http://www.openphacts.org/

Bringing together pharmacological data resources

in an integrated, interoperable infrastructure

Data sources integrated and linked together so that you can easily see the relationships between compounds, targets, pathways, diseases and tissues.

ChEBI, ChEMBL, ChemSpider, ConceptWiki, DisGeNET, DrugBank, FAERS, Gene Ontology, neXtProt, UniProt, WikiPathways

http://www.openphacts.org/

Web  explorer.openphacts.org

REST API  dev.openphacts.org

Workflows myexperiment.org
    (KNIME, Pipeline Pilot, Taverna)

Third-party applications

Docker github.com/openphacts/ops-docker

Download data.openphacts.org

Using Open PHACTS

http://www.openphacts.org/

Example workflow

For a given compound, give me the interaction profile with targets

http://www.myexperiment.org/workflows/4509

http://www.openphacts.org/

doi:10.1371/journal.pone.0115460

http://commonwl.org/

Common format for bioinformatics tool execution
Community based standards effort, not specific software
Implement CWL in your own workflow engine
Defined with a schema, specification & test suite
Designed for shared-nothing cluster & cloud environments
Designed for containers (e.g. Docker)

Main focus: command line tools

Adapted from  Peter Amstutz' Broad Institute CWL meetup 2015-11-13

http://commonwl.org/

https://github.com/common-workflow-language/workflows/tree/master/workflows/FestivalDemo

class: CommandLineTool
inputs:
  - id: "#infile"
    type: {type: array, items: File}
    inputBinding: {position: 1}
outputs:
  - id: "#outfile"
    type: File
    outputBinding: {glob: "out.txt"}
baseCommand: ["wc", -l]
stdout: out.txt

#!/usr/bin/env cwl-runner
class: Workflow
requirements:
  - class: ScatterFeatureRequirement
  - class: DockerRequirement
    dockerPull: "debian:8"

inputs:
  - id: "#pattern"
    type: string
  - id: "#infile"
    type: {type: array, items: File}

steps:
  - id: "#grep"
    run: {import: grep.cwl.yaml}
    scatter: "#grep.infile"
    inputs:
      - id: "#grep.infile"
        source: "#infile"
      - id: "#grep.pattern"
        source: "#pattern"
    outputs:
      - id: "#grep.outfile"


  - id: "#wc"
    run: {import: wc.cwl.yaml}
    inputs:
      - id: "#wc.infile"
        source: "#grep.outfile"
    outputs:
      - id: "#wc.outfile"

outputs:
  - id: "#outfile"
    type: File
    source: "#wc.outfile"

class: CommandLineTool
inputs:
  - id: "#pattern"
    type: string
    inputBinding: {position: 0}
  - id: "#infile"
    type: File
    inputBinding: {position: 1}
outputs:
  - id: "#outfile"
    type: File
    outputBinding: {glob: "out.txt"}
baseCommand: "grep"
stdout: out.txt

http://commonwl.org/

Rich: Linked Data allows for infinite metadata annotations and reasoning

Runnable: not just an abstract sketch; runs in containers, clouds, & (HPC) clusters

Portable: both reference & vendor implementations available

Community Driven: started at the Bioinformatics Open Source Conference; lazy consensus & do-ocracy approach

Adapted from Michael R Crusoe's #CommonWL talk at @scilifelab https://goo.gl/fR2shQ 

http://commonwl.org/

Implementers

cwltool reference impl.
Rabix
Arvados
Galaxy
Parallel Recipes
Toil
CancerCollaboratory
Airflow (SciDAP)

cwl2script

Apache Taverna planning

How can BioExcel help Open PHACTS?

Making Open PHACTS workflow components

swagger.json → CWL tools

"Call API" command line

Docker/CWL support in KNIME/Taverna/Galaxy

Improve local deployment of Open PHACTS

Virtualization and data management

Automate cloud installation

Tutorials and training

Community building