Lab Notebooks as Data Management (SLA Winter Virtual Conference 2012)

LAB NOTEBOOKS AS DATA MANAGEMENTSupporting Good Practices and the Transition from Paper to Electronic Notebooks

Dr. Kristin A. BrineyThe University of Wisconsin-Madison

SLA Winter Virtual Conference7 December 2012

Pre-publication v. Post-publication Data

• Lot of management work done in second area• This talk focuses on first area

• Scientists need most help here

• Data management very important in pre-publication• Help scientists find their own data, saving time and effort• Help scientist share data

• Even within a lab this is important!

• Help senior researchers/PIs keep track of data-long term as subordinates leave

• Makes post-publication management smoother

The Scientific Process• Literature review• Experiment design and grant writing• Acquire raw data• Data analysis• Repeat acquisition and analysis• (Maybe share data)• Make data presentational and write paper• Submit paper and eventually publish it• [Post-publication]

*Domain of the lab notebook

Data and Metadata Currently

Flickr: proteinbiochemist Flickr: jurvetson

Current Data and Metadata Problems• Searching is a huge problem

• Effectively need to search 2 difference systems to find one experiment

• Long-term concerns with keeping data and metadata together

• Back-ups are an issue• No standard for digital file organization

• Practices vary lab-to-lab AND researcher-to-researcher• Extremely difficult to find someone else’s data currently

Data and Metadata in the Future

• Electronic Lab Notebooks (ELNs)

Note: I am not endorsing any particular lab notebook software package. I will cover software that UW-Madison has looked into.

Data and Metadata in the Future• Easy searching• All files in one place• Linking between pages• Customization• Easier sharing

• Controlled access

• Audit trail• eSignatures• Revision history

Data and Metadata in the Future• Bugs, upgrades, and other digital issues• Effort to transition• Unsettled ELN market

• In first generation of ELNs

• Using files in 10 years• Data storage

• Location and ownership issues

• Data security and backups• Need to have reliable system in place

Recent UW-Madison ELN Pilot• Tested 2 notebooks, CERF and eCAT

• 55 users, majority never used an ELN before

• 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

How Librarians Can Help• Teach basic information organization• Help preserve old notebooks• Know the properties of a good ELN• Educate on how to choose an ELN• Support the transition to ELNs

Teach Basic Information Organization• Surrogate records!

• Record necessary metadata in notebook to point to file• How to organize digital files• This is our wheelhouse and will help scientists with searching

• Suggest file naming and organization conventions• Avoid “ / \ : * ? ‘ < > [ ] & $ characters• Use underscores not spaces• Date files and do it consistently (YYYY-MM-DD)• Label folders with reference to notebook

• Example: C:\Documents\BrineyNotebookIV\2012-12-07

http://researchdata.wisc.edu/manage-your-data/file-naming-and-versioning/

Preserve Old Paper Notebooks

• Add lab notebooks to library collection• Ask what do retiring

scientists do with their notebooks?

• Did you know?• Data for patents needs

to be retained >26 yrFlickr: mabelsound

Know the Properties of a Good ELN• Note taking and searching ability• Adding external files• Adding links between pages• Ability to export• Access permissions• eSignatures• Log of revision history

• Some researchers are using general note taking software, which doesn’t have this feature. I don’t recommend this software for a lab notebook because of this.

Educate on Choosing an ELN• Needs assessment• Test the software• Have an adoption plan• Have an exit strategy

• Note: I do not recommend free/demo version of software• Hosting may be outside US• No sharing

Needs Assessment• How much do I want to integrate the ELN into my

workflow?• How much customization do I want?• Do I need to share?

• PI should have access to all notebooks at very least

• Where should the information be stored?• If cloud-based, look for US-based hosting

• Can I support a local server hosting the ELN?• How much can I spend?

• Open Source up to $1000 per person per year

Test the Software• Can be big financial investment• One ELN software package will not work for everyone

• Ask to 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• Won’t buy a car without a test drive. Same for an ELN.

Have an Adoption Plan• Large shift in workflow in adoption of ELN• Adoption strategies

• Adopt at beginning of a project• Rolling adoption with new researchers• Or just plunge in!

• Put someone in charge of installation• Get software support• Get IT support

• Backups

Have an Exit Strategy• No guarantee that current notebooks 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

Support the Transition to ELNs• Transitioning to an ELN involves scientists, library and IT

• Who is going to train scientists?

• Library can offer important training on ELN software• Fold into information literacy instruction• Great opportunity to also teach basic data management skills• Target grad students (academia) and focus on research groups

• Keep an eye on the changing market• Products coalescing market share• Developing standards

The Future is ELNs• ELNs will help with data management in the laboratory• ELNs will become the norm in research by the end of my

career• Researchers in industry may be using ELNs now

• May be 5-10 years before market coalesces• Enterprise ahead of academic market• Good products available now

• Lots of benefits and some risks in adopting an ELN• Keeping a paper notebook has risks but they’re different• Need digital infrastructure to support ELN• If risks too big, wait a few years

Summary• Scientists need help with pre-publication data

management• Paper lab notebooks are problematic in a digital world• ELNs can solve these issues but have concerns of their

own• Librarians can help by

• Teaching good digital organization skills• Preserving old paper notebooks• Consult with scientist on good ELNs and transitioning to them

• ELNs are the future and scientists will need support with the transition

Resources• (2009). Guide for keeping laboratory records. Rockville,

MD: National Cancer Institute, Technology Transfer Center.

• Kanare, H. M. (1985). Writing the laboratory notebook. Washington, D.C.: American Chemical Society.

• DoIT Academic Technologies (2012). Electronic Lab Notebook Pilot at the University of Wisconsin-Madison. Madison, WI: University of Wisconsin-Madison http://academictech.doit.wisc.edu/ideas/electronic-lab-notebooks

Thanks!• SLA DCHE and PHT• Jan Cheetham, UW DoIT Academic Technologies• Victoria Sutton, UW WARF

• This presentation available under a Creative Commons Attribution-NonCommercial 3.0 license

• Slides will be available at: http://www.slideshare.net/kbriney