from py2cytoscape import cytoscapejs
import pandas as pd
cytoscapejs.render(pd.read_json("https://github.com/idekerlab/py2cytoscape/raw/develop/examples/initialisation.json"))
Kozo Nishida kozo2
kozo2
/ py2cytoscape.md
Last active
April 27, 2016 09:15
kozo2
/ file0.txt
Created
May 2, 2016 09:36
Ubuntu14.04 + InfiniBand で MPI を動かす ref: http://qiita.com/kozo2/items/4ccf4073d21bdc4db654
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| apt install opensm libmlx4-1 openmpi-bin libopenmpi-dev |
kozo2
/ kgml-biopython.ipynb
Created
May 6, 2016 09:35
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| library(SPARQL) # SPARQL querying package | |
| endpoint <- "http://sparql.uniprot.org/" | |
| # create query statement | |
| query <- | |
| " | |
| PREFIX up:<http://purl.uniprot.org/core/> | |
| SELECT ?taxon |
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| library(SPARQL) # SPARQL querying package | |
| endpoint <- "http://www.ebi.ac.uk/rdf/services/biomodels/sparql" | |
| query <- | |
| " | |
| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> |
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| from SPARQLWrapper import SPARQLWrapper, JSON | |
| #sparql = SPARQLWrapper("http://sparql.uniprot.org/") | |
| sparql = SPARQLWrapper("http://sparql.uniprot.org/sparql/") | |
| sparql.setQuery(""" | |
| PREFIX up:<http://purl.uniprot.org/core/> | |
| SELECT ?taxon | |
| FROM <http://sparql.uniprot.org/taxonomy/> | |
| WHERE | |
| { |
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| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> | |
| PREFIX dc: <http://purl.org/dc/elements/1.1/> | |
| PREFIX dcterms: <http://purl.org/dc/terms/> | |
| PREFIX foaf: <http://xmlns.com/foaf/0.1/> | |
| PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | |
| PREFIX biopax3: <http://www.biopax.org/release/biopax-level3.owl#> |
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| # Below is your R command history : | |
| InitDataObjects("conc", "msetora", FALSE) | |
| Setup.MapData(tmp.vec); | |
| CrossReferencing("hmdb"); | |
| SetMetabolomeFilter(F); | |
| SetCurrentMsetLib("pathway", 0, F); | |
| CalculateHyperScore() | |
| SaveTransformedData() |