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Agile Bioinformatics
Why do research projects fail?
Why do research projects fail?
          (in programming)
●   Time wasted using wrong tools / cleaning bad
    data / etc..
●   Insufficient programming skills
●   Objectives not defined clearly / bad planning
Why do research projects fail?
          (in programming)
●   Time wasted using wrong tools / cleaning bad
    data / etc.. ask for help
●   Insufficient programming skills practice
●   Objectives not defined clearly / bad planning
Why do research projects fail?
          (in programming)
●   Time wasted using wrong tools / cleaning bad
    data / etc.. ask for help
●   Insufficient programming skills practice
●   Objectives not defined clearly / bad
    planning
Example: last year's students
                 project
●   Day 1: Let's do a project to analyze a dataset
    of Alternative Splicing expression
Example: last year's students
                 project
●   Day 1: Let's do a project to analyze a dataset
    of Alternative Splicing expression
●   Day 3: Working on five different projects at
    once
Example: PhD thesis
●   Day 1: professor explains great idea of PhD
    thesis
Example: PhD thesis
●   Day 1: professor explains great idea of PhD
    thesis
●   After 3 years: student working on a completely
    different project
Planning and Programming
●   Planning is the most important part in
    programming
●   If your objective are not clear, you'll waste time
Planning is difficult,
         because objectives change!
●   Objectives always change over time
    –   New priorities
    –   New ideas
    –   Somebody else published it
    –   etc..
Planning is difficult,
         because objectives change!
●   Objectives always change over time
    –   New priorities
    –   New ideas
    –   Somebody else published it
    –   Etc..
●   What's the solution?
Scrum
●   Scrum is an approach to software
    programming
Scrum
●   Scrum is an approach to software
    programming
●   It's a set of guidelines to how to organize your
    work:
    –   How to define the objectives?
    –   How frequently objectives must be re-stated?
    –   How to organize daily work?
Scrum
●   Scrum is an approach to software
    programming
●   It's a set of guidelines to how to organize your
    work:
    –   How to define the objectives?
    –   How frequently objectives must be re-stated?
    –   How to organize daily work?
●   Guidelines, not rules
The scrum “sprint”
●   The basic of scrum is to split the work into
    “sprints” of 2-4 weeks each
The scrum “sprint”
●   The basic of scrum is to split the work into
    “sprints” of 2-4 weeks each
    –   Every 2-4 weeks, a meeting to redefine the
        objectives, and plan how to obtain them
    –   Short daily meetings to check that everything is ok
    –   A feedback meeting at the end, to discuss what
        went well or not
The planning meeting
●   A planning meeting is made every 2-3 weeks
    (beginning of the “sprint”)
●   Tasks:
    –   Define main objectives
    –   Divide work into single tasks
The planning meeting
●   A planning meeting is made every 2-3 weeks
    (beginning of the “sprint”)
●   Tasks:
    –   Define main objectives
    –   Divide work into single tasks




                                        http://blogs.microsoft.co.il/blogs/kolbis/
Planning table (post-its)




               Source of the image: wikipedia
The “post-it” rule
         ●   Ideally, a task can be
             decribed in paper of
             the size of a “Post-it”
         ●   If you can't explain it
             in a Post-it, then split
             it into two tasks
Objectives table




(sorry – I'll put this online when I submitted the paper)
Daily meeting
●   15 minutes meetings, every day in the
    morning
●   Each participant explains:
    –   What have you accomplished yesterday?
    –   What are you going to do today?
    –   Are there any impediments / stumbling blocks?
Daily planning table




(sorry – I'll put this online when I submitted the paper)
Daily Meeting example




 Barcelona runroom http://www.runroom.com/
Daily Meeting example




 Barcelona runroom http://www.runroom.com/
Daily meetings must be short!
●   The daily meeting must be necessarily not
    longer than 15 minutes
●   Anything that requires more than 15 minutes,
    should be discussed later
Never work more than 8 hours!
●   The day should be planned for 8 hours of work
●   If you consistently work more than 8 hours
    each day, you are not planning yourself well
Retrospective Meeting
●   At the end of each sprint (2-3 weeks)
    –   What has been accomplished?
    –   What has gone wrong?
    –   What can be improved?
Retrospective table




                      Image source:
                      www.it-zynergy.com
Retrospective Meeting
●   At the end of each sprint (2-3 weeks)
    –   What has been accomplished?
    –   What has gone wrong?
    –   What can be improved?
●   Tip: take a few days of “rest” after a sprint
Scrum - resume
●   Split your work into “sprints”, defining
    objectives that can be completed in 2-3 weeks
    –   One planning meeting at the beginning
    –   15 minutes meetings every day
    –   Feedback meeting at the end
Scrum - resume
●   Split your work into “sprints”, defining
    objectives that can be completed in 2-3 weeks
    –   One planning meeting at the beginning
    –   15 minutes meetings every day
    –   Feedback meeting at the end
●   These are guidelines, not rules
Example scrum calendar




          Image source: http://rocketninesolutions.com
How to know more?
●   Agile Barcelona
    –   http://agile-barcelona.org/
●   Barcelona gamestorming grou
    –   http://www.meetup.com/gamestorming-barcelona/
●   Look for the “Agile Programming” group in
    your city
●   Kane D, “Introducing Agile Development in
    Bioinformatics”, 2003

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Agile bioinf

  • 2. Why do research projects fail?
  • 3. Why do research projects fail? (in programming) ● Time wasted using wrong tools / cleaning bad data / etc.. ● Insufficient programming skills ● Objectives not defined clearly / bad planning
  • 4. Why do research projects fail? (in programming) ● Time wasted using wrong tools / cleaning bad data / etc.. ask for help ● Insufficient programming skills practice ● Objectives not defined clearly / bad planning
  • 5. Why do research projects fail? (in programming) ● Time wasted using wrong tools / cleaning bad data / etc.. ask for help ● Insufficient programming skills practice ● Objectives not defined clearly / bad planning
  • 6. Example: last year's students project ● Day 1: Let's do a project to analyze a dataset of Alternative Splicing expression
  • 7. Example: last year's students project ● Day 1: Let's do a project to analyze a dataset of Alternative Splicing expression ● Day 3: Working on five different projects at once
  • 8. Example: PhD thesis ● Day 1: professor explains great idea of PhD thesis
  • 9. Example: PhD thesis ● Day 1: professor explains great idea of PhD thesis ● After 3 years: student working on a completely different project
  • 10. Planning and Programming ● Planning is the most important part in programming ● If your objective are not clear, you'll waste time
  • 11. Planning is difficult, because objectives change! ● Objectives always change over time – New priorities – New ideas – Somebody else published it – etc..
  • 12. Planning is difficult, because objectives change! ● Objectives always change over time – New priorities – New ideas – Somebody else published it – Etc.. ● What's the solution?
  • 13. Scrum ● Scrum is an approach to software programming
  • 14. Scrum ● Scrum is an approach to software programming ● It's a set of guidelines to how to organize your work: – How to define the objectives? – How frequently objectives must be re-stated? – How to organize daily work?
  • 15. Scrum ● Scrum is an approach to software programming ● It's a set of guidelines to how to organize your work: – How to define the objectives? – How frequently objectives must be re-stated? – How to organize daily work? ● Guidelines, not rules
  • 16. The scrum “sprint” ● The basic of scrum is to split the work into “sprints” of 2-4 weeks each
  • 17. The scrum “sprint” ● The basic of scrum is to split the work into “sprints” of 2-4 weeks each – Every 2-4 weeks, a meeting to redefine the objectives, and plan how to obtain them – Short daily meetings to check that everything is ok – A feedback meeting at the end, to discuss what went well or not
  • 18. The planning meeting ● A planning meeting is made every 2-3 weeks (beginning of the “sprint”) ● Tasks: – Define main objectives – Divide work into single tasks
  • 19. The planning meeting ● A planning meeting is made every 2-3 weeks (beginning of the “sprint”) ● Tasks: – Define main objectives – Divide work into single tasks http://blogs.microsoft.co.il/blogs/kolbis/
  • 20. Planning table (post-its) Source of the image: wikipedia
  • 21. The “post-it” rule ● Ideally, a task can be decribed in paper of the size of a “Post-it” ● If you can't explain it in a Post-it, then split it into two tasks
  • 22. Objectives table (sorry – I'll put this online when I submitted the paper)
  • 23. Daily meeting ● 15 minutes meetings, every day in the morning ● Each participant explains: – What have you accomplished yesterday? – What are you going to do today? – Are there any impediments / stumbling blocks?
  • 24. Daily planning table (sorry – I'll put this online when I submitted the paper)
  • 25. Daily Meeting example Barcelona runroom http://www.runroom.com/
  • 26. Daily Meeting example Barcelona runroom http://www.runroom.com/
  • 27. Daily meetings must be short! ● The daily meeting must be necessarily not longer than 15 minutes ● Anything that requires more than 15 minutes, should be discussed later
  • 28. Never work more than 8 hours! ● The day should be planned for 8 hours of work ● If you consistently work more than 8 hours each day, you are not planning yourself well
  • 29. Retrospective Meeting ● At the end of each sprint (2-3 weeks) – What has been accomplished? – What has gone wrong? – What can be improved?
  • 30. Retrospective table Image source: www.it-zynergy.com
  • 31. Retrospective Meeting ● At the end of each sprint (2-3 weeks) – What has been accomplished? – What has gone wrong? – What can be improved? ● Tip: take a few days of “rest” after a sprint
  • 32. Scrum - resume ● Split your work into “sprints”, defining objectives that can be completed in 2-3 weeks – One planning meeting at the beginning – 15 minutes meetings every day – Feedback meeting at the end
  • 33. Scrum - resume ● Split your work into “sprints”, defining objectives that can be completed in 2-3 weeks – One planning meeting at the beginning – 15 minutes meetings every day – Feedback meeting at the end ● These are guidelines, not rules
  • 34. Example scrum calendar Image source: http://rocketninesolutions.com
  • 35. How to know more? ● Agile Barcelona – http://agile-barcelona.org/ ● Barcelona gamestorming grou – http://www.meetup.com/gamestorming-barcelona/ ● Look for the “Agile Programming” group in your city ● Kane D, “Introducing Agile Development in Bioinformatics”, 2003