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Www.nitrc.org nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI 2010 - September 24, 2010 Best Practices in Software Development: Users.

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Presentation on theme: "Www.nitrc.org nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI 2010 - September 24, 2010 Best Practices in Software Development: Users."— Presentation transcript:

1 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices in Software Development: Users and Developers Unite! Bennett Landman, Ph.D. David N. Kennedy, Ph.D. Xiaodong Tao, Ph.D. Paul A. Yushkevich, Ph.D. Gary Hui Zhang, Ph.D.

2 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Schedule 13: :00 Session 1: Presentations 13: :40 Introduction to the Tutorial 13: :00 Neuroimaging Informatics Tools and Resources Clearinghouse: NITRC David N. Kennedy 14: :20 3DSlicer3 Extension Modules: Concept and Implementation Xiaodong Tao 14: :40 Challenges of Collaborative Open-Source Development: Lessons learned from the early evolution of the Java Image Science Toolkit Bennett Landman 14: :00 Making others use your software: Lessons learned from ITK-SNAP Paul A. Yushkevich 15: :30 Tea/Coffee Break 15: :00 Session 2: Panel Discussion & Demonstrations 15: :15 Panel Discussion 16: :00 Demos

3 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Academic Objectives All participants should gain knowledge regarding: Methods for open source software development Methods for software distribution, including licensing issues Techniques for software validation Techniques for user interactions (documentation, tutorials, feedback/communication, etc.) Resources for finding existing relevant software projects. See

4 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Faculty Bennett Landman, Ph.D. Assistant Professor Department of Electrical Engineering Vanderbilt University Institute of Image Science David N. Kennedy, Ph.D. Professor, Department of Psychiatry University of Massachusetts Medical School Worcester, MA Xiaodong Tao, Ph.D. Computer Scientist GE Global Research Center Imaging Technologies Gary Hui Zhang, Ph.D. PICSL, Department of Radiology University of Pennsylvania School of Medicine 3600 Market Street, Suite 320 Philadelphia, PA Paul A. Yushkevich, Ph.D. Assistant Professor Penn Image Computing and Science Laboratory Department of Radiology University of Pennsylvania

5 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Neuroimaging Informatics Tools and Resources Clearinghouse - NITRC Software Tools - A Users Perspective David N. Kennedy, Ph.D. Director, Division of Neuroinformatics Department of Psychiatry, UMass Medical School Child and Adolescent NeuroDevelopment Initiative

6 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 With apologies and credit to Gary Larson - The Far Side

7 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 users developers How do I change the contrast? How do I add layers? How do I invert the transform? blah blah blah RTFM blah blah With apologies and credit to Gary Larson - The Far Side

8 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 users developers v Well, this is really a very complex piece of code. Have you read my paper from MICCAI? It’s probably too complex for you… With apologies and credit to Gary Larson - The Far Side

9 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Data Acquisition & Analysis - Normal Development and Studies in Child Psychiatry (Autism, Bipolar Disorder, etc.) –Structure –Diffusion –Resting State User Scope:

10 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Finding the Right Tool “MRI segmentation software brain” Google? –About 157,000 results –Top Hit: Rescue Source Forge? NITRC?

11 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Google Top Hit

12 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Finding the Right Tool “MRI segmentation software brain” Google? –About 157,000 results –Top Hit: Rescue –Results include: papers, pdfs, ppts, programs, pictures, videos, etc. Source Forge? NITRC?

13 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Finding the Right Tool “MRI segmentation software brain” Google? –About 157,000 results Source Forge? –15,539 results –Top Hit: PortableApps.com: Portable Software/USB –Results include: you name it… NITRC?

14 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Source Forge Results

15 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Finding the Right Tool “MRI segmentation software brain” Google? –About 157,000 results Source Forge? –15,539 results NITRC? –39 Software Packages –Top Hit: ITK-SNAP –Results include: All the ‘usual suspect’ tools, and more!

16 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 NITRC Result

17 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Refining the Search Operating System: MacOS Supported Image Type: DICOM Results in: 16 Resources

18 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 NITRC Result Refined

19 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion User RequirementsDeveloper Requirements

20 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Installation Findability is just first step. Can I install it, easily? Examples: –FSL –Mango

21 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 FSL Installation Steps 1.Click download link 2.Agree to license 3.Provide some personal information 4.Download appropriate release 5.Run FSL installer script (from command line) 6.Test the installation

22 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Mango Installation Steps 1.Click download link 2.Open the download w/ ‘Archive Utility’ 3.Run Installer (Double click from UI) - Answer usual questions 4.Run Program (Double click from ‘Applications’ directory)

23 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify User RequirementsDeveloper Requirements

24 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Ease of Use Now what? You’ve found and installed your program, how do you use it? From the UI, is it clear what to do?

25 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 User Interface

26 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Documentation Of course the software is very powerful, and it’s impossible for everything to be intuitively obvious from the UI, who do you think we are, Microsoft? Users are obligated to RTM (read the manual) prior to bugging the developers with questions. But, where is the manual? Is it easy to use? Are there examples? Tutorials? FAQ?

27 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 FSL Documentation

28 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive UI/Good Documentation User RequirementsDeveloper Requirements

29 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Help! OK, I REALLY did read the manual, and I just can’t figure out how to [insert problem here]… I checked the FAQ, and searched on the mail list archive… Oh, wait a minute, is there a FAQ? Is there a mail list? Is there a users ‘forum’? Where are they? OK, I checked those too, how do I get more help? –User Support Forums, Mailing Lists – an administrator? –What’s the preferred method for this project?

30 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive/Good Documentation 4.Get HelpBug Tracker/Forums/Mailing List User RequirementsDeveloper Requirements

31 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Latest Version? Once you succeed at contacting the developers, how often does the following happen to you? –Oh, you can’t do [blah]? ‘That’s been added in the ‘most recent’ version’ Or worse yet, ‘that’s only available in the development version’. Or, ‘that’s planned for release 3.X’. Users: Know your versions! Developers: Keep your public releases up to date! (yes, ALL of them…)

32 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive/Good Documentation 4.Get HelpBug Tracker/Forums/Mailing List 5.Up-to-Date Versioning/Synchronization/Dashboard User RequirementsDeveloper Requirements

33 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 I want the best! Of course, I only want to use the best software know to human kind for my research. Unfortunately, ‘best’ is exceedingly domain dependent, and many problems (and software packages) cross many domains in a specific problem (skull striping, registration, pre-filtering, statistical test, etc.). Also, ‘best’ is data dependent. The ‘best’ surface extraction in post mortem tissue may not be the best in patients w/ AD. Users: Know what best means in your context! Developers: Provide quality metrics (on standard cases) when possible!

34 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive/Good Documentation 4.Get HelpBug Tracker/Forums/Mailing List 5.Up-to-Date Versioning/Synchronization/Dashboard 6.High QualityValidation/Comparison Metrics User RequirementsDeveloper Requirements

35 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Say I’m not the only one… Even if using the ‘best’ tool, the user will run into publications problems if no one else has ever used that tool before. Have you gotten reviewers who say: “You should have used the Talairach coordinate system”, or “You should have used SPM…”? Even if it’s not fair or optimal, users need to know how popular a resource is. # of downloads  # of users  # of publications, etc.

36 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive/Good Documentation 4.Get HelpBug Tracker/Forums/Mailing List 5.Up-to-Date Versioning/Synchronization/Dashboard 6.High QualityValidation/Comparison Metrics 7.Use Metrics Downloads/Users/Publication Counts 8. User RequirementsDeveloper Requirements

37 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 I can make it better… I’ve found a great tool, it works really well for me, and does everything I need… almost. I submitted a ‘Feature Request’, and I completely understand that your funding and time is limited, and you will not get to my request until But hey, I’m a wicked good [insert programming language here] programmer myself. Let me at your source code… Open Source is not the solution for everything, but with proper management and policy, it’s an important tool for extensibility, transparency, and public relations. Besides, it ought to be the law…

38 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive/Good Documentation 4.Get HelpBug Tracker/Forums/Mailing List 5.Up-to-Date Versioning/Synchronization/Dashboard 6.High QualityValidation/Comparison Metrics 7.Use Metrics Downloads/Users/Publication Counts 8.Contribute/ExtendSource Code Availability/Policy User RequirementsDeveloper Requirements

39 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Summary Top 10 reasons users use a specific software package: 10. It’s what my lab uses… 9. Has the most publications… 8. Is easiest to use… 7. Is part of the LONI pipeline… 6. I wrote it… when I was a graduate student… 20 years ago…

40 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Summary Top 10 reasons users use a specific software package: 5. My graduate student wrote it… who is a botany major… with no formal programming training… 4. It works with 3D Slicer… 3. It’s written in ITK… 2. Everyone uses SPM… 1. At least it’s not SPM…

41 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Summary, continued Top 1 reason NOT listed as a reason to use a specific software package: 1. It is the best… This is where developers and users have to continue to work together to: Insist on the best Define the parameters of best Develop standards for performance Document the performance And use the guidelines of Best Practices for software development!

42 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Acknowledgements All NITRC Users and Developers Today’s Presenters & Audience MICCAI Organizers NITRC Development Team (Neuromorphometrics Inc, TCG Inc, UCSD) NITRC Sponsors (NIH Blueprint, NIBIB) The ‘tutorial’ lives on at

43 nitrc.nih.gov F-T4: Best Practices in Software Development MICCAI September 24, 2010 Best Practices Take-Home Points: 1.FindabilityDescription/Promotion 2.Easy to InstallEasy to Install/Verify 3.Easy to UseIntuitive/Good Documentation 4.Get HelpBug Tracker/Forums/Mailing List 5.Up-to-Date Versioning/Synchronization/Dashboard 6.High QualityValidation/Comparison Metrics 7.Use Metrics Downloads/Users/Publication Counts 8.Contribute/ExtendSource Code Availability/Policy User RequirementsDeveloper Requirements


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