Jun's Blog

Output, activities, memo and etc.

Bio-tech

Reflecting on 2023

This article reflects on the last year 2023. This is the 2023 version of my past article about the 2022 version. Note that I can not share some topics here for some reasons such as a private topic, a controversial topic, or a financial top…

Information, People, and Community as a catalyst of paradigm shift

I am in Casablanca, Morroco now. I visited in this country for the first time. And I have many new experiences here. There are many of information around us. But I think it's important for us to select information that we are exposed to. I…

A brain type quiz by Dr. Daniel Amen

I tried a quiz in the website https://www.brainhealthassessment.com/ by Daniel G. Amen, MD. And my type was the brain type 5. www.youtube.com The traits of the brain type 5 is below. Cautious Prepared Motivated Busy Mind Can Have Trouble R…

AI-based apps in biomedical literature and document mining

I am trying to install AI-based applications such as BioBERT and BioGPT to play. The following paper summarizes the list of applications and what we can do for the technologies very well. Applications of cutting-edge artificial intelligenc…

Genome data ecosystem

I think that in biology, the ecosystem Ecosystem - Wikipedia means a system of living things (organisms). You can imagine a variety of living things in the forest, jungle, or sea. But I am using the terminology "ecosystem" as another meani…

Nebula Genomics summary & thoughts

The process until getting the report I wrote I submitted Nebula Genomics on my past blog. I selected the Ultra-deep 100x coverage plan. If I checked my email history, it is below. I ordered it on 1st November 2022. I received the kit from …

Organisms are algorithms - A case of alcohol biochemical pathway

The famous historian Yuval Nora Halari mentioned "organisms are algorithms" in the main stage of the World Economic Forum in January 2018.[1] In this article, I want to show that the algorithms exist commonly in software, hardware, and bio…

HiFi / ONT genome asssembly pipeline with WDL in ECCB 2022

Last year in 2022, I helped to present the demo for HiFI / ONT (Oxford Nanopore Technology) genome assembly sequencing pipeline on WDL (Workflow Definition Language) in the event ECCB (European Conference on Computing Biology) 2022. It see…

Open Science and Research Assessment

I wrote a blog article about an incentivized system in academia. This article is also about the topic. I found the videos of the "Workshop on Open Science and Research Assessment - From a European to a Local perspective" published a few da…

An incentivized system in academia and a game changer in bio-tech

An incentivized system in academia Recently I learned Goodharts law by this article. If an incentivized system measures or evaluates people by strong force using something to achieve a goal, the something tends to be the goal itself. The o…

Reflecting on 2022

At the end of the year 2022, I would share my reflections on the year 2022 with this article. Previously I wrote the 2020 version of the article. In recent years, I learned how to work with big open-source projects. It was fun and meaningf…

Converting FASTQ format to FASTA format

The FASTQ format is to combine the FASTA format + Quality info. Therefore, we can convert the FASTQ format into FASTA format, removing only the quality info. Here is the way: https://bioinformaticsworkbook.org/dataWrangling/fastaq-manipula…

Use Docker on Fedora 36

I was trying to run the WDL file on locally by the dockstore command[1]. Because it's an easy way to check a WDL file rather than uploading it to the Dockstore site. Right now I couldn't find the dockstore command with the Podman[2][3], I …

Lowering LDL (bad cholesterol) level. - The Switch

I got a health check-up to understand what's happening in my body. Then while most of the numbers by check were very good, there was one bad value. That is the value of low-density lipoprotein (LDL), so-called "bad cholesterol". The number…

Book sumary: The Swtich - James W. Clement

Finally, I can summarize the book, The Switch - James W. Clement[1]. It has been long steps until now. I bought the Japanese edition, and read the Japanese edition at once. Then I bought the English original edition. Then I did read both b…

Biology online courses FutureLearn, Coursera

When I want to find online courses for biology. I found the Wellcome Connecting Science providing free online courses on the learning platform called FutureLearn [1]. [2][3] Unfortunately those courses are not always available, and there a…

Reference management tool: Mendeley

Mendeley [1][2] is a tool to manage and work with papers. I was looking for a way to read papers effectively. And it can be good for that. It's to import PDF files, and parse the metadata, and add annotation on the paper. I like the functi…

Paper summary: The hoverfly and the wasp: A critique of the hallmarks of aging as a paradigm

This page is a summary of the paper "Paper summary: The hoverfly and the wasp: A critique of the hallmarks of aging as a paradigm" [1][2], and my thoughts. The paper is a critique for famous paper "The hallmarks of aging" [3]. The "hoverfl…

Memo: List of countries by life expectancy

List of countries by life expectancy - Wikipedia Source: Life expectancy and Healthy life expectancy Data by country - WHO Countries ranked by life expectancy - www.worldometers.info

Aging biology: A small change for big changes

The paper "The hallmarks of Aging" cited, reviewed and verified by many researchers. A book about scientist mindset I am reading, suggests that publishing just one paper to change a paradigm rather than publishing many papers to verify som…

Paper summary: The Hallmarks of Aging

This is a summary of the paper "The Hallmarks of Aging" [1][2], and my thoughts. The summary is biased by my interest and experience. This paper is one of the most cited papers in aging biology, published in 2013. As I wrote on the past ar…

How to use PubMed, PubMed Central, Google Scholar, arXiv.org

In this article, I would introduce how to use PubMed, PubMed Central Google Scholar, and arXiv.org. These website are useful to search and manage especially science papers in biology, medical area. PubMed I am using PubMed [1] as a primary…

Czech National Library of Technology in Prague & DIY Bio

Today I visited Czech National Library of Technology [1] in Prague 6 to make my study fun. It was a big building with 6 floors. It looks like a good environment to study. It opens every day. I saw many students studying there. There are ar…

BioHackathon Europe

I joined the BioHackathon Europe in Barcelona. That's a hacking event, co-working event related to biology. This time it's to select one project from 37 projects (There are 38 projects on the page, but the "Single Cell Multi-Omics Analysis…

PacBio HiFi sequencing

When I joined Biohackathon Europe in Barcelona recently, I knew PacBio HiFi (High Fidelity) sequencing technology [1] that is highly accurate long read sequencing by circular consensus long-read [2]. For the long read sequencing, there is …

Miniconda, Bioconda on Fedora and Galaxy

This page is the memo about installing miniconda (conda command) on Fedora Linux. I referred the document [1]. I wanted to install a bioconda package. Because I wanted to build a Galaxy tool using Planemo [2]. The tutorial is using biocond…

Molecule Generation Experience

I wrote the article about the molecule recommendation before [1]. Now the interesting service called "IBM" MolGX" (IBM Molecule Generation Experience) was launched from IBM Research [2][3][4]. Updated by 12th March 2021. IBM Research also …

Nature Aging launched

Nature Aging [1] was launched on 14th January 2021. Here is the message. [2] One of the articles: "Artificial intelligence in longevity medicine" [3] looks interesting. One of the authors, Alex Zhavoronkov who published the book "THE AGELE…

Memo: WHO Model List of Essential Medicines

This one. [1][2]. According to [3] - definition, the essential medicines are those that satisfy the priority health care needs of the population. According to [1], are the medications considered to be most effective and safe to meet the mo…

Scaling the Scientific Method

2 challenges related to scaling scientific method I did read the book Lifespan [1], that is a new detailed inclusive report and history of aging biology. I see 2 challenges in the process of the science. First, verifying a hypothesis needs…