Another Japan in the World

Jun Aruga's blog.

yEd Graph Editor for Linux?

I love the tool yEd Graph Editor. yEd is freely available and runs on all major platforms: Windows, Unix/Linux, and macOS. It's available on Linux too. Is it packaged like FreeMind on Linux? www.yworks.com

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…

Madrid, Spain - Business area

Around Nuevos Ministerios metro station, and Chamartín Railway Station are local or business area. The place was not so crowed. Madrid airport was around 16 minutes from Nuevos Ministerios metro station. Maybe at a bookstore in Madrid airp…

Madrid, Spain - Tourist area, and Toledo

Months ago, I traveled Madrid Spain. That time, the route was Madrid, Toledo, Seville, and Arcos de la Frontera. Madrid - Tourist area The Atocha station is the main train station for the tourist. Museum of Ham (Museo del Jamón) is my favo…

RHEL 8, 7 and Fedora container images

IT

Something great is happening.. It's time to add RHEL8, 7 to your applications' CI test case. RHEL8 $ docker run --rm -t registry.access.redhat.com/ubi8 bash -cx "uname -a; cat /etc/os-release" + uname -a Linux b065f4dfb56b 4.4.74-boot2dock…

Cambridge UK

Months ago in Cambridge. ADC Theatre, Corpus Playroom [1] and Botanic Garden. [1] https://www.adctheatre.com/

Install podman & useful podman commands

IT

I would show you how to install podman the alternative docker. The difference between docker and podman is docker: Running the docker daemon to operate the containers. podman: Do not need to run a daemon to operate the containers. As a ini…

How to remove not removed container images & useful docker commands

IT

Before next blog for qemu-user-static. I would write some articles. How to remove not removed container images The subject is that I faced. The reason is after upgrading a docker, the actual storage to manage containers were changed. Then …

qemu-user-static - part 2 register

IT

qemu-user-static enables us to run multi architecture environment such as ARM on x86_64 like this. $ docker run --rm --privileged multiarch/qemu-user-static:register --reset $ docker run --rm -t multiarch/ubuntu-debootstrap:arm64-bionic un…

qemu-user-static - part 1 summary

IT

qemu-user-static [1] is a software to enable qemu [2] consumable to build and run multi architecture (ARM 64-bit, ARM 32-bit, Intel 32-bit and etc) on x86_64 Intel processor environment. If you run docker or a docker compatible software, y…

Install Debian 9 and how to report a bug

IT

I wanted to report a request for feature to bowtie2 package on Debian project Checking and asking how to report a bug to the bug tracking system (= BTS) on the project, it seems 2 ways. One is to send a report by email (https://www.debian.…

South of Spain

This time, Malaga -> Glranada -> Nerja -> Gibraltar and La Linea de la Concepcion -> Malaga Malaga Glranada Nerja Gibraltar and La Linea de la Concepcion Gibraltar is UK. It's interesting! La Linea de la Concepcion is Spain. It's fun and t…

How to use host os directory from chroot (mock) environment.

IT

On Fedora Project's work, a chroot environment is usually used to build and test. The environment is called "mock" environment. As I often forget the way, I save it to this page. There are 2 ways. 1. Using mount --bind Use below command. $…

Travis CI: A better alternative of travis_wait to output the command stdout

IT

I found a better way to run heavy command, seeing a code [1] by chance. If the command does not output log to stdout or stderr for 10 minutes, the job stops. The popular practice to prevent it is like this. But the problem is this command …

London, UK

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

Future of Cambridge, UK

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…

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 …

OpenStack vs AWS: comparing the services

IT

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…

Convert Markdown file to PDF file on Mac (2)

IT

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 $…

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…

Convert Markdown file to PDF file on Mac

IT

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…

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…

Heidelberg, Germany

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…

How to convert PDF file to PNG file with high quality on Fedora

IT

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…

South of London

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…

"The Future Starts Here" in London

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…

Camridge, UK

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