Charles Plessy @charles_plessy@mastodon.technology

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

Our research on the #genome of the #Oikopleura #zooplankton in #Okinawa is finally published in #BMC Genomics! https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07512-6

#Faculty positions open in "#Quantum Information Science and #Engineering", "#Artificial #Intelligence", "Molecular and #Cell #Biology" and other areas at #OIST, the #Okinawa Institute of #Science and #Technology Graduate University. Application deadline: April 30th. https://groups.oist.jp/facultypositions

Great to read advocacy the #Unix command-line in the scientific journal #Nature. By the way,

awk -F, '{ if ($4 > 50) print $0 }'

can be shortened to

awk -F, '$4 > 50''

Link to the article: https://www.nature.com/articles/d41586-021-00263-0

“Guidance on software citation created by the community for the community”, a blog post about the work of the #FORCE11 #Software #Citation Implementation Working Group.

https://blog.f1000.com/2021/01/26/guidance-on-software-citation-created-by-the-community-for-the-community/

4-figures pre-prints show the ambition of their authors but their most important information in in the “supplemental” material.

The Science festival of #OIST will be held online this January 30th.
https://sciencefest.oist.jp/

I was reading about "hardware-agnostic" code in a research article. According to Wiktionary, "agnostic" comes from Greek and stands for "ignorant". But Wiktionary also tells us that "ignorant" comes from Latin (via French) and means "unknowing". If we would replace words from our #vocabulary such as "agnostic" with simpler words like "unknowing", would it make #science more accessible to all? I do not know.