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Egon Willighagen egonw

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egonw / patientCalories.m
Created January 30, 2014 07:54
# Created by Octave 3.6.4, Thu Jan 26 08:52:32 2014 CET <egonw@elitebook>
# name: calories
# type: matrix
# rows: 73
# columns: 9
612.42 818.41 218.25 747.36 276.32 381.1 737.86 379.16 963.6799999999999
868.42 322.96 426.21 219.89 264.23 960.1900000000001 623.53 436.08 197.17
536.15 419.26 434.87 933.62 347.96 213.77 648.7 795.1 799.73
716.79 653.9 454.61 65.08 97.77 657.61 61.83 221.73 647.1900000000001
389.15 101.12 100.94 418.48 311.85 896.6799999999999 83.55 765.6900000000001 241.98
@egonw
egonw / c2w reply
Created March 3, 2014 10:24
Een vergelijkbaar systeem voor R bestaat al veel langer die het combineert met LaTeX: Sweave (zie bv. [0]). En het tellen van het aantal woorden in LaTeX is geen probleem. Knitr is hier een uitbreiding op en kan in meerdere formaten uitvoer geven [1].
En LaTeX is ook bekend onder chemici, en heeft pakketen om chemische structuren te tekenen [2], en R heeft pakketen om te rekenen aan structuren [3].
0.http://www.r-bloggers.com/getting-started-with-sweave-r-latex-eclipse-statet-texlipse/
1.http://yihui.name/knitr/
2.http://ctan.org/pkg/chemfig
3.http://cran.r-project.org/web/packages/rcdk/index.html
@egonw
egonw / Label "OH"
Last active August 29, 2015 14:01
Find things that could be protein states (Homo sapiens).
WP136 Phase I, non P450 Label "OH" -> db7
WP136 Phase I, non P450 Label "OH" -> e68
WP136 Phase I, non P450 Label "OH" -> e3d
WP136 Phase I, non P450 Label "OH" -> f1b
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> b92
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> aa2
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> d9a
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> a12
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> d94
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> a25
@egonw
egonw / QC report for hmdb_metabolites_20140516.bridge with BridgeDb 1.2.txt
Last active August 29, 2015 14:01
QC reports for hmdb_metabolites_20140516.bridge
WARNING: old DATASOURCENAME 'HMDB3' doesn't match new DATASOURCENAME 'HMDB35CHEBI'
INFO: Number of ids in Ce: 54081 (changed +82.2%)
INFO: Number of ids in Ch: 41513 (changed +0.0%)
INFO: Number of ids in Kd: 10 (changed +0.0%)
INFO: Number of ids in Ck: 8600 (changed +49.5%)
INFO: Number of ids in Cs: 16055 (changed +1.7%)
INFO: Wi is only in new database
INFO: Number of ids in Wi: 3300
INFO: Number of ids in Cpc: 16910 (changed +0.0%)
INFO: Number of ids in Ca: 24042 (changed +39.2%)
@egonw
egonw / orcids.csv
Last active August 29, 2015 14:02
ORCID identifiers of Maastricht University
0000-0001-7542-0286 FHML NUTRIM BiGCaT
0000-0002-9454-023X FHML CAPHRI Department of Family Medicine
0000-0002-5301-3142 FHML NUTRIM BiGCaT
0000-0002-6736-7814 Department of Molecular Genetics
@egonw
egonw / gist:504667713eb27f0ba3bb
Created August 20, 2014 14:01
@PREFIX w : <http://drugmet.rilspace.org/wiki/Special:URIResolver/> .
SELECT distinct ?o
WHERE {
?s <http://drugmet.rilspace.org/resource/hasPKaValue> ?s2 .
?s2 <http://semanticscience.org/resource/SIO_000300> ?o .
}
@egonw
egonw / report_human.txt
Created September 1, 2014 11:37
42 possible metabolites in WikiPathways encoded as Labels
Mon Sep 01 13:15:07 CEST 2014
Hs_Primary_Focal_Segmental_Glomerulosclerosis_FSGS_WP2572_76327.gpml: node a1b1e -> CALCIUM -> FAQLAUHZSGTTLN-UHFFFAOYSA-N -> CSID: []
Hs_Regulation_of_toll-like_receptor_signaling_pathway_WP1449_72114.gpml: node a02a3 -> Imidazoquinolin -> RHKWIGHJGOEUSM-UHFFFAOYSA-N -> CSID: [14697812]
Hs_Glucocorticoid_&_Mineralcorticoid_Metabolism_WP237_72079.gpml: node dc7 -> 3a,11b,21-Trihydroxy-20-Oxo-
5b-Pregnan-18-al -> YWTDWORQGPLRLL-UHFFFAOYSA-N -> CSID: [21233046, 4293559]
Hs_Glucocorticoid_&_Mineralcorticoid_Metabolism_WP237_72079.gpml: node f9a -> 5b-Pregnane-3,20-dione -> XMRPGKVKISIQBV-UHFFFAOYSA-N -> CSID: [21427590, 389575, 21232692, 21239075, 21237402]
Hs_Tryptophan_metabolism_WP465_71269.gpml: node adb -> 4-(2-Amino-5-hydroxyphenyl)
-2,4-dioxobutanoate -> MISPYSDHCLFNAO-UHFFFAOYSA-M -> CSID: [389617]
Hs_Tryptophan_metabolism_WP465_71269.gpml: node df7 -> 2,3-Dihydroxyindole -> PGNRLPTYNKQQDY-UHFFFAOYSA-N -> CSID: [20546]
Hs_Tryptophan_metabolism_WP465_71269.gpml: node e9f -> 2
@egonw
egonw / report_rat.txt
Created September 5, 2014 09:28
47 possible metabolites in rat WikiPathways encoded as Labels
Fri Sep 05 09:46:36 CEST 2014
Rn_Eicosanoid_Synthesis_WP293_71781.gpml: node e21 -> 12-Hydroperoxy Eicosatetraenoic Acid -> XCPNMPKPSWOLJW-UHFFFAOYSA-N -> CSID: [21233953, 10798777, 19198313]
Rn_Eicosanoid_Synthesis_WP293_71781.gpml: node b01 -> 15-Hydroperoxy Eicosatetraenoic Acid -> PYJFPHSZYWTSAS-UHFFFAOYSA-N -> CSID: [11409559, 20118045, 21402969]
Rn_Glutathione_metabolism_WP469_70700.gpml: node ea9 -> Taurine and hypotaurine -> OJFAFAAQEAAQJU-UHFFFAOYSA-N -> CSID: []
Rn_Glutathione_metabolism_WP469_70700.gpml: node dcc -> Glutathione -> RWSXRVCMGQZWBV-UHFFFAOYSA-N -> CSID: [725]
Rn_Glutathione_metabolism_WP469_70700.gpml: node ca2 -> Acetyl-CoA -> ZSLZBFCDCINBPY-UHFFFAOYSA-N -> CSID: [176, 21232084, 21236014, 21232302]
Rn_Glutathione_metabolism_WP469_70700.gpml: node d98 -> glycylspermidine -> CDXBTVMXHBTNRG-UHFFFAOYSA-N -> CSID: []
Rn_Alanine_and_aspartate_metabolism_WP104_72099.gpml: node ec9 -> Acetyl-CoA -> ZSLZBFCDCINBPY-UHFFFAOYSA-N -> CSID: [176, 21232084, 21236014, 21232302]
Rn_Alanine_and_aspart
@egonw
egonw / datadryad.output.txt
Last active August 29, 2015 14:11
Writing a CiteULike plugin for FigShare...
$ ./driver.tcl parse http://www.datadryad.org/resource/doi:10.5061/dryad.fr43s
parsing http://www.datadryad.org/resource/doi:10.5061/dryad.fr43s
keywords -> Ecological Genetics; Fish; Genomics/Proteomics; Life History Evolution; Empirical Population Genetics; Wildlife Management
linkouts -> {DRYAD {} 10.5061/dryad.fr43s {} {}} {DOI {} 10.5061/dryad.fr43s {} {}}
year -> 2014
type -> GEN
plugin_version -> 1
publisher -> Dryad Digital Repository
day -> 10
@egonw
egonw / example.ttl
Last active August 29, 2015 14:13
Wikidata mappings for 71 3char ISO country codes.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix cgn: <http://purl.org/cgngenis/accenumb/> .
@prefix xs: <http://www.w3.org/2001/XMLSchema> .
@prefix wikidata: <https://www.wikidata.org/wiki/> .
cgn:CGN22884 dwc:coordinateUncertaintyInMeters
"4342333"^^qudt:Meter ;
dwc:country wikidata:Q30 ;