kozo2

@prefix : <http://example.org/rules/> .
@prefix chebi: <http://purl.obolibrary.org/obo/chebi/> .
@prefix ex: <http://example.org/> .
@prefix fnml: <http://semweb.mmlab.be/ns/fnml#> .
@prefix fno: <https://w3id.org/function/ontology#> .
@prefix idlab-fn: <http://example.com/idlab/function/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix ql: <http://semweb.mmlab.be/ns/ql#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

kozo2

02:49:51 ERROR Fuseki          :: [line: 70691, col: 99] {W002} <http://purl.obolibrary.org/obo/ChemFont.owl#Adrenal Gland> Code: 17/WHITESPACE in FRAGMENT: A single whitespace character. These match no grammar rules of URIs/IRIs.

kozo2

version: '3.9'
services:
  R-notebook:
    image: jupyter/r-notebook
    ports:
      - '8888:8888'
    environment:
      - JUPYTER_TOKEN=easy
      - PASSWORD=easy
  cytoscape-desktop:

kozo2

• Quartoとは?

  • 画像は quarto.org のスクリーンショット

• Quartoの変換ができると何がうれしいのか？

• Quartoはどのように使うものなのか？

  • コマンドラインラインツールとして使う。
  • 入力ipynbをpdfやword、ウェブサイトに変換できる

• Quarto で ipynbをpdfやwordに変換できて何がうれしいのか？

  • 目次や図表へのクロスリファレンスを自動生成してくれる

• クロスリファレンスとは何か？

kozo2

Submitting Author: Kozo Nishida (@kozo2) All current maintainers: (@kozo2) Package Name: pywikipathways One-Line Description of Package: Python Client Package for the WikiPathways API Repository Link: https://github.com/kozo2/pywikipathways Version submitted: 0.0.2 Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD

kozo2

SELECT a #?uniprot_id #?xref_id
WHERE
{
 ?id ?label "ConA" .
 ?uniprot_id ?p ?id .
 ?uniprot_id a <http://purl.uniprot.org/core/Protein> .
# ?uniprot_id <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?xref_id .
# <http://purl.uniprot.org/pfam/PF00139> ?p ?o
# ?xref_id <http://purl.uniprot.org/core/database> <http://purl.uniprot.org/database/Pfam>
}

kozo2

Metadata-Version: 1.0
Name: ecell
Version: 4.0.0
Summary: A software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell.
Home-page: http://www.e-cell.org/ecell4
Author: Kazunari Kaizu
Author-email: kaizu@riken.jp
License: GPL-2
Description: see http://www.e-cell.org/ecell4
Platform: platform-independent

kozo2

# .bashrc

# User specific aliases and functions

alias rm='rm -i'
alias cp='cp -i'
alias mv='mv -i'

export CPATH=/root/hdf5-1.8.14-linux-centos5-x86_64-gcc482-shared/include:/root/boost_1_59_0
export LD_LIBRARY_PATH=/root/hdf5-1.8.14-linux-centos5-x86_64-gcc482-shared/lib:$LD_LIBRARY_PATH

kozo2

# Below is your R command history : 
InitDataObjects("conc", "msetora", FALSE)
Setup.MapData(tmp.vec);
CrossReferencing("hmdb");
SetMetabolomeFilter(F);
SetCurrentMsetLib("pathway", 0, F);
CalculateHyperScore()
SaveTransformedData()

kozo2

Docker container for E-Cell3

Docker allows software to be packaged into containers: self-contained environments that contain everything needed to run the software. Containers can be run anywhere (containers run in modern Linux kernels, but can be run on Windows and Mac as well using a virtual machine called boot2docker). E-Cell3's Docker image is stored in Docker Hub; the source Dockerfile is in Github. Our E-Cell3 image is based on ecell/spatiocyte.

E-Cell3 with CUI To run E-Cell3 docker container, run

docker run -i -t ecell/spatiocyte /bin/bash