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…

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…

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…

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…

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…

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 …

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…

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…

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:…

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,…

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…

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…

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…

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…

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 …

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…

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 …

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

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…

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 …

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…

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 …

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

This is not new information. I just found it today. Oxford Nanopore mobile portable genome sequencer MinION is supporting not only Windows and Mac but also Ubuntu Linux partly! [1][2] MinION Video: https://vimeo.com/211467532 I want it and…

Recently I was reading a book of Jennifer Doudna who is a RNA biologist and discovered how to edit gene with Crisper Cas9, the revolutional way for genome editing. [1] The book I am reading is the Japanese translation edition. It is a quit…

This person is ... [1] A software engineer with some training in bioinformatics, he was pursuing a PhD and thought it would really help to know some fundamentals of biology. "A software engineer with some training in bioinformatics" is lik…

To understand it, longevity.international: http://longevity.international/ The reports are good. Juvenescence: Investing in the age of longevity: https://www.amazon.co.jp/dp/B075WXX93Q Just started reading, the book and the structure of co…

I realized it recently. I am saving my memory's main structure as an image. It is something like the Tree trunk: saving as an image or sense. Small branches and leaves: saving as an text. To get information from my brain. Maybe I am access…

日本語で書きます。 理由は、日本語のゲノムの資料を今日読んで、「なんだ、そういうことだったのか」ということがあったからです。 残念なことに、まだまだ日本語の文章を読んだ方が格段に理解ができる、ということがわかりました。 国際ヒトゲノム参照配列…

Google Genomics, Microsoft Genomics, And now Amazon Web Services with Genomics. Partnership with DNAnexus, Illumina, and Seven Bridges. Getting to Know APN Genomics Partners BioTeam, DNAnexus, Illumina, and Seven Bridges | AWS Partner Netw…