Electronic Lab Notebooks
(ELNs)
Kristin A. Briney, PhD
Data Services Librarian, UWM
3 December 2013
Documentation

http://www.flickr.com/photos/jjpacres/3293117576/ (CC BY-NC-ND)
Good documentation is a critical
part of managing research data
well, now and into the future
Documentation - Content
• Scientific information
• Context of the experiment, measurement description, protocols, etc

• T...
Documentation - Audience
• For you
Documentation - Audience
• For you
• For future you
• For your boss
• For your colleagues
• For your collaborators
• For y...
Documentation - Provenance
• Intellectual property
• Accusations of misconduct
Documentation - Provenance
• Intellectual property
• Accusations of misconduct
 Why lab notebook best practices are impor...
Paper-Based System

http://www.flickr.com/photos/camknows/3821001012/ (CC BY-NC-SA)
Paper-Based System
• Flexible
• Easy to use
• Rich history and best practices
Paper-Based System
• Divide between handwritten notes and digital data
• Not easily searchable
• Not easy to use by others
Paper-Based System
• Notebooks not backed up
• Damage to paper (spills, fading ink, etc)
• Legibility issues
As data become larger and a more
valued research output, it will
become harder to rely solely on a
paper-based notebook
ELNs

http://www.flickr.com/photos/24801682@N08/4117012787/ (CC BY)
ELNs - Pros
• Add data files to ELN
• View data files in ELN

• Searching
• Linking between pages
ELNs - Pros
• Sharing
• Different access permissions by role
• May be able to share across institutions

• Developing work...
ELNs - Pros
• Audit trail (provenance)
• Revision history
• eSignatures

• Range of customizability
• Plugins
• Drawing to...
ELNs - Cons
• Digital system
• Bugs, upgrades, etc
• Security and storage concerns
• Limited access
ELNs - Cons
• Usability in 10 years
• Proprietary files
• Unsettled ELN market

• Adjusting your workflow
• Flexibility
• ...
Here at Wisconsin

http://www.flickr.com/photos/teemu08/7398639848/ (CC BY-SA)
UW-Madison ELN Pilot
• Tested 2 notebooks, CERF and eCAT
• 55 users, majority never used an ELN before

• CERF
• Pilot org...
UW-Madison ELN Pilot
• At end of pilot, 91% of respondents wanted to continue using an ELN
• 60% of CERF users wanted to t...
Future of ELNs on Campus
• Campus looking into purchasing software
• Currently in progress

• Great place to start
• Reali...
Demonstrations

http://www.flickr.com/photos/seanstayte/378461236/ (CC BY-NC-SA)
Demonstrations
• eCAT
•
•
•
•
•

CALS-supported installation from UW ELN pilot
Pilot testers liked this ELN
New version is...
Demonstrations Caveat
• I am showing free versions of software
• Free versions have limited features
• Also data security ...
Where To Go From Here?

http://www.flickr.com/photos/bulle_de/4672972586/ (CC BY)
1. What Are Your Needs?
• Will you be doing lots of searching, sharing, or reuse?
• Do you like the flexibility of a paper...
1. What Are Your Needs?
• Will you be doing lots of searching, sharing, or reuse?
• Do you like the flexibility of a paper...
2. How Much Does Discipline Matter?
• Many flavors of ELNs
• Different features by discipline

Rubacha, M.; Rattan, A. K.;...
3. What Resources Do You Have?
• Funding
• Open source ELNs
• May require tech ability

• Commercial ELNs
• Upward of $100...
3. What Resources Do You Have?
• Hardware
• Server
• Cloud storage*

• Point person
Minimum Requirements

http://www.flickr.com/photos/techbirmingham/167395997/ (CC-BY)
What to Look for in Software
• Note taking and searching ability
• Adding external files
• Adding links between pages
• Ac...
Provenance
• Way to create provenance
•
•
•
•

Audit trail
Lock pages once finished
Date stamps
Electronic signatures

• W...
Exporting Files
• No guarantee that current ELNs will be here in 5 years

• Ideally, write files to an open file format
•
...
Test Software
• One ELN software package will not work for everyone
• Test before purchase
• Ideally a week-to-month long ...
Future of ELNs

http://www.flickr.com/photos/simpologist/16734948/ (CC BY-NC)
Future of ELNs
• ELNs will become the norm in research in the future
• Graduates going into industry may be using ELNs now...
If You Want an ELN
• Identify needs
• Test the software out before converting
• If you adopt now, have an exit strategy
Final Word
• Lots of benefits and some risks in adopting an ELN
• Keeping a paper notebook has risks but they’re different...
Resources
• DoIT Academic Technologies
• http://academictech.doit.wisc.edu/ideas/electronic-lab-notebooks

• Research Data...
Thanks
• Ebling Library
• Trisha Adamus

• This presentation available under a Creative Commons Attribution 3.0
license
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Electronic Laboratory Notebooks

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Talk given for UW-Madison Ebling Library and School of Medicine and Public Health on 3 Dec 2013. It covers electronic laboratory notebooks and what to look for in the software.

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  • Thanks! This is a good set of important ideas to consider.

    For me, a lab notebook has always been a place for free flow of well-recorded documentation, scribbles, and hand-drawn pictures as the experiment progresses rather than a predefined template to fill systematically according to what someone else decides must fit the path. Being able to use a more general notebook software (on my iPad for example) that gives me the equivalent feel to working with a blank page of paper and that offers lots of good widgets handy (to draw and capture images or sound inputs) makes a lot better sense than using a commercially designed app that may have a slanted, biologist's view of what I as a chemical engineer should be recording during my lab experiment (not to slur biologists particularly here).

    With regard to provenance, a new service cloudHQ may offer the option to take content from such 'changeable' sources as Evernote and convert that content to time-stamped 'hard-coded' formats such as PDF. I suspect such services will become more common as other professions seek the same methods to 'hard-bind' their electronic 'hand-written' notes in legally-certifiable ways. Add to this that many general notebooks use a data format that is open source versus what may be the proprietary storage format of some ELN-specific apps, and you have a win-win case!

    Of course, we have also a plethora of cloud services at hand, and they are far cheaper in most cases than to use an ELN service. Why then tout anymore the advantages that any ELN company may have over any other for this?

    In the end, I have to wonder if the combined growth in cheaper, non-ELN-specific software tools (a high-powered, general note taking app + solid cloud services + a well-versioned, incremental, time-stamping archiving service) will eventually outpace any need or demand to use an application that is targeted solely as an ELN. I think the tipping point is near!

    --
    J J Weimer, Associate Professor
    Chemistry / Chemical & Materials Engineering, UAH
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Electronic Laboratory Notebooks

  1. 1. Electronic Lab Notebooks (ELNs) Kristin A. Briney, PhD Data Services Librarian, UWM 3 December 2013
  2. 2. Documentation http://www.flickr.com/photos/jjpacres/3293117576/ (CC BY-NC-ND)
  3. 3. Good documentation is a critical part of managing research data well, now and into the future
  4. 4. Documentation - Content • Scientific information • Context of the experiment, measurement description, protocols, etc • Technical information • Instrument calibrations, how the files fit together, etc • Data management information • Project information, data collector, data owner, etc
  5. 5. Documentation - Audience • For you
  6. 6. Documentation - Audience • For you • For future you • For your boss • For your colleagues • For your collaborators • For your peers • For other researchers • For the public
  7. 7. Documentation - Provenance • Intellectual property • Accusations of misconduct
  8. 8. Documentation - Provenance • Intellectual property • Accusations of misconduct  Why lab notebook best practices are important
  9. 9. Paper-Based System http://www.flickr.com/photos/camknows/3821001012/ (CC BY-NC-SA)
  10. 10. Paper-Based System • Flexible • Easy to use • Rich history and best practices
  11. 11. Paper-Based System • Divide between handwritten notes and digital data • Not easily searchable • Not easy to use by others
  12. 12. Paper-Based System • Notebooks not backed up • Damage to paper (spills, fading ink, etc) • Legibility issues
  13. 13. As data become larger and a more valued research output, it will become harder to rely solely on a paper-based notebook
  14. 14. ELNs http://www.flickr.com/photos/24801682@N08/4117012787/ (CC BY)
  15. 15. ELNs - Pros • Add data files to ELN • View data files in ELN • Searching • Linking between pages
  16. 16. ELNs - Pros • Sharing • Different access permissions by role • May be able to share across institutions • Developing workflows • Read data from instruments directly • Built in testing
  17. 17. ELNs - Pros • Audit trail (provenance) • Revision history • eSignatures • Range of customizability • Plugins • Drawing tools • Mobile versions
  18. 18. ELNs - Cons • Digital system • Bugs, upgrades, etc • Security and storage concerns • Limited access
  19. 19. ELNs - Cons • Usability in 10 years • Proprietary files • Unsettled ELN market • Adjusting your workflow • Flexibility • Lack of desired features • User interface matters
  20. 20. Here at Wisconsin http://www.flickr.com/photos/teemu08/7398639848/ (CC BY-SA)
  21. 21. UW-Madison ELN Pilot • Tested 2 notebooks, CERF and eCAT • 55 users, majority never used an ELN before • CERF • Pilot organizers liked this software • Did not live up to expectations in the lab • Did basic record keeping but other functionality disappointing • eCAT • • • • CALS installation supporting >30 people Users found easy to use and liked interface Users liked level of customization, though general template worked Majority felt they kept better records than before
  22. 22. UW-Madison ELN Pilot • At end of pilot, 91% of respondents wanted to continue using an ELN • 60% of CERF users wanted to try a different ELN • Required <12 hours to learn interface • Users employed training sessions and trial and error to learn • Users liked linking and adding data files • Drawing tools and mobile versions did not live up to expectations • http://academictech.doit.wisc.edu/ideas/electronic-lab-notebooks
  23. 23. Future of ELNs on Campus • Campus looking into purchasing software • Currently in progress • Great place to start • Realize ultimate product won’t work for all
  24. 24. Demonstrations http://www.flickr.com/photos/seanstayte/378461236/ (CC BY-NC-SA)
  25. 25. Demonstrations • eCAT • • • • • CALS-supported installation from UW ELN pilot Pilot testers liked this ELN New version is called ‘Research Space’ Has limited free version which I will demo http://www.researchspace.com/ • LabArchives • Was not part of pilot but an option that DoIT also looked into • Has limited free version which I will demo • http://www.labarchives.com/
  26. 26. Demonstrations Caveat • I am showing free versions of software • Free versions have limited features • Also data security and storage issues • Great for testing • May need to test with fake data • Don’t plan to use free versions in long term
  27. 27. Where To Go From Here? http://www.flickr.com/photos/bulle_de/4672972586/ (CC BY)
  28. 28. 1. What Are Your Needs? • Will you be doing lots of searching, sharing, or reuse? • Do you like the flexibility of a paper notebook? • Do you need a system for collaboration? • Do you need to protect your research notes for privacy reasons? • Will you be making a lot of drawings in your notes?
  29. 29. 1. What Are Your Needs? • Will you be doing lots of searching, sharing, or reuse? • Do you like the flexibility of a paper notebook? • Do you need a system for collaboration? • Do you need to protect your research notes for privacy reasons? • Will you be making a lot of drawings in your notes?  Do you even need an ELN?
  30. 30. 2. How Much Does Discipline Matter? • Many flavors of ELNs • Different features by discipline Rubacha, M.; Rattan, A. K.; Hosselet, S. C., A Review of Electronic Laboratory Notebooks Available in the Market Today. Journal of the Association for Laboratory Automation 2011, 16 (1), 9.
  31. 31. 3. What Resources Do You Have? • Funding • Open source ELNs • May require tech ability • Commercial ELNs • Upward of $1000 /person /year • Many ELNs getting into academic market
  32. 32. 3. What Resources Do You Have? • Hardware • Server • Cloud storage* • Point person
  33. 33. Minimum Requirements http://www.flickr.com/photos/techbirmingham/167395997/ (CC-BY)
  34. 34. What to Look for in Software • Note taking and searching ability • Adding external files • Adding links between pages • Access permissions • Ability to export
  35. 35. Provenance • Way to create provenance • • • • Audit trail Lock pages once finished Date stamps Electronic signatures • With provenance, ELNs acceptable for patents • Because of provenance, I don’t recommend • Blogs • Wikis • Note taking software
  36. 36. Exporting Files • No guarantee that current ELNs will be here in 5 years • Ideally, write files to an open file format • • • • PDF common XML HTML Word (.doc/.docx) • At worst, need to be able to print out all pages • Useful to have a batch method to do this
  37. 37. Test Software • One ELN software package will not work for everyone • Test before purchase • Ideally a week-to-month long test in the lab • Use as a notebook and look at features in depth • Keep both paper and electronic records during test  Takes time and effort to test but very important
  38. 38. Future of ELNs http://www.flickr.com/photos/simpologist/16734948/ (CC BY-NC)
  39. 39. Future of ELNs • ELNs will become the norm in research in the future • Graduates going into industry may be using ELNs now • May be 5-10 years before market coalesces • Enterprise ahead of academic market • Good product available now • UW-Madison wants to help with this transition
  40. 40. If You Want an ELN • Identify needs • Test the software out before converting • If you adopt now, have an exit strategy
  41. 41. Final Word • Lots of benefits and some risks in adopting an ELN • Keeping a paper notebook has risks but they’re different • Will be a workflow change to adopt an ELN • If risks too big, wait a few years
  42. 42. Resources • DoIT Academic Technologies • http://academictech.doit.wisc.edu/ideas/electronic-lab-notebooks • Research Data Services • http://researchdata.wisc.edu/ • WARF • http://www.warf.org/
  43. 43. Thanks • Ebling Library • Trisha Adamus • This presentation available under a Creative Commons Attribution 3.0 license
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