Ophthalmology (ARVO) https://timingliu.org/post/2023-04-15-why-i-am-still-in-healthcare/ Sat, 15 Apr 2023 00:00:00 +0000 https://timingliu.org/post/2023-04-15-why-i-am-still-in-healthcare/ Why medicine is still the top career choice for me https://timingliu.org/post/2023-03-12-dream-pawnshop/ Sun, 12 Mar 2023 00:00:00 +0000 https://timingliu.org/post/2023-03-12-dream-pawnshop/ A short story about that pawnshop for dreams https://timingliu.org/post/2022-11-13-the-pursuit-of-happyness/ Sun, 13 Nov 2022 00:00:00 +0000 https://timingliu.org/post/2022-11-13-the-pursuit-of-happyness/ Focusing on well-being maintenance https://timingliu.org/post/2022-08-03-a-case-for-the-full-stack-clinicians/ Wed, 03 Aug 2022 00:00:00 +0000 https://timingliu.org/post/2022-08-03-a-case-for-the-full-stack-clinicians/ Build a community of clinicians with various skills https://timingliu.org/post/2022-08-03-thoughts-about-leaving-medicine/ Wed, 03 Aug 2022 00:00:00 +0000 https://timingliu.org/post/2022-08-03-thoughts-about-leaving-medicine/ TL;DR: I am not leaving yet https://timingliu.org/post/2022-01-18-my-principles-of-entrepreneurship/ Tue, 18 Jan 2022 00:00:00 +0000 https://timingliu.org/post/2022-01-18-my-principles-of-entrepreneurship/ How to solve a problem worth solving https://timingliu.org/post/2022-01-01-engineering-my-way-to-engineering/ Sat, 01 Jan 2022 00:00:00 +0000 https://timingliu.org/post/2022-01-01-engineering-my-way-to-engineering/ Reflection on my engineering journey at Cambridge https://timingliu.org/post/2022-01-01-the-myth-of-being-self-made/ Sat, 01 Jan 2022 00:00:00 +0000 https://timingliu.org/post/2022-01-01-the-myth-of-being-self-made/ Without the support and inspirations from others, I will never be where I am https://timingliu.org/post/2021-12-25-full-stack-clinician-curriculum/ Sat, 25 Dec 2021 00:00:00 +0000 https://timingliu.org/post/2021-12-25-full-stack-clinician-curriculum/ https://timingliu.org/post/2021-12-19-setting-up-zenity-with-windows-python-go/ Sun, 19 Dec 2021 00:00:00 +0000 https://timingliu.org/post/2021-12-19-setting-up-zenity-with-windows-python-go/ Ask my computer to ask me questions https://timingliu.org/post/2021-08-27-let-s-be-emotionally-correct-instead/ Fri, 27 Aug 2021 00:00:00 +0000 https://timingliu.org/post/2021-08-27-let-s-be-emotionally-correct-instead/ We can discuss politically incorrect topics without hurting anyone if we are emotionally minded. https://timingliu.org/post/2021-08-21-problems-without-global-optima/ Sat, 21 Aug 2021 00:00:00 +0000 https://timingliu.org/post/2021-08-21-problems-without-global-optima/ We cannot find most solutions through discussions. https://timingliu.org/post/2021-08-05-personal-statement-that-got-me-into-cambridge/ Thu, 05 Aug 2021 00:00:00 +0000 https://timingliu.org/post/2021-08-05-personal-statement-that-got-me-into-cambridge/ Here is the personal statement that I used to apply to Cambridge. I removed sensitive information (about others) in []. Huge thanks to people1 who helped me proof-read this essay and I hope this helps you in pursuing your dreams. [INTRO] Medical science enthralls me for it integrates many fields to provide wide clinical applications: basic physical properties like nuclear decay are used in Tc99 to diagnose embolism. Each stage in the complex chemical reactions behind biological processes can be utilised to treat diseases. https://timingliu.org/post/2021-07-14-conda-command-to-live-by/ Wed, 14 Jul 2021 00:00:00 +0000 https://timingliu.org/post/2021-07-14-conda-command-to-live-by/ Export environment conda env export > environment.yml Recreate environment conda env create --name/--proxy xxx --file environment.yml https://timingliu.org/post/2021-06-27-my-first-paper/ Sun, 27 Jun 2021 00:00:00 +0000 https://timingliu.org/post/2021-06-27-my-first-paper/ My first paper is now published. It has been more than four years since I started on this project and I am thrilled to see its fruition. I remember asking myself this question in the year leading up to A levels: if I have only one year of life left, would I still want to work on this project? The answer was yes. As workaholic as it may sound, I hope my life could be part of some bigger cause - like improving the diagnosis of genetic diseases in this case. https://timingliu.org/post/2021-04-30-install-r-packages-on-an-offline-server/ Fri, 30 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-30-install-r-packages-on-an-offline-server/ Use renv to automatically manage installation and dependencies https://timingliu.org/post/2021-04-29-snp-analysis/ Thu, 29 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-29-snp-analysis/ ID naming TOPMED returns chr:pos:ref:alt. rsid REF:ALT to major:minor translation if (AF == MAF) => ALT = minor, REF = major SNP matching switching flipping SNP: chr:pos:alt:ref How do I know if it matches chr:pos:allele_1:allele_2 First: chr:pos are equivalent Second: Matching four scenarios If it matches, use the target variant id (often the variant in the plink files) as the new id. https://timingliu.org/post/2021-04-21-big-data-in-r/ Wed, 21 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-21-big-data-in-r/ Reading files vroom Skip columns: col_types = list(hp = col_integer(), cyl = col_skip(), gear = col_factor()) https://timingliu.org/post/2021-04-20-use-reprex-without-browsers/ Tue, 20 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-20-use-reprex-without-browsers/ The following code will generate a randomly named *_reprex.md file that can be copied for others. reprex::reprex( { library(tibble) library(purrr) library(dplyr) mutate(tibble(a=1),b = map(a, ~ tibble(c=1))) } , outfile = "reprex.html", html_preview=FALSE, session_info = TRUE ) https://timingliu.org/post/2021-04-15-debugging-python-with-vscode/ Thu, 15 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-15-debugging-python-with-vscode/ vscode tutorial create config file select python interpreter put stop points (you can add different conditions by right clicking) move to debug console for interacting with variables the variable will not show up unless you step in once how to add arguments https://timingliu.org/post/2021-04-12-book-review-share-your-work/ Mon, 12 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-12-book-review-share-your-work/ Learn in the public; share your progress https://timingliu.org/post/2021-04-11-how-i-read-history-books/ Sun, 11 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-11-how-i-read-history-books/ I divide history reading into two categories: micro and macro. The best example of macro history books is Homo Sapiens which is full of mental models applicable to different historical contexts and therefore our times. Microhistory include books that focus on individual experiences (like fictions), and they are used as wisdom-training tools. When reading these books, I pause and reflect: given the existing data, what would my next action be if I were the protagonist. https://timingliu.org/post/2021-04-10-theories-about-learning/ Sat, 10 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-10-theories-about-learning/ Facts, models, wisdom, insights, and practice https://timingliu.org/post/2021-04-08-base-r-notes/ Thu, 08 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-08-base-r-notes/ Many functions in base R has faded away from my daily use of R because of tidyverse and the paradigm to do as many operations as possible in a data.frame. Get the variable name deparse(substitute(variable)) Indexing and subsetting which to return a logical vector that can be used in [] for subsetting Tidyverse alterantive (notes for myself) Imagine that I have a list of data.frames (group_split split a dataframe into lists of dataframes by the value of column specified) https://timingliu.org/post/2021-04-08-learning-dt/ Thu, 08 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-08-learning-dt/ {DT} is a package to render html tables. It is an interface to the datatables javascript library. It should not be confused with the {data.table} package, which is a package useful for data wrangling. A similar package of the same purpose is {kableExtra}. I found that {kableExtra} is more suitable for making static tables, whereas {DT} is more suitable for making interactive tables. DT Adding captions DT::datatable(iris[1:10,],caption = htmltools::tags$caption( style = 'caption-side: top; text-align: center; color:black; font-size:200% ;','Table1: Iris Dataset Table') ) https://timingliu.org/post/2021-04-08-rmarkdown-notes/ Thu, 08 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-08-rmarkdown-notes/ This contains notes for Rmarkdown and markdown. All notes for markdown are generally applicable for Rmarkdown. markdown Footnote Rmarkdown Markdown extras Adding toggle <details><summary>toggle title</summary> toggle content </details> Image quality knitr::opts_chunk$set(dpi=300) Share html report A report should be self-contained. In xaringan, set self_cotained = TRUE in yaml and download html with Chrome, not Firefox. For DT, downloaded html from browser does not work - see here. https://timingliu.org/post/2021-04-08-string-processing-in-r/ Thu, 08 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-08-string-processing-in-r/ Case snakecase::to_any_case() help to fix the case of words - useful for converting between presentation data and processing data. Regex The regex in R is not 100% perl flavored. For example, escape character is \\ instead of \. I love the [{rev}](https://github.com/kevinushey/rex package). The most salient point that this package solves is on the interpretation of regex. When not to use regex Not all strings are interpreted as a regex. Sometimes, one needs to opt-in via a parameter in the function. https://timingliu.org/post/2021-04-08-the-bright-side-of-plots/ Thu, 08 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-08-the-bright-side-of-plots/ Font Font size Font format (e.g. subscripts) Font family Combine plots Helpful packages: Colours 3D rendering Rough plots It will be useful to consult Rmarkdown notes because I often use Rmarkdown to render ggplot. Font Font size Global adjustment (e.g. the default font size is small when rendering with Rmarkdown with ) theme’s basic size See individual adjustment here and also in this RStudio2021 conference talk and this https://timingliu.org/post/2021-04-08-working-with-na-in-r/ Thu, 08 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-08-working-with-na-in-r/ NA are necessary markers for missing data. However, Working with them can be tricky because of their special properties. Care should also be taken when reading in and presenting the data. Properties of NA Types There are different types of NA that are denoted by the NA_*. This shhould be noted when working with NA data in a data.frame. Operations like case_when require all output data to be of the same type. https://timingliu.org/post/2021-04-07-learning-functional-programming-in-r/ Wed, 07 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-07-learning-functional-programming-in-r/ Why use functional programming Avoid intermediate objects In any loop, the standard practice is to create a new list before the loop, do some processing for each element of the list in the loop and then add the processing result as an element to the new list (following the same index). It makes programming more fun Thinking about that index i is simply not as fun as working with the whole list. https://timingliu.org/post/2021-04-04-medical-school-application/ Sun, 04 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-04-medical-school-application/ This is a summary post of the medical school application process. If you read Chinese, this Zhihu answer is where things got started. The whole application can be broken down to the following aspects: Curriculum Class performance Research Other interests BMAT Interview Leadership The central theme is about being interesting. In fact, I believe this is everything that I need to write… The specifics are more or less repeated elsewhere, so I will come to them only when I got time. https://timingliu.org/post/2021-04-04-bioconductor-packages/ Sun, 04 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-04-bioconductor-packages/ This is not intended to be a comprehensive review of Bioconductor packages - there are too many of them. These are my personal notes. First of all, I must declare a love-hate relationship with many Bioconductor packages. On one hand, they are very useful for specific purposes. On the other hand, there is often less underlying logic for these packages as compared to the tidyverse ecosystem. Even the authors admit that sometimes they forget what functions are there in their packages (I should link here to a Bioconductor support page, but not in the mood to do so). https://timingliu.org/post/2021-04-04-ai-powered-research-tools/ Sun, 04 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-04-ai-powered-research-tools/ Semantic scholar A NLP-powered “PubMed” that generates quick summaries for articles Scite For each article, it indicates the nature of the citation i.e. approving, neutral, disproving Meta A research feed generator Others Connected Papers and CORE. Both are available on aRxiv and show relationship between papers. Connected Papers show a map. https://timingliu.org/post/2021-04-04-what-does-interesting-mean-to-me/ Sun, 04 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-04-what-does-interesting-mean-to-me/ This is an important mental model that I have been building over the past few years. Interesting means attention-capturing. Attention is the currency that we are trading in the information age. Thus, the value of almost everything can be assessed on whether they are interesting. Being interesting has two components: relevance and uniqueness. To me, a film star’s divorce is unique but not relevant; medical school applications from a student with straight-A grades but nothing else is relevant but not unique. https://timingliu.org/post/2021-04-03-caveats-when-working-with-bioinformatics-data/ Sat, 03 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-03-caveats-when-working-with-bioinformatics-data/ This documents the common pitfalls when working with Bioinformatics data and how to prevent them. Headers Case use janitor::clean_names to standardize names to snakecases. Names use a standardized name: chr for chromosome, instead of chrom, seqnames etc. Sometimes you have to change the name to fit a certain software (e.g. GenomicRanages), but only convert the name within the call of the function itself, and immediately change back. Never propagate the name change to the next function because it will then be a headache to deal with the dependencies between functions. https://timingliu.org/post/2021-04-03-how-to-split-a-string-column-by-length/ Sat, 03 Apr 2021 00:00:00 +0000 https://timingliu.org/post/2021-04-03-how-to-split-a-string-column-by-length/ Intro This is a documentation of how I split a string type column by its length, and combine them together in a directory format (which was a necessary step for me to check whether each directory existed in my analysis). library(tidyverse) data <- tibble(string = c("123456", "987654")) print(data) ## # A tibble: 2 x 1 ## string ## <chr> ## 1 123456 ## 2 987654 Step 1 strsplit splits the string into a list of strings, and in tibble it will show up as a column of list type. https://timingliu.org/post/2021-03-28-how-i-would-learn-programming-in-7-days/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-how-i-would-learn-programming-in-7-days/ This will be a part of a series of articles on learning programming and data science. There are many articles on this topic already, but these are for my friends. This post focuses on learning programming. Most data scientists use Python and R. Between the two, I think Python is a more programming-oriented language. The types of objects are more straightforward, the syntax is easier, the object-oriented approach is clearer, too. https://timingliu.org/post/2021-03-28-how-to-make-superstitions-work/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-how-to-make-superstitions-work/ As a student of life, I’ve come to embrace certain superstitious concepts, despite considering myself a rational person. I believe that denying these beliefs at face value would be foolish, and have found two specific superstitions that have proven useful in my life. The first is fortune-telling, a common form of superstition. While many may scoff at the idea of predicting the future, I have found that reading the ancient Chinese book, I Ching, has offered valuable insights into life’s different states. https://timingliu.org/post/2021-03-28-is-anything-enjoyable-also-meaningful/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-is-anything-enjoyable-also-meaningful/ Being an extremely (>3 s.d.) future-focused person, I have been conditioned to think that unpleasant things can be good for my future, medications, running the last lap etc. There is of course a bias here. Unpleasant things are much more reflection-provoking than pleasant things. I am more inclined to ask myself “why am I going through all these” when things are unpleasant. Unpleasant things also provoke learning. I learn much better (or so I think) when I have a question that I want to seek an answer to. https://timingliu.org/post/2021-03-28-learning-philosophy/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-learning-philosophy/ The learning of philosophy is to see things as they are. To possess no internal judgement over external things. In Buddhism, there is a saying “无明是苦”, which can be translated to “suffering comes from the lack of clarity”. Incidentally, 明, or clarity, is part of my Chinese name, so I am constantly reminded that things can be a bit clearer than they are. Learning philosphy has no destination. One question that has bothered me for a while is why we are constantly searching answers for the same questions. https://timingliu.org/post/2021-03-28-like-and-desire/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-like-and-desire/ I like good films, but I do not always desire to watch them. I enjoy flowers blossoming in the botanic garden, but I do not always desire to bring them back home and keep them for myself. Liking something or someone means there is concordance with your value. It is natural. There is no need to suppress it. All we have to do is to acknowledge its existence and also acknowledge that this idea, like any other, is flowing down our thought stream, and we should not mistake it as ourselves. https://timingliu.org/post/2021-03-28-tips-to-apply-to-research-labs-for-undergraduates-high-school-students/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-tips-to-apply-to-research-labs-for-undergraduates-high-school-students/ I have been working on research projects since age 15 and here are the tips that I often share with my friends regarding research project application. How to approach the whole process It is normal to experience frustration because honestly, it is not meant for someone who first joins the field: 1. it is a far more natural process if you have been reading papers in the field for 1-2+ years and much easier to articulate why the work done by the researcher is important and interesting (and what skills do you bring to the table) 2. https://timingliu.org/post/2021-03-28-my-name/ Sun, 28 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-28-my-name/ “What does your name mean” was the first question I got during the most important interview in my life. This also becomes the question that I like to ask others. I enjoy listening to these backdrop stories of a person’s life and what meanings they derive from it. I was born to Chinese parents who hardly speak any English. By family tradition, like everyone else in my generation, my name should have a character “明 Ming”, or clarity in English. https://timingliu.org/post/2021-03-26-live-through-phases-not-days/ Fri, 26 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-26-live-through-phases-not-days/ Dividing my days into phases is one of my favourite habits. The basic idea of phasing is to divide our awake hours into phases and devote each phase to a single project and nothing else. Conversely, the projects will be attended only during their designated phases. Here are the few benefits that I have found. Work expands so as to fill the time available for its completion - Parkinson’s Law https://timingliu.org/post/2021-03-26-philosophy-of-haircut/ Fri, 26 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-26-philosophy-of-haircut/ Cutting all my hair away has become a regular practice during the lockdown. The practical reasons include hygiene and convenience. Long hair takes a long time to groom. The whole process of delicate grooming as the first thing in the morning takes away too much willpower and decision-making capacity that could have been better spent elsewhere. There are also schools of philosophy that I am constantly reminded of by this new haircut. https://timingliu.org/post/2021-03-20-am-i-overthinking/ Sat, 20 Mar 2021 00:00:00 +0000 https://timingliu.org/post/2021-03-20-am-i-overthinking/ It feels a bit strange to write a post on overthinking because then I can be accused of overthinking about overthinking :P This question stems from the observation that my conversations seldom end after talking. I always take pleasure in writing down the sparkles generated in the conversation and producing more thoughts afterwards. I realise that my dad loves it, too - he always writes to me essays after some kind of discussion. https://timingliu.org/post/2021-02-28-the-problem-solving-approach-to-cv-building/ Sun, 28 Feb 2021 00:00:00 +0000 https://timingliu.org/post/2021-02-28-the-problem-solving-approach-to-cv-building/ why even intrinsic goals can be harmful https://timingliu.org/post/service/ Wed, 13 Jan 2021 00:00:00 +0000 https://timingliu.org/post/service/ Let me know if I can be of any help. https://timingliu.org/post/2021-01-03-should-i-reflect-daily-or-hourly/ Sun, 03 Jan 2021 00:00:00 +0000 https://timingliu.org/post/2021-01-03-should-i-reflect-daily-or-hourly/ This is a fun and quick Christmas project and a reflection on whether I overthink too much. Compound interest is the eighth wonder of the world. He who understands it, earns it … he who doesn’t … pays it. - Einstein Regardless whether Einstein actually said that, it is no doubt that even small incremental improvement makes a large difference in the long term. Here I decide to apply the model to personal growth. https://timingliu.org/post/2020-11-07-book-review-hell-yeah-or-no/ Sat, 07 Nov 2020 00:00:00 +0000 https://timingliu.org/post/2020-11-07-book-review-hell-yeah-or-no/ Rating: 10/10 It was a second masterpiece written by Derek. Don’t let the word masterpiece deter you since it was written in such an approachable way. To continue with my analogy with Confucianism last time, this book is more like 论语 (Analects of Confucius). So different from Anything you want which is centred around Derek’s entrepreneur journey, this book is organized in different themes. As I read through Derek’s reflections in the book, I can’t help reflecting on my life: https://timingliu.org/post/2020-11-03-retreat/ Tue, 03 Nov 2020 00:00:00 +0000 https://timingliu.org/post/2020-11-03-retreat/ 非淡泊无以明志，非宁静无以致远 -诸葛亮 I went to the woods because I wished to live deliberately, …, and not, when I came to die, discover that I had not lived. - Henry David Thoreau I will be on a retreat from today onwards. This involves reading, writing and meditating more time for self-reflection Why better understand myself and the world become a more empathetic person to others and myself make progress on projects that help others (instead of getting drowned in replying messages) experiment - an unexamined life is not worth living This implies https://timingliu.org/post/2020-10-25-book-review-anything-you-want/ Sun, 25 Oct 2020 00:00:00 +0000 https://timingliu.org/post/2020-10-25-book-review-anything-you-want/ Rating: Life-changing After reading this book, I simply felt touched. I love how Derek simplified the whole entrepreneurship business into one phrase: creating happiness for you and your customers. It is that simple. This is a book written for the purest ideal in everyone’s heart. It also has the power of transforming that idea into practical actions that make a difference to the world. In Confucianism, he seems to have achieved the state of Junzi(君子), someone who projects his positive energy to benefit the society and cares more about the virtue, Ren (仁), than personal gains. https://timingliu.org/post/2020-10-25-communication-published-my-first-document-with-bookdown/ Sun, 25 Oct 2020 00:00:00 +0000 https://timingliu.org/post/2020-10-25-communication-published-my-first-document-with-bookdown/ I have just published my first document with bookdown and I am feeling euphoric at the moment. Somehow this gives me a very different satisfaction as compared to creating just a google document. Yes, they serve almost the same function, but the presentation of a bookdown document is much better. It also provides more functionalities and flexibilities than a google doc. Here are the minimal steps needed to customize a document from Yihui’s guide. https://timingliu.org/post/2020-10-24-book-review-4-hour-work-week/ Sat, 24 Oct 2020 00:00:00 +0000 https://timingliu.org/post/2020-10-24-book-review-4-hour-work-week/ What to do trumps how much you do https://timingliu.org/post/2020-10-24-book-review-the-modern-medical-student-manual/ Sat, 24 Oct 2020 00:00:00 +0000 https://timingliu.org/post/2020-10-24-book-review-the-modern-medical-student-manual/ Rating: 10/10 This is the kind of book that you want to finish once you have read the first page. Chris Lovejoy is a Cambridge medical graduate and physician-data scientist. He shares great content about productivity, data science and medicine on his blog and YouTube Channel so do check it out. This is the book that every medical student should read - the earlier the better. ❓ The material in questions: How to have a fulfilling career in medicine What is your definition of a successful career trail of whys attending your own funeral How to expand one’s impact incoporate soomething you like work on self-directed research projects How to cope with down time When and how to leave medicine (consciously) How to be an effective medical student How to study content effectively spaced repetition flashcards periodic review system understanding question-based learning (what this review is about! https://timingliu.org/post/2020-10-22-2020-summer-update/ Thu, 22 Oct 2020 00:00:00 +0000 https://timingliu.org/post/2020-10-22-2020-summer-update/ It was the season of light, it was the season of darkness - Charles Dickens, A Tale of Two Cities Here are some lessons I learned from this summer, organized by projects: MedTech CovMD.org It was my first attempt to set up a startup. The aim was to create a forum to connect doctors on COVID-19 related topics. The project did not go as smoothly as we expected after 1-2 month and I have to personally pivot it by creating another platform. https://timingliu.org/post/are-we-searching-for-communities-or-power/ Tue, 13 Oct 2020 00:00:00 +0000 https://timingliu.org/post/are-we-searching-for-communities-or-power/ TL;DR: look for communities, not just to seek help, but to help others. We are in a loneliness pandemic (in addition to the ongoing COVID-19, of course). To find a solution, I have been very keen on looking for a community, where I can connect with like-minded people and collaborate to solve exciting problems. The idea of community resonated with me particularly well when I watched this video by the school of thought. https://timingliu.org/post/book-review-mindset-by-carol-dweck/ Tue, 13 Oct 2020 00:00:00 +0000 https://timingliu.org/post/book-review-mindset-by-carol-dweck/ Rating: 8/10 Growth mindset used to be a quite trendy topic about 5 years ago and I remember myself being determined to develop the growth mindset. This book is sort of a revisit to the concepts that I was exposed to earlier. What I learned from the book: if fixed mindset people want to validate themselves, why don’t they stop after validating themselves once? there will always be challenges in life and fixed mindset people treat each of the challenges as a potential pitfall that can depreciate their worth, instead of an opportunity to grow. https://timingliu.org/post/medical-school-interview-my-two-cents/ Sat, 10 Oct 2020 00:00:00 +0000 https://timingliu.org/post/medical-school-interview-my-two-cents/ Recently I have received many questions on medical school interview so I thought it might be good to share my tips with you. First, congratulations on receiving an interview invitation. It means that your application has passed the first few steps of screening and now you should discard any inferiority complex (if you have any) and believe that you have as much chance of getting in like any other people if you can shine in the interview. https://timingliu.org/post/reply/ Sat, 10 Oct 2020 00:00:00 +0000 https://timingliu.org/post/reply/ TL;DR: I reply to non-urgent messages over the weekend. If a sooner response is expected, I will appreciate a reminder of the importance and urgency of the message via a desktop-based platform. https://timingliu.org/post/why-i-write/ Sat, 15 Aug 2020 00:00:00 +0000 https://timingliu.org/post/why-i-write/ I started writing daily when I was 16. Most of the writings were just dumping my thoughts so that my brain can be less burdened by them. It is the exact reason why computers have hard disks in addition to RAM. Writing thoughts down is simply a much less costly way to store them than holding them in the mind. It was only until recently that I started to write down my thoughts on my blog and I would like to share why. https://timingliu.org/post/getting-scammed-what-happened-and-why/ Fri, 07 Aug 2020 00:00:00 +0000 https://timingliu.org/post/getting-scammed-what-happened-and-why/ This is an article written to properly document my experience about the first scam that I fell prey to, and the reasons why (I think) this happened. Note that this article is probably doomed with attribution errors and may not reflect what truly happened. Nevertheless, I believe through attributions we seek meanings and through meanings, we regain the confidence to live hopefully more wisely. The protagonist behind the scam, who preferred to remain anonymous and refused to comment on this incident (as if I could ever contact them), hacked @mikkasmusic’s verified twitter account and changed its display name and profile to Elon Musk’s. https://timingliu.org/post/pitfalls-of-shopping/ Fri, 07 Aug 2020 00:00:00 +0000 https://timingliu.org/post/pitfalls-of-shopping/ Nothing is unhealthy when exercised at a moderate amount. Whether or not certain activities can be considered as excessive depends on how well our values align with the underlying motives of the activity. Shopping, though a harmless activity in itself, can be intrinsically outward-seeking and mind-manipulating if we do not approach it with an understanding of its repercussions. For one, shopping encourages us to own possessions so that we can please other people. https://timingliu.org/post/the-myth-of-rest/ Thu, 06 Aug 2020 00:00:00 +0000 https://timingliu.org/post/the-myth-of-rest/ While I initially intended to write about rest being a myth, but after contemplating and discussing with friends, it will perhaps be more reasonable to write about our often mythical thinking about rest. Rest here is defined as the time outside our standard working hours and time required to meet our physiological needs (e.g. sleep). We all can roughly divide our 24 hour day into three parts. We spend 8 hours on sleep, 8 hours on contracted jobs, and it is how we spend the last 8 hours that defines our life. https://timingliu.org/post/the-downside-of-control/ Fri, 31 Jul 2020 00:00:00 +0000 https://timingliu.org/post/the-downside-of-control/ Recently, a new identity has been added to my list – a scam victim. The price I had to pay for this new identity is the funding that I had for the whole summer. For the past few days, I have been trying to draw wisdom from this experience in life, and here is the first post on the many thoughts that I had. If we divide everything in life into internal and external categories, money probably belongs to the external one for most people. https://timingliu.org/post/set-up-server/ Mon, 04 May 2020 00:00:00 +0000 https://timingliu.org/post/set-up-server/ Recently I have been working on a project to set up a customized Wiki with MediaWiki. It is a new challenge for me because it is the first time that I am building a dynamic website that requires the setup of a server. The end goal is to host it on Azure, but there have been some challenges in using either a web app or a virtual machine. So I decided to localize the issue and first set up the website on a local machine. https://timingliu.org/post/bioinformtatics-data-integrity/ Mon, 16 Sep 2019 00:00:00 +0000 https://timingliu.org/post/bioinformtatics-data-integrity/ Recently I have been tidying up data for my research projects in NUS. This process of dealing with a few TBs of data in one day made me slightly paranoid of the integrity of the data: where should they be stored, which archiving + compresssion protocal should be used, which local/remote file transferring algorithms should be used and even what kind of media - should they be transferred via USB or ethernet. https://timingliu.org/post/opinion-why-plain-text-files-shall-prevail/ Sun, 25 Aug 2019 00:00:00 +0000 https://timingliu.org/post/opinion-why-plain-text-files-shall-prevail/ This is an opinionated post on my belief how the future of text editing should be. I have been editing my CV recently. The purpose of a CV is to illustrate a person’s relevant professional experience in a field and basically to sell someone out. Since it is about selling, then some customization is required for each post to achieve the best impression. The basic content across all documents is likely to be similar or the same, but the sequence may need to be rearranged to highlight different expertise for different audience. https://timingliu.org/post/utilisation-of-bioinformatics-data/ Sun, 11 Aug 2019 00:00:00 +0000 https://timingliu.org/post/utilisation-of-bioinformatics-data/ I am writing this post not as a guideline, but mainly for self-reference and hopefully a prompt for discussion. The boom of bioinformatics in recent years is coupled with cheaper technologies and consequently the surge of the amount of data available. The rapid development of the field itself is an anti-estblishment movement - even the most experienced bioinformaticians must spend a significant amount of time getting updated with the resources and toolkits. https://timingliu.org/post/conda-and-snakemake-for-reproducible-command-line/ Sun, 28 Jul 2019 00:00:00 +0000 https://timingliu.org/post/conda-and-snakemake-for-reproducible-command-line/ This compiles my notes for conda and snakemake. conda command update conda environment from yaml source activate myenv conda env update --file environment.yaml snakemake notes Snakemake is a fantastic tool to keep the running environment constant, document data processing and reproduce the analysis when necessary. I think it currently lacks the functionality of recording down the thought process behind each data processing decision, but perhaps that can be left as comments in the file and finally documented somewhere else. https://timingliu.org/post/working-with-multi-thread-machine/ Fri, 12 Jul 2019 00:00:00 +0000 https://timingliu.org/post/working-with-multi-thread-machine/ Compreesion tar cf - paths-to-archive | pigz -9 -p 32 > archive.tar.gz https://timingliu.org/post/a-r-package-that-creates-blank-rmd-files/ Thu, 27 Jun 2019 00:00:00 +0000 https://timingliu.org/post/a-r-package-that-creates-blank-rmd-files/ I have created this package to create a blank Rmd file by saving a nearly blank Rmd template to the menu when you create Rmd files. I think it at least follows the first half of the UNIX orthodox: programs that do one thing and do it well. 😂 Reflection: the main purpose for me to create this package, other than making life easier, is to practise how to publish a R package onto github and to install it from there. https://timingliu.org/post/ubuntu-server-commands/ Wed, 26 Jun 2019 00:00:00 +0000 https://timingliu.org/post/ubuntu-server-commands/ Here is a collection of commands relevant to using a remote server that I find helpful. Establish connection ssh -X -p *port* user_name@server_ip ssh command establishes a ssh connection with the server. -X opens an X-server, which allows you to open GUI software (e.g. firefox) on the server and convey the display to your local computer -p selects the specific port the connection is going to be established. Not all ports of a computer are always open for security reasons. https://timingliu.org/post/helpful-software-for-bioinformatics/ Mon, 24 Jun 2019 00:00:00 +0000 https://timingliu.org/post/helpful-software-for-bioinformatics/ Here are some of the life savers that are not commonly introduced in standard bioinformatics curriculum. I think these toolkits encapsulate my understanding of the spirit of programming: there must be an easier way to do it. To Compare directory and text files Although unfavorable, sometimes it happens that one project directory is duplicated and the progress of analysis differs between each other. The tools that I have found to be very helpful for comparing different directories and files so that you can merge the two directory into one and keep the most updated files from each folder is Meld. https://timingliu.org/post/git-commands/ Mon, 17 Jun 2019 00:00:00 +0000 https://timingliu.org/post/git-commands/ This is a collection of common git commands that I use very often in my daily work. I have only touched on GitHub and find it fairly sufficient for my needs, and thus this post will base on GitHub as well. Case 1: start a new repository Let’s say we want to upload ~/analysis/ to GitHub On GitHub: create a new repository The only things I will set here are the repository name and the choice whether it is public or private. https://timingliu.org/post/set-up-ubuntu-machine/ Mon, 17 Jun 2019 00:00:00 +0000 https://timingliu.org/post/set-up-ubuntu-machine/ System Choice I chose Ubuntu 18.04 LTS. Not any earlier version because to my knowledge most, if not all software for bioinformatics analysis will support 18.04. One exception to this is Nanopore’s Albacore base caller, but it is being replaced by Guppy anyways. 18.10 (the current highest version) was not chosen , because the improvements in features do not seem to justify an upgrade away from LTS. Hardware GPU Ubuntu seems to dislike some high-spec GPUs. https://timingliu.org/post/background-tasks/ Tue, 04 Jun 2019 00:00:00 +0000 https://timingliu.org/post/background-tasks/ This post will cover how to start running a programme in a terminal’s background monitor the programme and stop the programme I decided to write this post beacuse I did not find any comprehensive tutorial to cover this aspect. start running a programme in a terminal’s background To do so, simply add & at the end of the line. What occurs after the enter is hit is that the first line will be run at the background and the terminal will prompt you another line of input. https://timingliu.org/post/bar-plot-with-bars-and-labels-between-tick-marks/ Fri, 31 May 2019 00:00:00 +0000 https://timingliu.org/post/bar-plot-with-bars-and-labels-between-tick-marks/ I had this quesition when preparing my manuscript and a quick search brings me to this stackoverflow question by Johanna. I find the answer by Henrick to be highly effective, but can be further elaborated so that readers can be clearer about the functions of each line. Thus, I will base my post largely on Henrick’s answer but at the same time add my explanation to the rationale behind the lines. https://timingliu.org/post/var-path-vs-echo-path/ Thu, 30 May 2019 00:00:00 +0000 https://timingliu.org/post/var-path-vs-echo-path/ TL;DR: $PATH will call the value stored in the environmental variable PATH as a command, but echo $PATH will print out the value stored in the variable PATH. How I found out: Recently I have been trying to integrate WSL with RStudio. One thing intrigues me is that the bash in Rmd has a different PATH with WSL. For example, one cannot run the software installed with conda directly from Rmd - the conda bin directory needs to be added into PATH (using export . https://timingliu.org/post/hello-world/ Tue, 28 May 2019 00:00:00 +0000 https://timingliu.org/post/hello-world/ Yes I have built this website. It is definitely not an easy process though. I can confirm this because by the time this post is being written, the website itself has not been deployed yet. Well but I just want to briefly explain the reasons why I am putting this website up. The most important reason is that I increasingly feel a need to host a place on the internet (not a typo) for me to outreach to other people. https://timingliu.org/post/2020-07-19-opinion-a-case-for-full-stack-clinician/ Mon, 01 Jan 0001 00:00:00 +0000 https://timingliu.org/post/2020-07-19-opinion-a-case-for-full-stack-clinician/