| born stunted born stunted whether the individual was born stunted (LAZ less than -2) parent | |
| severely stunted at sampling severely stunted at sampling whether the individual was found severely stunted at sampling (LAZ less than -3) Anthropometry | |
| stunted 3 months after sampling stunted 3 months after sampling whether the individual was found stunted 3 months aftet sampling (LAZ less than -2) Anthropometry | |
| stunted at sampling stunted at sampling whether the individual was found severely stunted 3 months after sampling (LAZ less than -3) Anthropometry | |
| laz 1 month after sampling LAZ 1 month after sampling Length-to-height Z-score 1 month after sampling Anthropometry | |
| laz 3 months after sampling LAZ 3 months after sampling Length-to-height Z-score 3 months after sampling Anthropometry | |
| laz at enrollment LAZ at enrollment Length-to-height Z-score at enrollment Anthropometry | |
| laz at sampling LAZ at sampling Length-to-height Z-score at sampling Anthropometry | |
| mean daily feeds at breast mean daily feeds at breast Mean dail |
To use this technology, we need Singularity installed in the target environment by root, which is possibly the largest obstacle for us.
Here is a container for analysing 16s rRNA data in MicrobiomeDB, requiring an R package DADA2. DADA2 releases to BioConductor, but we want the ability to load an arbitrary commit for development.
We can build on somebody's container with r-devtools, and add our libraries:
| Protopolystoma xenopodis (PRJEB1201) | 26263 | 37906 | 0.69 | |
|---|---|---|---|---|
| Romanomermis culicivorax (PRJEB1358) | 24769 | 48376 | 0.51 | |
| Gyrodactylus salaris (PRJNA244375) | 7929 | 15436 | 0.51 | |
| Heterorhabditis bacteriophora (PRJNA13977) | 8366 | 20964 | 0.40 | |
| Soboliphyme baturini (PRJEB516) | 4960 | 13193 | 0.38 | |
| Saccharomyces cerevisiae | 2516 | 6692 | 0.38 | |
| Parascaris equorum (PRJEB514) | 5558 | 14472 | 0.38 | |
| Ixodes scapularis | 7405 | 20486 | 0.36 | |
| Steinernema glaseri (PRJNA204943) | 11383 | 34137 | 0.33 | |
| Meloidogyne floridensis (PRJEB6016) | 16701 | 49938 | 0.33 |
| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta name="viewport" content="width=device-width, initial-scale=1.0"> | |
| <title>Lab meeting 24.07.2018</title> | |
| <link rel="stylesheet" href="https://stackedit.io/style.css" /> | |
| </head> |
| sampleAttributes() { | |
| curl -s "https://www.ebi.ac.uk/ena/data/view/$1&display=xml " \ | |
| | perl -MXML::LibXML -e ' | |
| for my $attr (XML::LibXML->load_xml(string => do {local $/ ; <> }) -> findnodes("./ROOT/SAMPLE/SAMPLE_ATTRIBUTES/*")) { | |
| print $attr->findvalue("./TAG") . "\t" . $attr->findvalue("./VALUE"). "\n" | |
| } ' | |
| } | |
| sampleAttributes SRS1334254 |
| >HmN_000814400.1 Hymenolepis microstoma WormBase ParaSite 9 | |
| MDVKRLQIEIDHSKLQTAIDAASGALRRTRSNQERATIVRQAMDDRYGPAWSCVTGMDFG | |
| SEIPYLPENFAFFTVNNVSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
| XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
| echo "$(date +%H) < 21" | bc | xargs test 1 -eq || say "This is your reminder" |
| [13:04] <huf> once again i managed to buy socks that are nearly the same color but not quite | |
| [13:04] == pmurias [~pmurias@89-79-102-79.dynamic.chello.pl] has left #perl [] | |
| [13:04] <huf> what fun i'll have mispairing them | |
| [13:08] == Secret113 [a37869e1@gateway/web/freenode/ip.163.120.105.225] has quit [Ping timeout: 260 seconds] | |
| [13:09] == orannis_ [~orannis@c-76-102-252-86.hsd1.ca.comcast.net] has joined #perl | |
| [13:09] <sibiria> in hungary one buys socks a piece? as in, "i need to buy a sock, i hope i can get one that looks like one of my others" | |
| [13:09] <jantje> huf: put rfid tags in 'm and scan 'm ! | |
| [13:10] <sibiria> i cannot imagine this plight | |
| [13:10] <huf> sibiria: um, you should ponder this a bit more | |
| [13:10] <huf> there must be an explanation that's reasonable |