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kozo2 / MSBNK-RIKEN-PR010017.ttl
Last active March 22, 2024 06:31
@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
kozo2 / error_in_fuseki.txt
Last active January 23, 2024 18:23
ChemFOnt version 1.0 OWL file import error
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
kozo2 / docker-compose.yml
Created September 8, 2023 03:28
version: '3.9'
services:
R-notebook:
image: jupyter/r-notebook
ports:
- '8888:8888'
environment:
- JUPYTER_TOKEN=easy
- PASSWORD=easy
cytoscape-desktop:
@kozo2
kozo2 / RubyQuartoSlides.md
Last active August 28, 2023 04:11

  • 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
kozo2 / pyopensci.md
Created August 18, 2023 08:07

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
kozo2 / msfexp_new.tsv
Created June 5, 2023 06:49
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 14 columns, instead of 13. in line 2.
File path File name Title MS1 count MSMS count PRECURSORMZ PRECURSORTYPE Structure rank Total score Databases Formula Ontology InChIKey SMILES
C:\Users\knishida\Desktop\MS-FINDER demo files\2-Deoxycytidine 5-diphosphate Trial 193 Neg.msp 2-Deoxycytidine 5-diphosphate Trial 193 Neg 2'-Deoxycytidine 5'-diphosphate; LC-ESI-QTOF; MS2; CE 0 8 386.015991 [M-H]- dCDP 8.0345 HMDB=HMDB0001245,ChEBI=CHEBI:28846;CHEBI:58593,SMPDB=PW_C000962,YMDB=YMDB00916,FooDB=FDB022510,BMDB=BMDB01245,ECMDB=ECMDB01245,PubChem=21122964;150855,PlantCyc=DCDP,BLEXP=BLEXPDB00000000623,COCONUT=CNP0142861 C9H15N3O10P2 Organic pyrophosphates FTDHDKPUHBLBTL-SHYZEUOFSA-N O=C1N=C(N)C=CN1C2OC(COP(=O)(O)OP(=O)(O)O)C(O)C2
C:\Users\knishida\Desktop\MS-FINDER demo files\2-Deoxycytidine 5-diphosphate Trial 193 Neg.msp 2-Deoxycytidine 5-diphosphate Trial 193 Neg 2'-Deoxycytidine 5'-diphosphate; LC-ESI-QTOF; MS2; CE 0 8 386.015991 [M-H]- UNPD122004 7.1501 UNPD=UNPD122004,COCONUT=CNP0270287 C9H15N3O10P2 Pyrimidine deoxyribonucleoside 3',5'-bisphosphates P
@kozo2
kozo2 / msfexp_old.tsv
Created June 5, 2023 06:32
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 78 columns, instead of 1. in line 2.
File path File name Title MS1 count MSMS count PRECURSORMZ PRECURSORTYPE Structure rank 1 Total score Databases Formula Ontology InChIKey SMILES Structure rank 2 Total score Databases Formula Ontology InChIKey SMILES Structure rank 3 Total score Databases Formula Ontology InChIKey SMILES Structure rank 4 Total score Databases Formula Ontology InChIKey SMILES Structure rank 5 Total score Databases Formula Ontology InChIKey SMILES Structure rank 6 Total score Databases Formula Ontology InChIKey SMILES Structure rank 7 Total score Databases Formula Ontology InChIKey SMILES Structure rank 8 Total score Databases Formula Ontology InChIKey SMILES Structure rank 9 Total score Databases Formula Ontology InChIKey SMILES Structure rank 10 Total score Databases Formula Ontology InChIKey SMILES
C:\Users\knishida\Desktop\MS-FINDER demo files\S-propylmercaptoglutathione.mat S-propylmercaptoglutathione Unknown 18 36 382.1105 [M+H]+
C:\Users\knishida\Des
@kozo2
kozo2 / pywikipathways-and-py4cytoscape.md
Last active July 8, 2023 14:09
pywikipathways

pywikipathways and py4cytoscape

by Kozo Nishida, Barry Demchak, Alexander Pico

pywikipathways 0.0.2
py4cytoscape 0.0.10

WikiPathways is a well-known repository for biological pathways that provides unique tools to the research community for content creation, editing and utilization [@Pico2008].

Python is a powerful programming language and environment for statistical and exploratory data analysis.

@kozo2
kozo2 / basics.md
Last active December 28, 2020 19:25
ナウいSnakemake Tutorial和訳2

この記事はWorkflow Advent Calendar 2020の4日目の記事です。 4日に分けてSnakemake Tutorialを和訳します。 これはその4日のうちの第2日目です。

Basics: An example workflow

Please make sure that you have activated the environment we created before, and that you have an open terminal in the working directory you have created. 以前に作成した環境をアクティブ化したこと、加えて作成した作業ディレクトリでターミナルを開いていることを確認してください。

A Snakemake workflow is defined by specifying rules in a Snakefile. Rules decompose the workflow into small steps (e.g., the application of a single tool) by specifying how to create sets of output files from sets of input files.

@kozo2
kozo2 / AnnotationWorkshop_Japanese.md
Created September 9, 2020 07:56