The document outlines current challenges in radio astronomy and potential solutions using scientific workflows and research objects. It introduces the speaker and their background and interests in bringing computational tools and the virtual observatory to radio astronomy. Specific challenges discussed include an overabundance of data that is difficult to find, document, share and reproduce. The talk proposes that workflows and research objects could help address these issues by defining computations and dependencies, enabling distributed and interactive computing, and providing tools for workflow storage, discovery and provenance.
Wf4Ever: Scientific Workflows and Research Objects as tools for scientific insight and methodology curation
1. Wf4Ever: Scientific Workflows
and Research Objects as tools
for scientific insight and
methodology curation
Juande Santander-Vela jdsant@iaa.es
Instituto de Astrofísica de Andalucía-CSIC
4. Who am I?
Member of the AMIGA international collaboration,
based at IAA-CSIC
Ph.D. on bringing Radio Astronomical data archives and
tools into the VO
Applied Scientist at ESO VLT archive, Software
Engineer/Astronomy Specialist at ALMA archive
(May 2009-Dec 2011)
Back to IAA-CSIC as VIA-SKA Project Manager,
Radio Astroinformatician
GROUP INTEREST IN TECH
DEVELOPMENTS FOR BETTER SCIENCE
5. Why I’m here?
Collaboration with Stephane Leon and the ALMA
Data Management Group
Helping bring the ALMA Science Archive to the VO
Modelling radio data cubes
Finding use cases for workflow technology (see later)
6. AMIGA
Analysis of the interstellar Medium of Isolated GAlaxies
Multi-wavelength, multi-object study on isolated galaxies
with strict isolation criteria
Careful curation of data
Very careful processing of new parameters from
Group’s own observation programs and data reduction
Literature table scanning
Virtual Observatory table harvesting and parsing
Emphasis on marrying astronomy and computer science,
and buy-in of the VO
E-SCIENCE USERS
7. AMIGA
Analysis of the interstellar Medium of Isolated GAlaxies
Multi-wavelength, multi-object study on isolated galaxies
with strict isolation criteria
Careful curation of data
Very careful processing of new parameters from
Group’s own observation programs and data reduction
Literature table scanning
Virtual Observatory table harvesting and parsing
Emphasis on marrying astronomy and computer science,
and buy-in of the VO
E-SCIENCE DEVELOPERS!
8. AMIGA
Project goal: providing a baseline for galaxy
properties to compare with other environments
Interaction-free sample, ideal for tracing HI infall:
we can use CIG galaxies to detect the cosmic web
Need for very sensitive telescopes able to resolve
faint HI ➡ Square Kilometre Array & pathfinders
PARTICIPATING IN SKA.TEL.SDP CONSORTIUM
WE NEED TOOLS FOR OUR OWN SCIENCE ANALYSIS
⤷
10. Data over-abundance
Moore’s Law for Detectors ➡ Exponential increase
of individual and accumulated data sets
We have more data than ever… but we can’t use it:
Because we can’t:
Difficult to set up (for sharing)
Difficult to find (for using)
Difficult to document (both using and sharing)
Difficult to deal with (because of size, formatting, purpose…)
Because it is not in our best interest
FULLY
?
13. Data sharing
Search Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Archive Audio & Video For Authors
SPECIALS See all specials
Editorial Feature Opinion Elsewhere in Nature
DATA SHARING
Sharing data is good. But sharing your own data? That can get complicated. As two research
communities who held meetings in May on the issue report their proposals to promote data sharing
in biology, a special issue of Nature examines the cultural and technical hurdles that can get in the
way of good intentions.
Data SharingSpecials & supplements archiveArchive
DATA FLIRTING
DATA HOARDING
IRREPRODUCIBLE
RESEARCH
?
14. Irreproducible researchSearch Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Archive Audio & Video For Authors
SPECIAL See all specials
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCH
No research paper can ever be considered to be the final word, and the replication and
corroboration of research results is key to the scientific process. In studying complex entities,
especially animals and human beings, the complexity of the system and of the techniques can all
too easily lead to results that seem robust in the lab, and valid to editors and referees of journals,
but which do not stand the test of further studies. Nature has published a series of articles about
the worrying extent to which research results have been found wanting in this respect. The editors
of Nature and the Nature life sciences research journals have also taken substantive steps to put
our own houses in order, in improving the transparency and robustness of what we publish.
Journals, research laboratories and institutions and funders all have an interest in tackling issues
of irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Challenges in irreproducible researchSpecials & supplements archiveArchive
nature.com Sitemap Cart Login Register
Search Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Audio & Video For Authors
SPECIAL See all specials
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCH
No research paper can ever be considered to be the final word, and the replication and
corroboration of research results is key to the scientific process. In studying complex entities,
especially animals and human beings, the complexity of the system and of the techniques can all
too easily lead to results that seem robust in the lab, and valid to editors and referees of journals,
but which do not stand the test of further studies. Nature has published a series of articles about
the worrying extent to which research results have been found wanting in this respect. The editors
of Nature and the Nature life sciences research journals have also taken substantive steps to put
our own houses in order, in improving the transparency and robustness of what we publish.
Journals, research laboratories and institutions and funders all have an interest in tackling issues
of irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Challenges in irreproducible researchSpecials & supplements archiveArchive
15. Irreproducible researchSearch Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Archive Audio & Video For Authors
SPECIAL See all specials
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCH
No research paper can ever be considered to be the final word, and the replication and
corroboration of research results is key to the scientific process. In studying complex entities,
especially animals and human beings, the complexity of the system and of the techniques can all
too easily lead to results that seem robust in the lab, and valid to editors and referees of journals,
but which do not stand the test of further studies. Nature has published a series of articles about
the worrying extent to which research results have been found wanting in this respect. The editors
of Nature and the Nature life sciences research journals have also taken substantive steps to put
our own houses in order, in improving the transparency and robustness of what we publish.
Journals, research laboratories and institutions and funders all have an interest in tackling issues
of irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Challenges in irreproducible researchSpecials & supplements archiveArchive
CHALLENGES IN IRREPRODUCIBLE RESEARCH
No research paper can ever be considered to be the final word, and the replication and
corroboration of research results is key to the scientific process. In studying complex entities,
especially animals and human beings, the complexity of the system and of the techniques can all
too easily lead to results that seem robust in the lab, and valid to editors and referees of journals,
but which do not stand the test of further studies. Nature has published a series of articles about
the worrying extent to which research results have been found wanting in this respect. The editors
of Nature and the Nature life sciences research journals have also taken substantive steps to put
our own houses in order, in improving the transparency and robustness of what we publish.
Journals, research laboratories and institutions and funders all have an interest in tackling issues
of irreproducibility. We hope that the articles contained in this collection will help.
Free full access
17. Starship Asterisk*
APOD and General Astronomy Discussion Forum
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*Web Resources and Tools for Astrophysicists/Astronomers*
by owlice » Sat Jul 16, 2011 12:01 pm 22 2750 by owlice
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2011 and 2012 Additions to the ASCL
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3DEX: Fast Fourier-Bessel Decomposition of Spherical 3D Surv
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AAOGlimpse: Three-dimensional Data Viewer
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Sat Oct 15, 2011 11:29 am
ACORNS-ADI: Calibration, Registration and Nulling in Imaging
by kcd » Sat Mar 30, 2013 7:40 am 0 177 by kcd
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ACS: ALMA Common Software
by kcd » Sat Feb 09, 2013 3:44 am 0 269 by kcd
Sat Feb 09, 2013 3:44 am
671 topics • Page 1 of 7 •
23. Workflows define
computations
Events & Processes
Dependencies
Resources
Local & Remote Processes
Sequences
Concurrences
Triggers
FORMALLY,
OR AT LEAST
MACHINE READABLE
➡
WORKFLOW
DEFINITION
LANGUAGES
24. Workflows enable
distributed computing
Distributed computing paradigm
Move computation to the data
Computing services
Collaborative environments
Linked data }
FOR SCIENTIFIC
DISCUSSION &
SCIENCE EXTRACTION
➡ Science-computing
25. Workflows enable
distributed computing
Data can be anywhere
Workflows can be constructed hierarchicaly
Each workflow does useful work on its own
The data flow can be easily followed
26. Workflows enable
interactive computing
Each workflow run records it’s inputs, outputs,
and intermediate results
You can build and run workflows incrementally
You can get (almost) immediate feedback on
changes
27. Tools for workflow
storage and discovery
About | Give us Feedback | Publications Juandesant
New Workflow GO Workflows Search
View
Download (v7)
Taverna 2
Original
Uploader
Paul
Fisher
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Taverna 2
Taverna 1
RapidMiner
Kepler
Bioclipse Scri…
LONI Pipeline
GWorkflowDL
KNIME
BioExtract Ser…
Galaxy
Filter by tag
example
Home Users Groups Workflows Files Packs Topics
Home > Workflows
Workflows
Showing 2207 results. Use the filters on the left and the search box below to refine the results.
Search
Pathways and Gene annotations for QTL region (7)
Created: 19/11/09 @ 18:18:52 | Last updated: 07/09/12 @ 18:23:36
Credits: Paul Fisher
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the
mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL
start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate
each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to
obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in
the KEGG path...
28. Tools for workflow
storage and discovery
About | Give us Feedback | Publications Juandesant
New Workflow GO Astrotaverna Workflows Search
View
Download (v3)
Taverna 2
Original
Uploader
Julian
Garrido
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9
9
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Taverna 2
Filter by tag
astronomy
astrotaverna
votable
virtual observ…
starter pack
local processes
taverna
workflow
galfit
sextractor
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Home > Workflows
Workflows
Showing 44 results. Use the filters on the left and the search box below to refine the results.
Astrotaverna Search
Remove search query
Cocatenates several VOTables into one (3)
Created: 30/08/12 @ 10:05:29 | Last updated: 22/04/13 @ 16:52:00
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input
is four VOTables with the same number of columns. The result if using sample values provided
will be a four times vertically duplicated VOTable.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
29. View
Download (v3)
Taverna 2
Original
Uploader
Julian
Garrido
View
Download (v1)
Taverna 2
Original
Uploader
Julian
Garrido
View
Download (v1)
Taverna 2
Original
Uploader
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Filter by type
Taverna 2
Filter by tag
astronomy
astrotaverna
votable
virtual observ…
starter pack
local processes
taverna
workflow
galfit
sextractor
Filter by user
Jose Enrique …
Julian Garrido
Filter by licence
by-sa
BSD
Filter by group
AMIGA
Wf4Ever
Showing 44 results. Use the filters on the left and the search box below to refine the results.
Astrotaverna Search
Remove search query
Cocatenates several VOTables into one (3)
Created: 30/08/12 @ 10:05:29 | Last updated: 22/04/13 @ 16:52:00
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input
is four VOTables with the same number of columns. The result if using sample values provided
will be a four times vertically duplicated VOTable.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 12 times
Tags (4):
astronomy | astrotaverna | cat | votable
Create configuration files from a template... (1)
Created: 26/07/12 @ 10:56:46 | Last updated: 04/09/12 @ 07:30:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow uses astrotaverna artifacts. It creates files by using a template whose keys are
replaced by data from a votable. A configuration file is created for every row in the votable. The
keys must appear also in the vocabulary file and match column names in the votable. A column
in the votable must contain the name of the result configuration file.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 14 times | Downloaded: 15 times
Tags (4):
astronomy | astrotaverna | local processes | votable
Simulates the physical, dynamical, and che... (1)
Created: 17/05/13 @ 08:03:13
Credits: Julian Garrido
30. View
Download (v3)
Taverna 2
Original
Uploader
Julian
Garrido
View
Download (v1)
Taverna 2
Original
Uploader
Julian
Garrido
View
Download (v1)
Taverna 2
Original
Uploader
Sort by: Relevance« Previous 1 2 3 4 5 Next »
44
43
42
40
26
23
9
9
9
5
5
27
17
40
4
16
4
Search filter terms
Filter by type
Taverna 2
Filter by tag
astronomy
astrotaverna
votable
virtual observ…
starter pack
local processes
taverna
workflow
galfit
sextractor
Filter by user
Jose Enrique …
Julian Garrido
Filter by licence
by-sa
BSD
Filter by group
AMIGA
Wf4Ever
Showing 44 results. Use the filters on the left and the search box below to refine the results.
Astrotaverna Search
Remove search query
Cocatenates several VOTables into one (3)
Created: 30/08/12 @ 10:05:29 | Last updated: 22/04/13 @ 16:52:00
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input
is four VOTables with the same number of columns. The result if using sample values provided
will be a four times vertically duplicated VOTable.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 12 times
Tags (4):
astronomy | astrotaverna | cat | votable
Create configuration files from a template... (1)
Created: 26/07/12 @ 10:56:46 | Last updated: 04/09/12 @ 07:30:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow uses astrotaverna artifacts. It creates files by using a template whose keys are
replaced by data from a votable. A configuration file is created for every row in the votable. The
keys must appear also in the vocabulary file and match column names in the votable. A column
in the votable must contain the name of the result configuration file.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 14 times | Downloaded: 15 times
Tags (4):
astronomy | astrotaverna | local processes | votable
Simulates the physical, dynamical, and che... (1)
Created: 17/05/13 @ 08:03:13
Credits: Julian Garrido
31. About | Give us Feedback | Publications Juandesant
New Workflow GO All Search
Version 3 (latest) (of 3) View version: 3 (latest)
Version created on: 22/04/13 @ 16:52:00 by: Julian Garrido
Title: Cocatenates several VOTables into one
Type: Taverna 2
Preview
(Click on the image to get the full size)
Workflow Type
Taverna 2
Original Uploader
Julian
Garrido
License
All versions of this Workflow are licensed
under:
Credits (1)
(People/Groups)
Julian Garrido
Attributions (0)
(Workflows/Files)
None
Home Users Groups Workflows Files Packs Topics
Home > Workflows > Cocatenates several VOTables into one
Workflow Entry: Cocatenates several VOTables into one
Created at: 30/08/12 @ 10:05:29 Last updated: 22/04/13 @ 16:52:00
| License | Credits (1) | Attributions (0) | Tags (4) | Featured in Packs (1) | Ratings (0) | Attributed By (0) | Favourited By (0) |
| Citations (0) | Version History | Reviews (0) | Comments (0) |
32. Version 3 (latest) (of 3) View version: 3 (latest)
Version created on: 22/04/13 @ 16:52:00 by: Julian Garrido
Title: Cocatenates several VOTables into one
Type: Taverna 2
Preview
(Click on the image to get the full size)
Download Scalable Diagram (SVG)
Description
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input is four
VOTables with the same number of columns. The result if using sample values provided will be a four times
vertically duplicated VOTable.
Download
Download Workflow File/Package (T2FLOW)
Workflow Type
Taverna 2
Original Uploader
Julian
Garrido
License
All versions of this Workflow are licensed
under:
Credits (1)
(People/Groups)
Julian Garrido
Attributions (0)
(Workflows/Files)
None
Tags (4)
Original Uploader tags
astronomy | astrotaverna | cat |
votable
Add Tags
Shared with Groups (1)
AMIGA
Featured In Packs (1)
AstroTaverna Starter Pack
Ratings (0)
33. Download
Download Workflow File/Package (T2FLOW)
Download Workflow as a Galaxy tool
Run
Run this Workflow in the Taverna Workbench...
Option 1:
Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/3130/download?version=3
[ More Info ]
Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
Dependencies (0)
Inputs (4)
Processors (1)
Beanshells (0)
Outputs (1)
Datalinks (5)
Coordinations (0)
Featured In Packs (1)
AstroTaverna Starter Pack
Ratings (0)
Hover and click to rate
Current:
0.0 / 5
(0 ratings)
You haven't rated yet
Breakdown
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Add to your Favourites
Statistics
53 viewings
75 downloads
[ see breakdown ]
More
35. 3
7
4
1
6
5
2
1. Intelligent Software Components
(iSOCO, Spain)
2. University of Manchester (UNIMAN,
UK)
3. Universidad Politécnica de Madrid
(UPM, Spain)
4. Poznan Supercomputing and
Networking Centre (PSNC, Poland)
5. University of Oxford (OXF, UK)
6. Instituto de Astrofísica de Andalucía
(IAA, Spain)
7. Leiden University Medical Centre
(LUMC, NL)
EU FUNDED FP7 STREP PROJECT
DECEMBER 2010 – DECEMBER 2013
36. • Astronomy (IAA-CSIC)
• Genome-wide Analysis and Biobanking
Case Studies
Archival, classification, and indexing
of scientific workflows and their
associated materials in scalable
semantic repositories, providing
advanced access and recommendation
capabilities
Creation of scientific communities to
collaboratively share, reuse, and evolve
workflows and their parts, stimulating
the development of new scientific
knowledge
Goals
• Digital Libraries
• Workflow Management
• Semantic Web
• Integrity & Authenticity
• Provenance
• Information Quality
Core Competencies (Tech)
• One SME
• Six public organisations
Partners
Technological infrastructure for the preservation and efficient
retrieval and reuse of scientific workflows in a range of
disciplines
TARGETING ALREADY ESTABLISHED
COMMUNITIES: MYEXPERIMENT,
VIRTUAL OBSERVATORY
37. 3
What is a Scientific Workflow?
Workflows to Access and Massage VO Data
» A mechanism for coordinating the execution of
services and codes, and linking together resources.
» The combination of data and processes into a
configurable, modular, structured set of steps that
implement semi-automated computational solutions
in scientific problem-solving.
» The implementation of a scientific method.
COURTESY J.E. RUIZ
NOT A PIPELINE!
38. AMIGA4GAS
3D KINEMATICAL MODELING
INPUT FILES
ROTCUR
12 RUNS
POSSIBLE COMBINATIONS
IN INPUT PARAMETERS
12 ASCII FILES
GALMOD
12 CUBES
4 APPROACHING
4 RECEEDING
4 BOTH
COPY
8 CUBES
4 APPROACHING + RECEEDING
4 BOTH
MOMENTS
8 VELOCITY MAPS
1 DATACUBE
1 VELOCITY MAP
1 CONFIG FILE ROTCUR
1 CONFIG FILE GALMOD
SUB
8 RESIDUAL CUBES
8 RESIDUAL MAPS
SUB
MNMX 8 VALUES FOR PEAKS IN CUBES
8 VALUES FOR PEAKS IN MAPS
VARIABLE
PARAMS
INSET
RADII, WIDTHS
WEIGHT
TOLERANCE
DENS
NV
Z0
VDISP
40. AstroTaverna
Taverna plugin for retrieving and manipulating
VO Data + Catalogs on HTML Pages
VO Services: ConeSearch, SIA, SSA, TAP coming soon
Tabular Data (VOTables, converters from other formats)
Crossmatching, Filtering, NameResolving, Coordinates and reference
system transformation, Data massage.. (STILTS)
Source catalog overplotting on Images and filtering, overplot circles,
ellipses, etc. as a function of physical magnitude. Resampling, crops,
blinks, mosaics, movies, blinks, RGBs, fusion, diff.. (through Aladin)
VO Table rendering, SAMP for final inspection
Image support, Spectra not yet PLUS ADDITIONAL
ANALYSIS USING
SCRIPTS
52. Home RO at 5000 feet Examples Ontologies Tools Collaboration Publications History About
Search
Research Objects
53. Research Objects
Content
Process (workflows), data, external resources and bibliography
Execution environment set-up and local software dependencies
Experimental protocol followed
Roles, types and relationships among all digital components
Provenance of intermediate and final results
Decomposable attribution and authoring
Fine-grained access control and permissions
Example datasets for demonstration, reproducibility, monitoring, etc
Templates
Placeholders to ease the aggregation process
Completeness checking/quality assessment
54. Research Objects
Target Audiencies
Scientists [producers] who want to share their research
outcomes so that they are more reusable and
reproducible – ease of sharing and citation.
Scientists [consumers] who want to understand, reuse,
validate and further extend existing RO’s.
Publishers can adopt the concept and principles of
Research Object to enable the sharing of and access to
the actual data and methods.
Librarians who want to support research preservation.
55. Semantic annotations
Author of an annotation
Author and co-authors of a workflow; reference link to a re-used workflow and its
author
WhohasperformedtheexecutionofaworkflowleadingtotheresultsprovidedintheRO
Computing execution environment of the RO and local software dependencies
Special access requirements to web services
Datasets provider: person, webpage, survey, data release, etc.
How much time does it take to run a workflow using the full data and the provided
subsample
The number of elements of the sample dataset where one workflow and/or RO iterates
Previous and subsequent workflows to be executed, as in the experimental
protocol
Research institution, country, and scientific domain of the RO
The actual size of the RO and/or a folder
58. ROs in Astronomy
ADSLabs Research Objects
Authors
Publications
Journals
Objects SIMBAD
Tabular data behind the plots CDS
ASCL reference of used software
Observing time Proposals
Used facilities, surveys or missions
NOT JUST FROM WORKFLOWS
POTENTIAL FOR
RESEARCH OBJECT
INDEXING IN ADS
59. RO Incentive
PAPERS WITH DATA LINKS ARE CITED MORE THAN THOSE WITHOUT
Effect of E-printing on Citation Rates in Astronomy and Physics
2006. Edwin A. Henneken et al.
60. RO Incentive
PAPERS WITH DATA LINKS ARE CITED MORE THAN THOSE WITHOUT
Effect of E-printing on Citation Rates in Astronomy and Physics
2006. Edwin A. Henneken et al.
NOW YOU CAN
CITE DATA AND
PROCESSES, TOO
61. Roadmap
AstroTaverna, mostly ready: you can publish
workflows and packs to myExperiment from
Taverna
myExperiment, building support for ROs
ADS will populate myExperiment with literature-
ROs
Taverna will be able to publish ROs to
myExperiment
62. Final points
We need something like workflows to describe
computations in a distributed environment
Workflows are not enough for supporting reuse
and methodology preservation
Research Objects are meaningful associations of
data, operations, provenance, which can also be
cited CAN EMBED
COMPUTATIONS IN
SCIENCE ARCHIVES