Tip: use instead of the 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`. gnu.org/software/time/

`if zcat bigfile | head | grep…` considered harmful 

It took me some time to understand why an if / else statement was giving me opposite results when run in a container via a pipeline. The reason was that it sets `-o pipefail` on the 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! stackoverflow.com/questions/41

I am at the yearly of the Molecular Society of , in , from today to Friday. I will present our work the rapid scrambling of coordinates during . www2.aeplan.co.jp/mbsj2021/eng

`zip -FF` or `7z x` to rescue big "corrupted" ZIP file. 

I received a big file containing data, version 6.0.0 would not open it and instead report that it is . Thanks to an old discussion on .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 or systems: (bitsgalore.org/2020/03/11/does). It seems that the command from package can also open some.

Speed fluctuations of bacterial replisomes. I am co-author in this preprint. In this work, three units joined their forces to produce experimental data of abundance in exponentially growing Escherichia coli, and to formulate a that permits to infer the 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 . Our slides are here: github.com/Rafael-Ayala/R-pack

RTF-EXPAR: Isothermal and exponential detection of the SARS-CoV-2 RNA under 10 minutes. 

In today, an article from the University of , using the BstNI enzyme to nick a oligonucleotide annealed to the of the SARS-CoV-2 (causing ) produce the trigger for detection under 10 min with an exponential amplification system called . pnas.org/content/118/35/e21003

Call for applications for the Interdisciplinary Postdoctoral Scholar Fellowship Program at OIST. 

The Scholar (IPSF) program provides a unique opportunity to advance researchers' academic careers by conducting full-time research and training at the Institute for and (). Follow this link to apply: apply.interfolio.com/75577

Co-first, equal authorship is great ! 

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. nature.com/articles/d41586-021

positions open in " Information Science and ", " ", "Molecular and " and other areas at , the Institute of and Graduate University. Application deadline: April 30th. groups.oist.jp/facultyposition

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

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

can be shortened to

awk -F, '$4 > 50''

Link to the article: nature.com/articles/d41586-021

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


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

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 such as "agnostic" with simpler words like "unknowing", would it make more accessible to all? I do not know.

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