Charles Plessy @charles_plessy@mastodon.technology

What I read

Immense progress for #OpenScience: more than 60 million articles in the #CrossRef database now have also information about which other articles they cite. https://i4oc.org/#progress

Inflation news: the impact factor of the scientific journal #Cell has increased from 41.584 to 66.850 in one year, a 61% growth.

What is a biological #species? Do we need the definition to be sharply precise, or to be broadly useful? These are questions that our scientific community need to solve now that we shown that the #zooplankton #Oikopleura dioica, thought to be the same species across the whole world, is at least 3 different populations. Surprisingly, the one found in #Okinawa near #OIST is so genetically different from the one found near #Japan's main islands that they can not cross breed. https://www.biorxiv.org/content/10.1101/2022.08.09.503427v1

Our CAGEr package for #transcription start site analysis is updated to version 2.2.0 in the latest release of #Bioconductor (version 3.15). This is a bug fix release where the main change is the re-enabling of the correctSystematicG option. https://bioconductor.org/packages/CAGEr

Published in #GenomeBiology, by Paul P. Gardner and colleagues from the University of Canterbury, Christchurch, New Zealand, the study of 68 #bioinformatic #scientific #software benchmarks shows that speed and accuracy correlates with number of commits and closed issues, and not by #journal #impact factor.

The #OIST Foundation is raising funds to help scholars and students from #Ukraine who seek for support in #Japan. https://secure.givelively.org/donate/okinawa-institute-of-science-and-technology-foundation-inc/ukraine-scholar-and-student-support-fund

Tip: use #GNU #time instead of the #shell builtin to get more information about how much resource was used by a command. One way to shortcut the builtin is to call the command from an absolute path, such as `/usr/bin/time`. https://www.gnu.org/software/time/

Online #seminar on #ageing organised by former colleagues from #RIKEN: https://www2.bdr.riken.jp/sympo/aging2022/

It took me some time to understand why an if / else statement was giving me opposite results when run in a container via a #Nextflow pipeline. The reason was that it sets `-o pipefail` on the #shell scripts, and `zcat` exits with an error since `head` does not not consume all of its input. The solution I found was to avoid a pipe between them, for instance `head <(zcat bigfile) | grep…` Merci StackOverflow for the hint! https://stackoverflow.com/questions/41516177/bash-zcat-head-causes-pipefail

I am at the yearly #conference of the Molecular #Biology Society of #Japan, in #Yokohama, from today to Friday. I will present our work the rapid scrambling of #Oikopleura #genome coordinates during #evolution. https://www2.aeplan.co.jp/mbsj2021/english/

I received a big #zip file containing data, #unzip version 6.0.0 would not open it and instead report that it is #corrupted. Thanks to an old discussion on #comp.os.linux.misc I found that it could be rescued with the `zip -FF` command. Further research shows that different kinds of corrupted big zip files can originate from #Microsoft or #Apple systems: (https://www.bitsgalore.org/2020/03/11/does-microsoft-onedrive-export-large-ZIP-files-that-are-corrupt). It seems that the #7z command from #p7zip package can also open some.

Speed fluctuations of bacterial replisomes. I am co-author in this #bioRxiv preprint. In this work, three #OIST units joined their forces to produce experimental data of #DNA abundance in exponentially growing Escherichia coli, and to formulate a #theory that permits to infer the #dynamics of replisomes from the DNA abundance distribution. Big congratulations to my colleagues Deepak and Simone who lead that work.

Just gave a presentation on R packaging this morning in a mini-course at #OIST. Our slides are here: https://github.com/Rafael-Ayala/R-packages-minicourse #rstats

In #PNAS today, an article from the University of #Birmingham, using the BstNI enzyme to nick a #DNA oligonucleotide annealed to the #RNA of the SARS-CoV-2 #virus (causing #COVID19) produce the trigger for detection under 10 min with an #isothermal exponential amplification system called #EXPAR. https://www.pnas.org/content/118/35/e2100347118

The #Interdisciplinary #Postdoctoral Scholar #Fellowship (IPSF) program provides a unique opportunity to advance researchers' academic careers by conducting full-time #interdisciplinary research and training at the #Okinawa Institute for #Science and #Technology (#OIST). Follow this link to apply: https://apply.interfolio.com/75577

Scientists are being judged – and too much – on their publication list, and on their contribution to these publications. Often, there is more than one person who was essential to the work.

I disagree with the negative image given to co-first authorship in this career feature article in the Nature journal. Co-first authorship is a win, not a loss. Employers who consider shared authorship as lessening someone's contribution are wrong. https://www.nature.com/articles/d41586-021-01574-y

Learn more about the #PhDProgram at the #Okinawa Institute of #Science and #Technology Graduate University (#OIST) in our #NetCafé today! https://groups.oist.jp/grad/event/oist-cafe-online-202106

Join us to study #plankton genomes!

Our research unit is #hiring a post-doctoral researcher to study #Plankton #genomics at #OIST (#Okinawa Institute of Science and Technology Graduate University). https://www.oist.jp/careers/postdoctoral-researcher-plankton-genomics-luscombe-unit