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Date: 22/10/2014 
Workflow Reuse in Practice: 
A Study of Neuroimaging Pipeline Users 
Daniel Garijo *, Oscar Corcho *, Yolanda Gil Ŧ, Meredith N. Braskieⱡ, Derrek Hibarⱡ, Xue Huaⱡ, Neda Jahanshadⱡ, Paul Thompsonⱡ, and Arthur W. Togaⱡ 
* Universidad Politécnica de Madrid, 
Ŧ USC Information Sciences Institute, 
ⱡ USC Laboratory of Neuroimaging
Main Contributions 
•Highlight the benefits of workflows and workflow fragments 
reported by users in a neuroscience research lab 
•Survey of workflow users 
•Quantitative perspective on the identified benefits. 
IEEE eScience 2014. Guarujá, Brasil 
2 
repurpose 
reuse 
repository 
Create, collaborate
Background 
•Workflows are software artifacts that capture computational experiments 
•Addition to paper publication 
•Provenance of results 
•Reuse 
•Existing repositories of workflows (Galaxy, myExperiment, the LONI Pipeline, CrowdLabs, etc.) 
•Sharing workflows 
•Exploring existing workflows 
•PROBLEMS to address: 
•How does workflow reuse happen in a research lab environment? 
•Are workflow fragments more useful than workflows? 
3 
IEEE eScience 2014. Guarujá, Brasil
Use case: The LONI Pipeline 
Workflow system for neuroimaging analysis 
http://pipeline.loni.usc.edu/explore/library-navigator/ 
IEEE eScience 2014. Guarujá, Brasil 
4
Why LONI Pipeline? 
•Need for reuse 
•Grouping Tools 
•Manual annotation of workflow fragments 
•Workflow Miner 
5 
IEEE eScience 2014. Guarujá, Brasil
Approach 
IEEE eScience 2014. Guarujá, Brasil 
6 
Discussions with scientists 
User survey 
Collect responses from users 
21 responses 
Discuss results
Possible benefits of workflows and workflow fragments 
•Sharing workflows with collaborators 
•Time savings 
•Copy & paste fragments of workflows 
•Reuse existent workflows 
•Teaching 
•Reduce the learning curve of new students 
•Visualization 
•Simplify workflows 
•Design for modularity 
•Highlight the most relevant steps on a workflow 
IEEE eScience 2014. Guarujá, Brasil 
7
Possible benefits of workflows and workflow fragments (2) 
•Design for understandability 
•Design for standardization 
•Debugging 
•Provenance exploration 
•Paper writing 
•Linking papers to pipelines 
•Reproducibility and inspectability 
IEEE eScience 2014. Guarujá, Brasil 
8
Survey Analysis 
9 
IEEE eScience 2014. Guarujá, Brasil
Writing and Sharing Code 
•Writing code is considered very important for this area of research. 
•Sharing code is not considered to be as important. 
10 
IEEE eScience 2014. Guarujá, Brasil
Adopting a Workflow System 
The overwhelming majority of responders found the workflow system useful. 
•Creation of workflows. 
IEEE eScience 2014. Guarujá, Brasil 
11
Adopting a workflow system: workflow size 
•Workflows of fewer than 10 steps seem to be the most preferred by scientists 
IEEE eScience 2014. Guarujá, Brasil 
12 
0	 2	 4	 6	 8	 10	 12	 14	 1	2	3	4	1-5	5-10	10-20	>20	 Number	of	workflow	components
Reusing workflows 
•Respondents answered that creating workflows is very useful 
•Reuse of workflows was seen as less useful 
•Reuse is not the only reason why workflows are created 
•Reusing workflows from a user’s prior work is considered as useful as reusing workflows from others 
IEEE eScience 2014. Guarujá, Brasil 
13
Reusing workflows (2) 
According to the respondents, the major benefits of workflows include: 
• Time savings 
•Organizing and storing code 
• Having a visualization of the overall analysis 
•Facilitating reproducibility 
IEEE eScience 2014. Guarujá, Brasil 
14 
Workflows save time 
13 
Easier to track and debug complex code 
9 
Convenient way to organize/store code 
11 
Help write more organized code 
6 
Help make code more modular/reusable 
4 
Help make methods more understandable 
8 
Visualization of overall analysis 
11 
Workflows facilitate reproducibility 
10
Reusing workflows (3) 
•The overwhelming majority of respondents said workflows are useful for both non-programmers and for teaching new students 
IEEE eScience 2014. Guarujá, Brasil 
15 
Non-programmers can use them 
20 
New students can easily learn 
19 
No need for others to re-implement code 
14 
Adoption of standard ways to do things 
9
Reusing workflows (4) 
•Respondents did not offer very overwhelming reasons for not sharing workflows 
•Respondents did not offer very overwhelming reasons for not reusing workflows from others 
IEEE eScience 2014. Guarujá, Brasil 
16 
Others would not want to use them 
1 
Others ask too many questions of the creators 
2 
Workflows from others are difficult to understand 
3 
It is difficult to understand how to prepare data for a workflow 
3 
Workflows from others are difficult to understand 
4 
It is difficult to understand how to prepare data for a workflow 
2 
Workflows created by others are too specific 
1 
It is hard to take workflows created by others and make them work 
2
Reusing groupings 
•Reuse is not the only reason why groupings are created. Unlike workflows, reusing groupings from one’s own work is more useful than reusing groupings from others 
IEEE eScience 2014. Guarujá, Brasil 
17
Reusing groupings (2) 
•Most respondents agreed that groupings help simplify workflows. Groupings also make workflows more understandable by others 
•Other grouping benefits: 
•Time savings 
•Help making modular and understandable code, more so than workflows 
•Seen as useful to non-programmers and students 
IEEE eScience 2014. Guarujá, Brasil 
18 
Visualization of the analysis 
10 
To simplify workflows that are complex overall 
12 
To make workflows more understandable to others 
12 
Groupings save time 
12 
Help make code more modular/reusable 
10 
Help make methods more understandable 
7
Reusing groupings (3) 
Very few responses motivated any reasons for not sharing groupings or not reusing groupings from others In general, workflows are considered generally more useful than groupings. On the other hand, more respondents said that groupings help make their code more modular and understandable 
IEEE eScience 2014. Guarujá, Brasil 
19 
Others would not want to use them 
0 
Others ask too many questions of the creators 
1 
Workflows from others are difficult to understand 
4 
It is difficult to understand how to prepare data for a grouping 
1 
Groupings from others are difficult to understand 
2 
It is difficult to understand how to prepare data for a grouping 
3 
Groupings created by others are too specific 
1 
It is hard to take groupings created by others and make them work 
4
Paper Writing 
Workflows are not systematically linked to publications 
•Most responders believe that the link between a workflow and a publication is kept in private laboratory notes, rather than in a publicly accessible manner 
IEEE eScience 2014. Guarujá, Brasil 
20
Discussion 
Workflows have a clear benefit to the lab. There are important directions of future research suggested by this work: 
•Improve the use of groupings. 
•If users had more assistance in specifying and finding groupings, it is possible that workflows and fragments would be more reused 
•Debugging and checking results 
•Better mechanisms to handle checking intermediate execution results would allow users to define larger workflows 
•Better documentation of workflows. 
•Documentation of workflows tends to be private and scattered, and not usually linked to papers 
•Facilitating workflows publication and linking to papers 
•Papers provide important context and documentation for workflows 
IEEE eScience 2014. Guarujá, Brasil 
21
Conclusions 
•Contributions: 
•Highlight the benefits of workflows and workflow fragments reported by users in a neuroscience research lab 
•Quantitative survey of the benefits by workflow users 
•Our work can be expanded by 
•Validating our findings with more respondents 
•Reflecting the experience level of the respondents on the questionnaire 
•Including statistics of the groupings usage on the workflows they create 
•There are clear opportunities to develop best practices for designing workflow components and modularizing code, encouraging standards adoption, and facilitating understanding by other users 
IEEE eScience 2014. Guarujá, Brasil 
22 
All materials used and the survey are available at: http://purl.org/net/wfSurvey-eScience2014
23 
Who are we? 
•Daniel Garijo, Oscar Corcho Ontology Engineering Group, UPM 
•Yolanda Gil Information Sciences Institute, USC 
•Meredith N. Braskie, Derrek Hibar, Xue Hua, Neda Jahanshad, Paul Thompson Arthur W. Toga. USC Laboratory of Neuro Imaging 
IEEE eScience 2014. Guarujá, Brasil
24 
Questions? 
IEEE eScience 2014. Guarujá, Brasil
Date: 22/10/2014 
Workflow Reuse in Practice: 
A Study of Neuroimaging Pipeline Users 
Daniel Garijo *, Oscar Corcho *, Yolanda Gil Ŧ, Meredith N. Braskieⱡ, Derrek Hibarⱡ, Xue Huaⱡ, Neda Jahanshadⱡ, Paul Thompsonⱡ, and Arthur W. Togaⱡ 
* Universidad Politécnica de Madrid, 
Ŧ USC Information Sciences Institute, 
ⱡ USC Laboratory of Neuroimaging

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Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users

  • 1. Date: 22/10/2014 Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users Daniel Garijo *, Oscar Corcho *, Yolanda Gil Ŧ, Meredith N. Braskieⱡ, Derrek Hibarⱡ, Xue Huaⱡ, Neda Jahanshadⱡ, Paul Thompsonⱡ, and Arthur W. Togaⱡ * Universidad Politécnica de Madrid, Ŧ USC Information Sciences Institute, ⱡ USC Laboratory of Neuroimaging
  • 2. Main Contributions •Highlight the benefits of workflows and workflow fragments reported by users in a neuroscience research lab •Survey of workflow users •Quantitative perspective on the identified benefits. IEEE eScience 2014. Guarujá, Brasil 2 repurpose reuse repository Create, collaborate
  • 3. Background •Workflows are software artifacts that capture computational experiments •Addition to paper publication •Provenance of results •Reuse •Existing repositories of workflows (Galaxy, myExperiment, the LONI Pipeline, CrowdLabs, etc.) •Sharing workflows •Exploring existing workflows •PROBLEMS to address: •How does workflow reuse happen in a research lab environment? •Are workflow fragments more useful than workflows? 3 IEEE eScience 2014. Guarujá, Brasil
  • 4. Use case: The LONI Pipeline Workflow system for neuroimaging analysis http://pipeline.loni.usc.edu/explore/library-navigator/ IEEE eScience 2014. Guarujá, Brasil 4
  • 5. Why LONI Pipeline? •Need for reuse •Grouping Tools •Manual annotation of workflow fragments •Workflow Miner 5 IEEE eScience 2014. Guarujá, Brasil
  • 6. Approach IEEE eScience 2014. Guarujá, Brasil 6 Discussions with scientists User survey Collect responses from users 21 responses Discuss results
  • 7. Possible benefits of workflows and workflow fragments •Sharing workflows with collaborators •Time savings •Copy & paste fragments of workflows •Reuse existent workflows •Teaching •Reduce the learning curve of new students •Visualization •Simplify workflows •Design for modularity •Highlight the most relevant steps on a workflow IEEE eScience 2014. Guarujá, Brasil 7
  • 8. Possible benefits of workflows and workflow fragments (2) •Design for understandability •Design for standardization •Debugging •Provenance exploration •Paper writing •Linking papers to pipelines •Reproducibility and inspectability IEEE eScience 2014. Guarujá, Brasil 8
  • 9. Survey Analysis 9 IEEE eScience 2014. Guarujá, Brasil
  • 10. Writing and Sharing Code •Writing code is considered very important for this area of research. •Sharing code is not considered to be as important. 10 IEEE eScience 2014. Guarujá, Brasil
  • 11. Adopting a Workflow System The overwhelming majority of responders found the workflow system useful. •Creation of workflows. IEEE eScience 2014. Guarujá, Brasil 11
  • 12. Adopting a workflow system: workflow size •Workflows of fewer than 10 steps seem to be the most preferred by scientists IEEE eScience 2014. Guarujá, Brasil 12 0 2 4 6 8 10 12 14 1 2 3 4 1-5 5-10 10-20 >20 Number of workflow components
  • 13. Reusing workflows •Respondents answered that creating workflows is very useful •Reuse of workflows was seen as less useful •Reuse is not the only reason why workflows are created •Reusing workflows from a user’s prior work is considered as useful as reusing workflows from others IEEE eScience 2014. Guarujá, Brasil 13
  • 14. Reusing workflows (2) According to the respondents, the major benefits of workflows include: • Time savings •Organizing and storing code • Having a visualization of the overall analysis •Facilitating reproducibility IEEE eScience 2014. Guarujá, Brasil 14 Workflows save time 13 Easier to track and debug complex code 9 Convenient way to organize/store code 11 Help write more organized code 6 Help make code more modular/reusable 4 Help make methods more understandable 8 Visualization of overall analysis 11 Workflows facilitate reproducibility 10
  • 15. Reusing workflows (3) •The overwhelming majority of respondents said workflows are useful for both non-programmers and for teaching new students IEEE eScience 2014. Guarujá, Brasil 15 Non-programmers can use them 20 New students can easily learn 19 No need for others to re-implement code 14 Adoption of standard ways to do things 9
  • 16. Reusing workflows (4) •Respondents did not offer very overwhelming reasons for not sharing workflows •Respondents did not offer very overwhelming reasons for not reusing workflows from others IEEE eScience 2014. Guarujá, Brasil 16 Others would not want to use them 1 Others ask too many questions of the creators 2 Workflows from others are difficult to understand 3 It is difficult to understand how to prepare data for a workflow 3 Workflows from others are difficult to understand 4 It is difficult to understand how to prepare data for a workflow 2 Workflows created by others are too specific 1 It is hard to take workflows created by others and make them work 2
  • 17. Reusing groupings •Reuse is not the only reason why groupings are created. Unlike workflows, reusing groupings from one’s own work is more useful than reusing groupings from others IEEE eScience 2014. Guarujá, Brasil 17
  • 18. Reusing groupings (2) •Most respondents agreed that groupings help simplify workflows. Groupings also make workflows more understandable by others •Other grouping benefits: •Time savings •Help making modular and understandable code, more so than workflows •Seen as useful to non-programmers and students IEEE eScience 2014. Guarujá, Brasil 18 Visualization of the analysis 10 To simplify workflows that are complex overall 12 To make workflows more understandable to others 12 Groupings save time 12 Help make code more modular/reusable 10 Help make methods more understandable 7
  • 19. Reusing groupings (3) Very few responses motivated any reasons for not sharing groupings or not reusing groupings from others In general, workflows are considered generally more useful than groupings. On the other hand, more respondents said that groupings help make their code more modular and understandable IEEE eScience 2014. Guarujá, Brasil 19 Others would not want to use them 0 Others ask too many questions of the creators 1 Workflows from others are difficult to understand 4 It is difficult to understand how to prepare data for a grouping 1 Groupings from others are difficult to understand 2 It is difficult to understand how to prepare data for a grouping 3 Groupings created by others are too specific 1 It is hard to take groupings created by others and make them work 4
  • 20. Paper Writing Workflows are not systematically linked to publications •Most responders believe that the link between a workflow and a publication is kept in private laboratory notes, rather than in a publicly accessible manner IEEE eScience 2014. Guarujá, Brasil 20
  • 21. Discussion Workflows have a clear benefit to the lab. There are important directions of future research suggested by this work: •Improve the use of groupings. •If users had more assistance in specifying and finding groupings, it is possible that workflows and fragments would be more reused •Debugging and checking results •Better mechanisms to handle checking intermediate execution results would allow users to define larger workflows •Better documentation of workflows. •Documentation of workflows tends to be private and scattered, and not usually linked to papers •Facilitating workflows publication and linking to papers •Papers provide important context and documentation for workflows IEEE eScience 2014. Guarujá, Brasil 21
  • 22. Conclusions •Contributions: •Highlight the benefits of workflows and workflow fragments reported by users in a neuroscience research lab •Quantitative survey of the benefits by workflow users •Our work can be expanded by •Validating our findings with more respondents •Reflecting the experience level of the respondents on the questionnaire •Including statistics of the groupings usage on the workflows they create •There are clear opportunities to develop best practices for designing workflow components and modularizing code, encouraging standards adoption, and facilitating understanding by other users IEEE eScience 2014. Guarujá, Brasil 22 All materials used and the survey are available at: http://purl.org/net/wfSurvey-eScience2014
  • 23. 23 Who are we? •Daniel Garijo, Oscar Corcho Ontology Engineering Group, UPM •Yolanda Gil Information Sciences Institute, USC •Meredith N. Braskie, Derrek Hibar, Xue Hua, Neda Jahanshad, Paul Thompson Arthur W. Toga. USC Laboratory of Neuro Imaging IEEE eScience 2014. Guarujá, Brasil
  • 24. 24 Questions? IEEE eScience 2014. Guarujá, Brasil
  • 25. Date: 22/10/2014 Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users Daniel Garijo *, Oscar Corcho *, Yolanda Gil Ŧ, Meredith N. Braskieⱡ, Derrek Hibarⱡ, Xue Huaⱡ, Neda Jahanshadⱡ, Paul Thompsonⱡ, and Arthur W. Togaⱡ * Universidad Politécnica de Madrid, Ŧ USC Information Sciences Institute, ⱡ USC Laboratory of Neuroimaging