SuLab/Applied-Bioinformatics

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SuLab/Applied-Bioinformatics

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Student course material for the Applied Bioinformatics course at Scripps Research

WikidataIntegrator

A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint

DrugMechDB

A database of paths that represent the mechanism of action from a drug to a disease in an indication.

Jupyter Notebook

YPet

Javascript library to rapidly annotate paragraphs of text on websites with the goal of making the annotation process as fast and simple as possible.

mark2cure

Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery.

sparql_to_pandas

Example for accessing SPARQL endpoints in Python with Pandas

Jupyter Notebook

scheduled-bots

GeneWiki Scheduled Bots

Jupyter Notebook

WikiGenomesBase

A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.

genewikiworld

Generate a network of all items we care about, and some we don't....

Jupyter Notebook

MechRepoNet

Jupyter Notebook

GeneWikiCentral

GeneWiki Organization

fiSSEA

Functional Impact SNP Set Enrichment Analysis

TSRI-CBB

This is the Github repository for The Scripps Research Institute Computational Biology and Bioinformatics (CBB) community and affiliated core track for graduate students.

genewiki

The GeneWiki Project

bioshovel

Biological text mining tool.

WD-rephetio-analysis

Jupyter Notebook

Wikidata-phenomizer

Incorporate wikidata statements into phenomizer

Jupyter Notebook

garbanzo

Wikidata Semantic Query API

wikidatasparqlexamples

WikiGenomes.org

Genome data portal for the GeneWiki Project in Wikidata

M2C_rel_nb

Jupyter Notebook

Antibody-Clustering-Challenge

This the material for our TopCoder Challenge

wikigenomes_base_DEPRECATED

A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. LactoBase.org)

Krusty

neo4j <-> wikibase import/export tool

decision-tree-viewer

The decision tree visualization tests for COMBO

single_cell_macrophage

crowdflower_relation_verification

Verification of EU-ADR drug-disease relationships using crowdsourcing.

biogps_plugin_checker

Check public plugins in the BioGPS plugin library for any access errors