apraga/org - Change SYWVRVTSQFTJTEOZOEIIRDGPSJUEIIXT6FLFGXK7MJGL2P2C7MOQC

Notes on reviewing Jakobs paper

Created by Alexis Praga on November 26, 2023

SYWVRVTSQFTJTEOZOEIIRDGPSJUEIIXT6FLFGXK7MJGL2P2C7MOQC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 6922 [7.1]

[6.163]

* <2023-11-26 Sun> Running
53min avec 1 petite montée

Replacement in site.hs at line 14 [8.9907]

B:BD[2.98] → [2.98:145]

           , "notes/medecine/hématologie.org"

[2.98]

[2.145]

           , "notes/medecine/hematologie.org"

Replacement in projects.org at line 77 [7.123895]

B:BD[3.2500] → [3.2500:2554]

** TODO Command minoxidil
SCHEDULED: <2023-11-26 Sun>

[3.2500]

[3.2554]

** DONE Command minoxidil
CLOSED: [2023-11-26 Sun 21:56] SCHEDULED: <2023-11-26 Sun>

Replacement in projects.org at line 423 [7.123895]

B:BD[9.656] → [3.6751:6782]

∅:D[3.6782] → [9.656:690]

B:BD[9.656] → [9.656:690]

**** TODO Examens d'hémostase
SCHEDULED: <2023-11-25 Sat 19:00>

[9.656]

[10.614]

**** DONE Examens d'hémostase
CLOSED: [2023-11-26 Sun 20:50] SCHEDULED: <2023-11-25 Sat 19:00>

Replacement in projects.org at line 430 [7.123895]
B:BD[10.705] → [6.175:208]
```
SCHEDULED: <2023-11-26 Sun .+1d>
```
[10.705]
[10.738]
```
SCHEDULED: <2023-11-27 Mon .+1d>
```
Replacement in projects.org at line 433 [7.123895]
B:BD[10.768] → [6.209:246]
```
:LAST_REPEAT: [2023-11-25 Sat 22:37]
```
[10.768]
[10.805]
```
:LAST_REPEAT: [2023-11-26 Sun 21:57]
```

Insertion in projects.org at line 435 [7.123895]

[10.811]

[6.247]

- State "DONE"       from "TODO"       [2023-11-26 Sun 22:13]

Deletion in projects.org at line 455 [7.123895]

B:BD[3.6928] → [3.6928:7056]

**** DONE Location (blackfriday)
CLOSED: [2023-11-20 Mon 19:32] SCHEDULED: <2023-11-20 Mon>
/Entered on/ [2023-11-20 Mon 18:29]

Replacement in projects.org at line 459 [7.123895]

B:BD[3.7183] → [3.7183:7582]

**** DONE Configurer rtorrent
CLOSED: [2023-11-20 Mon 22:53] SCHEDULED: <2023-11-21 Tue>
**** DONE Tester 1 livres :mam:
CLOSED: [2023-11-20 Mon 22:05] SCHEDULED: <2023-11-21 Tue>
**** DONE Ouvrir IP :mam:
CLOSED: [2023-11-20 Mon 22:22] SCHEDULED: <2023-11-21 Tue>
**** DONE Vérifier connectivity :mam:
CLOSED: [2023-11-20 Mon 22:22] SCHEDULED: <2023-11-21 Tue>
/Entered on/ [2023-11-20 Mon 22:04]

[3.7183]

[3.7582]

**** TODO Convertir FLAC en mp3 V0 et 320
 #+begin_src sh
 perl ~/softwares/flac2mp3/flac2mp3.pl --preset=320 test test320
 #+end_src
***** DONE Jacques Amade
CLOSED: [2023-11-26 Sun 19:13]

Replacement in projects.org at line 866 [7.123895]

B:BD[11.313] → [3.14641:14712]

**** TODO Correction v2 + envoi co-auteurs
SCHEDULED: <2023-11-26 Sun>

[11.313]

[12.997]

**** DONE Correction v2 + envoi co-auteurs
CLOSED: [2023-11-26 Sun 18:54] SCHEDULED: <2023-11-26 Sun>

Replacement in projects/bisonex.org at line 65 [13.35]

B:BD[5.57375] → [5.57375:65567]

uery=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur  les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** DONE Mail cento pour demande le type de capture
CLOSED: [2023-10-07 Sat 17:59]
/Entered on/ [2023-08-07 Mon 20:40]
Twist exome
*** PROJ Comparer happy et happy-vcfeval :giab:
** TODO Données syndip (CHM-eval) ! :syndip:
https://github.com/lh3/CHM-eval
*** KILL Données officielles : non car génome !!
CLOSED: [2023-11-19 Sun 23:43]
**** KILL Run ERR1341793
CLOSED: [2023-11-19 Sun 23:43] SCHEDULED: <2023-11-18 Sat>
(raw reads ERR1341793_1.fastq.gz and ERR1341793_2.fastq.gz downloaded from https://www.ebi.ac.uk/ena/browser/view/ERR1341793)
**** KILL Run ERR1341796
CLOSED: [2023-11-19 Sun 23:43] SCHEDULED: <2023-11-18 Sat>
*** TODO Données exome Broad institute (nextflow)
SCHEDULED: <2023-11-25 Sat 21:00>
https://console.cloud.google.com/storage/browser/broad-public-datasets/CHM1_CHM13_WES;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false
*** TODO Télécharger VCF
SCHEDULED: <2023-12-01 Fri>
https://github.com/lh3/CHM-eval/releases
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel   l et nettoyée à la main.
On générer une liste de variant pour variant_rec            oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
  prepareVariantRecod   er "variant_success.csv" "renamed.csv"
  runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
:     Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
    foreach(rm, variantRecoderInput())
    foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits ont juste été supprimé
- [X] Erreur de parsing, manque souvent un -
#+begin_src julia
lastTryMobidetails("recoded-failures-mobidetails.csv")
#+end_src
***** DONE Fusionner données
CLOSED: [2023-04-26 Wed 22:35]
#+begin_src julia
function mergeAllGenomic()
    dNew = mergeAll("recoded-success.csv",
                    "recoded-failures-mobidetails.csv",
                    "recoded-failures-mobidetails-redo.csv")
    dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin
        @transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange
        @select :file :transcript :classification :zygosity
        @rename :classificationCento = :classification
    end
    dTmp = outerjoin(dInit, dNew, on = :transcript)
    CSV.write("variant_genomic.csv", dTmp)
end
fSuccess = "recoded-success.csv"
fFailures = "recoded-failures.csv"
# variantRecoder(fSuccess, fFailures)
# mobidetailsOnFailures(fFailures)
# lastTryMobidetails("recoded-failures-mobidetails.csv")
mergeAllGenomic()
#+end_src
***** DONE Formatter donner pour simuscop
CLOSED: [2023-04-28 Fri 11:55] SCHEDULED: <2023-04-26 Wed>
**** KILL Extraire liste des CNVs
CLOSED: [2023-08-12 Sat 15:54]
SCHEDULED: <2023-04-17 Mon>
**** KILL Simuscop :simuscop:
CLOSED: [2023-08-12 Sat 15:54]
***** DONE Entrainer le modèle sur 63003856/
CLOSED: [2023-04-29 Sat 19:56]
Relancer le modèle pour être sûr
***** DONE Générer fastq avec simuscop (del et ins seulement) 20x
CLOSED: [2023-04-28 Fri 23:35] SCHEDULED: <2023-04-22 Sat>
****** DONE Génerer un profile avec bed de centogène
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
NA12878 mais à refaire avec un vrai séquencage
Voir [[*Centogène][Bed Centogène]] pour choix
****** DONE Générer les données en 20x
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
capture de cento
****** DONE Regénérer en supprimant les doublons
CLOSED: [2023-04-28 Fri 17:28]
***** DONE Quelle couverture ?
CLOSED: [2023-04-29 Sat 18:26]
ex sur chr11:16,014,966 où on a 11 reads dans la simulation contre 200 !
****** 200 est la plus proche
#+attr_html: :width 500px
[[./simuscop-200-chr1-1.png]]
#+attr_html: :width 500px
[[./simuscop-200-chr1-2.png]]
****** DONE 20x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 50x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 100x
CLOSED: [2023-04-29 Sat 15:39]
****** DONE 200x
CLOSED: [2023-04-29 Sat 15:39]
***** DONE Reads mal centrés sur des petits exons seuls
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
Capture ok : [[https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A153817168%2D153817824&hgsid=296556270_F4fkENLPXHXidi2oALXls2jxNH9l][UCSC]] (track noire)
Mais mauvaise répartitiopn
#+attr_html: :width 800px
[[./simuscop-error.png]]
À tester
- Problème de profile ?
  - mauvais patient ?
  - mauvaise génération ? -> comparer avec ceux donnés sur github
- nom des chromosomes ?
****** DONE [#A] Tester sur exon 6 GATAD2B pour NC_000001.11:g.153817496A>T
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
******* DONE Configuration + Profile 63003856.profile: idem, mal centré
CLOSED: [2023-04-29 Sat 19:18]
Téléchargement des données
#+begin_src sh :dir ~/code/bisonex/test-simuscop
scp meso:/Work/Projects/bisonex/data/genome/GRCh38.p14/genomeRef.fna .
scp meso:Work/Projects/bisonex/data/simuscop/*.profile .
scp -r meso:/Work/Projects/bisonex/data/genome/GRCh38.p13/bwa .
#+end_src
On récupère l'exon (NB: org-mode ne lance pas le code

[5.57375]

[5.65567]

uery=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur  les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** DONE Mail cento pour demande le type de capture
CLOSED: [2023-10-07 Sat 17:59]
/Entered on/ [2023-08-07 Mon 20:40]
Twist exome
*** PROJ Comparer happy et happy-vcfeval :giab:
** TODO Données syndip (CHM-eval) ! :syndip:
https://github.com/lh3/CHM-eval
*** KILL Données officielles : non car génome !!
CLOSED: [2023-11-19 Sun 23:43]
**** KILL Run ERR1341793
CLOSED: [2023-11-19 Sun 23:43] SCHEDULED: <2023-11-18 Sat>
(raw reads ERR1341793_1.fastq.gz and ERR1341793_2.fastq.gz downloaded from https://www.ebi.ac.uk/ena/browser/view/ERR1341793)
**** KILL Run ERR1341796
CLOSED: [2023-11-19 Sun 23:43] SCHEDULED: <2023-11-18 Sat>
*** TODO Données exome Broad institute (nextflow)
SCHEDULED: <2023-12-03 Sun>
https://console.cloud.google.com/storage/browser/broad-public-datasets/CHM1_CHM13_WES;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false
*** TODO Télécharger VCF
SCHEDULED: <2023-12-01 Fri>
https://github.com/lh3/CHM-eval/releases
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel   l et nettoyée à la main.
On générer une liste de variant pour variant_rec            oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
  prepareVariantRecod   er "variant_success.csv" "renamed.csv"
  runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
:     Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
    foreach(rm, variantRecoderInput())
    foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits ont juste été supprimé
- [X] Erreur de parsing, manque souvent un -
#+begin_src julia
lastTryMobidetails("recoded-failures-mobidetails.csv")
#+end_src
***** DONE Fusionner données
CLOSED: [2023-04-26 Wed 22:35]
#+begin_src julia
function mergeAllGenomic()
    dNew = mergeAll("recoded-success.csv",
                    "recoded-failures-mobidetails.csv",
                    "recoded-failures-mobidetails-redo.csv")
    dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin
        @transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange
        @select :file :transcript :classification :zygosity
        @rename :classificationCento = :classification
    end
    dTmp = outerjoin(dInit, dNew, on = :transcript)
    CSV.write("variant_genomic.csv", dTmp)
end
fSuccess = "recoded-success.csv"
fFailures = "recoded-failures.csv"
# variantRecoder(fSuccess, fFailures)
# mobidetailsOnFailures(fFailures)
# lastTryMobidetails("recoded-failures-mobidetails.csv")
mergeAllGenomic()
#+end_src
***** DONE Formatter donner pour simuscop
CLOSED: [2023-04-28 Fri 11:55] SCHEDULED: <2023-04-26 Wed>
**** KILL Extraire liste des CNVs
CLOSED: [2023-08-12 Sat 15:54]
SCHEDULED: <2023-04-17 Mon>
**** KILL Simuscop :simuscop:
CLOSED: [2023-08-12 Sat 15:54]
***** DONE Entrainer le modèle sur 63003856/
CLOSED: [2023-04-29 Sat 19:56]
Relancer le modèle pour être sûr
***** DONE Générer fastq avec simuscop (del et ins seulement) 20x
CLOSED: [2023-04-28 Fri 23:35] SCHEDULED: <2023-04-22 Sat>
****** DONE Génerer un profile avec bed de centogène
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
NA12878 mais à refaire avec un vrai séquencage
Voir [[*Centogène][Bed Centogène]] pour choix
****** DONE Générer les données en 20x
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
capture de cento
****** DONE Regénérer en supprimant les doublons
CLOSED: [2023-04-28 Fri 17:28]
***** DONE Quelle couverture ?
CLOSED: [2023-04-29 Sat 18:26]
ex sur chr11:16,014,966 où on a 11 reads dans la simulation contre 200 !
****** 200 est la plus proche
#+attr_html: :width 500px
[[./simuscop-200-chr1-1.png]]
#+attr_html: :width 500px
[[./simuscop-200-chr1-2.png]]
****** DONE 20x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 50x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 100x
CLOSED: [2023-04-29 Sat 15:39]
****** DONE 200x
CLOSED: [2023-04-29 Sat 15:39]
***** DONE Reads mal centrés sur des petits exons seuls
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
Capture ok : [[https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A153817168%2D153817824&hgsid=296556270_F4fkENLPXHXidi2oALXls2jxNH9l][UCSC]] (track noire)
Mais mauvaise répartitiopn
#+attr_html: :width 800px
[[./simuscop-error.png]]
À tester
- Problème de profile ?
  - mauvais patient ?
  - mauvaise génération ? -> comparer avec ceux donnés sur github
- nom des chromosomes ?
****** DONE [#A] Tester sur exon 6 GATAD2B pour NC_000001.11:g.153817496A>T
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
******* DONE Configuration + Profile 63003856.profile: idem, mal centré
CLOSED: [2023-04-29 Sat 19:18]
Téléchargement des données
#+begin_src sh :dir ~/code/bisonex/test-simuscop
scp meso:/Work/Projects/bisonex/data/genome/GRCh38.p14/genomeRef.fna .
scp meso:Work/Projects/bisonex/data/simuscop/*.profile .
scp -r meso:/Work/Projects/bisonex/data/genome/GRCh38.p13/bwa .
#+end_src
On récupère l'exon (NB: org-mode ne lance pas le code

File addition: reviews (d--x------)
[14.29]

File addition: jakobs2023.org (----------)

[0.8990]

Commentaire général : féliciter pour reprendre le code et publier les résultats de manière honnête
Contexte:
- version 6 déjà parallélisée : en C (CPU ?): speed 216, avec opeacc (67) et CUDA (4-5)
- version 7 : la grèle est une catégorie supplémentaire (et non pas simplement de la "neige roulée" -> pas clair, voir Bae 2018 [[file:~/research/biblio.org::*Development of a Single-Moment Cloud Microphysics Scheme with Prognostic Hail for the Weather Research and Forecasting (WRF) Model][Bae 2018]]] )
#+begin_quote
the WSM6 model is extended to a four-ice microphysics scheme by considering the
hydrometeor hail as an additional category rather than solely relying on graupel.
#+end_quote
* Intro
- Contexte: https://link.springer.com/article/10.1007/s13143-018-0066-3 Ajout de la grêle dans le modèle
- Grille : régulière ? À préciser
- Étendue du modèle (national probablement)
* 3
Argument sur le choix du C au lieu de Fortran n'est pas très clair
#+begin_quote
for this work the Fortran version is reimplemented in C++ using CUDA due
to the extensive usage of object orientation for the creation of GPU tasks, which only
can be represented insufficiently in Fortran based approaches like CUDA-Fortran.
#+end_quote
** Parallélisation :
- comment sont réparties les tâches de calcul (1 colonne = 1 tache a priori) ? Simple pile ou algorithme plus compliqué ?
#+begin_quote
Each column can be simulated in parallel allowing for a simultane-
ous calculation along the horizontal mesh points following the longitude and latitude
coordinates
#+end_quote
Cette phrase peut être supprimée car redondante
- Question: charge de calcul équilibrée horizontalement ? Et verticalement ? Il serait intéressant de voir la charge de calcul au cours du temps
Figure 2 : type "Daten" -> data, type "direkt" -> direct
* 4
- WPS = ?
CONUS = ?
MM5 ?
- Erreur : single float donc en-dessous du seuil ???
Précision:
- Comparaison entre Fortran et GPU: ok pour la non-régression mais par rapport aux observations ?? Le modèle a échoué à prédire (à vérifier) mais la version parallèle semble mieux prédite. Due à la meilleure précision ou artefact de la parallilésation ?
- testé sur le modèle 2D de Bae et al 2018 ?

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```
- déficit en fibrinogène : le plus souvent acquis mais congénital possible
```
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```
fact [label="VIII, IV, XI, XII"];
```
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```
fact [label="VIII, IX, XI, XII"];
```

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subgraph {"XI seul" -> "Infection\nGrosseses\nDéficit constit\nInhibiteur"}

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subgraph {"XI seul" -> "Infection\nGrossesse\nDéficit constit\nInhibiteur"}

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[5.82725]


** Variations physiologiques
- Grossesse :
  - augmentation facteur VIII, Willebrand *fibrinogène*, diminution XI
  - augmentation TP (VII, X, fibrinogène)
- Nouveau-né : carence en vitamine K (donc doser TP, TCA)
** Facteurs
- VIII: 50-150%, évolue parallèlement au willebrand (augmenté grossesse/inflammation mais aussi cirrhose hépatique par synthèse endothéliale)
- IX : 50-150% : diminué avant 3 mois
- XI: 60-140% : diminué avec 1 ans, diminué si IHC
** D-dimère
Produit de dégradation de la fibrine
- augmenté si CIVD
- bonne VPN pour thrombose/embolie pulmonaire (<450-550)

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```
...
```
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* DONE Location (blackfriday)
CLOSED: [2023-11-20 Mon 19:32] SCHEDULED: <2023-11-20 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-11-20 Mon 18:29]
* DONE Configurer rtorrent
CLOSED: [2023-11-20 Mon 22:53] SCHEDULED: <2023-11-21 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
* DONE Tester 1 livres :mam:
CLOSED: [2023-11-20 Mon 22:05] SCHEDULED: <2023-11-21 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
* DONE Ouvrir IP :mam:
CLOSED: [2023-11-20 Mon 22:22] SCHEDULED: <2023-11-21 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
* DONE Vérifier connectivity :mam:
CLOSED: [2023-11-20 Mon 22:22] SCHEDULED: <2023-11-21 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-11-20 Mon 22:04]

Notes on reviewing Jakobs paper

Dependencies

In channels

Change contents

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