View spectre.c
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#ifdef _MSC_VER
#include <intrin.h> /* for rdtscp and clflush */
#pragma optimize("gt",on)
#include <x86intrin.h> /* for rdtscp and clflush */
View query.rq
PREFIX dcterms: <>
PREFIX wp: <>
SELECT DISTINCT ?sourceWD ?sourceWDLabel ?sourceSMILEScan ?sourceSMILESiso ?targetWD ?targetWDLabel ?targetSMILEScan ?targetSMILESiso WITH {
SELECT ?sourceWD ?targetWD WHERE {
?pathway a wp:Pathway .
?interaction dcterms:isPartOf ?pathway .
?interaction a wp:Interaction, wp:Conversion .
?interaction wp:source ?source . ?source a wp:Metabolite; wp:bdbWikidata ?sourceWD .
View curation1.groovy
// Copyright (C) 2017 Egon Willighagen
// MIT license
// see
/* results (2017-10-29):
Number of missing InChIs: 2098
InChI too long: 1736
With undefined stereo: 348
View calcuateMZs.groovy
// download all GPML files for a species, and save those in /WikiPathways/data/
// first, calculate m/z values for everything in Wikidata
referenceFile = "/WikiPathways/mz_smiles.tsv"
mzData = new java.util.HashMap()
new File(bioclipse.fullPath(referenceFile)).eachLine { line ->
tokens = line.tokenize( '\t' )
if (tokens[0] != "compound") {
wkid = tokens[0].substring(31)
View bbl processor
* LaTeX .bbl output.
* (Code contributed by Egon Willighagen, based on the prototype.text code.)
CSL.Output.Formats.prototype.latex = {
"text_escape": function (text) {
if (!text) {
text = "";
View cites
View gist:553e1329936135699c641e3c32750c27
author = {van Rijswijk, Merlijn and Beirnaert, Charlie and Caron, Christophe and Cascante, Marta and Dominguez, Victoria and Dunn, Warwick B. and Ebbels, Timothy M. D. and Giacomoni, Franck and Gonzalez-Beltran, Alejandra and Hankemeier, Thomas and Haug, Kenneth and Izquierdo-Garcia, Jose L. and Jimenez, Rafael C. and Jourdan, Fabien and Kale, Namrata and Klapa, Maria I. and Kohlbacher, Oliver and Koort, Kairi and Kultima, Kim and Le Corguill\'{e}, Gildas and Moschonas, Nicholas K. and Neumann, Steffen and O'Donovan, Claire and Reczko, Martin and Rocca-Serra, Philippe and Rosato, Antonio and Salek, Reza M. and Sansone, Susanna-Assunta and Satagopam, Venkata and Schober, Daniel and Shimmo, Ruth and Spicer, Rachel A. and Spjuth, Ola and Th\'{e}venot, Etienne A. and Viant, Mark R. and Weber, Ralf J. M. and Willighagen, Egon L. and Zanetti, Gianluigi and Steinbeck, Christoph},
day = {6},
NOdoi = {10.12688/f1000research.12342.1},
issn = {2046-1402},
journal = {F1000Resear
View nms.ttl
@prefix void: <> .
@prefix owl: <> .
@prefix enm: <> .
@prefix xsd: <> .
@prefix rdfs: <> .
@prefix npo: <> .
@prefix sso: <> .
@prefix cito: <> .
@prefix bao: <> .
@prefix rdf: <> .
View README.txt
$ curl -s | sudo apt-key add -
$ sudo nano /etc/apt/sources.list.d/nodesource.list
deb stretch main
# deb-src stretch main
$ sudo npm install --global getpapers
View All Reactome pathways in WikiPathways
PREFIX cur: <>
SELECT DISTINCT ?pathway (str(?titleLit) as ?title)
?pathway wp:ontologyTag cur:Reactome_Approved ;
dc:title ?titleLit .