I visited London, and enjoyed live music at theatre and IMAX 2D. Thriller Live at Lyric Theatre China town Christmas Market at Leicester Square ODEON BFI IMAX near Waterloo Station Hungerford Bridge and Golden Jubilee Bridges

I visited to Cambridge, UK for a Bio IT event. In front of station. Under constraction for a building Apartment COSTA near the station Near The Grafton Centre at PRET (Petty Cury street) ADC Theatre Wasabi Spanish restaurant in Mill Road A…

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 …

I am comparing between OpenStack [1][2] and AWS services. [3] is all the services of OpenStack. [4] is the comparing document. I have an experience for AWS. But I do not have for OpenStack. The intent to compare those services is to rememb…

Previously I used markdown-pdf. But I found another tool to convert GitHub style PDF mdpdf [1]. And I would prefer it. junaruga.hatenablog.com mdpdf Install $ npm install mdpdf $ which mdpdf /Users/jun.aruga/node_modules/.bin/mdpdf Usage $…

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…

I was looking for how to covert from a Markdown file to PDF file. After finding a Stackoverflow page [1], I found markdown-pdf [2]. Install Install Nodejs at first, download "10.13.0 LTS" for Mac. $ which node /usr/local/bin/node $ node -v…

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…

This time's route: Brno, Czech - bus (student agency) or train - Prague, Czech: 2 hours 40 mins (same time for bus and train) Prague, Czech - bus (Flixbus) - (Germany, Frankfurt - bus (Flixbus) -) Germany, Heidelberg: 7 hours or 8 hours 30…

Here is the way to convert PDF file to PNG files (1 PNG for 1 page of the PDF) with convert command, according to [1]. Maybe output image file type are recognized automatically from the file extension name ".png". $ convert \ -verbose \ -d…

From the UK travel 1 month ago. Brighton Seven Sisters Near Brighton Isle of Wight This time the route is Brighton -> (Train) -> Portsmouth and Southsea Station -> (Bus) -> Southsea Hoverport stop -> (Hovercraft) -> Ryde In the island, the…

I wrote a blog about how attractive "Future starts here" in Victoria and Albert Museum was 2 month ago. Last month I visited there. It was one of the most interesting and affected experience. Let's see the photos together. That is to under…

I like Mill Rd in Cambridge, UK. A variety of country's restaurants. Chinese, Korean, African, and etc restaurants.

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 would note how to install perl with thread, as I needed it to use RNA Sequencing tool: Trinity [1]. I needed to upgrade Perlbrew [2] itself, as I got an error to install perl. Upgrade Perlbrew. $ \curl -L https://install.perlbrew.pl | ba…

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…

news.harvard.edu My favorite parts in the speech. "I’ve sat with children in juvenile detention and opioid addicts, who told me their lives could have turned out differently if they just had something to do, an after school program or some…

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 …

The Future Starts Here I found interesting event " The Future Starts Here" in Victoria and Albert Museum, in London. Maybe I am going to visit there soon. You can feel what's interesting from below URLs. Victoria and Albert Museum (now unt…

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 …

London King's Cross station => Cambridge station => Stansted Airport

London Paddington station => Oxford station Oxford station The biggest only shopping mall in Oxford A street A popular Jamaican restaurant A covered market A Market A park

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

To care and clean my intestine. A cup of spoon every morning, with water. So far, I could see the good effect.

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…