Lack of appropriate funding leads to cutting corners to the point that some results may not be worth the price of the paper to describe them. I had a passing experience with epigenetics. Even experiments with basically free of ethics issues cell lines could be screwed up by using single end, too short sequencing reads. Combined with too low coverage, less than perfect controls it gives the input data I which the state of the art peak callers will just throw the towel. So the "trick" is to use some way more forgiving peak caller and get a rather crappy results.
Using the outdated human genome assembly (hg19), and old genome mapping programs just puts an extra cherry on the cake...
I belive you are mixing assembling the genome by combining sequences of individual, overlapping inserts of cosmids, fosmids, PACs and BACs (bacterial vectors with human DNA inserts of 40-150kbp) to whole genome shotgun.
The inserts of the above bacterial vectors were sequenced using shotgun, but the gaps in the sequence were closed with custom primers.
Thank you for your kind words. Sorry for the Captain's Obvious a bit rude comment. It just happened that me and my partner were battling traffic using rickety road through the hills above the Barcelona to get on time for a chemotherapy session. Just to be told that due to the blackout it must be postponed for a few days. Luckily nothing serious in the long run, but nevertheless rather annoying. Because of the traffic jams and lack of mobile coverage for many hours in various locations in Spain I am quite sure there were some extra fatalities.
Thinking about it, there is nothing wrong writing about unexpected pleasures of that day. Just that we keep in mind the fact that blackouts have this non-hipstery, rather serious aspects.
PS I am doing ok-eish, splendid even considering the initial diagnosis (pancreatic cancer 1b stage diagnosed in December 2024). Maybe still way too touchy about some topic apparently triggering me.
If you would have a family member having a scheduled chemotherapy treatment for that day the thrill would be gone. Not every day is great for the chill out.
Spain does have few (probably 4 according to ESP Wikipedia) pumped-storage hydroelectricity plants. Supposedly these are being used nowadays to store excess of energy produced by fotovoltaic plants. No idea how fast these can switch from storing energy to producing it and if these were used to help during the blackout.
Also missing in vast majority of the dams is a lower reservoir. Pumping up the water from a river/canal below the dam would result in a dry river bed just below the dam rather quickly
Small thing: keeping old books is a bit like a physical memory palace. Granted, it may be pointless/way to costly to cling to a collection of say outdated books read as an adolescent, but we tend to remember better if we can access at least the visual image of the cover.
So my advice is to take the pictures of book covers you have to get rid of. And organize them be it by the time period you have read them, topic or something else. One day you may be able to fish out memories you didn't think exist anymore.
Re science: yes and no. Meaning: the old way of compiling programs from sources on HPC systems while not dead is becoming rare. I can only speak about bioinformatics: the majority of programs one can get up and running in no time using either conda environments or apptainer containers. It may take few weeks for the brand new shiny version to get packaged by the maintainers, but this is seldom the problem.
Even if you want to compile some program you will save yourself the time and frustration using either conda env or a container with a required toolchain/libraries. Even on a box with root access you need to avoid conflicting system wide installed library versions where program A requires lib version X and program B lib version Y.
Well, call them lazy but once you have i.e. biocontainers in which individual bioinformatics programs are prepackaged, hardly any scientist in that field would be reinventing the wheel and often just waste te time trying to install all the requirements and compile a program already running "good enough" using downloaded SIF.
Sure, at times with say limited resources one can try to speed up some frequently used software creating SIF from scratch with say newer or more optimized Linux distro (if memory serves me right containers using Alpine Linux/musl library were a bit slower than containers using Ubuntu). But in the end splitting the input into smaller chunks, running i.e genome mapping on multiple nodes then combining the results, should be way faster than "turbo-charging" the genome mapping program run on a single node even with a big number of cores.
The whole idea of maintaining module systems in a perfect sync on several systems as compared to i.e. just rsync-ing SIFs sounds strange to me. Often HPC systems (or rather their admins) are fairly (and for a good reason) conservative, keeping old system and libraries versions. Your mileage may vary, but in a small benchmark of a bioinformatics program called samtools depending on the version the fastest binaries were either run in a conda environment or inside singularity container using Clear Linux distro. Binaries compiled using either system's GCC or from a module were slower.
One would have to repeat it throwing in at least Spack to see if this still holds water.
Frankly I have a problem with one of your problem as described. Who on the planet Earth creates a container with GCC, may I guess, to compile programs? and then complains about make being located in another container.
If you miss some utility just convert the apptainer container to a sandbox, install utilities you need and convert the sandbox to .sif as needed.
Also the whole point of building the program using compilers/libraries in the container is to use such container to run the aforementioned program in that very environment and not worry about libraryX or utility Y not installed in some box in a galaxy far, far away...
I have gave up on E. once they supported GWB over Gore. I can barely understand over the top devotion to neoliberalism and deregulation. But the shortcomings of GWB were sticking out in the campaign, so closing the eyes and singing "la la liberalism" was way too much for me.
You may check Europe. I can assure you that patients getting PD-1 inhibitors etc. while if I am not mistaken at least in part recruited for clinical trials pay zilch, nada for the drugs there are taking (in Spain).
I am not sure I want to have the same painting or a poster on the wall not even for the rest of my life but for 5-10 years. Apart from maybe a tattoo with one's blood group frankly I am puzzled by the idea of getting even the most artsy-fartsy tattoo anywhere on my body.
While it is an important finding blocking either EPO production in the cancer cells or it's receptor on tumor infiltration macrophages is not trivial.
One can end up with a severe anemia.
Ignoring for the moment issues of syncing a database where the source DB may be running inserts/updates:
if one dumps tables as separate CSV files/streams and using DuckDB converts them to individual parquet files the rsync should run faster since hopefully not every table is modified between each new syncing. There is an obvious overhead of the back and forth conversions but DuckDB can directly export a database to SQLite.
I have not tested it myself, so it is just a brainstorming.
Last but not least: when compressing/decompressing text dumps use igzip or pigz if you want to speed things up. Also benchmark the compression levels.