Jun Aruga's Blog

Output, activities, memo and etc.

Bio-tech

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…

Anatomy

Book The books "カラー図解 新しい人体の教科書" ("Color pictured book: New textbook of Human Body" in English) I bought was very interesting unexpectedly. カラー図解 新しい人体の教科書 上 (ブルーバックス) | 山科正平 | 医学・薬学 | Kindleス…

Desire for big picture - Siddhartha Mukherjee

Let's say that you are at a restaurant, you are hungry. Do you like ordering a food without seeing all the menu? Or you want to order it after seeing all the menu, checking which is the best? The second pattern connects to the desire for s…

DNA sequencing: Standing of the shoulders of giants

Learning materials of DNA sequencing I found the teaching materials of Ben Langmead who is the author of bowtie and bowtie2. This is a great material to learn DNA sequencing. Langmead Lab @ Johns Hopkins University - Teaching Materials: ht…

Videos: Sequncing and history

Just put interesting videos about the DNA sequencing and the history. Reading DNA - Clive Brown, CTO of Oxford Nanopore Technologies www.youtube.com Broad@15 Talk Series; From bases to bytes (Live Stream) https://www.youtube.com/watch?v=GU…

Biomakespace to start training for gene editiong and sequencing with MinION

Very exciting news. https://biomake.space/home/blog/mozilla-grant-win-biomakespace-facilitates-accessible-gene-editing-and-dna-sequencing-technology Publicly-available datasets, open hardware, and good open-science practices will be used t…

The European Open Science Cloud was officially launched

When seeing the world, I tend to see it with a frame of Yuval Harari. The consequence of a quite popular futurist predicting the future, and saying the opinion makes the real situation happen affected by the opinion itself. Yuval Harari's …

Genome (base pair) size and gene number by Organism

As I installed Trinity RNA Seq tool, I want to do de novo sequencing to something. Genome size is base pair (= bp) size, not gene number. As to check the behavior of Trinity, small genome size (base pairs) is better. I found this NCBI's pa…

Install and test Trinity, the De novo assemble tool

This article is about how to install and test Trinity RNA seq de novo assemble tool on Mac OSX [1]. Install Seeing Trinity .travis.yml [2] is good to know it. First, we need to use a compiler supporting Open MP [3] (= Open Multi-Processing…

EMBL-EBI resources: An introduction

I watched this video today. Introduction to EMBL EBI resources www.youtube.com Literally this video is great to understand the data sources in the view of bird eyes. The detail page is here [1]. EBI Search Example: Search by the gene name:…

The Open Targets

Today I want to introduce the genome service "Open Targets" [1], that I knew 2 month ago in a bio hackathon event at Genome Campus, Cambridge UK. Summary It is to find a drug "targeting" a gene. The philosophy of the service is "open". So,…

Nanopore Day@EMBL Heidelberg

The reason I visited Heidelberg was because of Nanopore Day, the community event held by Oxford Nanopore Technologies. The event was held at the EMBL office. That was good opportunity to know both EMBL Heidelberg and Nanopore. Easy route i…

A bio hackathon - Cambridge UK

Last month, I traveled Cambridge and London again 2nd time this year, then South of London, Brighton and Isle of Wight. I experienced so many things. As it was hard to clear my thoughts by the travel, I was delayed to output it on the blog…