Converting Scripts into Reproducible Workflow Research Object

This page shows supplementary resources used to demonstrate how our methodology works. Below we show the Reproducible Workflow Research Object Bundle created following our methodological steps defined in the article submitted to the 2016 IEEE 12th International Conference on eScience.

The bundle was created using the Research Object Bundle specification 1.0 and RO Manager. We created a script to define the resources to be aggregated in the bundle and invoke RO Manager.

Download the Reproducible Workflow Research Object Bundle

A Research Object Bundle provides a way to collect the resources that are aggregated in a research object, represented as files in a ZIP archive, in addition to their metadata and annotations. The ZIP archive thus becomes a single representation of a research object and which can be exported, archived, published and transferred like a regular file or resource.

Permanent URL to this page

https://w3id.org/w2share/s2rwro/

Methodology for Conversion of Scripts

Methodology for Conversion of Scripts into Reproducible Workflow Research Objects

The Methodology

The scientist is guided through five steps to convert scripts into Reproducible Workflow Research Objects.

View details »

Recent Publications

Authors

Case Study - Molecular Dynamics

Our case study is based on a molecular dynamics simulation defined in the following article:

Silveira, R.L. and Skaf, M. S. Molecular Dynamics Simulations of Family 7 Cellobiohydrolase Mutants Aimed at Reducing Product Inhibition. J. Phys. Chem. B 119, 9295-9303 (2015). DOI: https://doi.org/10.1021/jp509911m

Manifest

File Description
build/structure.pdbcrystal ​structure​ of the protein
build/water.pdbcoordinates of water molecules present in the crystal structure
build/protein.pdbcoordinates of the protein atoms​
build/cal.pdbcoordinates of calcium ions present in the crystal structure
toppar/par_all22_prot.prmforce field parameter for the non-standard residue PCA
toppar/par_all36_carb.prmforce field parameters for carbohydrates
toppar/pca.prmforce field parameter for the non-standard residue PCA
toppar/pca.rtftopology file for ​the non-standard residue PCA
toppar/top_all36_prot.rtftopology file for protein​s
toppar/top_all36_carb.rtftopology file for carbohydrates​
build/hyd.pdbcrystal structure with hydrogen atoms added​
build/hyd.psfstructure file for the crystal structure with hydrogen atoms added​
build/wbox.pdbcoordinates of the solvated system
build/wbox.psfstructure file of the solvated system
build/bglc.pdbcoordinates of the glucan chain present in the crystal structure
build/bglc.psfstructure file for the glucan chain
build/cbh1.pdbinitial coordinates for the simulations, containing protein, water, ions and glucan chain
build/cbh1.psfstructure file for the coordinate file cbh1.pdb
build/fixed.1.pdbcoordinates for the whole system (cbh1.pdb), indicating which atoms should be kept fixed along the simulation
build/fixed.2.pdbcoordinates for the whole system (cbh1.pdb), indicating which atoms should be kept fixed along the simulation
md1/dynamics-1.namdinput for MD simulation​ -- production runs, after equilibration steps
md1/equilibration-1.namdinput for MD simulation, with fixed atoms indicated by the file fixed.1.pdb​
md1/equilibration-2.namdinput for MD simulation, with fixed atoms indicated by the file fixed.2.pdb​
md1/equilibration-3.namdinput for MD simulation​, with all atoms free
md1/output/distanceprogram to compute distance between pairs of atoms​
md1/output/distance.datdistance between atoms in function of the simulation time​
md1/output/distance.inpinput for the program distance​
md1/output/READMEREADME
md1/output/trajectory.dcdoutput of the MD simulation: xyz coordinates of the protein in function of the time​
workflow/executable-workflow.t2flowinitial executable workflow
workflow/refined-workflow.t2flowrefined executable workflow
provenance/executable-workflow.provenance.bundle.zipprovenance traces bundle exported by Taverna from execution of the initial workflow
provenance/refined-workflow.provenance.bundle.zipprovenance traces bundle exported by Taverna from execution of the refined workflow
build/build.shoriginal MD script
yesworkflow/abstract-workflow.pngabstract workflow derived from the script
script-workflow.prov.ttlPROV statements wrt workflow derived from the script blocks

PROV Statements

PROV statements to declare derivation of workflows from scripts. In the article the listing containing the PROV statements was not complete due to lack of space. View Complete Listing

Requirements

These softwares are required to run the workflows.

Images

Abstract Workflow

Workflow-view derived from the annotated script using YesWorkflow tool.

View Full Image View Annotated Script

Executable Workflow

Workflow derived from the script blocks.

View Full Image Download Workflow

Refined Workflow

Workflow derived from the executable workflow.

View Full Image Download Workflow

Acknowledgments

Work partially financed by FAPESP (2014/23861-4), FAPESP/CEPID CCES (2013/08293-7), FAPESP-PRONEX (eScience project), INCT in Web Science (557128/2009-9), and individual grants from CNPq. We thank Prof. Munir Skaf and his group from the Institute of Chemistry at Unicamp for making their scripts and data available and for their valuable feedback.