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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Blog
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Tutorials
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Posts
Scuba diving in Okinawa Part 1
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Sharing my passion for scuba diving and marine life in the pristine waters around Okinawa.
EMBL single-cell workshop in Heidelberg, Germany
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My experience attending an EMBO practical course on single-cell omics at EMBL Heidelberg campus.
Publishing my first research paper
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After a year long review, my first paper on NF-kB transcription factor was finally published in PLoS Genetics.
Landing a PhD position
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My journey to securing a PhD position at Okinawa Institute of Science and Technology after finishing my Master’s degree.
What happened to my research?
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COVID struck while I learned new experimental techniques, got a conference award, and published my first review article.
Getting into Japanese graduate school and getting a “full” scholarship
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My journey into Japanese graduate school and securing a scholarship to fund my studies.
Laboratory assignment, current research, and my first international conference presentation
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It’s getting really busy lately, so I haven’t had time to update my blog in a veeeeery long time. To sum up: I am currently a 4thyear student, and I am currently doing my undergraduate thesis research…
My research projects
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Hi, haven’t updated my blog in a very very long time but here I am lol. Happy new year to everyone! How was 2018? 2018 was a rather productive year for me, I started 2 new research projects and probab…
Shirahama Marine Biology Field Trip 2017
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At the end of the first year, we have an optional (used to be compulsory) trip to Shirahama. If you don’t know what Shirahama is, it is basically a beach in Southern Wakayama which is located South of…
2nd Semester: Labs
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Hello there, different from 1st semester, we have labs on our 2nd semester. A rather good thing knowing that we almost never had any lab experience during the course of first semester
2nd Semester in CBCMP: Circles and Clubs
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I haven’t updated this blog in a while lol… A lot of stuff happened in the 2nd semester honestly. Firstly I joined circles. For those of you who don’t know what a circle is, it basically is a club w…
First Semester in the CBCMP
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Haven’t posted in a while, first sem was really hectic… Let me sum up my first sem in the CBCMP then..
Reaching Osaka University
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Usually it takes about some 7-8 hours to get from Indonesia to Japan. However, MEXT somehow managed to book a ticket with a layover at Denpasar (Bali) and so I had to spend a total of around 14 hours …
Choosing a department at Osaka University
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About a month after the announcement of passing into the university, I was asked to choose among 4 departments:Department of Biological sciences (School of science),DepartmentofBiotechnology (School o…
The Next Step to 阪大
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So, I’m gonna save the language school post for later and the Osaka University post for today.
Why Japan?
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Out of the countries that I could have chosen to go to, why Japan?
How I managed to get into Japan
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So I went to this University fair about 2 years ago and got some info regarding this Osaka University Global 30 program, however I didn’t really look further into this program and ended up spending mo…
Why this blog and who am I
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Maybe a little too late to make a blog, but maybe not too late to share stories.
tutorials
Tutorial: TPM calculation with library size normalization
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Calculating transcripts per million (TPM) from raw RNA-seq counts in R, with library size normalization using edgeR.
Tutorial: Visualizing genomic tracks with Gviz
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Plotting bigWig ChIP-seq tracks alongside gene models and an ideogram in R using Gviz.
Tutorial: Running R on machine without administrator rights using Singularity
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Learn how to use Singularity to run R on HPC systems without administrator privileges.
Tutorial: Running RStudio using Docker for smoother collaboration
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Guide to setting up RStudio in Docker containers for consistent development environments across teams.
Tutorial: Docker and singularity image containing R and Renv for package version control
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Learn how to create reproducible R environments using Renv with Docker and Singularity containers.
Tutorial: Deploying JBrowse 2 on AWS EC2
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Complete guide to deploying JBrowse 2, a next-generation genome browser, on AWS EC2 instances.
Tutorial: Genome assembly and scaffolding of small eukaryotic genomes
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Learn genome assembly and scaffolding techniques for small eukaryotic genomes using NOVOloci and hifiasm.