Another Japan in the World

Jun Aruga's blog.

Genomics

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…

Synthetic Biology and Microsoft

I did read the book "The impact of Synthetic Biology". Unfortunately, this book is only written in Japanese. It's about Synthetic Biology, that is to write a genome. The world first Artificial Cell, Minimal Cell was created by Craig Venter…

Sequencing: Run mapping by bowtie2 and view it on IGV

Previously I ran mapping by Hisat2, and did view it by IGV Sequencing: Run mapping - Another Japan in the World Sequencing: view mapped genome on IGV (Integrative Genomics Viewer) - Another Japan in the World This time, I try to do mapping…

Sequencing: view mapped genome on IGV (Integrative Genomics Viewer)

Install Integrative Genomics Viewer (IGV) [1] to view mapped genome. Use bam file that was created previously. See the blog page. java is used. Install it if it is not installed. $ java -version java version "1.8.0_25" Java(TM) SE Runtime …

Sequencing: Run mapping

This is the next article from Sequencing: Install mapping tools - Another Japan in the World. Try to do mapping by Hisat2 with previous fastq files trimmed by FastQC. Go to Hisat2 official web [1], click H. sapiens GRCh38 "genome" link, an…

An age of DIYBio

I found an interesting open science community. That is Mozilla Science Lab [1]. You can see several projects there. In the past posts on my blog, maybe I have introduced similar communities Elixir Europe [2] and GA4GH [3]. Also I found an …

London, UK

Stansted Airport => Train (Stansted Express) => Liverpool station South Kensington station, Museums => Walking => Hyde Park => Walking => Green Park station => KIng's Cross station Around Kings Cross Francis Crick Institute

Sequencing: Install mapping tools

I tried to do mapping the genome data I used before. I tried to install a tool for mapping of the genome. I tried 2 tools: TopHat 2 [1], HISAT2 [2] for that. The result is TopHat 2: I could not install it. HISAT 2: I could install it. This…

Sequencing: Trimming FASTQ file

This article to trim .fastq files. .fastq files outputted from a sequencer can include data with a bad quality score. In the case, we would do trimming the bad data. Use the data used in previous blog post. Genome Sequening: Quality Check …

Sequencing: Quality Check by fastqc

This article to demonstrate how to do quality check for the data from Illumina Sequencer. Download FASTQ file Use publicly uploaded sequencing data on DRA (DDBJ Sequence Read Archive) [1]. You can also download same data from SRA (NCBI Seq…

Reading "実験医学" as e-book

It is no doubt that Amazon and the Kindle store have changed how to read books. Nowadays, people can easily buy and read not only books in their region but also English books, and other books in any region around the world, if those books …

Developments in NGS

X axis: Read length => Read length for each reads Y axis: Gigabses per run => Total read bases per run (unit: Giga) Detail is [1] [1] Detail: Developments in high throughput sequencing – July 2016 edition | In between lines of code