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Stian Soiland-Reyes

Login: stain

Company: eScience lab, University of Manchester

Location: Manchester, UK

Bio: Open Source research software engineer with interests in Linked Data, RESTful web services, provenance, annotations, open science, reproducible research

Blog: http://orcid.org/0000-0001-9842-9718

Member of

Repositories

2015-bosc: Abstract and presentation material for the Bioinformatics Open Source Conference 2015
2016-provweek-tavernaprov: Abstract submitted to http://provenanceweek.org/2016/p3yl/
7XX-rfc: An RFC for a new series of HTTP status codes covering developer fouls.
activity-monitoring-own-queuesize: A Taverna 2.x activity that monitors its own queue size (ie. jobs waiting to be done)
alibaba: Alibaba from http://www.openrdf.org/alibaba.jsp
alibaba-bug-con-person: Bug: Can't find con:Person on Windows
ApacheWombat: Apache worked LICENSE and NOTICE example
arcmedia: "archive" Top-Level Media Type
arcp-py: Create/parse arcp (Archive and Package) URIs
artifactory-with-mysql: Run Artifactory in a Docker container
asfrelease: Draft of proposed changes to Apache release policy.
AstroTaverna-AA-article: GitHub for the editing of the Astronomy & Astrophysics article on AstroTaverna
AtDataCruncher: Annotopia Data Cruncher provides display of analitics.
audiveris: Latest generation of Audiveris OMR engine
awesome-oss-mentors: List of OSS contributors willing to help others with their first pull requests!
bagit-docker: Docker packaging of bagit-java
bagit-profiles: null
bagitspec: null
banana-rdf: Banana RDF
bdbag: Big Data Bag Utilities
beanshell: beanshell (moved from apache-extras.org)
beanshell2: Cloned from http://beanshell2.googlecode.com/svn/
bioconda-recipes: Conda recipes for the bioconda channel.
biotoolsDocs: Documentation for bio.tools and related community projects
bosc2015-apachetaverna: Abstract about Apache Taverna to be submitted for BOSC 2015
bower: A curses terminal client for the Notmuch email system
branchandtagtest: Testing GitHub's management of branches and tags
BridgeDb: The BridgeDb Library source code
bridgedb-vocabulary: Source files for the BridgeDb ontology
bunny: Reproducible Analyses for Bioinformatics - Java
cdk-taverna: CDK-Taverna for Taverna 2.x
ClAnnotatorjs: Annotator.js Client Connector
clerezza: Mirror of Apache Clerezza
clerezza-rdf-core: Fork of https://git-wip-us.apache.org/repos/asf/clerezza-rdf-core.git
cliche: null
clinicalcodes.article5: null
clj-owlapi: OWL API wrapper for Clojure
clj-plaza: clojure's rdf framework
CnEbiConnector: EBI Connector
CnPubMedConnector: PubMed Connector
combinearchive.org: null
commons-beanutils: Mirror of Apache Commons Beanutils
commons-lang: Mirror of Apache Commons Lang
commons-rdf: Stian's fork of Apache Commons RDF
commonsrdf-parser-jena: Parsers for Apache Commons RDF, backed by Apache Jena
common-workflow-language: Repository for CWL Specfications
composer: Visual and code editor for Common Workflow Language
com.stralo.site: Stralo is an open-source linked data framework with the intention to make linked data easy.
conservancy-website: Website sources of Software Freedom Conservancy. This repository is *not* canonical, we're on our Kallithea instance instead: https://k.sfconservancy.org/website/ . This is a backup of the repository & here for those who already work on Github to fork.
cottontail: null
cottontail-editors: null
cottontail-electron: null
cpython: Semi-official read-only mirror of the CPython Mercurial repository
crowd-ldap-server: Implementation of an LDAP server that delegates authentication to an Atlassian Crowd installation using the Crowd REST API.
CsCircles: Circles management
cwl-svg: A library for generating an interactive SVG visualization of CWL workflows
cwl-ts: Typescript data model for Common Workflow Language
cxf: Mirror of Apache CXF
databundle: API for Taverna Data Bundles
data-dependency-test: Testing Maven for data dependency management
data-maven-plugin: Data management plugin for Apache Maven
dcm4che2: dcm4che2 with modifications to handle some dcm2dcm failures
docker-gradle: Docker image for building gradle projects
dret-I-D: Internet Drafts I've authored or contributed to.
ea-rdf: Experiments with Elegant Objects https://gitter.im/yegor256/elegantobjects
ebi-metagenomics-cwl: This repository contains the CWL description of EBI Metagenomics pipeline
eea.elasticsearch.river.rdf: EEA ElasticSearch RDF River Plugin
encoding-test-files: Encoding test files
EnsemblLinksetExtractor: Extracts Linksets for Open PHACTS IMS
eo: EO programming language
eolang-clj: Experimental Clojure mapping of eolang.org
eSC-plugin: Taverna plugin running in e-SC platform
e-SC-plugin-with-Taverna-workbench: e-SC plugin with Taverna workbench
explorer2: Ember JS web application used for browsing the Open PHACTS Discovery Platform
FAIRifier: A tool to make data FAIR
fda-hive: FDA High-performance Integrated Virtual Environment (HIVE)
filepath-example-activity: null
finance-quote: Finance::Quote module for Perl
flowing-clj: Flowing - Define and execute workflows in Clojure
forgetSQL: Python ORM wrapper for SQL databases (no longer maintained)
ga4gh_challenge: Workflow for GA4GH/DREAM challenge (phase 2)
github2jenkins: Create Jenkins jobs per Github repository
go-rdf: Gene Ontology (GO) RDF
gromacs-docker: docker and gromacs and copernicus
gs-maven: Building Java Projects with Maven :: Learn how to build a Java project with Maven.
GTP-RDF: Building a Linked Data version of the IUPHAR/BPS Guide to Pharmacology
HCLSDatasetDescriptions: null
helio-vo: Clone from http://sourceforge.net/p/helio-vo/code/HEAD/tree/trunk/helio-taverna-suite/
helloworld: Maven Hello World example (for debugging Jenkins)
hiccup: Fast library for rendering HTML in Clojure
highlight.js: Javascript syntax highlighter
hive-cwl-examples: Example BioCompute as Research Object with CWL
I-D: My attempt to write Internet Drafts
identifier-rules: 10 simple rules for identifiers
incubator-brooklyn: Mirror of Apache Brooklyn
incubator-example: Mirror of Apache Website Template
incubator-juneau: Mirror of Apache Juneau (Incubating)
incubator-taverna-language: Mirror of Apache Taverna Language (incubating)
incubator-taverna-maven-parent: Apache Taverna Maven Parent POM (staging)
incubator-taverna-maven-parent-1: Mirror of Apache Taverna Maven Parent (incubating)
incubator-taverna-mobile: Mirror of Apache Taverna Mobile (Incubating)
incubator-taverna-osgi: Mirror of Apache Taverna Osgi (incubating)
incubator-taverna-plugin-gis: Mirror of Apache Taverna Plugin GIS Incubator
incubator-taverna-server: Mirror of Apache Taverna Server (incubating)
incubator-taverna-site: Mirror of Apache Taverna (Incubating) Web Site
infrastructure-puppet: Mirror of Apache Infrastructure Puppet
install4j-support: Install4j Support
iobox: Extract, Transform, Load (ETL) utilities for ERMrest+Hatrac
jai-imageio-core: JAI ImageIO Core (without javax.media.jai dependencies)
jai-imageio-jpeg2000: JPEG2000 support for Java Advanced Imaging Image I/O Tools API
japicmp: Comparison of two versions of a jar archive
jaxb-any: Example of jaxb @AnyElement bug
jdk8u: Manually mirrored from mercurial at http://hg.openjdk.java.net/jdk8u/jdk8u/jdk/
jena: Mirror of Apache Jena
jena-docker: Docker image for Apache Jena riot
jena-jsonld: jena-jsonld
jena-test-unregistered-iana: Tests for UNREGISTERED_IANA_SCHEME bug in Jena
JERMOntology: The JERM Ontology is an application ontology designed to describe the items in SEEK and the relationships between them (for example, data, models, experiment descriptions, results, samples, protocols, standard operating procedures and publications); and to enable these relationships to be expressed with formal semantics.
jersey: This is an active mirror of Jersey 2.x workspace from http://jersey.java.net. Any changes made here are automatically propagated to java.net and vice versa. Forks and pull requests are welcome!
jsonld-java: JSON-LD implementation for Java
json-ld.org: JSON for Linked Data
junit-contracts: Contract test suite runner
kramdown-rfc2629: An RFC2629 (XML2RFC) backend for Thomas Leitner's kramdown markdown parser
ldn-tests: Linked Data Notifications tests
license-maven-plugin: Manage license headers in your source files
linkedISA: Package to convert ISA-TAB files into RDF data relying on different semantic frameworks (OWL ontologies).
linkedresearch.org: linkedresearch.org
lintian: Static analysis tool for Debian packages
LODE: Live OWL Documentation Environment, to convert OWL ontologies into HTML human-readable pages.
lr-example: Example of Linked Research as GitHub repo
lr-example-repo1: Example of Linked Research repo to be imported as git submodule
ltatakis.github.io: null
mailer: Mass-mailer in Python
mayktso: :milky_way: makytso: encounters at an endpoint
mesos: Mirror of Apache Mesos
miapa: MIAPA vocabularies and tools
moxo: Moxo S3 DAV proxy
myExperiment: Software running http://www.myexperiment.org/
mysql-for-artifactory: Docker image for mySQL tuned for Artifactory
net.sf.taverna.t2.core.provenance-derby: Temporary repository mirroring https://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.core.provenance-derby/
Nightweb: An anonymous P2P social network in Clojure
nio-zipfs: java.util.nio zipfs file system - from OpenJDK8u demo code
notes-stain: My work-related notes - open for public scrutiny
NumTab: Gold standard for numerical Wikidata values, mapping DBpedia properties to Wikidata
oa: Schemas for http://www.openannotation.org/spec/core/
opdsr: Fork of https://spotlite.nih.gov/ncats/opdsr. Data generated as part of the Open Phenotypic Drug Screening Resource, a collaboration between NCATS, Eli Lilly & Data2Discovery, Inc
OpenProvenanceModel: The overarching project of Java code related to the Open Provenance specifications.
ops-ensembl-linksets: Open PHACTS Ensembl linksets Maven project
ops-linkeddataapi-docker: Docker image of Open PHACTS Linked Data API (OPS-LinkedDataAPI)
orc: Mirror of Apache Orc
orcid-rdf-tests: Simple tests of ORCID's RDF
ORCID-Source: ORCID Open Source Project
ore: Contributions for www.openarchives.org/ore/
owl2jsonld: Convert RDFS/OWL ontology to JSON-LD context
owlapi: clone of the sourceForge owlapi repository
owlapi-jsonld: JSON-LD parser and writer for OWL API
owlapitools: clone of the SourceForge owlapitools project
owlview: OWL viewer
paq: Example of using PROV-AQ
pebble-notifier: Pebble notifier for Android
perfs: PerFS Peer-to-peer distributed file system
persistenturls: NOT MAINTAINED - just a backup from http://code.google.com/p/persistenturls
pizza-ontology: The pizza ontology
player: Almost certainly the first MP3 player of it's kind.
profilechecker: OWL API profile checker
prov-constraints-validator-spin: An implementation of PROV-Constraints using SPINRDF
provenance-corpus: Provenance corpus
prov-lodspeakr: Models and Views for W3C Provenance Working Group's OWL Ontology
ProvToolbox: Java toolbox to create and convert Provenance Interchange data Model representations
prov-viewer: Provenance Visualization Tool
Python-LRU-cache: An in-memory LRU cache for python
rabix: Reproducible Analyses for Bioinformatics
rabix-cliche: Rabix tool command line generator
rash-framework.github.io: Website for the RASH Framework
rdf4j: RDF4J Project
rdf-clj: RDF for Clojure, integrates with Commons RDF, Jena, RDF4J
rdfsplit: Split large RDF files into reasonably sized N-Quads files
rdf-tests: Repository for the RDF Tests Community Group
registry: null
reprozip: ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.
ro-combine-archive: Convert Combine Archive (OMEX) to RO Bundle
rubyzip: Offical Rubyzip repository
s: Skype redirection
scalability-reproducibility-chapter: Data and workflow examples
scape-component-profiles: Holds the SCAPE component profile ontology and profile XML files.
scholmd: Learn how to use scholarly markdown
scrapbook: Various small utillities
script-maven-plugin: script-maven-plugin
scufl2-awf: Reader for AWE workflows - see https://github.com/MG-RAST/AWE
scufl2-clojure: Using Scufl2 from Clojure
scufl2-info: SCUFL2 information web service
scufl2-iwir: Convert Taverna Scufl2 workflow bundle to SHIWA IWIR description
scufl2-paper: Paper: scufl2 and wfdesc
scufl2-wfdesc: Convert from Scufl2 to wfdesc from Wf4Ever RO ontology
seek: null
Shakespeare-s-Sonnets_1041: Shakespeare's Sonnets by Shakespeare, William, 1564-1616 is a Project Gutenberg book, now on Github.
shootout-docker-maven: A comparison between the four major docker-maven-plugins
soapdenovo2: SOAPdenovo2 case study website
specifications: Research Object Specifications
specref: A list of spec references and related API.
SPP_Command_Line_Tool: A repository that hosts the Semantic Provenance Processor command-line line tool
staged-recipes: A place to submit conda recipes before they become fully fledged conda-forge feedstocks
strigidoc: A documentation generator for OWL ontologies
sustaining-research-projects: sustainability models for research software projects
t2-server-jar-android-0.1: Taverna Server Android API v0.1
taverna: Automatically exported from code.google.com/p/taverna
taverna-grid: The taverna-grid repository is a Taverna Workbench plug-in to support invocation of caGrid 1.x services.
taverna-jekyll-site: Draft website for Apache Taverna (Jekyll-based)
Taverna-mobile-0.1: Taverna Server Android Client v0.1
Taverna_Provenance: A repository that hosts files related to my MSc dissertation on Taverna's provenance
taverna-sandbox: null
taverna-server: Taverna Server is an implementation of the Taverna Platform execution model as a REST and SOAP web service.
Taverna.server.android.client: null
taverna-workbench-product: Taverna Workbench product build and installers
test1: Example of Junit tests with Maven
test-orcid-gitauthor: Can we use ORCIDs as git's user.name or user.email ?
virtuoso-docker: Virtuoso docker image
Void-Editor: null
w3id-csv: Attempt to populate https://w3id.org/ .htaccess files from CSV (notably exported from purl.org's database)
w3id.org: Website source code for w3id.org
web-annotation: Web Annotation Working Group repository
Wf4Ever-PROV: The repository for the Wf4Ever team.
wikitest: null
workflow-to-galaxy: cloned from https://trac.nbic.nl/svn/elabfactory/galaxy-taverna/workflow-to-galaxy/
worldcupbingo: FIFA World Cup 2012 bingo
WPS: The 52�North Web Processing Service enables the deployment of geo-processes on the web in a standardized way.
xws-taverna: XWS Plugin for Taverna

Commits To

Repository	Most Recent Commit	# Commits
ruebot/bagit-profiles	2015-08-06 14:40:48.0	4
openphacts/ops-ncats-opdsr-rdf	2015-09-14 12:47:16.0	2

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.